| Year |
Citation |
Score |
| 2024 |
Wang K, Lo CH, Mehta RS, Nguyen LH, Wang Y, Ma W, Ugai T, Kawamura H, Ugai S, Takashima Y, Mima K, Arima K, Okadome K, Giannakis M, Sears CL, ... ... Huttenhower C, et al. An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk. Gastroenterology. PMID 39117122 DOI: 10.1053/j.gastro.2024.07.040 |
0.466 |
|
| 2024 |
Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, ... ... Huttenhower C, et al. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell. PMID 38981480 DOI: 10.1016/j.cell.2024.06.018 |
0.488 |
|
| 2024 |
Bhosle A, Bae S, Zhang Y, Chun E, Avila-Pacheco J, Geistlinger L, Pishchany G, Glickman JN, Michaud M, Waldron L, Clish CB, Xavier RJ, Vlamakis H, Franzosa EA, Garrett WS, ... Huttenhower C, et al. Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease. Molecular Systems Biology. PMID 38467837 DOI: 10.1038/s44320-024-00027-8 |
0.596 |
|
| 2024 |
Zolfo M, Silverj A, Blanco-Miguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, et al. Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. Biorxiv : the Preprint Server For Biology. PMID 38464031 DOI: 10.1101/2024.02.19.580813 |
0.536 |
|
| 2023 |
Wang Y, Ma W, Mehta R, Nguyen LH, Song M, Drew DA, Asnicar F, Huttenhower C, Segata N, Wolf J, Spector T, Berry S, Staller K, Chan AT. Diet and gut microbial associations in irritable bowel syndrome according to disease subtype. Gut Microbes. 15: 2262130. PMID 37786251 DOI: 10.1080/19490976.2023.2262130 |
0.486 |
|
| 2023 |
Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, ... ... Huttenhower C, et al. BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nature Biotechnology. PMID 37697152 DOI: 10.1038/s41587-023-01872-y |
0.71 |
|
| 2023 |
Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, ... ... Huttenhower C, et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology. PMID 36823356 DOI: 10.1038/s41587-023-01688-w |
0.553 |
|
| 2023 |
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, ... ... Huttenhower C, et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 613: 639-649. PMID 36697862 DOI: 10.1038/s41586-022-05546-8 |
0.53 |
|
| 2022 |
Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C. High-sensitivity pattern discovery in large, paired multiomic datasets. Bioinformatics (Oxford, England). 38: i378-i385. PMID 35758795 DOI: 10.1093/bioinformatics/btac232 |
0.568 |
|
| 2021 |
Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, ... ... Huttenhower C, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. PMID 34789871 DOI: 10.1038/s41591-021-01552-x |
0.681 |
|
| 2021 |
Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, ... ... Huttenhower C, et al. Multivariable association discovery in population-scale meta-omics studies. Plos Computational Biology. 17: e1009442. PMID 34784344 DOI: 10.1371/journal.pcbi.1009442 |
0.609 |
|
| 2021 |
Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 10. PMID 33944776 DOI: 10.7554/eLife.65088 |
0.562 |
|
| 2021 |
Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, ... ... Huttenhower C, et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature Medicine. PMID 33432175 DOI: 10.1038/s41591-020-01183-8 |
0.782 |
|
| 2020 |
Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Medicine. 12: 71. PMID 32791981 DOI: 10.1186/S13073-020-00765-Y |
0.332 |
|
| 2020 |
Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, ... ... Huttenhower C, et al. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biology. 21: 138. PMID 32513234 DOI: 10.1186/S13059-020-02042-Y |
0.568 |
|
| 2020 |
Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, ... ... Huttenhower C, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications. 11: 2500. PMID 32427907 DOI: 10.1038/S41467-020-16366-7 |
0.582 |
|
| 2020 |
Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, ... ... Huttenhower C, et al. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host & Microbe. PMID 32240601 DOI: 10.1016/J.Chom.2020.03.005 |
0.345 |
|
| 2020 |
Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, ... ... Huttenhower C, et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. PMID 32103176 DOI: 10.1038/S41586-020-2047-9 |
0.302 |
|
| 2020 |
Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, ... ... Huttenhower C, et al. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. PMID 31972239 DOI: 10.1053/J.Gastro.2019.12.029 |
0.301 |
|
| 2020 |
Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, Huttenhower C, Hartmann EM. Mobilizable antibiotic resistance genes are present in dust microbial communities. Plos Pathogens. 16: e1008211. PMID 31971995 DOI: 10.1371/Journal.Ppat.1008211 |
0.356 |
|
| 2020 |
Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, et al. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nature Microbiology. PMID 31959971 DOI: 10.1038/S41564-019-0655-7 |
0.344 |
|
| 2019 |
Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, ... ... Huttenhower C, et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications. 10: 5477. PMID 31792218 DOI: 10.1038/S41467-019-13443-4 |
0.599 |
|
| 2019 |
Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, ... ... Huttenhower C, et al. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host & Microbe. PMID 31607556 DOI: 10.1016/J.Chom.2019.08.018 |
0.554 |
|
| 2019 |
