Publications from the Gogarten Lab › University of Connecticut

Publications in refereed journals

Dissertations, books, non-refereed articles, and book chapters

Non-refereed published abstracts

Invited seminars

Other presentations

JPG's Erdös number = 3 via Lars S. Jermiin and Brendan Damien McKay, or via Ron Shamir and Noga Alon (list)

Publications in Refereed Journals

Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP.(2024):
Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. ,
mBio 15:e00408-24.
https://doi.org/10.1128/mbio.00408-24

Weiner S, Feng Y, Gogarten JP, Bansal MS(2024):
Assessing the potential of gene tree parsimony for microbial phylogenomics
RECOMB International Workshop on Comparative Genomics , 129-149;
Lecture Notes in Computer Science ((LNBI,volume 14616))
https://doi.org/10.1007/978-3-031-58072-7_7

Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U.(2023):
Neighboring inteins interfere with one another's homing capacity.
PNAS Nexus, 27 Oct 2023, 2(11):pgad354
https://doi.org/10.1093/pnasnexus/pgad354

Lee, I.P.A., Eldakar, O.T., Gogarten, J.P., and Andam, C.P. (2023):
Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience 26.
https://doi.org/10.1016/j.isci.2023.107344

Gosselin SP, Arsenault DR, Jennings CA$, Gogarten JP* (2022):
The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.
Genes (Basel) 14, 288
https://doi.org/10.3390/genes14020288

Podgorski JM, Freeman K, Gosselin S, Huet A, Conway JF, Bird M, Grecco J, Patel S, Jacobs-Sera D, Hatfull G, Gogarten JP, Ravantti J, White SJ* (2022):
A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.
TStructure 2, 282-294.e5.
https://doi.org/10.1016/j.str.2022.12.012

Lee IPA, Eldakar OT, Gogarten JP, Andam CP (2021):
Bacterial cooperation through horizontal gene transfer.
Trends in Ecology & Evolution
https://doi.org/10.1016/j.tree.2021.11.006

Gosselin S. Fullmer MS, Feng Y, Gogarten JP (2021):
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support
Systematic Biology, syab060,
https://doi.org/10.1093/sysbio/syab060

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP (2021):
An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets.
Genome Biology and Evolution, 2021, evab187,
https://doi.org/10.1093/gbe/evab187

Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP (2021):
IThe Evolutionary Origins of Extreme Halophilic Archaeal Lineages.
Genome Biology and Evolution 13 (8) evab166
https://doi.org/10.1093/gbe/evab166

Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS (2021):
Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes.
Mol Biol Evol. 38(6):2639-2659
https://doi.org/10.1093/molbev/msab043

Goldman A, Fournier G, Gogarten JP, Petrov AS, Rothschild L, Segrè D, Smith E, Williams L (2021):
Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life.
Bulletin of the AAS, 53(4).
https://doi.org/10.3847/25c2cfeb.cb78fd8a

Fournier G , Gogarten JP, Goldman AD, Petrov AS, Rothschild L, Segrè D, Smith E, Williams,L (2021):
Understanding the Early Major Transitions in Evolutionary History Part 2: Ancient Evolution of Biological Systems and the Biosphere.
Bulletin of the AAS, 53(4).
https://doi.org/10.3847/25c2cfeb.2e749fbd

Makkay AM, Louyakis AS, Ram‐Mohan N, Gophna U, Gogarten JP, Papke T (2020):
Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.
Sci Rep 10, 22297
https://doi.org/10.1038/s41598-020-79296-w

Pyatibratov MG, Syutkin AS, QuaxTEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV(2020):
Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum.
MicrobiologyOpen 2020;00:e1047
https://doi.org/10.1002/mbo3.1047

Rangel LT#, Marden J#, Colston S, Setubal JC, Graf J, Gogarten JP (2019):
**Identification and characterization of putative Aeromonas spp. T3SS effectors** PLoS One 14(6): e0214035.
https://doi.org/10.1371/journal.pone.0214035

Fullmer MS#, Ouellette M#, Louyakis AS#, Papke RT, Gogarten JP (2019)
The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.
Genes (Special Issue on Genetics of Halophilic Microorganisms) 10(3), 233.
doi: 10.3390/genes10030233

Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP (2019)
**Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21**
Microbiol Resour Announc 8 (12), e00096-19. doi: 10.1128/MRA.00096-19

Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J (2018)
Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients.
MBio. doi: 10.1128/mBio.01328-18 ( Reviews )

Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S (2018)
Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire.
ISME J. 2018 Jun 28. doi: 10.1038/s41396-018-0166-1.

Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT (2018)
Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.
Gene - Section: Microbial Genetics and Genomics, Genetics and Genomics of Extremophiles 9(3). pii: E129. doi: 10.3390/genes9030129

Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U (2018)
Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax.
Gene - Section: Microbial Genetics and Genomics, Genetics and Genomics of Extremophiles9(3), 172; doi:10.3390/genes9030172

Dick AA, Harlow TJ, Gogarten JP (2017)
Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction.
Mol Phylogenet 107: 338-344. doi: 10.1016/j.ympev.2016.11.016

Omer S, Harlow TJ, GogartenJP (2017)
Does Sequence Conservation Provide Evidence for Biological Function?
Trends in Microbiology 25(1):11-18, doi: 10.1016/j.tim.2016.09.010

Soucy SM, Gogarten JP (2017)
Inteins as Indicators of Bio-Communication,
Biocommunication of Archaea, 265-275, Authors' submitted version, doi: 10.1007/978-3-319-65536-9_16

Gogarten JP, Deamer D (2016)
Is LUCA a thermophilic progenote?
Nature Microbiology 1, 16229; doi: 10.1038/nmicrobiol.2016.229

Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV Balunas MJ (2016)
Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.
Frontiers in Microbiology 7, 1342; doi: 10.3389/fmicb.2016.01342

Naor A.#, Altman-Price N#, Soucy SM, Green AG, Mitiagin Y, Turgeman I, Davidovich N, Gogarten JP, Gophna U (2016)
The impact of a homing intein on recombination frequency and organismal fitness.
PNAS 113 (32): E4654–E4661 doi:10.1073/pnas.1606416113

Soucy SM, Huang J, Gogarten JP (2015)
Horizontal gene transfer: building the web of life.
Nature Reviews in Genetics 16, 472–482. doi: 10.1038/nrg3962

Fullmer MS, Soucy SM, Gogarten JP (2015)
The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis.
Frontiers in Microbiology 6, 728. doi: 10.3389/fmicb.2015.00728

Fournier G, Andam CP, Gogarten JP (2015)
Ancient horizontal gene transfer and the last common ancestors.
BMC Evolutionary Biology 15 (1) p. 70 doi: 10.1186/s12862-015-0350-0 (Highly Accessed)

Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV (2015):
Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.
Frontiers in Microbiology 6. doi:10.3389/fmicb.2015.00123

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J (2014):
**Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.**
MBio 18;5(6):e02136. doi: 10.1128/mBio.02136-14.

Soucy SM, Fullmer MS, Papke RT, and Gogarten JP (2014):
Inteins as Indicators of Gene Flow in the Halobacteria.
Frontiers in Microbiology 5: 299, 25 June 2014 | doi: 10.3389/fmicb.2014.00299

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y (2014):
AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.
PLos One 9(6):e98844. doi: 10.1371/journal.pone.0098844

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
Population and genomic analysis of the genus Halorubrum.
Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler RW, Ventosa A, Naor A, Gogarten JP, Papke RT:
Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.
Frontiers in Microbiology 2014, 5:143. doi: 10.3389/fmicb.2014.00143

Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2014)
The impact of HGT on phylogenomic reconstruction methods
Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050

Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM (2013)
Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.
PLoS One. 8(12):e84300. doi: 10.1371/journal.pone.0084300.

Swithers S, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP (2013)
Distribution and Evolution of the Mobile vma-1b Intein
Molecular Biology and Evolution 30 (12): 2676-2687 doi: 10.1093/molbev/mst164

Butzin N, Secinaro M, Swithers KS, Gogarten JP, and Noll K (2013)
Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12
Applied and Environmental Microbiology 79 (22) 7006-7012. doi: 10.1128/AEM.01800-13

Green AG, Swithers KS, Gogarten JF, Gogarten JP (2013)
Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum.
Molecular Biology and Evolution 30 (11): 2463-2474. doi:10.1093/molbev/mst145

Lasek-Nesselquist E, Gogarten, JP (2013)
The effects of model choice and mitigating bias on the ribosomal tree of life.
Molecular Phylogenetics and Evolution 69 (1) 17–38 doi:10.1016/j.ympev.2013.05.006

Bansal MS, Banay, G, Harlow TJ, Gogarten JP, Shamir R
Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes
Bioinformatics 30 (11): 2463-2474 First published online: January 17, 2013 doi:10.1093/bioinformatics/btt021

Williams D, Gogarten JP, Papke RT (2012)
Quantifying homologous replacement of loci between haloarchaeal species.
Genome Biology and Evolution 4 (12) 1223-1244 doi:10.1093/gbe/evs098

Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM and Butzin NC (2012)
Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.
Genome Biology and Evolution 4 (8) 842-851 [Epub before print] doi:10.1093/gbe/evs057

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y (2012)
Quartet decomposition server: a platform for analyzing phylogenetic trees
BMC Bioinformatics 13:123 doi:10.1186/1471-2105-13-123

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM (2012)
Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs.
PLoS One 7(6):e40236 doi: 10.1371/journal.pone.0040236

Andam CP, Harlow TJ, Papke RT, Gogarten JP (2012)
Ancient origin of the divergent forms of leucyl-tRNA synthetases in the halobacteriales Journal:
BMC Evolutionary Biology 12:85 doi: 10.1186/1471-2148-12-85

Swithers KS, Soucy SM, Gogarten JP (2012)
The Role of Reticulate Evolution in Creating Innovation and Complexity.
International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi: 10.1155/2012/418964

Papke RT, Gogarten JP (2012)
How Bacterial Lineages Emerge.
Science 336: 45-46 doi: 10.1126/science.1219241

Fournier GP, Andam CP, Alm EJ, Gogarten JP (2012)
Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life.
Origins of Life and Evolution of Biospheres 41:621–632 [Authors' pre-proof version] doi: 10.1007/s11084-011-9261-2

Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L (2011)
Home and Away- The Evolutionary Dynamics of Homing Endonucleases.
BMC Evolutionary Biology 11:324 doi:10.1186/1471-2148-11-324

Andam CP, Gogarten JP (2011)
Biased gene transfer and its implications for the concept of lineage. (Research)
Biology Direct 6:47 doi:10.1186/1745-6150-6-47

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP and Gogarten JP (2011)
A Rooted Net of Life. (Review)(Highly Accessed)
Biology Direct 6:45 doi:10.1186/1745-6150-6-45

Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Saunders E, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Lykidis A, Land ML, Brettin T, Stetter KO, Nelson KE, Gogarten JP, Noll KM (2011)
Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores.
J Bacteriol 193(20):5869-70 pubmed

Andam CP, Gogarten JP (2011)
Biased gene transfer in microbial evolution. (Analysis)
Nature Reviews Microbiology 9(7): 543-555 , doi:10.1038/nrmicro2593 pubmed

Swithers KS, Dipippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM (2011)
Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea.
J Bacteriol 193(19):5566-7 pubmed

Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P.
Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.
PLoS One. 2011;6(8):e23774. pubmed doi:10.1371/journal.pone.0023774

Bansal MS, Banay G, Gogarten JP, Shamir R (2011)
Detecting highways of horizontal gene transfer.
J Comput Biol 18(9): 1087-1114. pubmed

Silver AC#, Williams D#, Faucher J, Horneman AJ, Gogarten JP, Graf J (2011)
Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data.
PLoS ONE 6(2): e16751. doi:10.1371/journal.pone.0016751

Andam CP, Fournier GP, Gogarten JP (2011)
Multi-level populations and the evolution of antibiotic resistance through horizontal gene transfer.
FEMS Microbiol Rev 35(5): 756-767 doi: 10.1111/j.1574-6976.2011.00274.x.

Fournier GP, Dick AA, Williams D, Gogarten JP (2011)
Evolution of the Archaea: Emerging views on origins and phylogeny.
Research in Microbiology 162(1):92-98 (Pubmed)

Andam CP, Williams D, Gogarten JP (2010)
Biased gene transfer mimics patterns created through shared ancestry.
PNAS 107(23):10679-84 [Epub 2010 May 21] doi:10.1073/pnas.1001418107
Reviewed by Yuri Wolf as a "Must Read" on Faculty of 1000.

Poptsova MS, Gogarten JP (2010)
Using comparative genome analysis to identify problems in annotated microbial genomes.
Microbiology 156, 1909-1917; DOI 10.1099/mic.0.033811-0

Fournier GP, Gogarten JP (2010)
Rooting the Ribosomal Tree of Life.
Molecular Biology and Evolution 27(8):1792-1801; doi:10.1093/molbev/msq057

Fournier GP, Neumann JE, Gogarten JP (2010)
Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders.
PLoS ONE 5(3): e9437. doi:10.1371/journal.pone.0009437

Andam CP, Williams D, Gogarten JP (2010)
Natural Taxonomy in Light of Horizontal Gene Transfer.
Special Issue on the Tree of Life
Biology and Philosophy 25 (4): 589-602, doi: 10.1007/s10539-010-9212-8

Williams D, Gogarten JP*, Lapierre P (2010)
Filling the gaps in the genomic landscape (opinion)
Genome Biology 11:103 (link to publisher's website)

Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009)
Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements.
BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303 (Highly Accessed)

Olendzenski L, Gogarten JP (2009)
Evolution of genes and organisms: The tree/web of life in light of horizontal gene transfer.
Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009)
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.
BMC Genomics. 2009 Oct 12;10(1):468

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009)
Prokaryotic evolution and the tree of life are two different things.
Biol Direct. 2009 Sep 29;4:34. (Highly Accessed)

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009)
Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
Genome Biology and Evolution 2009: 325-339 pubmed GBE

Swithers KS, Gogarten JP, Fournier GP (2009)
Trees in the Web of Life,
Journal of Biology 2009, 8:54doi:10.1186/jbiol160 (Highly Accessed)

Fournier GP, Huang JL, Gogarten JP (2009)
Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.
Philosophical Transactions of the Royal Society, London, Section B Biol Sci. 364(1527): 2229-39.

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, and Noll KM (2009)
On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales.
Proc Nat Acad Sci USA 106(14):5865-70.

See book section for "Horizontal Gene Transfer: Genomes in Flux".

Huang J, Gogarten JP (2009)
Ancient gene transfer as a tool in phylogenetic reconstruction.
Methods Mol Biol. 2009; 532:127-39.

Olendzenski L, Gogarten JP (2009)
Gene transfer: who benefits?
Methods Mol Biol. 2009;532:3-9.

Poptsova M (2009)
Testing phylogenetic methods to identify horizontal gene transfer.
Methods Mol Biol. 2009;532:227-40.

Fournier G (2009)
Horizontal gene transfer and the evolution of methanogenic pathways.
Methods Mol Biol. 2009;532:163-79.

Lapierre P, Gogarten JP (2009)
Estimating the size of the bacterial pan-genome
Trends in Genetics, doi:10.1016/j.tig.2008.12.004 (pdf incl. supplementary materials)

Reviewed in Nature Reviews Microbiology 7, 258-259 (April 2009) | doi:10.1038/nrmicro2123 under the title “Genome watch: Sequencing the species pan-genome” by Stephen Bentley

See book section for "Computational Methods for Understanding Bacterial and Archaeal Genomes"

Huang, Jinling and J. Peter Gogarten (2008)
Concerted gene recruitment in early plant evolution
Genome Biology 9(7): R109 (Highly Accessed)

Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008)
Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
BMC Evolutionary Biology 2008, 8:7

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2008)
Unsupervised Learning in Detection of Gene Transfer.
Journal of Biomedicine and Biotechnology (full text open access) doi: 10.1155/2008/472719

Fournier, Gregory P., and Gogarten, J. Peter (2008)
Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia.
J. Bacteriol. 190(3):1124-7 [Abstract] online [PDF]

Fournier GP, Gogarten JP (2007)
Signature of a Primitive Genetic Code in Ancient Protein Lineages.
J Mol Evol 65 (4), 425-436

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2007)
Proceeding of the IEEE Conference Frontiers in the Convergence of Bioscience and Information Technologies (FBIT 2007), October 2007, pp317 - 321, IEEE Press, ISBN 0-7695-2999-2

Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007)
GPX: A Tool for the Exploration and Visualization of Genome Evolution.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 - 1342,
IEEE Press, ISBN 1-4244-1509-8.

