Curtis Huttenhower, Ph.D. - Publications

Affiliations: 
2009 Princeton University, Princeton, NJ 
Area:
Bioinformatics Biology, Computer Science

166 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, ... ... Huttenhower C, et al. Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biology. 19: 142. PMID 30253799 DOI: 10.1186/s13059-018-1511-4  0.44
2018 Kosumi K, Hamada T, Koh H, Borowsky J, Bullman S, Twombly TS, Nevo D, Masugi Y, Liu L, da Silva A, Chen Y, Du C, Gu M, Li C, Li W, ... ... Huttenhower C, et al. The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome. The American Journal of Pathology. PMID 30243655 DOI: 10.1016/j.ajpath.2018.08.015  0.56
2018 Cho Y, Abu-Ali G, Tashiro H, Brown TA, Osgood R, Kasahara DI, Huttenhower C, Shore SA. Sex Differences in Pulmonary Responses to Ozone in Mice: Role of the Microbiome. American Journal of Respiratory Cell and Molecular Biology. PMID 30240285 DOI: 10.1165/rcmb.2018-0099OC  0.32
2018 Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, ... ... Huttenhower C, et al. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host & Microbe. 24: 146-154.e4. PMID 30001517 DOI: 10.1016/j.chom.2018.06.007  1
2018 Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, ... ... Huttenhower C, et al. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host & Microbe. 24: 133-145.e5. PMID 30001516 DOI: 10.1016/j.chom.2018.06.005  1
2018 McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, ... ... Huttenhower C, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. Msystems. 3. PMID 29795809 DOI: 10.1128/mSystems.00031-18  0.32
2018 Cho Y, Abu-Ali G, Tashiro H, Kasahara DI, Brown TA, Brand JD, Mathews JA, Huttenhower C, Shore SA. The Microbiome Regulates Pulmonary Responses to Ozone in Mice. American Journal of Respiratory Cell and Molecular Biology. PMID 29529379 DOI: 10.1165/rcmb.2017-0404OC  0.32
2018 Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/s41564-018-0114-x  0.32
2018 Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C. Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Medicine. 10: 6. PMID 29378630 DOI: 10.1186/s13073-018-0515-8  0.56
2018 Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nature Microbiology. PMID 29335555 DOI: 10.1038/s41564-017-0084-4  0.44
2018 Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm EB, ... ... Huttenhower C, et al. Stability of the human faecal microbiome in a cohort of adult men. Nature Microbiology. PMID 29335554 DOI: 10.1038/s41564-017-0096-0  0.44
2018 Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, ... ... Huttenhower C, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nature Microbiology. PMID 29311644 DOI: 10.1038/s41564-017-0089-z  0.56
2018 Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 3: 8-16. PMID 29255284 DOI: 10.1038/s41564-017-0072-8  0.32
2017 Börnigen D, Ren B, Pickard R, Li J, Ozer E, Hartmann EM, Xiao W, Tickle T, Rider J, Gevers D, Franzosa EA, Davey ME, Gillison ML, Huttenhower C. Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer. Scientific Reports. 7: 17686. PMID 29247187 DOI: 10.1038/s41598-017-17795-z  0.56
2017 McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: A meta'omic analysis environment. Bioinformatics (Oxford, England). PMID 29194469 DOI: 10.1093/bioinformatics/btx754  1
2017 Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biology. 18: 228. PMID 29187204 DOI: 10.1186/s13059-017-1359-z  0.6
2017 Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, ... ... Huttenhower C, et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Medicine. 9: 103. PMID 29183332 DOI: 10.1186/s13073-017-0490-5  0.44
2017 Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L. Accessible, curated metagenomic data through ExperimentHub. Nature Methods. 14: 1023-1024. PMID 29088129 DOI: 10.1038/nmeth.4468  1
2017 Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. PMID 29022944 DOI: 10.1038/nature24485  0.56