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, ... ... Huttenhower C, et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31399723 DOI: 10.1038/S41587-019-0252-6 |
0.516 |
|
| 2019 |
McBurney MI, Davis C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe ME. Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. The Journal of Nutrition. PMID 31373365 DOI: 10.1093/Jn/Nxz154 |
0.364 |
|
| 2019 |
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, ... ... Huttenhower C, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31341288 DOI: 10.1038/S41587-019-0209-9 |
0.487 |
|
| 2019 |
Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nature Communications. 10: 3136. PMID 31316056 DOI: 10.1038/S41467-019-10927-1 |
0.409 |
|
| 2019 |
Hsu T, Gemmell MR, Franzosa EA, Berry S, Mukhopadhya I, Hansen R, Michaud M, Nielsen H, Miller WG, Nielsen H, Bajaj-Elliott M, Huttenhower C, Garrett WS, Hold GL. Comparative genomics and genome biology of . Emerging Microbes & Infections. 8: 827-840. PMID 31169073 DOI: 10.1080/22221751.2019.1622455 |
0.362 |
|
| 2019 |
Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, ... ... Huttenhower C, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 569: 655-662. PMID 31142855 DOI: 10.1038/S41586-019-1237-9 |
0.341 |
|
| 2019 |
Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, et al. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host & Microbe. 25: 668-680.e7. PMID 31071294 DOI: 10.1016/J.Chom.2019.04.002 |
0.337 |
|
| 2019 |
Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, ... ... Huttenhower C, et al. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell. 176: 649-662.e20. PMID 30661755 DOI: 10.1016/J.Cell.2019.01.001 |
0.597 |
|
| 2019 |
Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L. HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. American Journal of Epidemiology. PMID 30649166 DOI: 10.1093/Aje/Kwz006 |
0.71 |
|
| 2019 |
Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, ... ... Huttenhower C, et al. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nature Communications. 10: 38. PMID 30604764 DOI: 10.1038/S41467-018-07841-3 |
0.342 |
|
| 2018 |
Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, ... ... Huttenhower C, et al. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nature Microbiology. PMID 30559407 DOI: 10.1038/S41564-018-0321-5 |
0.37 |
|
| 2018 |
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, ... ... Huttenhower C, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nature Microbiology. PMID 30531976 DOI: 10.1038/S41564-018-0306-4 |
0.361 |
|
| 2018 |
Sinha R, Ahsan H, Blaser M, Caporaso JG, Carmical JR, Chan AT, Fodor A, Gail MH, Harris CC, Helzlsouer K, Huttenhower C, Knight R, Kong HH, Lai GY, Hutchinson DLS, et al. Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017. Microbiome. 6: 210. PMID 30477563 DOI: 10.1186/S40168-018-0596-Z |
0.309 |
|
| 2018 |
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods. 15: 962-968. PMID 30377376 DOI: 10.1038/S41592-018-0176-Y |
0.599 |
|
| 2018 |
Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 562: 583-588. PMID 30356187 DOI: 10.1038/S41586-018-0617-X |
0.313 |
|
| 2018 |
Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, ... ... Huttenhower C, et al. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 562: 589-594. PMID 30356183 DOI: 10.1038/S41586-018-0620-2 |
0.347 |
|
| 2018 |
Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, Betancourt-Román CM, Brown GZ, Fretz M, Northcutt D, Siemens KN, Huttenhower C, Green JL, Van Den Wymelenberg K. Daylight exposure modulates bacterial communities associated with household dust. Microbiome. 6: 175. PMID 30333051 DOI: 10.1186/S40168-018-0559-4 |
0.303 |
|
| 2018 |
Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, ... ... Huttenhower C, et al. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Cell Host & Microbe. 24: 600-610.e4. PMID 30308161 DOI: 10.1016/J.Chom.2018.09.009 |
0.308 |
|
| 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 |
0.606 |
|
| 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 |
0.515 |
|
| 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 |
0.501 |
|
| 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 |
0.32 |
|
| 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 |
0.363 |
|
| 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 |
0.319 |
|
| 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 |
0.387 |
|
| 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 |
0.355 |
|
| 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 |
0.718 |
|
| 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 |
0.377 |
|
| 2017 |
Schwager E, Mallick H, Ventz S, Huttenhower C. A Bayesian method for detecting pairwise associations in compositional data. Plos Computational Biology. 13: e1005852. PMID 29140991 DOI: 10.1371/Journal.Pcbi.1005852 |
0.329 |
|
| 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 |
0.692 |
|
| 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 |
0.362 |
|
| 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 |
0.38 |
|
| 2017 |
Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Lima IGP, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, ... ... Huttenhower C, et al. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 5: 86. PMID 28810907 DOI: 10.1186/S40168-017-0285-3 |
0.36 |
|