J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2007)
Gene transfer and the reconstruction of life's early history from the molecular record.
Space Science Reviews [Epub ahead of print] DOI: 10.1007/s11214-007-9253-8

Zhaxybayeva O, Gogarten JP, Doolittle WF (2007)
A hyperconserved protein in Prochlorococcus and marine Synechococcus.
FEMS Microbiol Lett. 274 (1): 30-4. [Pre-Review Manuscript]

Martin, Willian, Tal Dagan, Eugene V. Koonin, Jonathan L. Dipippo, J. Peter Gogarten, and James A. Lake (2007)
The Evolution of Eukaryotes, Letter on "Genomics and the irreducible nature of eukaryotic cells".
Science 316, 542-543

Huang, Jinling and J. Peter Gogarten (2007)
Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
Genome Biology 8(6): R99
A very complimentary review of this paper is at www.chlamydiae.com

Maria S. Poptsova, J. Peter Gogarten (2007)
BranchClust: A phylogenetic algorithm for selecting gene families.
BMC Bioinformatics 8:120 (Highly Accessed)

Maria S. Poptsova, J. Peter Gogarten (2007)
The power of phylogenetic approaches to detect horizontally transferred genes.
BMC Evolutionary Biology 7:45 (Highly Accessed)

Alireza G. Senejani and J. Peter Gogarten (2007)
Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
Int J Biol Sci 2007; 3:205-211

Philippe Normand, Pascal Lapierre, Louis S. Tisa, Johann Peter GOGARTEN, Nicole Alloisio, Emilie Bagnarol, Carla A. Bassi, Alison M. Berry, Derek M. Bickhart, Nathalie Choisne, Arnaud Couloux, Benoit Cournoyer, Stephane Cruveiller, Vincent Daubin, Nadia Demange, Maria Pilar Francino, Eugene Goltsman, Ying Huang, Olga R. Kopp, Laurent Labarre, Alla Lapidus, Celine Lavire, Joelle Marechal, Michele Martinez, Juliana E. Mastronunzio, Beth C. Mullin, James Niemann, Pierre Pujic, Tania Rawnsley, Zoe Rouy, Chantal Schenowitz, Anita Sellstedt, Fernando Tavares, Jeffrey P. Tomkins, David Vallenet, Claudio Valverde, Luis G. Wall, Ying Wang, Claudine Medigue, and David R. Benson (2007):
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
Genome Research 17: 7-15 Open Access, pdf

Gogarten, J. Peter and Elena Hilario (2006)
Inteins, introns, and homing endonucleases: Recent revelations about the life cycle of parasitic genetic elements.
BMC Evolutionary Biology 6:94 Open Access (Highly Accessed)

Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., Papke, R.T. (2006)
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events.
Genome Res. 16(9):1099-108. Epub 2006 Aug 9 pubmed, Open Access

Huang, J. and Gogarten, J.P. (2006)
Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
Trends in Genetics 22 (7):361-6. Epub 2006 May 30 pubmed

LAPIERRE, P., SHIAL,R., and GOGARTEN, J.P. (2006):
Distribution of F- and A/V- type ATPases in Thermus scotoductus and Other Closely Related Species.
Systematic and Applied Microbiology, 29(1):15-23

ZHAXYBAYEVA, O., LAPIERRE P., and GOGARTEN, J. P.(2006):
Ancient Gene Duplications and the Root(s) of the Tree of Life.
Protoplasma 227(1):53-64

GOGARTEN, J. P. and TOWNSEND, J. P. (2005):
Horizontal gene transfer, genome innovation, and evolution
Nature Reviews in Microbiology 3(9) 679-687 (online version, pdf)

HUANG J., XU, Y., and GOGARTEN, J.P. (2005):
The Presence of a Haloarchaeal Type Tyrosyl tRNA Synthetase Marks the Opisthokonts as Monophyletic
Molecular Biology and Evolution, 22(11):2142-6

MORANDI, A., ZHAXYBAYEVA, O., GOGARTEN, J.P. and GRAF, J. (2005):
Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the16S rRNA Gene in Aeromonas Strains,
Journal of Bacteriology 187, 6561–6564 (pdf)

HAMEL, L., ZHAXYBAYEVA, O., GOGARTEN J.P. (2005):
PentaPlot: A software tool for the illustration of genome mosaicism.
BMC Bioinformatics 2005,6:139

SOLLOD, B. L., WILSON, D., ZHAXYEVA, O., GOGARTEN, J. P., DRINKWATER, R., and KING, G. F. (2005):
Were arachnids the first to use combinatorial peptide libraries?
Peptides26, 131-139 (pdf)

ZHAXYBAYEVA, O.,GOGARTEN, J. P. (2005):
Book Review: Cladistics: A Practical Primer on CD-ROM. By Peter Skelton and Andrew Smith, withaccompanying booklet by NealeMonks.
Origins of Life and Evolution of Biospheres 35, 1, 69 – 71 (pdf)

HARLOW, Timothy J, GOGARTEN, J. Peter, and RAGAN, Mark A (2004):
A hybrid clustering approach to recognition of protein families in 114 microbial genomes,
BMC Bioinformatics 2004, 5:45

ZHAXYBAYEVA, O., LAPIERRE, P. and GOGARTEN J.P. (2004):
Genome Mosaicism and Organismal Lineages.
Trends in Genetics, 20 (5): 254-260 (Link to Science direct) (pdf)

ZHAXYBAYEVA, Olga and GOGARTEN, J.Peter (2004):
Cladogenesis, Coalescence and the Evolution of the Three Domains of Life.
Trends in Genetics 20 (4): 182- 187 (Link to Science direct) (pdf)

ZHAXYBAYEVA, Olga, Lutz HAMEL, Jason RAYMOND, and J Peter GOGARTEN (2004):Visualization of the phylogenetic content of five genomes using dekapentagonal maps
Genome Biology 2004, 5:R20

ZHAXYBAYEVA, Olga and GOGARTEN, J. Peter (2003):
An Improved Probability Mapping Approach to Assess Genome Mosaicism,
BMC Genomics 2003 4: 37

ZHAXYBAYEVA, Olga and GOGARTEN, J. Peter (2003):
Spliceosomal Introns: New Insights into Their Evolution.
Curr Biol.;13 (19):R764-6.

GOGARTEN J.P. (2003):
Horizontal Gene Transfer: Gene Swapping Craze Reaches the Eukaryotic Domain.
Current Biology 13 (2):R53-4

RAYMOND, J.#, ZHAXYBAYEVA, O.#, GOGARTEN, J.P., GERDES, S., BLANKENSHIP, R.E (2002).:
Whole Genome Analysis of Photosynthetic Prokaryotes.
Science 298: 1616-1620.

RAYMOND, J., ZHAXYBAYEVA, O., GOGARTEN, J.P. AND BLANKENSHIP, R.E. (2003):
Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.
Philosophical Transactions of the Royal Society: Biological Sciences Volume: 358 Number: 1429 Page: 223 -- 230

GOGARTEN, J. P., DOOLITTLE, W. F. and LAWRENCE, J. G. (2002):
Prokaryotic Evolution in Light of Gene Transfer,
Molecular Biology and Evolution 19: 2226-2238.

GOGARTEN, J. P.*, SENEJANI, A. G., ZHAXYBAYEVA, O., OLENDZENSKI, L. and HILARIO, E. (2002)
Inteins: Structure, Function, and Evolution. (pdf)
Annu. Rev. Microbiol. 2002, 56: 263-287

ZHAXYBAYEVA, Olga, and GOGARTEN, J Peter (2002)
Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses.
BMC Genomics 2002, 3:4,1-13 [Supplementary Data] (Highly Accessed)

MAGNOTTA, Scot, and GOGARTEN, J Peter (2002)
Multi site polyadenylation and transcriptional response to stress of a vacuolar type H+-ATPase subunit A gene in Arabidopsis thaliana.
BMC Plant Biology 2002, 2:3

SENEJANI, A.G., HILARIO, E., and GOGARTEN, J.P. (2001)
The intein of the Thermoplasma A-ATPase A subunit: Structure, evolution and expression in E. coli.
BMC Biochem 2(1): 13,1-10

OLENDZENSKI, L., LIU, L., ZHAXYBAYEVA, O., MURPHEY, R., SHIN, D.-G., and GOGARTEN, J.P. (2000):
Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by molecular and computer based approaches.
Journal of Molecular Evolution, 51(6): 587-599 (at Springer Verlag, link to full text for subscribers only).

GOGARTEN, J.P, and OLENDZENSKI, L. (1999)
Orthologs, paralogs and genome comparisons
Current Opinion in Genetics and Development Dec; 9(6) :630-6 (pdf) Full text version

GOGARTEN, J.P., MURPHEY, R. (UGA), and OLENDZENSKI, L. (1999)
Horizontal Gene Transfer: Pitfalls and Promises
Biological Bulletins 196:359-62 (pdf)

HILARIO, E., and GOGARTEN, J.P. (1998) The prokaryote to eukaryote transition reflected in the evolution of the V/F/A-ATPase catalytic and proteolipid subunits. J. Mol. Evol. 46(6):703-715

LIU, L., LAUFER, H., GOGARTEN, P.J., and WANG, M. (1997)
cDNA cloning of a mandibular organ inhibiting hormone from the spider crab Libinia emarginata.
Invert Neurosci 3:199-204, doi: 10.1007/BF02480375

MAGNOTTA, S., and GOGARTEN, J.P.(1997)
Characterization and isolation of a vacuolar type H+-ATPase subunit A cDNA from Arabidopsis thaliana.
Plant Physiol. 115, 1730

GOGARTEN, J.P.*, OLENDZENSKI, L., HILARIO, E., SIMON, C., and HOLSINGER, K.E. (1996)
Dating the Cenancester of Organisms - Technical Comment,
Science 274, 1750-1751. (pdf)

GOGARTEN, J.P.*, HILARIO, E., OLENDZENSKI, L. (1996):
Gene Duplications and Horizontal Gene Transfer during Early Evolution. In: "Evolution of Microbial Life",
Society for General Microbiology, 54, 267-292.

HILARIO, E., GOGARTEN, J.P.(1995):
The V-ATPase A Subunit Gene (vma-1) from Giardia lamblia.
Biochimica et Biophysica Acta, 128, 94-98.

GOGARTEN, J.P. (1995):
The early evolution of cellular life,
Trends in Ecology and Evolution, 10, 147-151. (pdf)

MERCIER, R. W., GOGARTEN, J.P. (1995):
A second cell wall acid invertase gene in Arabidopsis thaliana.
Plant Physiology, 107, 659-660.

GOGARTEN-BOEKELS, M., HILARIO, E., GOGARTEN, J.P. (1995):
The effects of heavy meteorite bombardment on the early evolution - the emergence of the three domains of life.
Origin of Life and Evolution of the Biosphere, 25, 251-264.

GOGARTEN JP (1994):
Which is the Most Conserved Group of Proteins? Homology - Orthology, Paralogy, Xenology and the Fusion of Independent Lineages.
Journal of Molecular Evolution 39: 541-543 (pdf).

MERCIER, R.W., CHAIVISUTHANGKURA, P., GOGARTEN, J.P. (1993):
Letter to the editor on ß-fructosidase homologues.
Plant Molecular Biology 23, 229-230.

HILARIO, E, GOGARTEN, J.P. (1993):
Horizontal Transfer of ATPase Genes -The Tree of Life becomes a Net of Life, (pdf)
BioSystems 31, 111-119.

STARKE,T., GOGARTEN, J. P. (1993):
A conserved intron in the V-ATPase A subunit genes of plants and algae.
Federation of European Biochemical Societies Letters 315, 252-258.

GOGARTEN, J.P.*, STARKE, T, KIBAK, H., FICHMANN, J., TAIZ, L., (1992)
Evolution and Isoforms of V-ATPase Subunits.
The Journal of Experimental Biology 172, 137-147.

GOGARTEN, J.P., TAIZ, L. (1992):
Evolution of Proton Pumping ATPases: Rooting the Tree of Life.
Photosynthesis Research 33, 137-146. (pdf)

KIBAK, H., Taiz, L., STARKE, T., BERNASCONI, P., GOGARTEN, J.P (1992):
Evolution of Structure and Function of V-ATPases.
Journal of Bioenergetics and Biomembranes 24, 415-424.

GOGARTEN, J.P. , FICHMANN, J., BRAUN, Y., MORGAN, L., STYLES, P.,TAIZ, S. L., DELAPP, K., TAIZ, L. (1992):
The Use of Antisense mRNA to Inhibit the Tonoplast ATPase in Carrot.
The Plant Cell 4, 851-864.

STARKE, T., LINKKILA, T.P., GOGARTEN, J.P. (1991):
Two separate genes encode the catalytic 70kDa -ATPase subunit in Psilotum and Equisetum.
Zeitschrift für Naturforschung, A Journal of Biosciences, Section C 46, 613-620.

Linkkila, T.P., Gogarten, J.P. (1991): Tracing origins with molecular sequences: Rooting the universal tree of life, Trends in Biochemical Sciences 16, 287-288 (pdf).

BERNASCONI, P., RAUSCH, T., GOGARTEN J.P., TAIZ, L. (1990):
The H+-ATPase regulatory subunit of Methanococcus thermolithotrophicus: amplification of an 800bp fragment by polymerase chain reaction,
Federation of European Biochemical Societies Letters 259, 227-229.

GOGARTEN, J.P., KIBAK, H., DITTRICH, P. TAIZ, L.*, BOWMAN, E.J., BOWMAN, B., MANOLSON, M., POOLE, R., DATE, T., OSHIMA, T., KONISHI, J., DENDA, K., YOSHIDA, M. (1989):
The evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes.
Proceedings of the National Academy of Sciences U.S.A. 86, 6661-6665.

GOGARTEN J.P., RAUSCH, T., BERNASCONI, P., KIBAK, H., TAIZ, L. (1989):
Molecular evolution of H+-ATPases. I. Methanococcus and Sulfolobus are monophyletic with respect to eukaryotes and eubacteria,
Zeitschrift für Naturforschung, A Journal of Biosciences, Section C 44, 641-650.

GOGARTEN, J.P., BENTRUP, F.-W. (1989):
Substrate specifity of the hexose carrier in the plasmalemma of Chenopodium suspension cells probed by transmembrane exchange diffusion.
Planta 178, 52-60. (pdf)

GOGARTEN, J.P., BENTRUP, F.-W. (1989):
The electrogenic proton/hexose carrier in the plasmalemma of Chenopodium rubrum suspension cells: Effects of delta c, delta pH and delta psi on hexose exchange diffusion
Biochimica et Biophysica Acta 978, 43-50.

ZIMNIAK, L., DITTRICH, P., GOGARTEN, J.P., KIBAK, H., TAIZ, L. (1988):
The cDNA sequence of the 69kDa subunit of the carrot vacuolar H+-ATPase: homology to the beta-chain of F0F1-ATPases. Journal of Biological Chemistry 263, 9102-9112.

GOGARTEN-BOEKELS, M., GOGARTEN, J.P., BENTRUP, F.-W. (1988):
Sugar nucleotides dissipate ATP-generated transmembrane pH gradient in Golgi vesicles from suspension-cell protoplasts of Chenopodium rubrum L.,
Planta 174, 349-57. doi: 10.1007/BF00959520

GOGARTEN, J. P. (1988):
Physical properties of the cell-wall of photoautotrophic suspension cells from Chenopodium rubrum L..
Planta 174, 333-339. doi: 10.1007/BF00959518

BENTRUP, F.-W., HOFFMANN, B., GOGARTEN-BOEKELS, M., GOGARTEN, J.P., BAUMANN, C. (1986):
ATP-dependent acidification and tonoplast hyperpolarization in isolated vacuoles from Chenopodium rubrum L.,
Proceedings of the National Academy of Sciences U.S.A. 83, 2431-2433. pdf

GOGARTEN, J.P., BENTRUP, F.-W. (1985):
Lateral electrophoresis versus 2D-diffusion,
Trends in Biochemical Sciences 10, 471-472 (pdf).

BENTRUP, F.-W., HOFFMANN, B., GOGARTEN-BOEKELS, M., GOGARTEN, J.P., BAUMANN, C. (1985):
A patch clamp study of tonoplast electrical properties in vacuoles isolated from Chenopodium rubrum suspension cells,
Zeitschrift für Naturforschung, A Journal of Biosciences, Section C 40, 886-890.

GOGARTEN-BOEKELS, M., GOGARTEN, J.P., BENTRUP, F.-W. (1985):
Kinetics and specifity of ATP-dependent proton translocation measured with acridine orange in microsomal fractions from green suspension cells of Chenopodium rubrum L.
Journal of Plant Physiology 118, 309-325. doi: 10.1016/S0176-1617(85)80190-5

GOGARTEN, J.P., BENTRUP, F.-W. (1983):
Fluxes and compartmentation of 3-O-methyl-D-glucose in Riccia fluitans L.,
Planta 159, 423-431 (pdf).

FELLE, H., GOGARTEN, J.P., BENTRUP, F.-W. (1983):
Phlorizin inhibits the hexose transport across the plasmalemma of Riccia fluitans,
Planta 157, 267-270. doi: 10.1007/BF00405192

* Communicating Author, # these authors contributed equally to the published work.

Dissertations, Books, Non-refereed Articles, and Book Chapters

Jennifer M. Podgorski, Krista Freeman, Sophia Gosselin, Alexis Huet, James F. Conway, Mary Bird, John Grecco, Shreya Patel, Deborah Jacobs-Sera, Graham Hatfull, Johann Peter Gogarten, Janne Ravantti, Simon White (2022) bioRxiv 2022.09.09.507160 . A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability. DOI:/10.1101/2022.09.09.507160 Link to PDF.

Wiemann J, de Queiroz K, Rowe TB, Planavsky NJ, Anderson RP, Gogarten JP, Turner PE, Gauthier JA (2020) Biota. in Phylonyms: A Companion to the PhyloCode (Eds: Kevin de Queiroz, Philip D. Cantino, Jacques A. Gauthier) CRC Press. Link to PDF.