2017 Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Abnet CC, Knight R, White O, Huttenhower C. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nature Biotechnology. PMID 28967885 DOI: 10.1038/nbt.3981  0.32
2017 Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. PMID 28953883 DOI: 10.1038/nature23889  0.56
2017 Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, ... ... Huttenhower C, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science (New York, N.Y.). 357: 1156-1160. PMID 28912244 DOI: 10.1126/science.aah5043  0.56
2017 Golombos DM, Ayangbesan A, O'Malley P, Lewicki P, Barlow L, Barbieri CE, Chan C, DuLong C, Abu-Ali G, Huttenhower C, Scherr DS. The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: a Prospective, Pilot Study. Urology. PMID 28888753 DOI: 10.1016/j.urology.2017.08.039  0.32
2017 Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC. Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. Msystems. 2. PMID 28808691 DOI: 10.1128/mSystems.00047-17  0.6
2017 Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, ... ... Huttenhower C, et al. Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host & Microbe. 22: 25-37.e6. PMID 28704649 DOI: 10.1016/j.chom.2017.06.007  0.56
2017 Cao Y, Wu K, Mehta R, Drew DA, Song M, Lochhead P, Nguyen LH, Izard J, Fuchs CS, Garrett WS, Huttenhower C, Ogino S, Giovannucci EL, Chan AT. Long-term use of antibiotics and risk of colorectal adenoma. Gut. PMID 28377387 DOI: 10.1136/gutjnl-2016-313413  0.56
2017 Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Research. PMID 28167665 DOI: 10.1101/gr.216242.116  1
2017 Mehta RS, Nishihara R, Cao Y, Song M, Mima K, Qian ZR, Nowak JA, Kosumi K, Hamada T, Masugi Y, Bullman S, Drew DA, Kostic AD, Fung TT, Garrett WS, ... Huttenhower C, et al. Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium Nucleatum in Tumor Tissue. Jama Oncology. PMID 28125762 DOI: 10.1001/jamaoncol.2016.6374  0.56
2017 Gosmann C, Anahtar MN, Handley SA, Farcasanu M, Abu-Ali G, Bowman BA, Padavattan N, Desai C, Droit L, Moodley A, Dong M, Chen Y, Ismail N, Ndung'u T, Ghebremichael MS, ... ... Huttenhower C, et al. Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women. Immunity. PMID 28087240 DOI: 10.1016/j.immuni.2016.12.013  0.32
2016 Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, et al. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 167: 1897. PMID 27984736 DOI: 10.1016/j.cell.2016.11.046  0.56
2016 Rooks MG, Veiga P, Reeves AZ, Lavoie S, Yasuda K, Asano Y, Yoshihara K, Michaud M, Wardwell-Scott L, Gallini CA, Glickman JN, Sudo N, Huttenhower C, Lesser CF, Garrett WS. QseC inhibition as an antivirulence approach for colitis-associated bacteria. Proceedings of the National Academy of Sciences of the United States of America. PMID 27980034 DOI: 10.1073/pnas.1612836114  0.56
2016 Hill JH, Franzosa EA, Huttenhower C, Guillemin K. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife. 5. PMID 27960075 DOI: 10.7554/eLife.20145  0.56
2016 Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C. Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. Msystems. 1. PMID 27822528 DOI: 10.1128/mSystems.00018-16  0.6
2016 Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, et al. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 167: 1125-1136.e8. PMID 27814509 DOI: 10.1016/j.cell.2016.10.020  0.56
2016 Mima K, Cao Y, Chan AT, Qian ZR, Nowak JA, Masugi Y, Shi Y, Song M, da Silva A, Gu M, Li W, Hamada T, Kosumi K, Hanyuda A, Liu L, ... ... Huttenhower C, et al. Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location. Clinical and Translational Gastroenterology. 7: e200. PMID 27811909 DOI: 10.1038/ctg.2016.53  0.56
2016 Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. PMID 27802154 DOI: 10.1136/gutjnl-2016-312135  0.44
2016 Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biology. 17: 201. PMID 27687735 DOI: 10.1186/s13059-016-1062-5  0.44
