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Exploring prokaryotic diversity in the genomic era
Philip Hugenholtz
Genome Biol. 2002; 3(2): reviews0003.1–reviews0003.8. Published online 2002 January 29.
PMCID:
PMC139013
Abstract Full Text PDF–175K

Is Cited by the Following 41 Articles in this Archive:

Disturbance of deep-sea environments induced by the M9.0 Tohoku Earthquake
Shinsuke Kawagucci, Yukari T. Yoshida, Takuroh Noguchi, Makio C. Honda, Hiroshi Uchida, Hidenori Ishibashi, Fumiko Nakagawa, Urumu Tsunogai, Kei Okamura, Yoshihiro Takaki, Takuro Nunoura, Junichi Miyazaki, Miho Hirai, Weiren Lin, Hiroshi Kitazato, Ken Takai
Sci Rep. 2012; 2: 270. Published online 2012 February 16. doi: 10.1038/srep00270
PMCID:
PMC3280601
Abstract Full Text PDF–495K Supplementary Material
Polytomy identification in microbial phylogenetic reconstruction
Guan Ning Lin, Chao Zhang, Dong Xu
BMC Syst Biol. 2011; 5(Suppl 3): S2. Published online 2011 December 23. doi: 10.1186/1752-0509-5-S3-S2
PMCID:
PMC3287570
Abstract Full Text PDF–1.1M
Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats
Thomas C. Jeffries, Justin R. Seymour, Jack A. Gilbert, Elizabeth A. Dinsdale, Kelly Newton, Sophie S. C. Leterme, Ben Roudnew, Renee J. Smith, Laurent Seuront, James G. Mitchell
PLoS One. 2011; 6(9): e25173. Published online 2011 September 23. doi: 10.1371/journal.pone.0025173
PMCID:
PMC3179486
Abstract Full Text PDF–671K Supplementary Material
Taxonomic classification of metagenomic shotgun sequences with CARMA3
Wolfgang Gerlach, Jens Stoye
Nucleic Acids Res. 2011 August; 39(14): e91. Published online 2011 May 17. doi: 10.1093/nar/gkr225
PMCID:
PMC3152360
Abstract Full Text PDF–309K Supplementary Material
OTUbase: an R infrastructure package for operational taxonomic unit data
Daniel Beck, Matt Settles, James A. Foster
Bioinformatics. 2011 June 15; 27(12): 1700–1701. Published online 2011 April 15. doi: 10.1093/bioinformatics/btr196
PMCID:
PMC3106189
Free in PMC on 2012/06/15
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective
Samuel A Smits, Cleber C Ouverney
BMC Bioinformatics. 2010; 11(Suppl 6): S18. Published online 2010 October 7. doi: 10.1186/1471-2105-11-S6-S18
PMCID:
PMC3026365
Abstract Full Text PDF–1.5M
Structure of the human gastric bacterial community in relation to Helicobacter pylori status
Ana Maldonado-Contreras, Kate C Goldfarb, Filipa Godoy-Vitorino, Ulas Karaoz, Mónica Contreras, Martin J Blaser, Eoin L Brodie, Maria G Dominguez-Bello
ISME J. 2011 April; 5(4): 574–579. Published online 2010 October 7. doi: 10.1038/ismej.2010.149
PMCID:
PMC3105737
Abstract Full Text PDF–360K Supplementary Material
FragGeneScan: predicting genes in short and error-prone reads
Mina Rho, Haixu Tang, Yuzhen Ye
Nucleic Acids Res. 2010 November; 38(20): e191. Published online 2010 August 28. doi: 10.1093/nar/gkq747
PMCID:
PMC2978382
Abstract Full Text PDF–3.2M Supplementary Material
MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Manuel Stark, Simon A Berger, Alexandros Stamatakis, Christian von Mering
BMC Genomics. 2010; 11: 461. Published online 2010 August 5. doi: 10.1186/1471-2164-11-461
PMCID:
PMC3091657
Abstract Full Text PDF–3.6M
Occupancy Modeling, Maximum Contig Size Probabilities and Designing Metagenomics Experiments
Stephen A. Stanhope
PLoS One. 2010; 5(7): e11652. Published online 2010 July 29. doi: 10.1371/journal.pone.0011652
PMCID:
PMC2912229
Abstract Full Text PDF–609K Supplementary Material
Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx
Katherine P. Lemon, Vanja Klepac-Ceraj, Hilary K. Schiffer, Eoin L. Brodie, Susan V. Lynch, Roberto Kolter
mBio. 2010 Jul-Aug; 1(3): e00129-10. Published online 2010 June 22. doi: 10.1128/mBio.00129-10
PMCID:
PMC2925076
Abstract Full Text PDF–599K Supplementary Material
Archaic chaos: intrinsically disordered proteins in Archaea
Bin Xue, Robert W Williams, Christopher J Oldfield, A Keith Dunker, Vladimir N Uversky
BMC Syst Biol. 2010; 4(Suppl 1): S1. Published online 2010 May 28. doi: 10.1186/1752-0509-4-S1-S1
PMCID:
PMC2880407
Abstract Full Text PDF–1.2M Supplementary Material
Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics
Luis David Alcaraz, Gabriel Moreno-Hagelsieb, Luis E Eguiarte, Valeria Souza, Luis Herrera-Estrella, Gabriela Olmedo
BMC Genomics. 2010; 11: 332. Published online 2010 May 26. doi: 10.1186/1471-2164-11-332
PMCID:
PMC2890564
Abstract Full Text PDF–1.7M Supplementary Material
Bacterial diversity in the oral cavity of ten healthy individuals
Elisabeth M. Bik, Clara Davis Long, Gary C. Armitage, Peter Loomer, Joanne Emerson, Emmanuel F. Mongodin, Karen E. Nelson, Steven R. Gill, Claire M. Fraser-Liggett, David A. Relman
ISME J. Author manuscript; available in PMC 2010 September 18.