Gogarten, JP (2019) The progenote, LUCA, and the root of the cellular tree of life. Link to author's version. Chapter 8.1 in the Handbook of Astrobiology, 1st Edition, Edited by Vera M. Kolb, CRC Press, Taylor & Francis Group, LLC, Boca Raton, FL, USA

Gogarten, JP and Papke, RT (2019):Horizontal Gene Transfer in Microbial Evolution. Link to authors version. Chapter 8.2 in the Handbook of Astrobiology, 1st Edition, Edited by Vera M. Kolb, CRC Press, Taylor & Francis Group, LLC, Boca Raton, FL, USA

Cheryl P. Andam and J. Peter Gogarten (2013): Biased Gene Transfer Contributes to Maintaining the Tree of Life.
In: Lateral Gene Transfer in Evolution, edited by Uri Gophna
Springer, ISBN: 978-1-4614-7779-2

Shannon Soucy, LorraineOlendzenski, and J Peter Gogarten, (March 2013) Orthologues, Paralogues and Horizontal Gene Transfer in the Human Holobiont.
In: eLS 2013, John Wiley & Sons Ltd: Chichester http://www.els.net/
[DOI: 10.1002/9780470015902.a0005298]
pre-proof version available here

Kristen S. Swithers and J. Peter Gogarten (2011):
Introns and Inteins. In: Bacterial Integrative Mobile Genetic Elements, edited by Adam P. Roberts and Peter Mullany. Landes Bioscience.
Pre-proof version of the manuscript is availabe here

Borodovsky, M.; Gogarten, J.P.; Przytycka, T.; Rajasekaran, S. (Eds.) (2010) Bioinformatics Research and Applications. Bioinformatics Research and Applications Bioinformatics Research and Applications 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings. Lecture Notes in Bioinformatics, Vol. 6053. 1st Edition., 253 p., Softcover ISBN: 978-3-642-13077-9
Amazon Link Publisher Link

David Williams, Cheryl P. Andam and J. Peter Gogarten (2010)
Horizontal Gene Transfer and the Formation of Groups of Microorganisms.
In: Molecular Phylogeny of Microorganisms, Aharon Oren and R. Thane Papke (editors),
Caister Academic Press, ISBN: 978-1-904455-67-7.
Pre-proof version of the manuscript is availabe here

Mukul S. Bansal, J. Peter Gogarten, Ron Shamir (2010)
Detecting highways of horizontal gene transfer.
In: Lecture Notes in Bioinformatics 6398, Proceedings of the Eighth Annual RECOMB Satellite Workshop on Comparative Genomics, Eric Tannier (ed.) Springer, Berlin Heidelberg, New York. ISBN-13: 978 3 642 16180 4

Maria B. Gogarten, Johann Peter Gogarten, Lorraine C. Olendzenski (Editors) Horizontal Gene Transfer: Genomes in Flux. Humana Press - Springer; 1 edition (February 13, 2009), ISBN-13: 978-1603278522
Amazon LInk Publisher Link

Ying Xu and J Peter Gogarten (eds.) (2008) Computational Methods for Understanding Bacterial and Archaeal Genomes. Imperial College Press, London, ISBN-13: 978-1-86094-982-1.
Amazon Link

Tisa LS, Benson DR, Smejkal GB, Lapierre P, Gogarten JP, Normand P, Francino MP, Richardson P (2008)
Living Large: Elucidation of the Frankia EAN1pec Genome Sequence Shows Gene Expansion and Metabolic Versatility
Current Plant Science and Biotechnology in Agriculture, Volume 42, II, Part 9, 255, DOI: 10.1007/978-1-4020-8252-8_97

NAHAR, N., POPTSOVA, M. S., HAMEL, L., and GOGARTEN, J. P. (2007):
GPX: A tool for the exploration and visualization of genome evolution.
In Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07)

GOGARTEN, J. Peter, and ZHAXYBAYEVA, Olga(2007):
Horizontal gene transfer, gene histories and the root of the tree of life.
Chapter 9 in "Planetary systems and the Origins of Life", RE Pudritz, PG Higgs and J Stone (eds.), Cambridge University Press.

OLENDZENSKI, L., ZHAXYBAYEVA, O., and GOGARTEN, J.P. (2007):
Orthologs, Paralogs and Xenologs in Human and other Genomes.
In Encyclopedia of Life Sciences, John Liley and Sons, Ltd. (same as below, Wiley baught the Encyclopedia and merged articles into their Encyclopedia of Life Sciences)

OLENDZENSKI, L., ZHAXYBAYEVA, O., and GOGARTEN, J.P.:
Orthologs, Paralogs and Xenologs in Human and other Genomes.
In Encyclopedia of the Human Genome, Nature Publishing Group,

OLENDZENSKI, L. ZHAXYBAYEVA, O., and GOGARTEN JP. (2004)
A Brief History on Views of Prokaryotic Evolution and Taxonomy.
In "Microbial Genomes", CM Fraser, T Read and KE Nelson (eds), Humana Press, pp. 143-154

OLENDZENSKI, L., ZHAXYBAYEVA, O., and GOGARTEN, J.P. 2002.
Horizontal Gene Transfer: A new taxonomic principle?
Chapter 34 in: Horizontal Gene Transfer 2nd ed., Syvanen, M. and Kado C.I. (eds.) Academic Press, London. pp 427-435

Zhaxybayeva, Olga and Gogarten, J. Peter:
Review of "Cladistics: a practical primer on CD-ROM", by Peter Skelton and Andrew Smith. Origin of Life and Evolution of Biosphere

BLANKENSHIP, R.E., RAYMOND, J., LINCE, M., LARKUM, A.W.D., JERMIIN, L.S., LOCKHART, P.J., ZHAXYBAYEVA, O., GOGARTEN, J.P. (2001)
Evolution of photosynthetic antennas and reaction centers.
In: PS2001 Proceedings: 12th International Congress on Photosynthesis. PL13 (CSIRO Publishing: Melbourne, Australia) (ISBN 0643 067 116)

OLENDZENSKI, L., ZHAXYBAYEVA, O., and GOGARTEN, J.P. 2001.
What's in a Tree?: Does Horizontal Gene Transfer Determine Microbial Taxonomy?
In: Cellular Origin and Life in Extreme Habitats, Vol 4.:Symbioses, Seckbach, J. (ed.) Kluwer Academic Publishers, Netherlands. pp. 65-78.

OLENDZENSKI L., HILARIO E., AND J.P. GOGARTEN (1998)
Horizontal Gene Transfer and Fusing Lines of Descent: the Archaebacteria - a Chimera?
In "Horizontal Gene Transfer", M. Syvanen and C. Kado (eds.), Chapman and Hall, London. pp 349-362

GOGARTEN, J.P., OLENDZENSKI, L. (2001)
Articles on "Bacteria" and "Archaea" for Plant Sciences for Students, Richard Robinson, editor. MacMillan Library Reference; ISBN: 0028654315

GOGARTEN, J.P., OLENDZENSKI, L. (1999)
Gene Transfer in Early Evolution.
In : "Enigmatic Microbes and Life in Extreme Environments", Joseph Seckbach, ed., Kluwer Academic Publishers, Netherlands pp 15-27

GOGARTEN J.P., OLENDZENSKI L., (1999)
The Progenote. In Encyclopedia of Molecular Biology, Thomas Creighton, ed., John Wiley and Sons, NY (submitted version here)

GOGARTEN, J. P. (1998)
Origin and early evolution of life: Deciphering the molecular record.
In "Origins, Astronomical Society of the Pacific Conference Series Vol.148", Ch. E. Woodward, J. M. Shull and H. A. Thronson, Jr. (eds.) pp 415-448

GOGARTEN, J.P., OLENDZENSKI, L., HILARIO, E. (1998) Gene Duplications and Horizontal Gene Transfer. In : "Thermophiles: the key to molecular evolution and the origin of life?" eds: Michael Adams and Jürgen Weigel, publ.; Taylor and Francis. pp. 165-176

OLENDZENSKI L., HILARIO E., AND J.P. GOGARTEN (1998) Horizontal Gene Transfer and Fusing Lines of Descent: the Archaebacteria - a Chimera? in "Horizontal Gene Transfer", M. Syvanen and C. Kado (eds.), Chapman and Hall, London. pp 349-362

GOGARTEN, J.P., HILARIO, E., OLENDZENSKI, L. (1997) The Tree of Life. American Society for Microbiol. News 63, 404-405.

GOGARTEN-BOEKELS, M, GOGARTEN, J. P (1996) The Effects of Heavy Meteorite Bombardment on Early Evolution - A New Look at the Molecular Record. In: Proceedings of the First International Conference on Circumstellar Habitable Zones. L.R. Doyle (editor), Travis House Publications, 379-391.

GOGARTEN, J. P and KIBAK, H (1992): The Bionergetics of the Last Common Ancestor and the Origin of the Eukaryotic Endomembrane System. In: The Origins and Evolution of the cell. H. Hartman and K. Matsuno (eds.), World Scientific Publ. Co., pp. 131-154. (pdf)

TAIZ, L., STRUVE, I., RAUSCH, T., BERNASCONI, P., GOGARTEN, J.P., KIBAK, H., TAIZ, S.L. (1990): The Vacuolar ATPase: Structure, Evolution and Promotor Analysis. In: Calcium in Plant Growth and Development, eds. R.T. Leonard, P.K. Hepler, Vol. 4 Current Topics in Plant Physiology, ASPP Press, pp. 55-59.

TAIZ, L., GOGARTEN, J.P., KIBAK, H., STRUVE, I., BERNASCONI, P., RAUSCH, T., TAIZ, S.L. (1990): Studies on the structure and evolution of the vacuolar H+-ATPase, in: Plant Membrane Transport, J. Dainty et al. eds., Elsevier Science Publishers, pp. 131-137.

GOGARTEN, J.P. (1986): Untersuchungen zum Zuckertransport an photoautotrophen Suspensionszellen von Chenopodium rubrum L., Dissertation, Universität Gießen.

GOGARTEN, J.P. BENTRUP, F.-W. (1984): Properties of a hexose carrier at the plasmalemma of green suspension cells from Chenopodium rubrum L., in: Membrane Transport in Plants, W. J. Cram, K. Janácek, R. Rybová, K. Sigler (eds.), Academia Publishing House of the Czechoslovak Academy of Sciences, Praha , pp. 183-188.

GOGARTEN, J.P. (1983): Untersuchungen zu Metabolismus, Transport und Kompartimentierung von 3-O-Methyl-D-Glukose bei Riccia fluitans L., Diplomarbeit, Universität Tübingen.

Published Abstracts (since 1991, incomplete)

Olga Zhaxybayeva, David Williams, Kristen Swithers and J. Peter Gogarten:
Quartet decomposition and its applications to study evolutionary histories of genes in genomes.
Proceedings ISBRA 2010

Fenglou Mao, Maria Poptsova, David Williams, Olga Zhaxybayeva, Peter Gogarten and Ying Xu:
Quartet Decomposition Server: A Platform for Analyzing Phylogenetic Trees
Proceedings ISBRA 2010

Pascal Lapierre, Olga Zhaxybayeva and J. Peter Gogarten:
"Whole genome analyses on the class levels: is there a consensus phylogeny?",
International Journal of Astrobiology, Supplement 1, 2004: p.48

Olga Zhaxybayeva and J. Peter Gogarten:
"Cladogenesis, Coalescence and the Evolution of the Three Domains of Life",
International Journal of Astrobiology, Supplement 1, 2004: p.52

J.P. Gogarten:
“The Early Evolution of Life as Reflected in the Molecular Record” Abstract # 13038, 2003 General NAI meeting at Arizona State University, Feb. 10-12, 2003,
Published in "Astrobiology 2(4) "

O. Zhaxybayeva and J.P. Gogarten:
“Detecting Ancient Duplications using Whole Genome Data” Abstract # 12547, 2003 General NAI meeting at Arizona State University, Feb. 10-12, 2003,
Published in "Astrobiology2(4): 475-476"

P. Lapierre,, R. Shial, and J.P. Gogarten: Evidence of an A/V type ATPase in Thermus scotoductus and Other Closely Related Species Abstract # 12646, 2003 General NAI meeting at Arizona State University, Feb. 10-12, 2003,
Published in Astrobiology2(4)

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten:
"Mosaicism in Genes and Genomes", poster presented at the 10th Issol Meeting in Oaxaca, Mexico, June 30 - July 5, 2002,
published in Origin of Life and Evolution of the Biosphere.

O. Zhaxybayeva, L. and J.P. Gogarten:
"Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses", poster presented at the 10th Issol Meeting in Oaxaca, Mexico, June 30 - July 5, 2002
published in Origin of Life and Evolution of the Biosphere.

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten:
"Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses." Poster at the 2nd Astrobiology Science Conference at NASA's Ames Research Center April 7-11, 2002.
Published in "Astrobiology"

Jason R. Raymond, Robert E. Blankenship, Olga Zhaxybayeva, and J. Peter Gogarten:
"Whole Genome Analyses of Photosynthetic Bacteria and the Evolution of Photosynthesis",
Poster presented at the Second Astrobiology Science Conference, NASA AMES Research Center, April 7 - 11, 2002.
Published in "Astrobiology"

MAGNOTTA, S, GOGARTEN, J. P (1997)
"Identification of a vacuolar type H+-ATPase subunit A cDNA and three putative subunit B isoforms in Arabidopsis thaliana.", Abstracts of the Annual ASPP meeting in Vancouver, Canada, Supplement to Plant Phys.

LIU, L., LAUFER, H., GOGARTEN, J.P., WANG, M. (1997)
"cDNA cloning of a mandibular organ inhibiting hormone from the spider crab Libinia emarginataI." Book of Abstracts of the 5th International Conference on Invertebrate Neurochemistry and Neurophysiology (ICINN), 9/7-11,'97, Eilat, Israel.

GOGARTEN, J. PETER, ELENA HILARIO, LORRAINE OLENDZENSKI (1996)
"Gene Duplications and Horizontal Gene Transfer during Early Evolution", Abstracts of the 11th International Conference on the Origin of Life, Orleans, France, # 103; also published in Origin of Life and Evolution of the Biosphere

CHAIVISUTHANGKURA, P., MERCIER, R.W., GOGARTEN, J.P. (1994)
The Role of Cell Wall Bound Acid Invertase in Photosynthate Partitioning, Abstracts of the Annual National Meeting of the American Society of Plant Physiologists, Portland, Oregon, USA, Supplement to Plant Physiology 105, 639.

MERCIER,R.W., CHAIVISUTHANGKURA, P., GOGARTEN, J.P. (1993)
The Role of Apoplastic Invertase in Photosynthate Partitioning, Abstracts of the Annual National Meeting of the American Society of Plant Physiologists, Minneapolis, Minnesota, USA, Supplement to Plant Physiology 102, 220.

GOGARTEN, J.P. (1993)
Phylogeny of Proton Pumping ATPases: Implications for the Early Evolution of Life, Abstracts of the 10th International Conference on the Origin of Life, Barcelona, Spain, # 103; also published in Origin of Life and Evolution of the Biosphere

HILARIO, E., GOGARTEN, J.P., SOSA-PEINADO, A., SILVA, E., LAZCANO, A. (1993)
Early Gene Duplication and the Origin of Biochemical Regulation, Abstracts of the 10th International Conference on the Origin of Life, Barcelona, Spain, # 144; also published in Origin of Life and Evolution of the Biosphere

GOGARTEN, J.P, STARKE, T., FICHMANN, J., TAIZ, L (1992)
Evolution and Isoforms of the Plant V-ATPase, Abstracts of the ninth international Workshop on Plant Membrane Biology, #43.

SCHADTLE, T., GOGARTEN, J.P. (1992)
Evolution of Proton Pumping ATPases: Indications for a Lateral Gene Transfer between the Primary Kingdoms", Proceedings of the 1st International Conference on Molecular Evolution, Pennsylvania State University.

MERCIER, R.W., SOILEAU, C., GOGARTEN, J.P., (1991):
The role of cell wall bound acid invertase in regulating the flow of photosynthate, Plant Physiology 86 (4), Supplement, #487.

GOGARTEN, J.P., FICHMANN, J., MORGAN, L., DELAPP, K., TAIZ, S., TAIZ, L., (1991):
The Use of Antisense DNA to probe function and isoforms of the plant vacuolar ATPase. Proceedings of the 30th Annual Meeting of the American Society of Cell Biology, San Diego, CA, Cell Biology Supplement 1991, #1763.

Invited Seminars and Lectures

Invited Talks and Lectures (since Fall 1991, incomplete)

“Inteins and Homingendonucleases:Long term survival and constructive neutral evolution.” Presentation at the colloquium on “Trash to treasure and treasure to trash: invasion, persistence, neofunctionalization, and gene decay in evolution” at the SMBE meeting in Yokohama, July 12th, 2018

"Organismal and molecular LUCAs in relation to the origin of life and the domain ancestors." Invited presentation at the Workshop on Biogeochemical Dating in Deep Time, UConn Storrs CT, May 10th to 11th, 2017

“Horizontal Gene Transfer, Antibiotic Resistance, Pan-genomes, and within PopulationDiversity”, Invited lecture at the ASM Microbe 2016 meeting in Boston

“Horizontal Gene Transfer: The Pan-Genome as shared genetic resource of a lineage”, Invited plenary lecture at the meeting “Molecules as Documents of Evolutionary History”, held in Roscoff (Brittany), France, May 9th to 13th, 2016

“Molecular evolution before the domain ancestors: Indications for dramatic planetary changes during life’s early evolution”, Invited plenary lecture at the meeting “From star and planet formation to early life” held in Vilnius, Lithuania, April 25th – 28th, 2016

“The Role of Horizontal Gene Transfer in Microbial Evolution”, Invited seminar in the Frontiers in Genomics series at the National University of México (UNAM), Campus Morelos, April 14th, 2016

“Inteins: Co-evolution between selfish genes and genomes”, Presentation to students in the Genomics program at National University of México (UNAM), Campus Morelos, April 14th, 2016

“The role of horizontal gene transfer in microbial evolution”, Invited seminar at the Instituto Politécnico Nacional, Mexico City, March 12th, 2016

“Gene transfer and antibiotic resistance in Aeromonas”, Presentation at the Collegio National, Mexico, as part of a conversation on “Genes ambulantes, Una conversación sobre transporte horizontal y resistencia a antibióticos.” March 4th, 2016

“Inteins: Co-evolution between selfish genes and genomes”, Seminar at the Universidad Nacional Autónoma de México February 22nd, 2016

“The role of horizontal gene transfer in microbial evolution”, Invited departmental Seminar at the Instituto de Fisiología Celular Universidad Nacional Autónoma de México, February 5th, 2016

"The roles of shared ancestry and shared genes in niche adaptation in Aeromonas", SMBE 2015 annual meeting, Vienna, July 12th to the 16th, 2015

"Molecular evolution before the domain ancestors: Indications for dramatic planetary changes during life’s early evolution", invited lecture at the IAP Lecture Series: The Origin of Life at MIT, Jan 28th, 2015

"Molecular evolution before the ancestors of the bacterial and archaeal domains and before the Last Universal Common Ancestor", invited plenary lecture at the ISSOL Meeting, Origins 2014, Nara, Japan, July 6-11, 2014

"Tracing evolution in Aeromonas: the role of shared ancestry and shared genes in niche adaptation", International Symposium on Aeromonas and Plesiomonas in Montpellier, France. (June 26, 2014).