2016 Hartmann EM, Hickey R, Hsu T, Betancourt Román CM, Chen J, Schwager R, Kline J, Brown GZ, Halden RU, Huttenhower C, Green JL. Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome. Environmental Science & Technology. PMID 27599587 DOI: 10.1021/acs.est.6b00262  0.72
2016 Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nature Microbiology. 1: 16070. PMID 27572971 DOI: 10.1038/nmicrobiol.2016.70  1
2016 Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, Xavier RJ. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Science Translational Medicine. 8: 343ra81. PMID 27306663 DOI: 10.1126/scitranslmed.aad0917  0.72
2016 Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, ... ... Huttenhower C, et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 165: 1551. PMID 27259157 DOI: 10.1016/j.cell.2016.05.056  0.56
2016 Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, ... ... Huttenhower C, et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. PMID 27133167 DOI: 10.1016/j.cell.2016.04.007  0.72
2016 Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, ... ... Huttenhower C, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science (New York, N.Y.). 352: 565-9. PMID 27126040 DOI: 10.1126/science.aad3369  0.72
2016 Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Medicine. 8: 51. PMID 27122046 DOI: 10.1186/s13073-016-0307-y  1
2016 Börnigen D, Tyekucheva S, Wang X, Rider JR, Lee GS, Mucci LA, Sweeney C, Huttenhower C. Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. Plos Computational Biology. 12: e1004820. PMID 27078000 DOI: 10.1371/journal.pcbi.1004820  1
2016 Lee KC, Stott MB, Dunfield PF, Huttenhower C, McDonald IR, Morgan XC. The Chthonomonas calidirosea genome is highly conserved across geography and distinct chemical and microbial environments in the Taupō Volcanic Zone, New Zealand. Applied and Environmental Microbiology. PMID 27060125 DOI: 10.1128/AEM.00139-16  0.72
2016 Drew DA, Lochhead P, Abu-Ali G, Chan AT, Huttenhower C, Izard J. "Fecal microbiome in epidemiologic studies" - Letter. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 26961995 DOI: 10.1158/1055-9965.EPI-16-0063  0.72
2016 Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C. Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Medicine. 8: 17. PMID 26884067 DOI: 10.1186/s13073-016-0271-6  1
2016 Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, No D, Gobourne A, Littmann E, Huttenhower C, Pamer EG, Wolchok JD. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nature Communications. 7: 10391. PMID 26837003 DOI: 10.1038/ncomms10391  0.72
2015 Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. Plos Computational Biology. 11: e1004557. PMID 26682918 DOI: 10.1371/journal.pcbi.1004557  1
2015 Sinha R, Abnet CC, White O, Knight R, Huttenhower C. The microbiome quality control project: baseline study design and future directions. Genome Biology. 16: 276. PMID 26653756 DOI: 10.1186/s13059-015-0841-8  0.72
2015 Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J. Cross-biome comparison of microbial association networks. Frontiers in Microbiology. 6: 1200. PMID 26579106 DOI: 10.3389/fmicb.2015.01200  0.72
2015 Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB. Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Standards in Genomic Sciences. 10: 101. PMID 26568784 DOI: 10.1186/s40793-015-0099-5  0.72
2015 Semenkovich CF, Danska J, Darsow T, Dunne JL, Huttenhower C, Insel RA, McElvaine AT, Ratner RE, Shuldiner AR, Blaser MJ. American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome. Diabetes. PMID 26420863 DOI: 10.2337/db15-0597  0.72
2015 Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature Methods. 12: 902-3. PMID 26418763 DOI: 10.1038/nmeth.3589  0.72
2015 Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, ... ... Huttenhower C, et al. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut. PMID 26311717 DOI: 10.1136/gutjnl-2015-310101  0.56
2015 Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, ... ... Huttenhower C, et al. Fusobacterium nucleatum and T Cells in Colorectal Carcinoma. Jama Oncology. PMID 26181352 DOI: 10.1001/jamaoncol.2015.1377  0.56