Published in final edited form as: ISME J. 2010 August; 4(8): 962–974. Published online 2010 March 25. doi: 10.1038/ismej.2010.30
PMCID:
PMC2941673
Abstract Full Text PDF–1.6M Supplementary Material
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies
James R White, Saket Navlakha, Niranjan Nagarajan, Mohammad-Reza Ghodsi, Carl Kingsford, Mihai Pop
BMC Bioinformatics. 2010; 11: 152. Published online 2010 March 24. doi: 10.1186/1471-2105-11-152
PMCID:
PMC2859756
Abstract Full Text PDF–1.6M Supplementary Material
Prevalence and Diversity of Microbes in the Amniotic Fluid, the Fetal Inflammatory Response, and Pregnancy Outcome in Women with Preterm Prelabor Rupture of Membranes
Daniel B. DiGiulio, Roberto Romero, Juan Pedro Kusanovic, Ricardo Gómez, Chong Jai Kim, Kimberley Seok, Francesca Gotsch, Shali Mazaki-Tovi, Edi Vaisbuch, Katherine Sanders, Elisabeth M. Bik, Tinnakorn Chaiworapongsa, Enrique Oyarzún, David A. Relman
Am J Reprod Immunol. Author manuscript; available in PMC 2011 July 1.
Published in final edited form as: Am J Reprod Immunol. 2010 July 1; 64(1): 38–57. Published online 2010 March 21. doi: 10.1111/j.1600-0897.2010.00830.x
PMCID:
PMC2907911
Abstract Full Text PDF–827K
Transposases are the most abundant, most ubiquitous genes in nature
Ramy K. Aziz, Mya Breitbart, Robert A. Edwards
Nucleic Acids Res. 2010 July; 38(13): 4207–4217. Published online 2010 March 9. doi: 10.1093/nar/gkq140
PMCID:
PMC2910039
Abstract Full Text PDF–5.8M Supplementary Material
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Dongying Wu, Philip Hugenholtz, Konstantinos Mavromatis, Rüdiger Pukall, Eileen Dalin, Natalia N. Ivanova, Victor Kunin, Lynne Goodwin, Martin Wu, Brian J. Tindall, Sean D. Hooper, Amrita Pati, Athanasios Lykidis, Stefan Spring, Iain J. Anderson, Patrik D’haeseleer, Adam Zemla, Mitchell Singer, Alla Lapidus, Matt Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng, Susan Lucas, Cheryl Kerfeld, Elke Lang, Sabine Gronow, Patrick Chain, David Bruce, Edward M. Rubin, Nikos C. Kyrpides, Hans-Peter Klenk, Jonathan A. Eisen
Nature. Author manuscript; available in PMC 2011 April 9.
Published in final edited form as: Nature. 2009 December 24; 462(7276): 1056–1060. doi: 10.1038/nature08656
PMCID:
PMC3073058
Abstract Full Text PDF–442K Supplementary Material
Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis
David A. Hill, Christian Hoffmann, Michael C. Abt, Yurong Du, Dmytro Kobuley, Thomas J. Kirn, Frederic D. Bushman, David Artis
Mucosal Immunol. Author manuscript; available in PMC 2010 September 1.