"Inteins as Indicators of Gene Flow in the Halobacteria", Annual SMBE Meeting. (June 8, 2014 - June 12, 2014).

"Molecular evolution before the ancestors of the bacterial and archaeal domains", Annual SMBE Meeting. (June 8, 2014 - June 12, 2014).

"Phylogenomics, Horizontal Gene Transfer, and Darwin's 'Coral-of-Life’", Invited Lecture at the University of Northern Texas, April 4th, 2014

"Microbial Evolution and Phylogenomics in Light of Horizontal Gene Transfer" Invited lecture at the 48th Annual ASM Region I Meeting, University of Connecticut, Storrs, CT, October 25th-26th, 2013

"Phylogenomics and Darwin's "Coral-of-Life" in light of horizontal gene transfer", invited lecture at the Massachusetts Institute of Technology, February 27th, 2013

"Coalescence, gene transfer, and the study of pre-LUCA molecular evolution" lecture at the Origin of Life Conference, Princeton, January 23rd, 2013

"Phylogenomics and Darwin's "Coral-of-Life" in light of horizontal gene transfer", invited lecture at the Graduate Program in Organismic and Evolutionary Biology, UMass & five college System, Amherst, November 9th, 2012

"Phylogenomics, Horizontal Gene Transfer, and Darwin's 'Coral of Life'", invited keynote lecture at Recomb Comparative Genomics, Niteroi. Brazil, October 17-19, 2012

"Horizontal Gene Transfer (HGT), Homeoalleles, NISEs, and the Formation and Maintenance of Higher Taxonomic Units in Bacteria and Archaea", oral presentation at the SMBE 2012 Annual Meeting, Dublin, June 23rd -26th, 2012

"The rooted Net of Life and molecular evolution before LUCA" Invited lecture at the 2012 Astrobiology Sciences Conference, Atlanta GA, April 16th, 2012

"Phylogenomics and Darwin's “Coral-of-Life” in Light of Horizontal Gene Transfer." Invited lecture at the MBL in Woods Hole, March 16th, 2012

"Darwin's Coral-of-Life, Horizontal Gene Transfer, and the Evolution of the Genetic Code." Invited lecture at the 8th Georgia Tech, Emory and the Oak Ridge National Lab. International Conference: "From Genomics to Synthetic Biology”, Nov. 10—12, 2011

"Biased Gene Transfer and Phylogenomics." Invited lecture at the Society for General Microbiology Autumn meeting, York, GB, September 5-7, 2011

"Phylogeny and Darwin's coral of life in light of horizontal gene transfer." Lecture at the Institute Pasteur, Paris, France, June 9th, 2011

"Molecular evolution before LUCA and the rooted Net of Life" Gogarten, J. Peter, Fournier, Gregory P., Andam, Cheryl P.; lecture by JPG at the 2011 ISSOL and Bioastronomy Joint International Conference, Montpellier, France, July 3rd- 8th, 2011

"Adventures in Molecular Evolution", invited lunch presentation at Yale University, West Campus, June 20th, 2011

"Impact of HGT on Phylogenomic Reconstruction", Presentation at the workshop “Challenges for large scale phylogeny and alignment estimation”, National Evolutionary Synthesis Center (NESCent), Durham, NC, April 1st, 2011

"Phylogenomics and Darwin's “Coral-of-Life” in Light of Horizontal Gene Transfer." Invited lecture at the Anthropology Department, UConn, Storrs, 2/24/2011

"Phylogenomics and Darwin's "Coral-of-Life" in Light of Horizontal Gene Transfer." Keynote Address at the 5th Biology New England South (BioNES) 2010 meeting, Roger Williams University, December 3rd, 2010

"Phylogenomics and Darwin's "Coral-of-Life" in Light of Horizontal Gene Transfer." Presentation at Bates College, Biology Department, November 30th, 2010

"Phylogenomics and Darwin's "Coral-of-Life" in Light of Horizontal Gene Transfer." Presentation at the University of Rhode Island, Biology Department, November 22nd, 2010.

"Phylogenomics and Darwin's "Coral-of-Life" in Light of Horizontal Gene Transfer." Presentation at the Research Highlights at Noon Series, Tuesday, November 9th, 2010, Homer Babbidge Library (flyer).

"Horizontal Gene Transfer as a Tool in Reconstructing the Net of Life", Tree of Life Workshop, London, UK July 10th and 11th, 2010

"Horizontal Gene Transfer as a Tool to Reconstruct the Net of Life", invited lecture at the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE) in Lyon, France, July 4th-8th, 2010

"The Tree/Web of Life in Light of Horizontal gene transfer." Invited lecture at UNAM Cuernavaca, Mexico, May 17 2010

"Horizontal Gene Transfer, Organismal Evolution, and Darwin's "Coral of Life." Invited seminar at the Undergraduate Program on Genomic Sciences at the Center for Genomic Sciences and the Biotechnology Institute in the city of Cuernavaca, Mexico, May 17 2010

“Phylogenomics and Darwin's “Coral-of-Life” in Light of Horizontal Gene Transfer.” Biology Departmental Seminar, Haifa University, January 10th, 2010

“Phylogenomics and Darwin's “Coral-of-Life” in Light of Horizontal Gene Transfer.” Invited Seminar at the Weizman Institute, BigRoc Seminar series (see http://bioinfo.weizmann.ac.il/BigRoc/), December 28th, 2009

“Rooting the ribosomal tree of life using the early expansion of the genetic code.” Presentation at the 23rd annual meeting of the ILASOL society (see http://www.ilasol.org.il/ ), Weizmann Institute of Science, December 13th, 2009

"Darwin's "Coral of Life" in Light of Horizontal Gene Transfer." Invited lecture at the Department of Life Sciences, Ben-Gurion University of the Negev, Israel, November 30th, 2009

"Intertwined evolutionary histories of marine Synecchococcus and Prochlorococcus." Seminar in Safir Bioinformatics program at Tel Aviv University November 11th, 2009

"Horizontal Gene Transfer, Organismal Evolution, and Darwin's "Coral of Life." Invited lecture at the Biochemistry Department, Tel Aviv University, October 20th, 2009

"ATPsynthases and Inteins: A Personal History." Seminar for Biotechnology group at Tel Aviv University, September 8th, 2009

“Population Genetics and the Evolution of higher taxonomic units” invited lecture at the Halifax Workshop on “Perspectives on the Tree of Life”, July 30th to August 1st, 2009

“The tree-of-life in light of horizontal gene transfer”, invited lecture at the "Archaea and the Tree of Life" meeting at the Les Treilles Foundation, France, May 11-15, 2009

“Phylogenetics in Light of Horizontal Gene Transfer”, invited seminar at the University of Georgia, Athens, April 10th, 2009

“Phylogenetics in Light of Horizontal Gene Transfer”, invited seminar at the School of Biology Georgia Institute of Technology, Atlanta, April 9th, 2009

“Phylogenetics in Light of Horizontal Gene Transfer”, invited seminar at the University of Vermont, Burlington, March 26. 2009

“Phylogenetics in Light of Horizontal Gene Transfer”, invited seminar at Dalhousie University, Halifax, NS, November 21st, 2008

“The Role of Gene Transfer in Innovation and Speciation”, invited lecture at the conference on Natural Genetic Engineering and Natural Genome Editing, Salzburg, 3-6 July, 2008

“Horizontal Gene Transfer, Organismal Evolution, and Darwin's "Coral of Life."” Departmental seminar at the Department of Biological Sciences at the University of Iowa, October 5th, 2007

“From gene trees to organismal evolution: properties of the Most Recent Common Ancestor, early metabolic pathways, and the origin of primary plastids.” Invited lecture at the “Structural, Functional & Evolutionary Genomics Gordon Research Conference, , Wellcome Trust Conference Centre, Hinxton, Cambridge, United Kingdom, July 29 - August 3, 2007

"Gene Transfer, Symbiosis, Membranes, and Most Recent Common Ancestors" invited presentation at the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Dalhousie University, Halifax, Nova Scotia, Canada; June 24-28, 2007

"Transferred genes as phylogenetically informative characters and gene transfer from extinct lineages" invited presentation at the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Dalhousie University, Halifax, Nova Scotia, Canada; June 24-28, 2007

"Tree-of-Life or Tangled-Web -- How Do Organisms Evolve?" invited seminar at Trinity College, Hartford Connecticut, November 30, 2006

"Organismal Evolution: Tree-of-Life or Tangled Web" invited seminar, Rutgers University, November 8th, 2006

"Organismal Evolution: Tree-of-Life or Tangled Web" invited seminar at the Seminar Series "Exceptions and the Unexpected", Swarthmore College, October 27, 2006

"Molecular Evolution and the Fossil Record: Is the Tree of Life a Tree?" Invited seminar at the Functional Genes Mini Symposium organized by the International GeoBiology Course, Catalina Island, CA, July 8th 2006

"Is there a “Tree of Life”?” Invited lecture at the ISSI ASTROBIOLOGY WORKSHOP “STRATEGIES OF LIFE DETECTION”, Bern, Switzerland, April 24-28, 2006

“Oxygen Producing Photosynthesis and the Molecular Record” Invited lecture at the Agouron Instute’s Oxygen meeting, Santa Fe, April 6-10, 2006

“Horizontal gene transfer and microbial evolution: Is the Tree-of-Life a Tree?” Invited seminar at the Astrobiology Forum, Harvard University, December 13th, 2005

“Horizontal gene transfer and microbial evolution: Is theTree-of-Life a Tree?” Invited seminar at the EEB Department at Yale University, November 30th, 2005

“Horizontal gene transfer and microbial evolution: Is the ‘Tree of Life’ a Tree?” Presentation at the Astrobiology/Exobiology PI meeting, NASA Ames, August 16, 2005

“Prokaryotic Evolution: Is the ‘Tree-of-Life’ a Tree?’ ” Invited lecture at the World Summit on Evolution in the Galapagos, June 9-12, 2005

“Is the “Tree of Life” a Tree?” talk at the Origins Institute conference/workshop on: "Astrobiology and the Origins of Life", May 24-28, 2005

“Horizontal Gene Transfer and Microbial Evolution: Is the “Tree of Life” a Tree?” Invited Seminar at the Bioinformatics Institute at the University of Georgia, Wednesday, May 4, 2005

"Horizontal gene transfer and the early evolution of life", Invited Departmental Seminar at the Department of Biology and Biochemistry at the University of Houston, Texas, January 26, 2005

"Horizontal gene transfer, coalescence and the early evolution of life", Invited lecture at the 15th Annual New England Molecular Evolutionary Biologists Meeting, November 6th, 2004

“Von Chenopodium rubrum zu den Wurzeln des Lebens: Eine persönliche and wissenschaftliche Historie”, Lecture at the Friedrich Wilhelm Bentrup Symposium, Salzburg, Austria, October 8th, 2004

“Probability Mapping and Bipartition Analysis to Study Genome Histories” DIMACS WorkshopDIMACS Workshop on Reticulated Evolution, DIMACS Center, Rutgers University, September 20 - 22, 2004

“Evolutionary events preceding eukaryotic times: coalescence, ancient duplications, and the nucleocytoplasmic component” Invited presentation at the meeting on “Lateral gene transfer and the origins of eukaryotes Harrison Hot Springs Resort, B.C., May 5-9, 2004

“The Early Evolution of Life as Reflected in the Molecular and Fossil Records:
Mass Extinctions, Radiations and Coalescence”, Invited Seminar at the University of Connecticut Geology Department, April 15, 2004

"Horizontal Gene Transfer and the Early Evolution of Life" invited lecture at the symposium on "Bioinformatics in the Post-Genomic Era" held at Puerto Vallarta, Jalisco, Mexico, March 14-16, 2004

“Genomics and the Early Evolution of Life”. Invited Departmental Seminar at at Lehigh University, November13, 2003

“Comparative Genomics and the Organismal Tree of Life” Invited lecture at the Frontiers in Bioinformatics Symposium at the UB Center of Excellence in Bioinformatics, University of Buffalo, SUNY, June 6-8, 2003

“Quantifying Horizontal Gene Transfer – Is there a single meaningful phylogeny for prokaryotes?”Invited presentation at the 103rd General Meeting of the American Society for Microbiology, Washington DC, May 18-25, 2003

“The Early Evolution of Life as Reflected in the Molecular Record” Invited lecture at the Mannheim University of Applied Sciences, Germany, April 4th, 2003

"What's in a tree? Exploration of Probability Mapping as a Tool in Comparative Genome Analyses” Invited lecture at the University of Rhode Island, Kingston, February 26th 2003

“The Early Evolution of Life as Reflected in the Molecular Record” Invited plenary lecture at the 2003 General Meeting of the NASA Astrobiology Institute held at Arizona State University, Feb. 10-12, 2003

"What's in a tree? Exploration of probability mapping as a tool in comparative genome analyses.” Invited seminar at the University of Queensland, Brisbane, Australia, 10/31/02.

"Use of probability mapping in comparative genome analysis"; Invited seminar at the Annual Meeting of the Canadian Institute for Advanced Research Evolutionary Biology Program at Harrison Hot Springs Resort, BC, Canada on 9/28/02 - 10/2/02.

Invited plenary lecture at the 10th Issol Meeting in Oaxaca, Mexico: "Genome Scale Analyses and the Early Evolution of Life", June 30 - July 5, 2002

Oral presentation at Molecular Evolution: Evolution, Genomics, Bioinformatics Meeting on “Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome Analyses”, Sorrento, Italy, June 13-16, 2002

Invited seminar on "Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses", Joint EEB-Statistics Seminar Series, University of Connecticut, April 12th, 2002

Invited lecture at the American Society for Microbiology Annual Joint Branch Meeting held at the University of Connecticut at Avery Point with the title: "What's in a Tree? Does Horizontal Gene Transfer Determine Microbial Taxonomy?", Oct. 25, 2001

Invited lecture at the Evolutionary Theory Conference of the Esalen Center for Theory & Research on “Microbial Evolution”, California, November 5-10, 2000

Invited lecture at the 14th meeting of the Canadian Institute for Advanced Research Evolutionary Biology Program on “Does horizontal gene transfer shape microbial taxonomy”, Dingby, Nova Scotia, Canada, October 11-15, 2000

Session Chair of the “Horizontal Gene Transfer” Session at the 2000 Gordon Research Conference on the Origin of Life at Plymouth State College New Hampshire, July 9-14, 2000

Invited lecture at the 50th Annual Meeting of the Canadian Society of Microbiologists in Winnipeg on “The Impact of Lateral Gene Transfer (LGT) on Microbial Evolution”, June 11 – 14, 2000

Invited lecture at the Marine Biological Laboratories on “Organismal Properties and Mechanisms of Evolution: Unscrambling the Molecular Record”, February 11, 2000

Invited lecture at the Carnegie Institution of Washington on “Organismal Properties and Mechanisms of Evolution: Unscrambling the Molecular Record”, December 6, 1999

Invited lecture at the 13th meeting of the Canadian Institute for Advanced Research Evolutionary Biology Program on "The search for infrequently transferred genes with low substitution rates: lessons for organismal evolution." in Banff Canada, 11/20-11/24/1999

Invited lecture at the 7th ESEB conference in Barcelona, Spain: on "Horizontal Gene transfer: Pitfalls and Promises". (8/24/99)

Invited lecture at Northeastern University, Boston, MA, on "Problems and Pitfalls in Deciphering the Molecular Record of Early Life". 4/28/1999

Invited Seminar at Origin of Life Gordon Conference, Ventura, CA "Organismal Properties and Mechanisms of Evolution: Unscrambling the Molecular Record ", 2/22-2/26/99

Invited Seminar at Dieter Söll's group at Yale University "Deciphering the Molecular Record of Early Life", 2/11/99

Invited lecture at the Fachhochschule Mannheim, FRG, on "Deciphering the molecular record for the early evolution of life", 1/14/99

Invited lecture at the Rensselaer Polytechnic Institute "Problems and Pitfalls in Deciphering the Molecular Record of Early Life". 26th of October 1998.

Invited lecture at the University of Rhode Island, Life in Extreme Environment Seminar Series: "Problems in deciphering the molecular record of early life", April 27, 1998

Invited lecture at Harvard University, Population Biology Seminar, Museum of Comparative Zoology: "Early Evolution of Life: Deciphering the Molecular Record", December 4, 1997

Lecture at IXth Symposium on Chemical Evolution and the Origin and Evolution of Life at the NASA Ames Resarch Center meeting at NASA Ames, November 17-20, 1997:" Horizontal Gene Transfer: Pitfalls and Promises "

Invited lecture at the workshop "Evolution: a Molecular Point of View: at the MBL in Woods Hole on "Horizontal Gene Transfer: Pitfalls and Promises", October 24-26, 1997

Invited lecture at the University of Dalhousie on "Deciphering the early molecular record", Sept.4, 1997.