2015 Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C. A reproducible approach to high-throughput biological data acquisition and integration. Peerj. 3: e791. PMID 26157642 DOI: 10.7717/peerj.791  1
2015 Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Peerj. 3: e1029. PMID 26157614 DOI: 10.7717/peerj.1029  0.72
2015 Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, Padavattan N, Ismail N, Moodley A, Sabatini ME, Ghebremichael MS, Nusbaum C, Huttenhower C, Virgin HW, Ndung'u T, et al. Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity. 42: 965-76. PMID 25992865 DOI: 10.1016/j.immuni.2015.04.019  1
2015 Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. Identifying personal microbiomes using metagenomic codes. Proceedings of the National Academy of Sciences of the United States of America. 112: E2930-8. PMID 25964341 DOI: 10.1073/pnas.1423854112  1
2015 Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nature Reviews. Microbiology. 13: 360-72. PMID 25915636 DOI: 10.1038/nrmicro3451  1
2015 Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biology. 16: 67. PMID 25887922 DOI: 10.1186/s13059-015-0637-x  1
2015 Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host & Microbe. 17: 385-91. PMID 25732063 DOI: 10.1016/j.chom.2015.01.015  1
2015 Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, ... Huttenhower C, et al. Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. The Journal of Clinical Investigation. 125: 1363. PMID 25729854 DOI: 10.1172/JCI79657  0.72
2015 Pelle KG, Oh K, Buchholz K, Narasimhan V, Joice R, Milner DA, Brancucci NM, Ma S, Voss TS, Ketman K, Seydel KB, Taylor TE, Barteneva NS, Huttenhower C, Marti M. Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection. Genome Medicine. 7: 19. PMID 25722744 DOI: 10.1186/s13073-015-0133-7  1
2015 Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, ... ... Huttenhower C, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host & Microbe. 17: 260-73. PMID 25662751 DOI: 10.1016/j.chom.2015.01.001  1
2015 Trippa L, Waldron L, Huttenhower C, Parmigiani G. Bayesian nonparametric cross-study validation of prediction methods Annals of Applied Statistics. 9: 402-428. DOI: 10.1214/14-AOAS798  1
2015 Schwager E, Luo C, Huttenhower C, Morgan XC. Sequencing and other tools for studying microbial communities: Genomics and “meta’omic” tools are enabling us to explore the Microbiome from three complementary perspectives–taxonomic, functional, and ecological Microbe. 10: 419-425.  0.72
2014 Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, ... ... Huttenhower C, et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Medicine. 6: 107. PMID 25587358 DOI: 10.1186/s13073-014-0107-1  1
2014 Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metabolism. 20: 731-41. PMID 25440055 DOI: 10.1016/j.cmet.2014.10.003  1
2014 Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell. 159: 227-30. PMID 25303518 DOI: 10.1016/j.cell.2014.09.022  1
2014 Zhao SD, Parmigiani G, Huttenhower C, Waldron L. Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics (Oxford, England). 30: 3062-9. PMID 25061068 DOI: 10.1093/bioinformatics/btu488  1
2014 Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, ... Huttenhower C, et al. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. The Journal of Clinical Investigation. 124: 3617-33. PMID 25003194 DOI: 10.1172/JCI75436  1
2014 Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 40: 843-54. PMID 24950204 DOI: 10.1016/j.immuni.2014.05.013  1
2014 Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L. Cross-study validation for the assessment of prediction algorithms. Bioinformatics (Oxford, England). 30: i105-12. PMID 24931973 DOI: 10.1093/bioinformatics/btu279  1
2014 Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C. Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences of the United States of America. 111: E2329-38. PMID 24843156 DOI: 10.1073/pnas.1319284111  1