| 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 |
0.333 |
|
| 2017 |
Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science (New York, N.Y.). 355. PMID 28183913 DOI: 10.1126/Science.Aai8386 |
0.321 |
|
| 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 |
0.553 |
|
| 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 |
0.358 |
|
| 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 |
0.37 |
|
| 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 |
0.342 |
|
| 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 |
0.621 |
|
| 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 |
0.576 |
|
| 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 |
0.319 |
|
| 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 |
0.333 |
|
| 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 |
0.357 |
|
| 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 |
0.329 |
|
| 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 |
0.364 |
|
| 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 |
0.335 |
|
| 2016 |
Liu TC, Gurram B, Baldridge M, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz M, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, ... Huttenhower C, et al. O-011 Paneth Cell Phenotypes Define a Subtype of Pediatric Crohn's Disease Through Alterations in Host-Microbial Interactions. Inflammatory Bowel Diseases. 22: S4. PMID 26849729 DOI: 10.1097/01.Mib.0000480097.23732.5E |
0.305 |
|
| 2016 |
Mukhopadhya I, Hsu T, Nielsen H, Berry S, Huttenhower C, Hold G. PWE-102 Elucidating The Role of Non JEJUNI/Coli-Campylobacter in The Development of Colorectal Cancer Utilising Comparative Genomics to Study Their Pathogenic Potential Gut. 65. DOI: 10.1136/Gutjnl-2016-312388.347 |
0.365 |
|
| 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 |
0.578 |
|
| 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 |
0.329 |
|
| 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 |
0.53 |
|
| 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 |
0.666 |
|
| 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 |
0.611 |
|
| 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 |
0.316 |
|
| 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 |
0.325 |
|
| 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 |
0.372 |
|
| 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 |
0.652 |
|
| 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 |
0.333 |
|
| 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 |
0.315 |
|
| 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 |
0.323 |
|
| 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. DOI: 10.1128/Microbe.10.419.1 |
0.388 |
|
| 2015 |
Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. Erratum: MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nature Methods. 13: 101-101. DOI: 10.1038/Nmeth0116-101B |
0.496 |
|
| 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 |
0.377 |
|
| 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 |
0.4 |
|
| 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 |
0.602 |
|
| 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 |
0.311 |
|
| 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 |
0.332 |
|
| 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 |
0.592 |
|
| 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 |
0.737 |
|
| 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 |
0.33 |
|
| 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 |
0.576 |
|
| 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 |
0.619 |
|
| 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 |
0.373 |
|
| 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 |
0.559 |
|
| 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 |
0.413 |
|
| 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 |
0.626 |
|
| 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 |
0.382 |
|
| 2014 |
Birrer MJ, Riester M, Wei W, Waldron L, Culhane A, Trippa L, Oliva E, Kim S, Michor F, Huttenhower C, Parmigiani G. Meta-analysis of public microarray databases for prognostic and predictive gene signatures of late-stage ovarian cancer. Journal of Clinical Oncology. 32: 5531-5531. DOI: 10.1200/Jco.2014.32.15_Suppl.5531 |
0.317 |
|
| 2014 |
Riester M, Wei W, Culhane AC, Trippa L, Michor F, Huttenhower C, Parmigiani G, Birrer M. Abstract 2355: Risk prediction for late-stage ovarian cancer by meta-analysis of 1,525 patient samples Cancer Research. 74: 2355-2355. DOI: 10.1158/1538-7445.Am2014-2355 |
0.311 |
|
| 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 |
0.394 |
|
| 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 |
0.307 |
|
| 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 |
0.55 |
|
| 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 |
0.405 |
|
| 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 |
0.707 |
|
| 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 |
0.577 |
|
| 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 |
0.32 |
|
| 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 |
0.393 |
|
| 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 |
0.365 |
|
| 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 |
0.616 |
|
| 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 |
0.634 |
|
| 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 |
0.596 |
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| 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 |