Invited lecture at the Canadian Institute for Advanced Research, Evolutionary Biology Program: "Horizontal gene transfer across domain boundaries", Ottawa, August 23-27, 1997.

Invited lecture at the Gordon conference "Dating Early events in the history of Life", New Hampshire 7/97.

Invited lecture at ’97 meeting of the Protein Society in Boston "Horizontal Gene Transfer and Fusing Lines of Descent". 7/97.

Invited lecture at the NASA Evolutionary Biology Workshop "Molecular Record of Evolution: Evolution of Proteins", Sunnyvale, California, April14-15.

Invited lecture at the Origins '97 conference "Microbial Ecology and The Common Ancestor", May 19-23, Colorado.

Invited lecture in the special Bioinformatics Seminar Series at the University of Connecticut on "Reconstructing Early Evolution of Life from Molecular Sequence Data Using Computational Methods", Dec.2, 1996.

Invited lecture at the Thermophiles '96 Workshop, Athens Georgia: "Gene Duplications and Horizontal Gene Transfer during Early Evolution", Sept. 9-12, 1996.

Oral contribution at the 11th ISSOL meeting, Orleans France: "Gene Duplications and Horizontal Gene Transfer during Early Evolution", July 7-12, 1996.

Invited lecture at the 134th meeting of the Society for General Microbiology, Symposium on the "Evolution of Microbial Life", University of Warwick: "Gene Duplications and Horizontal Gene Transfer during Early Evolution." March 1996.

Invited lecture at the Gordon Research Conference on "Origin of Life", Ventura, CA: "The last Common Ancestor." January 1996.

Invited lecture at the 6th New England Evolutionary Biologists Meeting, Storrs, CT, November 11, 1995.

Invited lecture at the 95th meeting of the American Society of Microbiologists, Washington, DC: "Phylogeny of ATPases: Horizontal Gene Transfer versus Duplicated Genes." May 25, 1995.

Invited lecture at the Friedrich Schiller University of Jena, FRG: "Function and Evolution of Proton Pumping ATPases", April 21, 1995.

Invited lecture at Dalhousie University, Canada: "Evolution of Proton Pumping ATPases, Horizontal Gene Transfer and the Three Domains of Life", October 8, 1994.

Invited presentation at the workshop on Bacteria from Ancient Salt Deposits, Washington, DC, August 18-21, 1994.

Invited lecture at the University of Guelph, Canada, Interdepartmental Seminar Series in Evolution and Systematics: "Evolution of Proton Pumping ATPases: Rooting the Universal Tree of Life", Feb. 18, 1994.

Invited lecture at the Exobiology-NSCORT (NASA specialized Center of Research and Training), University of San Diego, Salk & Scripps Institute: "Molecular Evolution of Proton Pumping ATPases: Scenarios for the Early Evolution of Life", Jan. 27, 1994.

Invited presentation at the 1st conference on "Circumstellar Habitable Zones" at NASA Ames: "The effects of heavy bombardment on the early evolution of cellular life - a new look at the molecular record." Jan 17-19, 1994.

Invited presentation at the workshop on Exobiology organized by the German Aeronautics and Space Agency in Bad Honneff (FRG) "Effects of Meteorite Bombardment on the Early Evolution of Life - a New Interpretation of the Molecular Records" Dec13-15, 1993).

Invited lecture at the University of Salzburg, Austria: "Evolution of proton pumping ATPases: Rooting the Universal Tree of Life" June 15, 1993.

Invited lecture at the University of Munich, Germany "Evolution of proton pumping ATPases: Rooting the Universal Tree of Life" June 17, 1993.

Invited lecture at the University of Regensburg, Germany; "Evolution of proton pumping ATPases: Rooting the Universal Tree of Life" June 18, 1993.

Invited lecture at the University of Tübingen, Germany, "Evolution of proton pumping ATPases: Rooting the Universal Tree of Life" June 24, 1993.

Invited Lecture entitled: "Phylogeny of Proton Pumping ATPases: Implications for the the Early Evolution of Life", given at 10th International Conference on the Origin of Life, Barcelona, Spain, July 5-9, 1993.

Invited Lecture entitled "Evolution and Isoforms of the Plant V-ATPase" given at the Ninth International Workshop on Plant Membrane Biology, Monterey, California, 8/92.

Invited Lecture entitled "Evolution and Isoforms of V-ATPase Subunits" given at the International Symposium on Membrane Energization by Vacuolar Type Proton Pumps, Telluride, Collorado, 6/92.

Invited Lecture entitled "Bioenergetics of the Last Common Ancestor and the Origin of the Eukaryotic Endomembrane System" given at the Symposium on " The Origin and Evolution of Prokaryotic and Eukaryotic Cells" held in Shimoda, Japan,4/92.

Invited lecture at the Univ. of Massachusetts at Amherst, Botany Dept., 2/91: "Function and Evolution of Vacuolar Type ATPases: Rooting of the Universal Tree of Life and the Evolution of the Eukaryotic Endomembrane System".

Other Presentations at Meetings (since Fall1991, incomplete):

Anna Green, Kristen Swithers, Kennth Noll, J. Peter Gogarten "Signals for thermophilic adaptation and phylogeny in the genomes of the Thermotogales." Poster presented by Anna Green at the Undergraduate Mentoring Program of the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE) in Lyon, France, July 4th-8th, 2010

Kristen S. Swithers Gregory P. Fournier and J. Peter Gogarten: Evolutionary Conservation of Intein and Intron Insertion Sites. 2nd ASM Conference on Mobile DNA April 24 - 28, 2010, Montreal, Canada (invited talk by KSS)

Kristen Swithers, Maria Poptsova, Pascal Lapierre, Kenneth Noll, J. Peter Gogarten: Evolutionary study of gene gains and losses in the Thermotogales genome. ASM General Meeting, San Diego, May 2010

Andam, C. P., Williams, D., Gogarten, J. P.: Phylogenetic analysis of tyrosyl tRNA synthetases: Biased gene transfer mimics patterns created through shared ancestry. ASM General Meeting, San Diego, May 2010

Pascal Lapierre and J. Peter Gogarten: Mapping the prokaryotic world using random protein samplings of genomes. ASM General Meeting, San Diego, May 2010

Fournier G. P., Gogarten J. P.: Inferring the Early Evolution of Translation: Ancestral Reconstruction, Compositional Analysis, and Functional Specificity. Astrobiology Science Conference April 26-29, 2010 League City, Texas (invited talk by GPF).

Nicholas C. Butzin, Danielle M. Bradnan, J. Peter Gogarten, and Kenneth M. Noll: A genome sequence-directed investigation of D-tagatose utilization by Kosmotoga olearia. Astrobiology Science Conference April 26-29, 2010 League City, Texas (Poster presented by Nicholas Butzin).

Amanda.Dick, David Williams, J. Peter Gogarten: Woese's Trinity, Eukaryogenesis, and the Tubulin/FtsZ family. Origin of Life GRC, January 10-15, 2010, Galveston, TX (Poster presented by AD).

M.Poptsova, K. Swithers, D. Williams, P. Lapierre, K. Noll, J.P. Gogarten. "Detection and Analysis of Horizontal Gene Transfer in Thermotogales" Poster presented by MP at the "Genome Informatics" meeting at Cold Spring Harbor, October 27-30, 2009,

Greg Fournier, J.Peter Gogarten: "Protein evolution before the MRCA: Ancestral Reconstruction, Compositional Analysis, and Functional Specificity", Origin of Life GRC, January 10-15, 2010, Galveston, TX (invited talk presented by GF)

P. Lapierre, J. P. Gogarten: Gene Transfer as a Problem for Phylogenomic Reconstruction, Poster Presented at the American Society for Microbiology 109th General Meeting, Philadelphia, PA, May 17-21, 2009

Greg Fournier, J.Peter Gogarten: “Horizontal Gene Transfer and the Evolution of Methanogenesis” Lecture Presented by Greg Fournier at the American Society for Microbiology 109th General Meeting, Philadelphia, PA, May 17-21, 2009

Greg Fournier, J.Peter Gogarten: "Rooting the Ribosomal Tree of Life" Poster Presented at the American Society for Microbiology 109th General Meeting, Philadelphia, PA, May 17-21, 2009

Cheryl Andam, David Williams, J. Peter Gogarten: Horizontal gene transfer shapes microbial taxonomy Poster presented at the 74th Cold Spring harbor Symposium on Quantitative Biology, Evolution: The molecular landscape, Cold Spring Harbor, NY, May 27 – June 1, 2009

Kristen Swithers, Derek Bickhart, Pascal Lapierre, Kenneth Noll, J. Peter Gogarten: "Mobile Genetic Elements and their Role in the Evolution of Genome Structure across the Thermotogales Order. Poster presented at American Society for Microbiology General 109th Meeting, Philadelphia PA , May 17-21, 2009."

C. P. Andam, J. P. Gogarten: "Horizontal Gene Transfer Shapes Microbial Taxonomy" Poster presented at American Society for Microbiology General 109th Meeting, Philladelphia, PA, May17-21, 2009

M. Poptsova: Computational Techniques for Orthologous Gene Prediction in Prokaryotes, Invited lecture at the Physic Department, Moscow State University, Moscow, Russia, October 29, 2008.

Kristen Swithers, Pascal Lapierre, Kenneth Noll and J. Peter Gogarten: "Genomic Analyses of the Thermotogales: New Revelations on an Old Order." Poster presented at American Society for Microbiology General 108th Meeting, Boston, Ma, June 1-5, 2008.

J. Peter Gogarten presented a poster on the"Evolutionary conservation of intron and intein insertion sites" (Alireza G. Senejani and J. Peter Gogarten) at the the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Dalhousie University, Halifax, Nova Scotia, Canada; June 24-28, 2007

Kristen Swithers, Pascal Lapierre and J. Peter Gogarten. Characterization of the F-ATPase and V-ATPase in Thermotogales. Poster presented at the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Dalhousie University, Halifax, Nova Scotia, Canada; June 24-28, 2007.

Kristen Swithers, Alireza Senejani and J Peter Gogarten. Evolutionary Conservation of Intron and Intein Insertion Sites. Poster presented at the New England Molecular Evolutionary Biologists (NEMEB), Queens College, New York City, NY. November 3, 2007.

Kristen Swithers, Alireza Senejani and J Peter Gogarten. Evolutionary Conservation of Intron and Intein Insertion Sites. Poster presented at 2008 Origin of Life Conference, Ventura, Ca. January 19-25, 2008

Greg Fournier presented a poster on the "Emergence of a Planetary Methane Ecology: Evolution of Aceticlastic Methanogenesis in Methanosarcinae via horizontal gene transfer from Clostridia" at the SMBE 2007 Annual Meeting, Halifax, NS, Canada, June 24-28

Olga Zhaxybayeva presented a poster on "A hyperconserved protein in Prochlorococcus and marine Synechococcus" (Olga Zhaxybayeva, J Peter Gogarten and W. Ford Doolittle)at the SMBE 2007 Annual Meeting, June 24 - June 28, 2007, Halifax, NS, Canada

Alireza Senejani presented a poster on "Insertion of a new GFP domain into PI-SceI homing endonuclease protein structure" (Alireza G. Senejani and J. Peter Gogarten) at the 3rd Annual North Eastern Structure Symposium (NESS), University of Connecticut, Storrs, CT, U.S.A.; September 30, 2006

Maria Poptsova (postdoc, Gogarten lab) gave an invited lecture on "Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes" at the The Life Science Society Computational Systems Bioinformatics Conference (CSB2006) Workshop on Comparative Genome Analysis of Bacterial Genomes and Applications in Stanford, CA, August 14-18, 2006

Greg Fournier presented a poster on the "Emergence of a Planetary Methane Ecology: Evolution of Aceticlastic Methanogenesis in Methanosarcinae via horizontal gene transfer from Clostridia" at the the The Center for Biodiversity and Conservation's Twelfth Annual Symposium entitled "Small Matters: Microbes and Their Role in Conservation" held at the American Museum of Natural History, New York City, NY, April 26-27, 2007

J. Peter Gogarten presented a poster on " The Size of the Bacterial Protein Universe " (Pascal Lapierre and J. Peter Gogarten) at the XVII NEMEB Meeting (New England Molecular Evolutionary Biologists), November 4, 2006, University of Massachusetts Amherst, MA

Maria Poptsova gave a lecture on "BranchClust: a phylogenetic algorithm for selecting gene families" (Maria Poptsova and J. Peter Gogarten) at the XVII NEMEB Meeting (New England Molecular Evolutionary Biologists), November 4, 2006, University of Massachusetts Amherst, MA

Greg Fournier presented a poster on "Evolution of Methanogenesis: An ancient transfer event?" (Greg Fournier and J. Peter Gogarten) at the Annual Meeting for the Society for Molecular Biology and Evolution (SMBE) Arizona State University, Arizona, May 24-28, 2006

Greg Fournier presented a poster on "Phylogenetic Evidence for a Methanogenic Sister Group to the Most Recent Common Ancestor" (Greg Fournier and J. Peter Gogarten) at the 2006 Origin of Life Gordon Research Conference at Bates College in Lewiston, ME, July 23 -28, 2006

Peter Gogarten presented a poster on "The Size of the Bacterial Protein Universe" (Pascal Lapierre and J. Peter Gogarten) at the 2006 Origin of Life Gordon Research Conference at Bates College in Lewiston, ME, July 23 -28, 2006

Maria Poptsova (postdoc, Gogarten lab) presented a poster on “The Power of Phylogenetic Approaches to Detect Horizontally Transferred Genes” (Maria Poptsova, Timothy J. Harlow, J. Peter Gogarten) at the Phylogeneomics Conference held in Sainte-Adele, Quebec, Canada, 15-19 March 2006

Olga Zhaxybayeva presented a poster on “Phylogenetic analyses of cynanobacterial genomes: Quantification of horizontal gene transfer events.” , J. Peter Gogarten, Robert Charlebois, W. Ford Doolittle, and R. Thane Papke) at the Phylogeneomics Conference held in Sainte-Adele, Quebec, Canada, 15-19 March 2006

Pascal Lapierre (grad student, Gogarten lab) was selected to give an oral presentation on the “Size of the Prokaryotic Protein Universe” at the Astrobiology Science Conference, Washington DC, March 26-30, 2006

Greg Fournier (grad student, Gogarten lab) is invited to give an oral presentation on "Evolution of Methanogenesis: An Ancient Transfer Event?" at the Gordon-Kenan Graduate Research Seminar on the Origin Of Life at Bates College in Lewiston, ME July 21-23, 2006

Kaiyuan Shi (grad student, Gogarten lab) was selected to give oral presentation on "Parametric Bootstrap Analyses of Bacterial 16S rRNA Mosaicism" (collaboration with Olga Zhaxybayeva, and Sushma Samala) at the National Academy of Sciences organized conference on the "Tapestry of Life: Lateral Transfers of Heritable Elements”, which was held at Beckman Center, Irvine, California USA, on December 12-13, 2005.

Jinling Huang (postdoc, Gogarten lab) presented a poster on “Ancient gene transfer benefits phylogenetic reconstruction” (Jinling Huang, Peter Gogarten) at the NAS Sackler Tapestry of Life Colloquium in Dec 2005

Alireza Senejani (grad student, Gogarten lab) was selected to give an oral presentation on "Homing endonucleases: Clever tools for evolving super selfish genes” at “The 16th Annual New England Molecular Evolutionary Biologists Meeting”, Wellesley College, Massachusetts; Nov, 2005

Olga Zhaxybayeva, R. Thane Papke, W. Ford Doolittle and J. Peter Gogarten: Spectral Analyses of Cyanobacterial Genomes: Quantification of Horizontally Transferred Genes, World Summit on Evolution, Galapagos Islands,Ecuador, June 9-12, 2005.

Olga Zhaxybayeva, R. Thane Papke, W. Ford Doolittle and J. Peter Gogarten: Spectral Analyses of Cyanobacterial Genomes: Quantification of Horizontally Transferred Genes, Annual Meeting of CIARProgram in Evolutionary Biology, Vancouver Island, BC, September 15-19, 2005.

Poster presented at the Exobiology PI meeting, NASA Ames California, August 15-19, 2005: Greg Fournier, and J.Peter Gogarten “Signature of a Primitive, Evolving Genetic Code in Ancient Conserved Proteins”

Poster presented at the Exobiology PI meeting, NASA Ames California, August 15-19, 2005: Pascal Lapierre and J.Peter Gogarten “Evaluation of the early substitution rates using cyanobacterial gene family Comparisons”.

Poster presented at the Annual NASA Astrobiology Institute Biannual Meeting at Bouder, CO (April 14-17): Jinling Huang and J.Peter Gogarten "Ancient Gene Transfer Marks the Opisthokonts"

Poster presented at the Origins Institute conference/workshop on: "Astrobiology and the Origins of Life", May 24-28, 2005:
Olga Zhaxybayeva, R. Thane Papke, Robert Charlebois, W. Ford Doolittle and J. Peter Gogarten:
”Spectral analyses of completely sequenced genomes using Bipartitions and embedded Quartets”

Posters presented at the International Conference on Microbial Genomes April 13 - 16, 2005; Halifax, Nova Scotia, Canada

Olga Zhaxybayeva, R. Thane Papke, W. Ford Doolittle and J. Peter Gogarten
Spectral Analyses of Cyanobacterial Genomes: Quantification of Horizontally Transferred Genes

P. Lapierre, J. P. Gogarten, Y. Huang, J. Mastronunzio, T. Rawnsley, C. A. Bassi,
L. S. Tisa, M. P. Francino, Alla Lapidus, P. Richardson, P. Normand, and D. R. Benson
Comparative analysis of three Frankia genomes: symbiotic interaction with actinorhizal host plants and genome plasticity

Poster presented at the Gordon Research Conference on Mammalian DNA Repair, Ventura, CA, January 2005: A. Senejani and J.P. Gogarten, "Towards an experimental system to evolve homing endonucleases through phage competition".