2014 Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ, Sonnenburg JL, McGovern DP, Borneman J, Braun J. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. The Isme Journal. 8: 2193-206. PMID 24781901 DOI: 10.1038/ismej.2014.64  1
2014 Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. Journal of the National Cancer Institute. 106. PMID 24700803 DOI: 10.1093/jnci/dju048  1
2014 Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. Journal of the National Cancer Institute. 106. PMID 24700801 DOI: 10.1093/jnci/dju049  1
2014 Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, ... ... Huttenhower C, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host & Microbe. 15: 382-92. PMID 24629344 DOI: 10.1016/j.chom.2014.02.005  1
2014 Shafquat A, Joice R, Simmons SL, Huttenhower C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends in Microbiology. 22: 261-6. PMID 24618403 DOI: 10.1016/j.tim.2014.01.011  1
2014 Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. The Isme Journal. 8: 1403-17. PMID 24500617 DOI: 10.1038/ismej.2014.3  1
2014 Morgan XC, Huttenhower C. Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology. 146: 1437-1448.e1. PMID 24486053 DOI: 10.1053/j.gastro.2014.01.049  1
2014 Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N. MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Research. 42: D617-24. PMID 24203705 DOI: 10.1093/nar/gkt1078  1
2014 Lee S, Cantarel B, Henrissat B, Gevers D, Birren BW, Huttenhower C, Ko G. Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. The Isme Journal. 8: 493-503. PMID 24108330 DOI: 10.1038/ismej.2013.167  1
2014 Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D. Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. Journal of Innate Immunity. 6: 253-62. PMID 23796786 DOI: 10.1159/000351912  1
2014 Gilbert JA, Ball M, Blainey P, Blaser MJ, Bohannan BJM, Bateman A, Bunge J, Dominguez-Bello MG, Epstein S, Fierer N, Gevers D, Grikscheit T, Hamdan LJ, Harvey J, Huttenhower C, et al. Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012 Standards in Genomic Sciences. DOI: 10.1186/1944-3277-9-13  1
2014 Ravel J, Blaser MJ, Braun J, Brown E, Bushman FD, Chang EB, Davies J, Dewey KG, Dinan T, Dominguez-Bello M, Erdman SE, Finlay BB, Garrett WS, Huffnagle GB, Huttenhower C, et al. Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 Microbiome. 2.  1
2013 McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ, Borneman J, Braun J. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome. 1: 17. PMID 24450808 DOI: 10.1186/2049-2618-1-17  1
2013 Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV, Kennedy MA, Huttenhower C, Newburg DS. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 1: 13. PMID 24450576 DOI: 10.1186/2049-2618-1-13  1
2013 Joice R, Narasimhan V, Montgomery J, Sidhu AB, Oh K, Meyer E, Pierre-Louis W, Seydel K, Milner D, Williamson K, Wiegand R, Ndiaye D, Daily J, Wirth D, Taylor T, ... Huttenhower C, et al. Inferring developmental stage composition from gene expression in human malaria. Plos Computational Biology. 9: e1003392. PMID 24348235 DOI: 10.1371/journal.pcbi.1003392  1
2013 Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJ. Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell. 155: 1296-308. PMID 24315099 DOI: 10.1016/j.cell.2013.10.045  1
2013 Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2: e01202. PMID 24192039 DOI: 10.7554/eLife.01202  1
2013 Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 31: 814-21. PMID 23975157 DOI: 10.1038/nbt.2676  1
2013 Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C. Two-stage microbial community experimental design. The Isme Journal. 7: 2330-9. PMID 23949665 DOI: 10.1038/ismej.2013.139  1
2013 Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature Communications. 4: 2304. PMID 23942190 DOI: 10.1038/ncomms3304  1
2013 Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology. Nucleic Acids Research. 41: e171. PMID 23921638 DOI: 10.1093/nar/gkt661  1