Published in final edited form as: Mucosal Immunol. 2010 March; 3(2): 148–158. Published online 2009 November 25. doi: 10.1038/mi.2009.132
PMCID:
PMC2824244
Abstract Full Text PDF–2.4M
UFO: a web server for ultra-fast functional profiling of whole genome protein sequences
Peter Meinicke
BMC Genomics. 2009; 10: 409. Published online 2009 September 2. doi: 10.1186/1471-2164-10-409
PMCID:
PMC2744726
Abstract Full Text PDF–784K Supplementary Material
The case for biocentric microbiology
Ramy Karam Aziz
Gut Pathog. 2009; 1: 16. Published online 2009 August 4. doi: 10.1186/1757-4749-1-16
PMCID:
PMC2731788
Abstract Full Text PDF–568K
A Flood of Microbial Genomes–Do We Need More?
Niyaz Ahmed
PLoS ONE. 2009; 4(6): e5831. Published online 2009 June 9. doi: 10.1371/journal.pone.0005831
PMCID:
PMC2688083
Full Text PDF–82K
Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum ‘Synergistetes’ isolated from the human oral cavity
Julia Downes, Sonia R. Vartoukian, Floyd E. Dewhirst, Jacques Izard, Tsute Chen, Wen-Han Yu, Iain C. Sutcliffe, William G. Wade
Int J Syst Evol Microbiol. 2009 May; 59(Pt 5): 972–980. doi: 10.1099/ijs.0.000364-0
PMCID:
PMC2868594
Abstract Full Text PDF–266K Supplementary Material
Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects
Jennifer Commins, Christina Toft, Mario A Fares
Biol Proced Online. 2009; 11: 52–78. Published online 2009 March 11. doi: 10.1007/s12575-009-9004-1
PMCID:
PMC3055744
Abstract Full Text PDF–550K
Metagenomic Pyrosequencing and Microbial Identification
Joseph F. Petrosino, Sarah Highlander, Ruth Ann Luna, Richard A. Gibbs, James Versalovic
Clin Chem. Author manuscript; available in PMC 2010 June 28.
Published in final edited form as: Clin Chem. 2009 May; 55(5): 856–866. Published online 2009 March 5. doi: 10.1373/clinchem.2008.107565
PMCID:
PMC2892905
Abstract Full Text PDF–507K
Heterogeneity of Vaginal Microbial Communities within Individuals
Tae Kyung Kim, Susan M. Thomas, Mengfei Ho, Shobha Sharma, Claudia I. Reich, Jeremy A. Frank, Kathleen M. Yeater, Diana R. Biggs, Noriko Nakamura, Rebecca Stumpf, Steven R. Leigh, Richard I. Tapping, Steven R. Blanke, James M. Slauch, H. Rex Gaskins, Jon S. Weisbaum, Gary J. Olsen, Lois L. Hoyer, Brenda A. Wilson
J Clin Microbiol. 2009 April; 47(4): 1181–1189. Published online 2009 January 21. doi: 10.1128/JCM.00854-08
PMCID:
PMC2668325
Abstract Full Text PDF–2.3M Supplementary Material
Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum
Dongying Wu, Jason Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank Robb, Albert Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi L. Ward, Jonathan A. Eisen
PLoS ONE. 2009; 4(1): e4207. Published online 2009 January 16. doi: 10.1371/journal.pone.0004207
PMCID:
PMC2615216
Abstract Full Text PDF–816K Supplementary Material
Microbial Prevalence, Diversity and Abundance in Amniotic Fluid During Preterm Labor: A Molecular and Culture-Based Investigation
Daniel B. DiGiulio, Roberto Romero, Harold P. Amogan, Juan Pedro Kusanovic, Elisabeth M. Bik, Francesca Gotsch, Chong Jai Kim, Offer Erez, Sam Edwin, David A. Relman
PLoS ONE. 2008; 3(8): e3056. Published online 2008 August 26. doi: 10.1371/journal.pone.0003056
PMCID:
PMC2516597
Abstract Full Text PDF–359K Supplementary Material
Bacterial Community in the Crop of the Hoatzin, a Neotropical Folivorous Flying Bird
Filipa Godoy-Vitorino, Ruth E. Ley, Zhan Gao, Zhiheng Pei, Humberto Ortiz-Zuazaga, Luis R. Pericchi, Maria A. Garcia-Amado, Fabian Michelangeli, Martin J. Blaser, Jeffrey I. Gordon, Maria G. Domínguez-Bello
Appl Environ Microbiol. 2008 October; 74(19): 5905–5912. Published online 2008 August 8. doi: 10.1128/AEM.00574-08
PMCID:
PMC2565963
Abstract Full Text PDF–936K Supplementary Material
Gene prediction in metagenomic fragments: A large scale machine learning approach
Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
BMC Bioinformatics. 2008; 9: 217. Published online 2008 April 28. doi: 10.1186/1471-2105-9-217
PMCID:
PMC2409338
Abstract Full Text PDF–441K Supplementary Material
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