Poster presented at the Gordon Conference on the Origin of Life,Ventura, CA, January 2005: Gregory Fournier and J. Peter Gogarten, “The Ribosomal Protein Core: Evidence for an Ancestral Genetic Code”.

Posters presented at the 15th Annual New England Evolutionary Biologists Meeting, Tuft University, Medford, MA , November 2004 :
P. Lapierre, O. Zhaxybayeva and J.P. Gogarten, "Evaluation of substitution rates in cyanobacteria".
O. Zhaxybayeva and J.P. Gogarten, "Spectral Analyses of Completely Sequenced Genomes using Bipartitions and Embedded Quartets".
Senejani and J.P. Gogarten, "Towards an experimental system to evolve homing endonucleases through phage competition".
G. Fournier and J. Peter Gogarten, “The early evolution of the genetic code”.

Poster presented at Genomes and Evolution Meeting, The Pennsylvania State University, University Park, PA, June 17-20, 2004:
Olga Zhaxybayeva and J. Peter Gogarten:
Cladogenesis, Coalescence and the Evolution of the Three Domains of Life

Poster presented at Genomes and Evolution Meeting, The Pennsylvania State University, University Park, PA, June 17-20, 2004:
Pascal Lapierre, Olga Zhaxybayeva and J. Peter Gogarten:
Whole genome analyses on the class levels: is there a consensus phylogeny?

Posters presented at the Annual Meeting of the CIAR Evolutionary Biology Program, Hotel du Lac Carling, Pine Hill, Quebec, October 13-17, 2004: Olga Zhaxybayeva and J. Peter Gogarten: “Spectral Analyses of Completely Sequenced Genomes using Bipartitions and Embedded Quartets”

Posters presented at Astrobiology Science Conference 2004, NASA Ames, March 28-April 1, 2004:
Pascal Lapierre, Olga Zhaxybayeva and J. Peter Gogarten. Whole genome analyses on the class levels: is there a consensus phylogeny?
Olga Zhaxybayeva and J. Peter Gogarten: Cladogenesis, Coalescence and the Evolution of the Three Domains of Life

Poster presented at the meeting on "Lateral Gene Transfer and the Origins of Eukaryotes", Harrison Hot Springs Resort, B.C., May 5-9, 2004: *Olga Zhaxybayeva and J. Peter Gogarten: Cladogenesis, Coalescence and the Evolution of the Three Domains of Life

Posters presented at the Annual Meeting of the Canadian Institute for Advanced Research Evolutionary Biology Program at White Point Beach, Nova Scotia, Canada September 10-14, 2003:
  Olga Zhaxybayeva and J. Peter Gogarten: Detecting Ancient Duplications Using Whole Genome Data*
  Olga Zhaxybayeva and J. Peter Gogarten: Cladogenesis, Coalescence and the Evolution of the Three Domains of Life*
  Olga Zhaxybayeva, Lutz Hamel, and J. Peter Gogarten: An Improved Probability Mapping Approach*
  Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan: A hybrid clustering approach to genome-scale recognition of protein families*.

Poster presented at the Gordon Research Conference on Molecular Evolution, Ventura, CA, February 1-6, 2004:
*Pascal Lapierre, Olga Zhaxybayeva and J. Peter Gogarten. Whole genome analyses on the class levels: is there a consensus phylogeny?

Poster presented at the Evolutionary Genomics Meeting, University of Arizona, Tucson, AZ, January 15-17, 2004:
*Olga Zhaxybayeva and J. Peter Gogarten: Visualization of Genome Mosaicism: New and Improved Methods

Posters presented at Exobiology Principal Investigators' Seventh Triennial Science Conference, NASA Ames Research Center, Moffett Field, CA, August 25-29, 2003:
  Olga Zhaxybayeva and J. Peter Gogarten: Detecting Ancient Duplications Using Whole Genome Data*
  Olga Zhaxybayeva and J. Peter Gogarten: Cladogenesis, Coalescence and the Evolution of the Three Domains of Life*
  * Pascal Lapierre and J. Peter Gogarten: Update on the molecular evolution of the bacterial A/V-type ATP synthases.
  Olga Zhaxybayeva, Lutz Hamel, and J. Peter Gogarten: An Improved Probability Mapping Approach*
  Olga Zhaxybayeva and J. Peter Gogarten: Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome Analyses*

Posters presented at the Gordon Research Conference on the Origin of Life, Bates College, Maine, July 13-18, 2003:
  Alireza Senejani, Gregory Roussos and J. Peter Gogarten: “Life Cycle” of Inteins: Time-scale, Horizontal Transfer and Homing.*
  Pascal Lapierre and J. Peter Gogarten: Update on the molecular evolution of the bacterial A/V-type ATP synthases.*
  O. Zhaxybayeva and J. Peter Gogarten: "Detecting Ancient Duplications Using Whole Genome Data".
  O. Zhaxybayeva and J. Peter Gogarten: "Cladogenesis, Coalescence and the Evolution of the Three Domains of Life"

Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan: A hybrid clustering approach to genome-scale recognition of protein families. Poster at the International conference on Intelligent Systems for Molecular Biology (ISMB), Brisbane, Australia, June 29 - July 3, 2003

Pascal Lapierre and J. Peter Gogarten: “Update on the Molecular Evolution of the Bacterial A/V- Type ATP Synthases” Posters presented at Gordon Research Conference on Molecular & Cellular Bioenergetics, Kimball Union Academy, Meriden, NH, June 22-27, 2003

Posters presented at the 2003 NAI meeting at Arizona state:|
O. Zhaxybayeva and J.P. Gogarten: “Detecting Ancient Duplications using Whole Genome Data”
P. Lapierre,, R. Shial, and J.P. Gogarten: “Evidence of an A/V type ATPase in Thermus scotoductus and Other Closely Related Species”

Zhaxybayeva, O., L. Olendzenski and J.P. Gogarten: "Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses." Poster at the Gordon Research Conference on Genomics and Structural/Evolutionary Bioinformatics, 7/28/02 - 8/2/02, Mount Holyoke College, South Hadley, MA.

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten: "Mosaicism in Genes and Genomes", poster presented at the 10^th Issol Meeting in Oaxaca, Mexico, June 30 - July 5, 2002

O. Zhaxybayeva, L. and J.P. Gogarten: "Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses", poster presented at the 10^th Issol Meeting in Oaxaca, Mexico, June 30 - July 5, 2002

Pascal Lapierre, Reshma Shial and J. Peter Gogarten: “Evidence of an A/V type ATPase in Thermus scotoductus and Other Closely Related Species” presented at NEMEB XIII, November 9, 2002, Lillie Auditorium, Marine Biological Laboratory
Woods Hole, MA

Robert E. Blankenship, Jason R. Raymond, Olga Zhaxybayeva, and J. Peter Gogarten: "Whole Genome Analyses of Photosynthetic Bacteria and the Evolution of Photosynthesis", Discussion Meeting: Comparative functional genomics of chloroplasts, mitochondria and their bacterial homologues - new perspectives on symbiosis in cell evolution, The Royal Society of London, Wednesday 26th and Thursday 27th June 2002.

Jason R. Raymond, Olga Zhaxybayeva, J. Peter Gogarten, and Robert E. Blankenship: "Whole Genome Analyses of Photosynthetic Bacteria and the Evolution of Photosynthesis", Gordon Research Conference on Photosynthesis, June 16-21, 2002, Roger Williams University, Bristol, RI.

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten: "Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses." Poster at the 2nd Astrobiology Science Conference at NASA's Ames Research Center April 7-11, 2002. A one page summary will be published in "Astrobiology"

Jason R. Raymond, Robert E. Blankenship, Olga Zhaxybayeva, and J. Peter Gogarten: "Whole Genome Analyses of Photosynthetic Bacteria and the Evolution of Photosynthesis", Poster presented at the Second Astrobiology Science Conference, NASA AMES Research Center, April 7 - 11, 2002. . A one page summary published in "Astrobiology

Posters presented at the 2002 Gordon Research Conference on the Origin of Lile in Ventura (CA):

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten: “Mosaicism in ribosomal RNA genes.”

O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten: Bootstrap, Bayesian Probability and Maximum Likelihood Mapping: Exploring New Tools for Comparative Genome analyses."

Posters presented at the 3rd Georgia Tech - Emory International Conference on Bioinformatics: In silico Biology: Bioinformatics after Human Genome, Atlanta, GA, November 15-18, 2001: Olga Zhaxybayeva, Lorraine Olendzenski and J. Peter Gogarten: Maximum Likelihood Mapping as Tool for Comparative Genome Analyses

Posters presented at New England Molecular Evolutionary Biologists (NEMEB) XII, Smith College on November 3, 2001:
- R. Shial, P. Lapierre, L. Olendzenski and J.P. Gogarten: “The Distribution of ATP synthases within the Deinococcales.”
- J. Draghi, O. Zhaxybayeva and J.P. Gogarten: "Resistor and Diode Networks as a Tool to Study"
- O. Zhaxybayeva, L. Olendzenski and J.P. Gogarten: “Mosaicism in 16S rRNA genes.”
- O. Zhaxybayeva and J.P. Gogarten: "Maximum Likelihood Mapping as Tool for Comparative Genome"
- A.G. Senejani and J.P. Gogarten: “The Intein of the Thermoplasma A-ATPase A subunit Structure, Evolution and Expression in E. coli.”
- L. Olendzenski and J.P. Gogarten: “Microsporidia as Fungi, Red Algae as Plants: Phylogenetic Relationships Among Eukaryotes based on the Vacuolar ATPase.”

Poster presented at the conference on Objects in Bio- & Chem-Informatics 2001 (OiBC-2001), Boston MA, July 9-10, 2001: Dong-Guk Shin, John Bluis, Ravi Nori, Hsin-Wei Wang, Pinglei Zhou, and J. Peter Gogarten: PhyloSource: An Interactive Phylogenetic Relationship Repository.
Poster presented by D.-G. Shin.

Posters presented at the 2001 meeting of the NASA Astrobiology Institute at the Carnegie Institution of Washington, Washington DC, April 10-12, 2001:

Olga A. Zhaxybayeva, Lorraine Olendzenski, J. Peter Gogarten: Mosaicism in 16S rRNA genes

Lorraine Olendzenski, Olga A. Zhaxybayeva, J. Peter Gogarten: How Much Did Horizontal Gene Transfer Contribute to Early Evolution?: Quantifying Archaeal Genes in Two Bacterial Lineages

Olga Zhaxybayeva and J. Peter Gogarten: Maximum Likelihood Mapping as Tool for Comparative Genome Analyses

Presentation ant the NASA Astrobiology meeting at Arizona State University on “Vertical and horizontal inheritance in microbial evolution”, Tempe, AZ, Jan. 11-12, 2001

Participation in the meeting of the NAS committee on the origins and evolution of life meeting at UCIrvine, Feb 26-28, 2001

Presentation at the International Conference on Complex Systems (ICCS) May 21-26, 2000 in Nashua, NH; J. Peter Gogarten (presenter), W. Ford Doolittle, & Lorraine Olendzenski; "Assessing Patterns in Microbial Evolution: Does Horizontal Gene Transfer Shape Microbial Taxonomy?"

Poster at the International Conference on Complex Systems (ICCS) May 21-26, 2000 in Nashua, NH; Olga Zhaxybayeva (presenter), Lorraine Olendzenski , Peter Gogarten, Dong-Guk Shin, Lei Liu. Comparative Analysis Of The Deinococcus Genome Indicates Infrequent Horizontal Transfer Between The Three Domains Of Life.

Poster presented at the First Astrobiology Science Conference meeting at NASA Ames, April 2^nd to April 5^th, 2000: Lorraine Olendzenski (presenter), Olga Zhaxybayeva, Peter Gogarten, Dong-Guk Shin, Lei Liu. Comparative Analysis Of The Deinococcus Genome Indicates Infrequent Horizontal Transfer Between The Three Domains Of Life.

Presentation at the First Astrobiology Science Conference meeting at NASA Ames, April 2^nd to April 5^th, 2000: J.P. Gogarten (presenter), F. Doolittle, L. Olendzenski, Assessing Patterns in Microbial Evolution: Does Horizontal Gene Transfer Shape Microbial Taxonomy?

Posters presented at the 1999 meeting of the New England Molecular Evolutionary Biologists at SUNY Albany (Nov. 6).
Olga Zhaxybayeva, Lorraine Olendzenski, Lei Liu, Peter Gogarten - Comparative analysis of the Deinococcus genome indicates infrequent horizonatal transfer between the three domains of life.
Elena Hilario and J. Peter Gogarten: The Intein in the Thermoplasma A-ATPase A-subunit: evolutionary and functional implications.
Lorraine Olendzenski and J. Peter Gogarten: - Early eukaryotes? - Molecular phylogenetics of the vacuolar ATPase and the search for eukaryotic origins.

Elena Hilario and J. Peter Gogarten: "The Intein in the Thermoplasma A-ATPase A-subunit: evolutionary and functional implications." Poster presented at the IX^th International Congress of Bacteriology and Applied Microbiology, August 16-20, 1999, Sydney, Australia

Lorraine Olendzenski and J. Peter Gogarten: "Early" Eukaryotes? - Molecular Phylogenetics of the Vacuolar ATPase and the Search for Eukaryotic Origins." Poster presented by LO at the 12^th ISSOL meeting in San Diego 7/99.

Olga Zhaxybayeva, Lorraine Olendzenski, Peter Gogarten, Lei Liu: Comparative analysis of the Deinococcus genome indicates infrequent horizontal transfer between the three domains of life. Poster presented by OZ at the 12^th ISSOL meeting in San Diego 7/99.

Lorraine Olendzenski, J. Peter Gogarten "The Vacuolar ATPase A-subunit: Implications for Early Eukaryote Evolution" talk presented by LO at the International Society for Evolutionary Protistology meeting in Flagstaff, AZ, July 31-Aug. 5, 1998.

Peter Gogarten, Lorraine Olendzenski: "The Vacuolar ATPase A subunit: Implications for Early Eukaryote Evolution", poster presented at the 1998 New England Molecular Evolutionary Biologist Annual Meeting in New York (NYU), Halloween 1998 [Abstract]

J.P. Gogarten "Horizontal Gene Transfer: Pitfalls and Promises. "Talk presented at the Evolution Societies meeting in Vancouver (June 20-23, 1998)

Olga Zhaxybayeva and Peter Gogarten: "The Effects of Among Site Rate Variation on Phylogenetic Reconstruction from Amino Acid Sequences" Poster presented at the First Internet-Extended Bioinformatics Conference, April 14 to April 24, 1998 at http://www.vei.co.uk/bioinfiec1/

Lei Liu, Dong-Guk Shin, J. Peter Gogarten, Ryan D. Murphey (UGA), and Lorraine Olendzenski: Comparison of Deinococcus radiodurans genome against archaeal, bacterial, and eucaryotic genomes: computer analysis of the genome indicates horizontal gene transfer. Poster presented at 7th Annual bioinformatics and genome research meeting at the Cambridge Health Institute, Boston June 15th, 1998

Scot Magnotta and J. Peter Gogarten: "Genetic analysis of vacuolar type H+-ATPase subunit A and B isoforms in Arabidopsis thaliana." Presented at the 1998 New York Area Plant Molecular Biology Meeting, New York City. Oral presentation given by SM, Jan 17 , 1998

Poster presentations at the IXth Symposium on Chemical Evolution and the Origin and Evolution of Life at the NASA Ames Resarch Center meeting at NASA Ames, November 17-20, 1997:
- J. Peter Gogarten and Olga Zhaxybayeva:
The Effects of Among Site Rate Variation on Phylogenetic Reconstruction from Amino Acid Sequences
- Ryan Murphy, Lorraine Olendzenski, Scott MacNamara, and J. Peter Gogarten:
Horizontal Gene Transfer of Archaeal Genes into the Deinococcaceae
- Lorraine Olendzenski, Elena Hilario, and J. Peter Gogarten:
The Phylogenetic Position of the Microsporidia: Death of an Early Branching Lineage?

Talk presented at the NEMEB –’97 meeting at Yale University (Nov. 2nd):
Elena Hilario (presenter) and J. Peter Gogarten: The prokaryote to eukaryote transition reflected in the evolution of the V/F/A-ATPase catalytic and proteolipid subunits.

Poster presentations at the NEMEB –’97 meeting at Yale University (Nov. 2nd):
- J. Peter Gogarten and Olga Zhaxybayeva:
The Effects of Among Site Rate Variation on Phylogenetic Reconstruction from Amino Acid Sequences
- Ryan Murphy, Lorraine Olendzenski, Scott MacNamara, and J. Peter Gogarten:
Horizontal Gene Transfer of Archaeal Genes into the Deinococcaceae
- Lorraine Olendzenski, Elena Hilario, and J. Peter Gogarten:
The Phylogenetic Position of the Microsporidia: Death of an Early Branching Lineage?
- Elena Hilario, Lisa Farino, Farzad Nowrouzzadeh, Torsten Schadtle, and J.Peter Gogarten:
The Intein in the Thermoplasma V-ATPase A-Subunit: Evolutionary musings and functional implications.