2013 Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Medicine. 5: 65. PMID 23906180 DOI: 10.1186/gm469  1
2013 Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. Plos One. 8: e64832. PMID 23741402 DOI: 10.1371/journal.pone.0064832  1
2013 Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Molecular Systems Biology. 9: 666. PMID 23670539 DOI: 10.1038/msb.2013.22  1
2013 Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biology. 14: 113. PMID 23651518 DOI: 10.1186/gb-2013-14-4-113  1
2013 Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 102: 1-7. PMID 23570996 DOI: 10.1016/j.ygeno.2013.03.009  1
2013 Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. Translating the human microbiome. Nature Biotechnology. 31: 304-8. PMID 23563424 DOI: 10.1038/nbt.2543  1
2013 Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L. curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database : the Journal of Biological Databases and Curation. 2013: bat013. PMID 23550061 DOI: 10.1093/database/bat013  1
2013 Ballarini A, Segata N, Huttenhower C, Jousson O. Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. Plos One. 8: e55764. PMID 23409037 DOI: 10.1371/journal.pone.0055764  1
2013 Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. Plos Computational Biology. 9: e1002863. PMID 23326225 DOI: 10.1371/journal.pcbi.1002863  1
2013 Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends in Genetics : Tig. 29: 51-8. PMID 23140990 DOI: 10.1016/j.tig.2012.09.005  1
2012 Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. Plos Computational Biology. 8: e1002808. PMID 23300406 DOI: 10.1371/journal.pcbi.1002808  1
2012 Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. Plos Computational Biology. 8: e1002779. PMID 23209389 DOI: 10.1371/journal.pcbi.1002779  1
2012 Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, ... ... Huttenhower C, et al. Expression profiling of archival tumors for long-term health studies. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 6136-46. PMID 23136189 DOI: 10.1158/1078-0432.CCR-12-1915  1
2012 Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ. Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. Plos Pathogens. 8: e1002946. PMID 23028335 DOI: 10.1371/journal.ppat.1002946  1
2012 Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biology. 13: R79. PMID 23013615 DOI: 10.1186/gb-2012-13-9-r79  1
2012 Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C. The Human Microbiome Project: a community resource for the healthy human microbiome. Plos Biology. 10: e1001377. PMID 22904687 DOI: 10.1371/journal.pbio.1001377  1
2012 Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. Plos Computational Biology. 8: e1002606. PMID 22807668 DOI: 10.1371/journal.pcbi.1002606  1
2012 Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. Plos One. 7: e36466. PMID 22719832 DOI: 10.1371/journal.pone.0036466  1
2012 Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA. A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). Plos One. 7: e29044. PMID 22719821 DOI: 10.1371/journal.pone.0029044  1
2012 Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, ... ... Huttenhower C, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. Plos Computational Biology. 8: e1002358. PMID 22719234 DOI: 10.1371/journal.pcbi.1002358  1
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/nature11209  1
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/nature11234  1
2012 Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology. 13: R42. PMID 22698087 DOI: 10.1186/gb-2012-13-6-r42  1
2012 Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. 9: 811-4. PMID 22688413 DOI: 10.1038/nmeth.2066  1
2012 Morikawa T, Tanaka N, Kuchiba A, Nosho K, Yamauchi M, Hornick JL, Swanson RS, Chan AT, Meyerhardt JA, Huttenhower C, Schrag D, Fuchs CS, Ogino S. Predictors of lymph node count in colorectal cancer resections: data from US nationwide prospective cohort studies. Archives of Surgery (Chicago, Ill. : 1960). 147: 715-23. PMID 22508672 DOI: 10.1001/archsurg.2012.353  1
