Cited by ..

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

Is Cited by the Following 37 Articles in this Archive:

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

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

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

The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

Philip McKenna, Christian Hoffmann, Nana Minkah, Pyone Pyone Aye, Andrew Lackner, Zongzhi Liu, Catherine A Lozupone, Micah Hamady, Rob Knight, Frederic D Bushman

PLoS Pathog. 2008 February; 4(2): e20. Published online 2008 February 1. doi: 10.1371/journal.ppat.0040020

PMCID:: PMC2222957

Abstract Full Text PDF–682K Supplementary Material

Novel Microarray Design Strategy To Study Complex Bacterial Communities

Antoine Huyghe, Patrice Francois, Yvan Charbonnier, Manuela Tangomo-Bento, Eve-Julie Bonetti, Bruce J. Paster, Ignacio Bolivar, Denise Baratti-Mayer, Didier Pittet, Jacques Schrenzel, and the Geneva Study Group on Noma (GESNOMA)

Appl Environ Microbiol. 2008 March; 74(6): 1876–1885. Published online 2008 January 18. doi: 10.1128/AEM.01722-07