Posters presented at the '97 MCB Departmental Retreat:
- Elena Hilario and J.Peter Gogarten: The vacuolar H+-ATPase from Giardia lamblia:
A potential model for the study of the evolution of the first eukaryotes.
- Parin Chaivisuthangkura, Richard Mercier and J.Peter Gogarten:
Antisense stimulation of apoplastic invertase in transgenic Arabidopsis thaliana
- J. Peter Gogarten and Olga Zhaxybayeva:
The Effects of Among Site Rate Variation on Phylogenetic Reconstruction from Amino Acid Sequences
- Ryan Murphy, Lorraine Olendzenski, Scott MacNamara, and J. Peter Gogarten:
Horizontal Gene Transfer of Archaeal Genes into the Deinococcaceae
- Lorraine Olendzenski, Elena Hilario, and J. Peter Gogarten:
The Phylogenetic Position of the Microsporidia: Death of an Early Branching Lineage?
- Elena Hilario, Lisa Farino, Farzad Nowrouzzadeh, Torsten Schadtle, and J.Peter Gogarten:
The Intein in the Thermoplasma V-ATPase A-Subunit: evolutionary musings and functional implications.
- Scot Magnotta and J.Peter Gogarten: Identification of a vacuolar type H+-ATPase subunit A cDNA and three putative subunit B isoforms in Arabidopsis thaliana

Gordon Research Conference on Microbial Population Biology, Plymouth New Hampshire, July 27-August 1, 1997. Hilario, E., Gogarten, J.P. (1997) "The vacuolar H+-ATPase from Giardia lamblia: a potential model for the study of the evolution of the first eukaryotes.." Poster at the Gordon conference on microbial evolution and Population, NH (poster by EH).

Annual ASPP meeting in Vancouver, Canada, August 1997, Magnotta, S and Gogarten, JP "Identification of a vacuolar type H+-ATPase subunit A cDNA and three putative subunit B isoforms in Arabidopsis thaliana." (poster by SM).

5th International Conference on Invertebrate Neurochemistry and Neurophysiology (ICINN), 9/7-11,'97, Eilat, Israel, Lei Liu, Hans Laufer, J. Peter Gogarten, Minhua Wang (1997) "cDNA cloning of a mandibular organ inhibiting hormone from the spider crab Libinia emarginataI." (poster by HL).

Seventh Annual Meeting of the New England Molecular Evolutionary Biologists at UNH, New Hampshire, October 19, 1996: Lorraine Olendzenski, Elena Hilario, J. Peter Gogarten:"Molecular Phylogeny of the Vacuolar ATPase Catalytic Subunit: Implicationsfor Early Eukaryotic Evolution" (poster by LO).

Tagung der Deutschen Botanischen Gesellschaft, August, 1996, Düsseldorf, FRG. Kranewitter, W., Gogarten, J.P., Pfeiffer, W., Bentrup, F.-W. : Cloning and Sequencing of the Vacuolar Ppiase from Chenopodium rubrum. (poster by WK).

11th International Conference on the Origin of Life, Orleans, France, July, 1996, J.Peter Gogarten: "Gene Duplications and Horizontal Gene Transfer during Early Evolution." (talk by JPG).

Sixth Annual Meeting of the New England Molecular Evolutionary Biologists, in Storrs, CT, November 11, 1995: Hilario E, Gogarten P: "The V-ATPase catalytic subunit of Giardia lamblia" (poster by EH).

Regional meeting of the American Society of Plant Physiologists in Rhode Island, North East Section, April 28, 1995, R. Mercier, P. Chaivisuthangkura, J.P. Gogarten: "The role of apoplastic invertase in photosynthate partitioning" (Poster presented by PC).

"Eastern Great Lakes Molecular Evolution Meeting" at McMaster University, Hamilton, Ontario: "Comparison of Molecular Phylogenies: Towards a Concsensus for the Tree/Net of Life", E. Hilario, J.P. Gogarten. May 13, 1995. (talk presented by E.H.).

Gordon Conference on the Origin if Life, RI, 1994: "Horizontal transfer of ATPase genes - The tree of life becomes a net of life", E. Hilario, J.P. Gogarten. (Poster presented by E.H.).

Gordon Conference on the Origin if Life, August 21-28, 1994: "Comparison of Molecular Phylogenies: Towards a Consensus for the Tree/Net of Life. ", J.Peter Gogarten (Poster).

Annual National Meeting of the American Society of Plant Physiologists, Portland, Oregon, USA, August 1994: P. Chaivisuthangkura, R. Mercier, J.P. Gogarten: "The Role of Cell Wall Bound Acid Invertase in Photosynthate Partitioning." (Poster presented by PC).

"Eastern Great Lakes Molecular Evolution Meeting" at the University of Rochester, NY: "Horizontal transfer of ATPase genes - The tree of life becomes a net of life", E. Hilario, J.P. Gogarten. May 7, 1994. (Poster presented by E.H.).

Fourth Annual Meeting of the New England Molecular Evolutionary Biologists, 11/93: Hilario E, Gogarten P: "Horizontal transfer of ATPase genes: the tree of life becomes the net of life." (Poster).

Annual National Meeting of the American Society of Plant Physiologists, Minneapolis, Minnesota, USA, August 1993: R. Mercier, P. Chaivisuthangkura, J.P. Gogarten: "The Role of Apoplastic Invertase in The Flow of Photosynthate in Higher Plants" (Poster by RM).

10th International Conference on the Origin of Life, Barcelona, Spain, July 5-9, 1993, E. Hilario, J.P.Gogarten, A. Sosa-Peinado, E. Silva and A. Lazcano: "Early Gene Duplication and the Origin of Biochemical Regulation" (Poster by EH).

NATO Advanced Study Institute on Plant Molecular Biology, Mallorca, Spain, May 9-19, 1993, R.W. Mercier, P. Chaivisuthangkura, J.P. Gogarten: "The Role of Invertase in Photosynthate Partitioning" (Poster by RM).

Regional meeting of the American Society of Plant Physiologists, North East Section, 5/93, R. Mercier, P. Chaivisuthangkura, J.P. Gogarten: "The Role of apoplastic invertase in Photosynthate Partitioning" (Poster by RM).

Posters at the "Third Annual Meeting of the New England Molecular Evolutionary Biologists", 11/92: Thomas Starke, J. PeterGogarten, " Intron Evolution: a case study in plants." (poster by JPG) Torsten Schadtle and J.Peter Gogarten "Evolution of Proton Pumping ATPases: Indications for a Lateral Gene Transfer between the Primary Kingdoms." (poster by TS).

International Conference on Molecular Evolution, Pennsylvania State University, 6/92: "Evolution of Proton Pumping ATPases: Indications for a Lateral Gene Transfer between the Primary Kingdoms.", Torsten Schadtle and J.Peter Gogarten (poster by TS).

Regional meeting of the American Society of Plant Physiologists, North East Section, 4/91: "The Role of cell wall bound acid invertase in directing the flow of photosynthate", Carmen Soileau, Richard Mercier, J.P. Gogarten (poster by RM).

UCONN-UMASS Plant Phys. meeting in Amherst, MA, 2/91: "V-ATPase Isoforms in in higher plants".

30th Annual Meeting of the American Society of Cell Biology, San Diego, CA, 1/91: "The Use of Antisense DNA to probe function and isoforms of the plant vacuolar ATPase" J.P.Gogarten, J. Fichmann, L. Morgan, K. DeLapp, S. Taiz, L. Taiz (poster by JF).

Gogarten Lab at UConn

Publications in Refereed Journals

Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP.(2024): Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. , mBio 15:e00408-24. https://doi.org/10.1128/mbio.00408-24

Weiner S, Feng Y, Gogarten JP, Bansal MS(2024): Assessing the potential of gene tree parsimony for microbial phylogenomics RECOMB International Workshop on Comparative Genomics , 129-149; Lecture Notes in Computer Science ((LNBI,volume 14616)) https://doi.org/10.1007/978-3-031-58072-7_7

Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U.(2023): Neighboring inteins interfere with one another's homing capacity. PNAS Nexus, 27 Oct 2023, 2(11):pgad354 https://doi.org/10.1093/pnasnexus/pgad354

Lee, I.P.A., Eldakar, O.T., Gogarten, J.P., and Andam, C.P. (2023): Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience 26. https://doi.org/10.1016/j.isci.2023.107344

Gosselin SP, Arsenault DR, Jennings CA$, Gogarten JP* (2022): The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination. Genes (Basel) 14, 288 https://doi.org/10.3390/genes14020288

Lee IPA, Eldakar OT, Gogarten JP, Andam CP (2021): Bacterial cooperation through horizontal gene transfer. Trends in Ecology & Evolution https://doi.org/10.1016/j.tree.2021.11.006

Gosselin S. Fullmer MS, Feng Y, Gogarten JP (2021): Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support Systematic Biology, syab060, https://doi.org/10.1093/sysbio/syab060

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP (2021): An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets. Genome Biology and Evolution, 2021, evab187, https://doi.org/10.1093/gbe/evab187

Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP (2021): IThe Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biology and Evolution 13 (8) evab166 https://doi.org/10.1093/gbe/evab166

Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS (2021): Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes. Mol Biol Evol. 38(6):2639-2659 https://doi.org/10.1093/molbev/msab043

Goldman A, Fournier G, Gogarten JP, Petrov AS, Rothschild L, Segrè D, Smith E, Williams L (2021): Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life. Bulletin of the AAS, 53(4). https://doi.org/10.3847/25c2cfeb.cb78fd8a

Makkay AM, Louyakis AS, Ram‐Mohan N, Gophna U, Gogarten JP, Papke T (2020): Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. Sci Rep 10, 22297 https://doi.org/10.1038/s41598-020-79296-w

Rangel LT#, Marden J#, Colston S, Setubal JC, Graf J, Gogarten JP (2019): Identification and characterization of putative Aeromonas spp. T3SS effectors PLoS One 14(6): e0214035. https://doi.org/10.1371/journal.pone.0214035

Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP (2019) Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21 Microbiol Resour Announc 8 (12), e00096-19. doi: 10.1128/MRA.00096-19

Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J (2018) Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients. MBio. doi: 10.1128/mBio.01328-18 ( Reviews )

Dick AA, Harlow TJ, Gogarten JP (2017) Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction. Mol Phylogenet 107: 338-344. doi: 10.1016/j.ympev.2016.11.016

Omer S, Harlow TJ, GogartenJP (2017) Does Sequence Conservation Provide Evidence for Biological Function? Trends in Microbiology 25(1):11-18, doi: 10.1016/j.tim.2016.09.010

Soucy SM, Gogarten JP (2017) Inteins as Indicators of Bio-Communication, Biocommunication of Archaea, 265-275, Authors' submitted version, doi: 10.1007/978-3-319-65536-9_16

Gogarten JP, Deamer D (2016) Is LUCA a thermophilic progenote? Nature Microbiology 1, 16229; doi: 10.1038/nmicrobiol.2016.229

Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV Balunas MJ (2016) Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios. Frontiers in Microbiology 7, 1342; doi: 10.3389/fmicb.2016.01342

Naor A.#, Altman-Price N#, Soucy SM, Green AG, Mitiagin Y, Turgeman I, Davidovich N, Gogarten JP*, Gophna U* (2016) The impact of a homing intein on recombination frequency and organismal fitness. PNAS 113 (32): E4654–E4661 doi:10.1073/pnas.1606416113

Soucy SM, Huang J, Gogarten JP (2015) Horizontal gene transfer: building the web of life. Nature Reviews in Genetics 16, 472–482. doi: 10.1038/nrg3962

Fullmer MS, Soucy SM, Gogarten JP (2015) The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis. Frontiers in Microbiology 6, 728. doi: 10.3389/fmicb.2015.00728

Fournier G, Andam CP, Gogarten JP (2015) Ancient horizontal gene transfer and the last common ancestors. BMC Evolutionary Biology 15 (1) p. 70 doi: 10.1186/s12862-015-0350-0 (Highly Accessed)

Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV (2015): Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes. Frontiers in Microbiology 6. doi:10.3389/fmicb.2015.00123

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J (2014): Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 18;5(6):e02136. doi: 10.1128/mBio.02136-14.

Soucy SM, Fullmer MS, Papke RT, and Gogarten JP (2014): Inteins as Indicators of Gene Flow in the Halobacteria. Frontiers in Microbiology 5: 299, 25 June 2014 | doi: 10.3389/fmicb.2014.00299

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y (2014): AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees. PLos One 9(6):e98844. doi: 10.1371/journal.pone.0098844

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT: Population and genomic analysis of the genus Halorubrum. Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler RW, Ventosa A, Naor A, Gogarten JP, Papke RT: Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Frontiers in Microbiology 2014, 5:143. doi: 10.3389/fmicb.2014.00143

Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2014) The impact of HGT on phylogenomic reconstruction methods Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050

Swithers S, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP (2013) Distribution and Evolution of the Mobile vma-1b Intein Molecular Biology and Evolution 30 (12): 2676-2687 doi: 10.1093/molbev/mst164

Butzin N, Secinaro M, Swithers KS, Gogarten JP, and Noll K (2013) Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12 Applied and Environmental Microbiology 79 (22) 7006-7012. doi: 10.1128/AEM.01800-13

Green AG, Swithers KS, Gogarten JF, Gogarten JP (2013) Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum. Molecular Biology and Evolution 30 (11): 2463-2474. doi:10.1093/molbev/mst145

Lasek-Nesselquist E, Gogarten, JP (2013) The effects of model choice and mitigating bias on the ribosomal tree of life. Molecular Phylogenetics and Evolution 69 (1) 17–38 doi:10.1016/j.ympev.2013.05.006

Bansal MS, Banay, G, Harlow TJ, Gogarten JP, Shamir R Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes Bioinformatics 30 (11): 2463-2474 First published online: January 17, 2013 doi:10.1093/bioinformatics/btt021

Williams D, Gogarten JP, Papke RT (2012) Quantifying homologous replacement of loci between haloarchaeal species. Genome Biology and Evolution 4 (12) 1223-1244 doi:10.1093/gbe/evs098

Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM and Butzin NC (2012) Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales. Genome Biology and Evolution 4 (8) 842-851 [Epub before print] doi:10.1093/gbe/evs057

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y (2012) Quartet decomposition server: a platform for analyzing phylogenetic trees BMC Bioinformatics 13:123 doi:10.1186/1471-2105-13-123

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM (2012) Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs. PLoS One 7(6):e40236 doi: 10.1371/journal.pone.0040236

Andam CP, Harlow TJ, Papke RT, Gogarten JP (2012) Ancient origin of the divergent forms of leucyl-tRNA synthetases in the halobacteriales Journal: BMC Evolutionary Biology 12:85 doi: 10.1186/1471-2148-12-85

Swithers KS, Soucy SM, Gogarten JP (2012) The Role of Reticulate Evolution in Creating Innovation and Complexity. International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi: 10.1155/2012/418964

Papke RT, Gogarten JP (2012) How Bacterial Lineages Emerge. Science 336: 45-46 doi: 10.1126/science.1219241

Fournier GP, Andam CP, Alm EJ, Gogarten JP (2012) Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life. Origins of Life and Evolution of Biospheres 41:621–632 [Authors' pre-proof version] doi: 10.1007/s11084-011-9261-2

Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L (2011) Home and Away- The Evolutionary Dynamics of Homing Endonucleases. BMC Evolutionary Biology 11:324 doi:10.1186/1471-2148-11-324

Andam CP, Gogarten JP (2011) Biased gene transfer and its implications for the concept of lineage. (Research) Biology Direct 6:47 doi:10.1186/1745-6150-6-47

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP and Gogarten JP (2011) A Rooted Net of Life. (Review)(Highly Accessed) Biology Direct 6:45 doi:10.1186/1745-6150-6-45

Andam CP, Gogarten JP (2011) Biased gene transfer in microbial evolution. (Analysis) Nature Reviews Microbiology 9(7): 543-555 , doi:10.1038/nrmicro2593 pubmed

Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P. Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PLoS One. 2011;6(8):e23774. pubmed doi:10.1371/journal.pone.0023774

Bansal MS, Banay G, Gogarten JP, Shamir R (2011) Detecting highways of horizontal gene transfer. J Comput Biol 18(9): 1087-1114. pubmed

Silver AC#, Williams D#, Faucher J, Horneman AJ, Gogarten JP, Graf J (2011) Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data. PLoS ONE 6(2): e16751. doi:10.1371/journal.pone.0016751

Andam CP, Fournier GP, Gogarten JP (2011) Multi-level populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev 35(5): 756-767 doi: 10.1111/j.1574-6976.2011.00274.x.

Fournier GP, Dick AA, Williams D, Gogarten JP (2011) Evolution of the Archaea: Emerging views on origins and phylogeny. Research in Microbiology 162(1):92-98 (Pubmed)

Andam CP, Williams D, Gogarten JP (2010) Biased gene transfer mimics patterns created through shared ancestry. PNAS 107(23):10679-84 [Epub 2010 May 21] doi:10.1073/pnas.1001418107 Reviewed by Yuri Wolf as a "Must Read" on Faculty of 1000.