2012 Yamauchi M, Lochhead P, Morikawa T, Huttenhower C, Chan AT, Giovannucci E, Fuchs C, Ogino S. Colorectal cancer: a tale of two sides or a continuum? Gut. 61: 794-7. PMID 22490520 DOI: 10.1136/gutjnl-2012-302014  1
2012 Waldron L, Simpson P, Parmigiani G, Huttenhower C. Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. Bmc Cancer. 12: 124. PMID 22458912 DOI: 10.1186/1471-2407-12-124  1
2012 Merrick CJ, Huttenhower C, Buckee C, Amambua-Ngwa A, Gomez-Escobar N, Walther M, Conway DJ, Duraisingh MT. Epigenetic dysregulation of virulence gene expression in severe Plasmodium falciparum malaria. The Journal of Infectious Diseases. 205: 1593-600. PMID 22448008 DOI: 10.1093/infdis/jis239  1
2012 Yamauchi M, Morikawa T, Kuchiba A, Imamura Y, Qian ZR, Nishihara R, Liao X, Waldron L, Hoshida Y, Huttenhower C, Chan AT, Giovannucci E, Fuchs C, Ogino S. Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum. Gut. 61: 847-54. PMID 22427238 DOI: 10.1136/gutjnl-2011-300865  1
2012 Waldron L, Coller HA, Huttenhower C. Integrative approaches for microarray data analysis. Methods in Molecular Biology (Clifton, N.J.). 802: 157-82. PMID 22130880 DOI: 10.1007/978-1-61779-400-1_11  1
2012 Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, ... Huttenhower C, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Research. 22: 292-8. PMID 22009990 DOI: 10.1101/gr.126573.111  1
2011 Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biology. 12: 137. PMID 22204305 DOI: 10.1186/gb-2011-12-12-137  1
2011 Waldron L, Pintilie M, Tsao MS, Shepherd FA, Huttenhower C, Jurisica I. Optimized application of penalized regression methods to diverse genomic data. Bioinformatics (Oxford, England). 27: 3399-406. PMID 22156367 DOI: 10.1093/bioinformatics/btr591  1
2011 Segata N, Huttenhower C. Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. Plos One. 6: e24704. PMID 21931822 DOI: 10.1371/journal.pone.0024704  1
2011 Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host & Microbe. 10: 260-72. PMID 21925113 DOI: 10.1016/j.chom.2011.08.005  1
2011 Huttenhower C. Computational biology: plus c'est la même chose, plus ça change. Genome Biology. 12: 307. PMID 21861851 DOI: 10.1186/gb-2011-12-8-307  1
2011 Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biology. 12: R60. PMID 21702898 DOI: 10.1186/gb-2011-12-6-r60  1
2011 Livstone MS, Oughtred R, Heinicke S, Vernot B, Huttenhower C, Durand D, Dolinski K. Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD). Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 6.11. PMID 21400696 DOI: 10.1002/0471250953.bi0611s33  1
2011 Ballal SA, Gallini CA, Segata N, Huttenhower C, Garrett WS. Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Cellular Microbiology. 13: 508-17. PMID 21314883 DOI: 10.1111/j.1462-5822.2011.01572.x  1
2011 Morikawa T, Baba Y, Yamauchi M, Kuchiba A, Nosho K, Shima K, Tanaka N, Huttenhower C, Frank DA, Fuchs CS, Ogino S. STAT3 expression, molecular features, inflammation patterns, and prognosis in a database of 724 colorectal cancers. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 17: 1452-62. PMID 21310826 DOI: 10.1158/1078-0432.CCR-10-2694  1
2011 Wardwell LH, Huttenhower C, Garrett WS. Current concepts of the intestinal microbiota and the pathogenesis of infection. Current Infectious Disease Reports. 13: 28-34. PMID 21308452 DOI: 10.1007/s11908-010-0147-7  1
2011 Sathirapongsasuti JF, Sathira N, Suzuki Y, Huttenhower C, Sugano S. Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing. Nucleic Acids Research. 39: 1967-79. PMID 21062826 DOI: 10.1093/nar/gkq949  1
2010 Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. Bmc Systems Biology. 4: 180. PMID 21194434 DOI: 10.1186/1752-0509-4-180  0.68
2010 Park CY, Hess DC, Huttenhower C, Troyanskaya OG. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. Plos Computational Biology. 6: e1001009. PMID 21124865 DOI: 10.1371/journal.pcbi.1001009  1