0.722 |
|
| 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 |
0.584 |
|
| 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. Author response: Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis Elife. DOI: 10.7554/Elife.01202.028 |
0.497 |
|
| 2013 |
Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ. Correction: Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis Plos Pathogens. 9. DOI: 10.1371/Annotation/4669E9E7-Fd12-4A01-Be2A-617B956Ec0Bb |
0.314 |
|
| 2013 |
McHardy I, Goudarzi M, Tong M, Ruegger P, Horvath S, Sonnenburg J, Graeber T, Huttenhower C, Borneman J, McGovern DP, Fornace A, Braun J. Tu1983 Comprehensive Inter-Omic Analysis Reveals Exquisite Metabolite-Driven Microbial Relationships Gastroenterology. 144: S-896-S-897. DOI: 10.1016/S0016-5085(13)63339-9 |
0.33 |
|
| 2013 |
Tong M, McHardy I, Ruegger P, Schwager E, Fleshner P, Li X, McGovern DP, Huttenhower C, Borneman J, Braun J. Sa1800 The Crohn's Disease Risk Locus FUT2 Selects for Microbial Functional Specialization in Normal Individuals That Predisposes to IBD Susceptibility Gastroenterology. 144: S-309. DOI: 10.1016/S0016-5085(13)61111-7 |
0.319 |
|
| 2012 |
Morgan XC, Huttenhower C. Chapter 12: Human microbiome analysis. Plos Computational Biology. 8: e1002808. PMID 23300406 DOI: 10.1371/Journal.Pcbi.1002808 |
0.4 |
|
| 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 |
0.371 |
|
| 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 |
0.688 |
|
| 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 |
0.341 |
|
| 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 |
0.373 |
|
| 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 |
0.6 |
|
| 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 |
0.591 |
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| 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 |
0.436 |
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| 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 |
0.618 |
|
| 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 |
0.398 |
|
| 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 |
0.368 |
|
| 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 |
0.718 |
|
| 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 |
0.75 |
|
| 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 |
0.617 |
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| 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 |
0.584 |
|
| 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 |
0.672 |
|
| 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 |
0.311 |
|
| 2012 |
Sokol H, Tickle TL, Korzenik JR, Sands BE, Xavier RJ, Huttenhower C. 190 Functional Aspects of the Intestinal Microbiome in Inflammatory Bowel Disease Gastroenterology. 142. DOI: 10.1016/S0016-5085(12)60179-6 |
0.367 |
|
| 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 |
0.575 |
|
| 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 |
0.632 |
|
| 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 |
0.613 |
|
| 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 |
0.591 |
|
| 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: 10.7490/F1000Research.1089522.1 |
0.716 |
|
| 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 |
0.578 |
|
| 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 |
0.337 |
|
| 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 |
0.303 |
|
| 2011 |
Segata N, Abubucker S, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Waldron L, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, ... ... Huttenhower C, et al. Microbial community function and biomarker discovery in the human microbiome Genome Biology. 12: P47. DOI: 10.1186/Gb-2011-12-S1-P47 |
0.639 |
|
| 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 |
0.572 |
|
| 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 |
0.584 |
|
| 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 |
0.425 |
|
| 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 |
0.571 |
|
| 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 |
0.62 |
|
| 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 |
0.789 |
|
| 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 |
0.721 |
|
| 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 |
0.797 |
|
| 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 |
0.802 |
|
| 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 |
0.771 |
|
| 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 |
0.791 |
|
| 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 |
0.672 |
|
| 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 |
0.594 |
|
| 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 |
0.737 |
|
| 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 |
0.64 |
|
| 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 |
0.8 |
|
| 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 |
0.774 |
|
| 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 |
0.537 |
|
| 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 |
0.55 |
|
| 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 |
0.781 |
|
| 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 |
0.724 |
|
| 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 |
0.795 |
|
| 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 |
0.508 |
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