Poptsova MS, Gogarten JP (2010) Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156, 1909-1917; DOI 10.1099/mic.0.033811-0

Fournier GP, Gogarten JP (2010) Rooting the Ribosomal Tree of Life. Molecular Biology and Evolution 27(8):1792-1801; doi:10.1093/molbev/msq057

Fournier GP, Neumann JE, Gogarten JP (2010) Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders. PLoS ONE 5(3): e9437. doi:10.1371/journal.pone.0009437

Andam CP, Williams D, Gogarten JP (2010) Natural Taxonomy in Light of Horizontal Gene Transfer. Special Issue on the Tree of Life Biology and Philosophy 25 (4): 589-602, doi: 10.1007/s10539-010-9212-8

Williams D, Gogarten JP*, Lapierre P (2010) Filling the gaps in the genomic landscape (opinion) Genome Biology 11:103 (link to publisher's website)

Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009) Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements. BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303 (Highly Accessed)

Olendzenski L, Gogarten JP (2009) Evolution of genes and organisms: The tree/web of life in light of horizontal gene transfer. Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009) Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia. BMC Genomics. 2009 Oct 12;10(1):468

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct. 2009 Sep 29;4:34. (Highly Accessed)

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus Genome Biology and Evolution 2009: 325-339 pubmed GBE

Swithers KS, Gogarten JP, Fournier GP (2009) Trees in the Web of Life, Journal of Biology 2009, 8:54doi:10.1186/jbiol160 (Highly Accessed)

Fournier GP, Huang JL, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philosophical Transactions of the Royal Society, London, Section B Biol Sci. 364(1527): 2229-39.

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, and Noll KM (2009) On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales. Proc Nat Acad Sci USA 106(14):5865-70.

See book section for "Horizontal Gene Transfer: Genomes in Flux".

Huang J, Gogarten JP (2009) Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol. 2009; 532:127-39.

Olendzenski L, Gogarten JP (2009) Gene transfer: who benefits? Methods Mol Biol. 2009;532:3-9.

Poptsova M (2009) Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. 2009;532:227-40.

Fournier G (2009) Horizontal gene transfer and the evolution of methanogenic pathways. Methods Mol Biol. 2009;532:163-79.

See book section for "Computational Methods for Understanding Bacterial and Archaeal Genomes"

Huang, Jinling and J. Peter Gogarten (2008) Concerted gene recruitment in early plant evolution Genome Biology 9(7): R109 (Highly Accessed)

Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008) Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales BMC Evolutionary Biology 2008, 8:7

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2008) Unsupervised Learning in Detection of Gene Transfer. Journal of Biomedicine and Biotechnology (full text open access) doi: 10.1155/2008/472719

Fournier, Gregory P., and Gogarten, J. Peter (2008) Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia. J. Bacteriol. 190(3):1124-7 [Abstract] online [PDF]

Fournier GP, Gogarten JP (2007) Signature of a Primitive Genetic Code in Ancient Protein Lineages. J Mol Evol 65 (4), 425-436

Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP.(2024):
Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. ,
mBio 15:e00408-24.
https://doi.org/10.1128/mbio.00408-24

Weiner S, Feng Y, Gogarten JP, Bansal MS(2024):
Assessing the potential of gene tree parsimony for microbial phylogenomics
RECOMB International Workshop on Comparative Genomics , 129-149;
Lecture Notes in Computer Science ((LNBI,volume 14616))
https://doi.org/10.1007/978-3-031-58072-7_7

Turgeman-Grott I, Arsenault D, Yahav D, Feng Y, Miezner G, Naki D, Peri O, Papke RT, Gogarten JP, Gophna U.(2023):
Neighboring inteins interfere with one another's homing capacity.
PNAS Nexus, 27 Oct 2023, 2(11):pgad354
https://doi.org/10.1093/pnasnexus/pgad354

Lee, I.P.A., Eldakar, O.T., Gogarten, J.P., and Andam, C.P. (2023):
Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience 26.
https://doi.org/10.1016/j.isci.2023.107344

Gosselin SP, Arsenault DR, Jennings CA$, Gogarten JP* (2022):
The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.
Genes (Basel) 14, 288
https://doi.org/10.3390/genes14020288

Lee IPA, Eldakar OT, Gogarten JP, Andam CP (2021):
Bacterial cooperation through horizontal gene transfer.
Trends in Ecology & Evolution
https://doi.org/10.1016/j.tree.2021.11.006

Gosselin S. Fullmer MS, Feng Y, Gogarten JP (2021):
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support
Systematic Biology, syab060,
https://doi.org/10.1093/sysbio/syab060

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP (2021):
An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets.
Genome Biology and Evolution, 2021, evab187,
https://doi.org/10.1093/gbe/evab187

Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP (2021):
IThe Evolutionary Origins of Extreme Halophilic Archaeal Lineages.
Genome Biology and Evolution 13 (8) evab166
https://doi.org/10.1093/gbe/evab166

Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS (2021):
Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes.
Mol Biol Evol. 38(6):2639-2659
https://doi.org/10.1093/molbev/msab043

Goldman A, Fournier G, Gogarten JP, Petrov AS, Rothschild L, Segrè D, Smith E, Williams L (2021):
Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life.
Bulletin of the AAS, 53(4).
https://doi.org/10.3847/25c2cfeb.cb78fd8a

Makkay AM, Louyakis AS, Ram‐Mohan N, Gophna U, Gogarten JP, Papke T (2020):
Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon.
Sci Rep 10, 22297
https://doi.org/10.1038/s41598-020-79296-w

Rangel LT#, Marden J#, Colston S, Setubal JC, Graf J, Gogarten JP (2019):
**Identification and characterization of putative Aeromonas spp. T3SS effectors** PLoS One 14(6): e0214035.
https://doi.org/10.1371/journal.pone.0214035

Feng Y, Louyakis AS, Makkay AM, Guerrero RO, Papke RT, Gogarten JP (2019)
**Complete Genome Sequence of Halorubrum ezzemoulense Strain Fb21**
Microbiol Resour Announc 8 (12), e00096-19. doi: 10.1128/MRA.00096-19

Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J (2018)
Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients.
MBio. doi: 10.1128/mBio.01328-18 ( Reviews )

Dick AA, Harlow TJ, Gogarten JP (2017)
Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction.
Mol Phylogenet 107: 338-344. doi: 10.1016/j.ympev.2016.11.016

Omer S, Harlow TJ, GogartenJP (2017)
Does Sequence Conservation Provide Evidence for Biological Function?
Trends in Microbiology 25(1):11-18, doi: 10.1016/j.tim.2016.09.010

Soucy SM, Gogarten JP (2017)
Inteins as Indicators of Bio-Communication,
Biocommunication of Archaea, 265-275, Authors' submitted version, doi: 10.1007/978-3-319-65536-9_16

Gogarten JP, Deamer D (2016)
Is LUCA a thermophilic progenote?
Nature Microbiology 1, 16229; doi: 10.1038/nmicrobiol.2016.229

Gromek SM, Suria AM, Fullmer MS, Garcia JL, Gogarten JP, Nyholm SV Balunas MJ (2016)
Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.
Frontiers in Microbiology 7, 1342; doi: 10.3389/fmicb.2016.01342

Naor A.#, Altman-Price N#, Soucy SM, Green AG, Mitiagin Y, Turgeman I, Davidovich N, Gogarten JP, Gophna U (2016)
The impact of a homing intein on recombination frequency and organismal fitness.
PNAS 113 (32): E4654–E4661 doi:10.1073/pnas.1606416113

Soucy SM, Huang J, Gogarten JP (2015)
Horizontal gene transfer: building the web of life.
Nature Reviews in Genetics 16, 472–482. doi: 10.1038/nrg3962

Fullmer MS, Soucy SM, Gogarten JP (2015)
The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis.
Frontiers in Microbiology 6, 728. doi: 10.3389/fmicb.2015.00728

Fournier G, Andam CP, Gogarten JP (2015)
Ancient horizontal gene transfer and the last common ancestors.
BMC Evolutionary Biology 15 (1) p. 70 doi: 10.1186/s12862-015-0350-0 (Highly Accessed)

Collins AJ, Fullmer MS, Gogarten JP, Nyholm SV (2015):
Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes.
Frontiers in Microbiology 6. doi:10.3389/fmicb.2015.00123

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J (2014):
**Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.**
MBio 18;5(6):e02136. doi: 10.1128/mBio.02136-14.

Soucy SM, Fullmer MS, Papke RT, and Gogarten JP (2014):
Inteins as Indicators of Gene Flow in the Halobacteria.
Frontiers in Microbiology 5: 299, 25 June 2014 | doi: 10.3389/fmicb.2014.00299

Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y (2014):
AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.
PLos One 9(6):e98844. doi: 10.1371/journal.pone.0098844

Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
Population and genomic analysis of the genus Halorubrum.
Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140

Ram Mohan N, Fullmer MS, Makkay AM, Wheeler RW, Ventosa A, Naor A, Gogarten JP, Papke RT:
Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.
Frontiers in Microbiology 2014, 5:143. doi: 10.3389/fmicb.2014.00143

Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2014)
The impact of HGT on phylogenomic reconstruction methods
Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050

Swithers S, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP (2013)
Distribution and Evolution of the Mobile vma-1b Intein
Molecular Biology and Evolution 30 (12): 2676-2687 doi: 10.1093/molbev/mst164

Butzin N, Secinaro M, Swithers KS, Gogarten JP, and Noll K (2013)
Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12
Applied and Environmental Microbiology 79 (22) 7006-7012. doi: 10.1128/AEM.01800-13

Green AG, Swithers KS, Gogarten JF, Gogarten JP (2013)
Reconstruction of Ancestral 16S rRNA Reveals Mutation Bias in the Evolution of Optimal Growth Temperature in the Thermotogae Phylum.
Molecular Biology and Evolution 30 (11): 2463-2474. doi:10.1093/molbev/mst145

Lasek-Nesselquist E, Gogarten, JP (2013)
The effects of model choice and mitigating bias on the ribosomal tree of life.
Molecular Phylogenetics and Evolution 69 (1) 17–38 doi:10.1016/j.ympev.2013.05.006

Bansal MS, Banay, G, Harlow TJ, Gogarten JP, Shamir R
Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes
Bioinformatics 30 (11): 2463-2474 First published online: January 17, 2013 doi:10.1093/bioinformatics/btt021

Williams D, Gogarten JP, Papke RT (2012)
Quantifying homologous replacement of loci between haloarchaeal species.
Genome Biology and Evolution 4 (12) 1223-1244 doi:10.1093/gbe/evs098

Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM and Butzin NC (2012)
Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.
Genome Biology and Evolution 4 (8) 842-851 [Epub before print] doi:10.1093/gbe/evs057

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y (2012)
Quartet decomposition server: a platform for analyzing phylogenetic trees
BMC Bioinformatics 13:123 doi:10.1186/1471-2105-13-123

Petrus AK, Swithers KS, Ranjit C, Wu S, Brewer HM, Gogarten JP, Pasa-Tolic L, Noll KM (2012)
Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs.
PLoS One 7(6):e40236 doi: 10.1371/journal.pone.0040236

Andam CP, Harlow TJ, Papke RT, Gogarten JP (2012)
Ancient origin of the divergent forms of leucyl-tRNA synthetases in the halobacteriales Journal:
BMC Evolutionary Biology 12:85 doi: 10.1186/1471-2148-12-85

Swithers KS, Soucy SM, Gogarten JP (2012)
The Role of Reticulate Evolution in Creating Innovation and Complexity.
International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi: 10.1155/2012/418964

Papke RT, Gogarten JP (2012)
How Bacterial Lineages Emerge.
Science 336: 45-46 doi: 10.1126/science.1219241

Fournier GP, Andam CP, Alm EJ, Gogarten JP (2012)
Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life.
Origins of Life and Evolution of Biospheres 41:621–632 [Authors' pre-proof version] doi: 10.1007/s11084-011-9261-2

Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L (2011)
Home and Away- The Evolutionary Dynamics of Homing Endonucleases.
BMC Evolutionary Biology 11:324 doi:10.1186/1471-2148-11-324

Andam CP, Gogarten JP (2011)
Biased gene transfer and its implications for the concept of lineage. (Research)
Biology Direct 6:47 doi:10.1186/1745-6150-6-47

Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP and Gogarten JP (2011)
A Rooted Net of Life. (Review)(Highly Accessed)
Biology Direct 6:45 doi:10.1186/1745-6150-6-45

Andam CP, Gogarten JP (2011)
Biased gene transfer in microbial evolution. (Analysis)
Nature Reviews Microbiology 9(7): 543-555 , doi:10.1038/nrmicro2593 pubmed

Swithers KS, Fournier GP, Green AG, Gogarten JP, Lapierre P.
Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.
PLoS One. 2011;6(8):e23774. pubmed doi:10.1371/journal.pone.0023774

Bansal MS, Banay G, Gogarten JP, Shamir R (2011)
Detecting highways of horizontal gene transfer.
J Comput Biol 18(9): 1087-1114. pubmed

Silver AC#, Williams D#, Faucher J, Horneman AJ, Gogarten JP, Graf J (2011)
Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data.
PLoS ONE 6(2): e16751. doi:10.1371/journal.pone.0016751

Andam CP, Fournier GP, Gogarten JP (2011)
Multi-level populations and the evolution of antibiotic resistance through horizontal gene transfer.
FEMS Microbiol Rev 35(5): 756-767 doi: 10.1111/j.1574-6976.2011.00274.x.

Fournier GP, Dick AA, Williams D, Gogarten JP (2011)
Evolution of the Archaea: Emerging views on origins and phylogeny.
Research in Microbiology 162(1):92-98 (Pubmed)

Andam CP, Williams D, Gogarten JP (2010)
Biased gene transfer mimics patterns created through shared ancestry.
PNAS 107(23):10679-84 [Epub 2010 May 21] doi:10.1073/pnas.1001418107
Reviewed by Yuri Wolf as a "Must Read" on Faculty of 1000.

Poptsova MS, Gogarten JP (2010)
Using comparative genome analysis to identify problems in annotated microbial genomes.
Microbiology 156, 1909-1917; DOI 10.1099/mic.0.033811-0

Fournier GP, Gogarten JP (2010)
Rooting the Ribosomal Tree of Life.
Molecular Biology and Evolution 27(8):1792-1801; doi:10.1093/molbev/msq057

Fournier GP, Neumann JE, Gogarten JP (2010)
Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders.
PLoS ONE 5(3): e9437. doi:10.1371/journal.pone.0009437

Andam CP, Williams D, Gogarten JP (2010)
Natural Taxonomy in Light of Horizontal Gene Transfer.
Special Issue on the Tree of Life
Biology and Philosophy 25 (4): 589-602, doi: 10.1007/s10539-010-9212-8

Williams D, Gogarten JP*, Lapierre P (2010)
Filling the gaps in the genomic landscape (opinion)
Genome Biology 11:103 (link to publisher's website)

Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009)
Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements.
BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303 (Highly Accessed)

Olendzenski L, Gogarten JP (2009)
Evolution of genes and organisms: The tree/web of life in light of horizontal gene transfer.
Annals of the New York Academy of Sciences 1178: 137-145 doi: 10.1111/j.1749-6632.2009.04998.x

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR (2009)
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.
BMC Genomics. 2009 Oct 12;10(1):468

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009)
Prokaryotic evolution and the tree of life are two different things.
Biol Direct. 2009 Sep 29;4:34. (Highly Accessed)

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009)
Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
Genome Biology and Evolution 2009: 325-339 pubmed GBE

Swithers KS, Gogarten JP, Fournier GP (2009)
Trees in the Web of Life,
Journal of Biology 2009, 8:54doi:10.1186/jbiol160 (Highly Accessed)

Fournier GP, Huang JL, Gogarten JP (2009)
Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.
Philosophical Transactions of the Royal Society, London, Section B Biol Sci. 364(1527): 2229-39.

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, and Noll KM (2009)
On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales.
Proc Nat Acad Sci USA 106(14):5865-70.

Huang J, Gogarten JP (2009)
Ancient gene transfer as a tool in phylogenetic reconstruction.
Methods Mol Biol. 2009; 532:127-39.

Olendzenski L, Gogarten JP (2009)
Gene transfer: who benefits?
Methods Mol Biol. 2009;532:3-9.

Poptsova M (2009)
Testing phylogenetic methods to identify horizontal gene transfer.
Methods Mol Biol. 2009;532:227-40.

Fournier G (2009)
Horizontal gene transfer and the evolution of methanogenic pathways.
Methods Mol Biol. 2009;532:163-79.

Huang, Jinling and J. Peter Gogarten (2008)
Concerted gene recruitment in early plant evolution
Genome Biology 9(7): R109 (Highly Accessed)

Noll KM, Lapierre P, Gogarten JP and Nanavati DM (2008)
Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
BMC Evolutionary Biology 2008, 8:7

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2008)
Unsupervised Learning in Detection of Gene Transfer.
Journal of Biomedicine and Biotechnology (full text open access) doi: 10.1155/2008/472719

Fournier, Gregory P., and Gogarten, J. Peter (2008)
Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia.
J. Bacteriol. 190(3):1124-7 [Abstract] online [PDF]

Fournier GP, Gogarten JP (2007)
Signature of a Primitive Genetic Code in Ancient Protein Lineages.
J Mol Evol 65 (4), 425-436

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2007)
Proceeding of the IEEE Conference Frontiers in the Convergence of Bioscience and Information Technologies (FBIT 2007), October 2007, pp317 - 321, IEEE Press, ISBN 0-7695-2999-2

Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007)
GPX: A Tool for the Exploration and Visualization of Genome Evolution.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 - 1342,
IEEE Press, ISBN 1-4244-1509-8.

J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva (2007)
Gene transfer and the reconstruction of life's early history from the molecular record.
Space Science Reviews [Epub ahead of print] DOI: 10.1007/s11214-007-9253-8

Zhaxybayeva O, Gogarten JP, Doolittle WF (2007)
A hyperconserved protein in Prochlorococcus and marine Synechococcus.
FEMS Microbiol Lett. 274 (1): 30-4. [Pre-Review Manuscript]