2010 Tanaka N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino S. Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer. The American Journal of Pathology. 177: 2731-40. PMID 21037082 DOI: 10.2353/ajpath.2010.100361  1
2010 Baba Y, Nosho K, Shima K, Huttenhower C, Tanaka N, Hazra A, Giovannucci EL, Fuchs CS, Ogino S. Hypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis. Gastroenterology. 139: 1855-64. PMID 20682317 DOI: 10.1053/j.gastro.2010.07.050  1
2010 Huttenhower C, Hofmann O. A quick guide to large-scale genomic data mining. Plos Computational Biology. 6: e1000779. PMID 20523745 DOI: 10.1371/journal.pcbi.1000779  1
2010 Baba Y, Huttenhower C, Nosho K, Tanaka N, Shima K, Hazra A, Schernhammer ES, Hunter DJ, Giovannucci EL, Fuchs CS, Ogino S. Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Molecular Cancer. 9: 125. PMID 20507599 DOI: 10.1186/1476-4598-9-125  1
2009 Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. Bmc Bioinformatics. 10: 417. PMID 20003429 DOI: 10.1186/1471-2105-10-417  1
2009 Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA. Detailing regulatory networks through large scale data integration. Bioinformatics (Oxford, England). 25: 3267-74. PMID 19825796 DOI: 10.1093/bioinformatics/btp588  1
2009 Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics (Oxford, England). 25: 2404-10. PMID 19561015 DOI: 10.1093/bioinformatics/btp397  1
2009 Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. Plos Computational Biology. 5: e1000417. PMID 19543383 DOI: 10.1371/journal.pcbi.1000417  1
2009 Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods in Molecular Biology (Clifton, N.J.). 548: 273-93. PMID 19521830 DOI: 10.1007/978-1-59745-540-4_15  1
2009 Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. Plos Computational Biology. 5: e1000322. PMID 19300515 DOI: 10.1371/journal.pcbi.1000322  1
2009 Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. Plos Genetics. 5: e1000407. PMID 19300474 DOI: 10.1371/journal.pgen.1000407  1
2009 Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Research. 19: 1093-106. PMID 19246570 DOI: 10.1101/gr.082214.108  1
2009 Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. Plos Computational Biology. 5: e1000257. PMID 19119411 DOI: 10.1371/journal.pcbi.1000257  1
2008 Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics (Oxford, England). 24: i330-8. PMID 18586732 DOI: 10.1093/bioinformatics/btn160  1
2008 Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. The Sleipnir library for computational functional genomics. Bioinformatics (Oxford, England). 24: 1559-61. PMID 18499696 DOI: 10.1093/bioinformatics/btn237  1
2008 Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Molecular Biology of the Cell. 19: 352-67. PMID 17959824 DOI: 10.1091/mbc.E07-08-0779  1
2007 Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (Oxford, England). 23: 2692-9. PMID 17724061 DOI: 10.1093/bioinformatics/btm403  1
2007 Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. Bmc Bioinformatics. 8: 250. PMID 17626636 DOI: 10.1186/1471-2105-8-250  1
2007 Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 104: 2193-8. PMID 17287358 DOI: 10.1073/pnas.0607084104  1
2006 Huttenhower C, Troyanskaya OG. Bayesian data integration: a functional perspective. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 341-51. PMID 17369653  1
2006 Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. Bmc Bioinformatics. 7: 443. PMID 17032457 DOI: 10.1186/1471-2105-7-443  1
2006 Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics (Oxford, England). 22: 2890-7. PMID 17005538 DOI: 10.1093/bioinformatics/btl492  1
2006 Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. Bmc Genomics. 7: 187. PMID 16869964 DOI: 10.1186/1471-2164-7-187  1
2005 Huttenhower C, Troyanskaya O. A general methodology for integration of microarray data 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 109. DOI: 10.1109/CSBW.2005.8  1
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