Human Microbiome Project

Science Publications


 
Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.
Chen, Jun; Bushman, Frederic D; Lewis, James D; Wu, Gary D; Li, Hongzhe
Biostatistics (Oxford, England). 2013 Apr. 244-58 
PMID: 23074263 [PubMed]
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.
Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin J
The Journal of infectious diseases. 2013 Apr. 1105-14 
PMID: 23300163 [PubMed]
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.
Ursell, Luke K; Knight, Rob
Cell metabolism. 2013 Mar 5. 317-8 
PMID: 23473028 [PubMed]
Secondary structure improves OTU assignments of 16S rRNA gene sequences.
Schloss, Patrick D
The ISME journal. 2013 Mar. 457-60 
PMID: 23018771 [PubMed]
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.
Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, James
FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2013 Mar. 1012-22 
PMID: 23165986 [PubMed]
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity.
Markle, Janet G M; Frank, Daniel N; Mortin-Toth, Steven; Robertson, Charles E; Feazel, Leah M; Rolle-Kampczyk, Ulrike; von Bergen, Martin; McCoy, Kathy D; Macpherson, Andrew J; Danska, Jayne S
Science (New York, N.Y.). 2013 Mar 1. 1084-8 
PMID: 23328391 [PubMed]
Shallow breathing: bacterial life at low O(2).
Morris, Rachel L; Schmidt, Thomas M
Nature reviews. Microbiology. 2013 Mar. 205-12 
PMID: 23411864 [PubMed]
Nestly--a framework for running software with nested parameter choices and aggregating results.
McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick A
Bioinformatics (Oxford, England). 2013 Feb 1. 387-8 
PMID: 23220574 [PubMed]
Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis.
Ansong, Charles; Ortega, Corrie; Payne, Samuel H; Haft, Daniel H; Chauvigne-Hines, Lacie M; Lewis, Michael P; Ollodart, Anja R; Purvine, Samuel O; Shukla, Anil K; Fortuin, Suereta; Smith, Richard D; Adkins, Joshua N; Grundner, Christoph; Wright, Aaron T
Chemistry & biology. 2013 Jan 24. 123-33 
PMID: 23352146 [PubMed]
Propionibacterium Acnes Strain Populations in the Human Skin Microbiome Associated with Acne.
Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying
The Journal of investigative dermatology. 2013 Jan 21.  
PMID: 23337890 [PubMed]
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.
Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, Mircea
Environmental microbiology. 2013 Jan 18.  
PMID: 23387867 [PubMed]
Genomic variation landscape of the human gut microbiome.
Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R; Weinstock, George M; Bork, Peer
Nature. 2013 Jan 3. 45-50 
PMID: 23222524 [PubMed]
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.
Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob
The ISME journal. 2013 Jan. 85-95 
PMID: 22895161 [PubMed]
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.
Zhu, Zhengwei; Niu, Beifang; Chen, Jing; Wu, Sitao; Sun, Shulei; Li, Weizhong
Bioinformatics (Oxford, England). 2013 Jan 1. 122-3 
PMID: 23044549 [PubMed]
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy.
Tran, Truc T; Panesso, Diana; Gao, Hongyu; Roh, Jung H; Munita, Jose M; Reyes, Jinnethe; Diaz, Lorena; Lobos, Elizabeth A; Shamoo, Yousif; Mishra, Nagendra N; Bayer, Arnold S; Murray, Barbara E; Weinstock, George M; Arias, Cesar A
Antimicrobial agents and chemotherapy. 2013 Jan. 261-8 
PMID: 23114757 [PubMed]
Biodiversity and functional genomics in the human microbiome.
Morgan, Xochitl C; Segata, Nicola; Huttenhower, Curtis
Trends in genetics : TIG. 2013 Jan. 51-8 
PMID: 23140990 [PubMed]
TIGRFAMs and Genome Properties in 2013.
Haft, Daniel H; Selengut, Jeremy D; Richter, Roland A; Harkins, Derek; Basu, Malay K; Beck, Erin
Nucleic acids research. 2013 Jan. D387-95 
PMID: 23197656 [PubMed]
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J; Gevers, Dirk; Gordon, Jeffrey I; Knight, Rob; Mills, David A; Caporaso, J Gregory
Nature methods. 2013 Jan. 57-9 
PMID: 23202435 [PubMed]
An analysis of online messages about probiotics.
Brinich, Margaret A; Mercer, Mary Beth; Sharp, Richard R
BMC gastroenterology. 2013. 5 
PMID: 23311418 [PubMed]
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.
Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E
PLoS computational biology. 2013 Jan. e1002863 
PMID: 23326225 [PubMed]
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Division of Program Coordination, Planning, and Strategic Initiatives  •  National Institutes of Health  •  Bethesda, Maryland 20892