Harvard Catalyst Profiles

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Eric A. Franzosa, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. VanEvery H, Franzosa EA, Nguyen LH, Huttenhower C. Microbiome epidemiology and association studies in human health. Nat Rev Genet. 2022 Oct 05. PMID: 36198908.
    Citations:    Fields:    
  2. Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C. Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. Genome Biol. 2022 10 03; 23(1):208. PMID: 36192803.
    Citations: 1     Fields:    Translation:Humans
  3. Bhosle A, Wang Y, Franzosa EA, Huttenhower C. Progress and opportunities in microbial community metabolomics. Curr Opin Microbiol. 2022 Dec; 70:102195. PMID: 36063685.
    Citations:    Fields:    
  4. Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS. A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Nat Microbiol. 2022 09; 7(9):1404-1418. PMID: 35982310.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  5. 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. 2022 06 24; 38(Suppl 1):i378-i385. PMID: 35758795; PMCID: PMC9235493.
    Citations:    Fields:    Translation:Cells
  6. Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature. 2022 06; 606(7915):754-760. PMID: 35614211.
    Citations:    Fields:    Translation:HumansCells
  7. Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS. Human gut bacteria produce ??17-modulating bile acid metabolites. Nature. 2022 03; 603(7903):907-912. PMID: 35296854; PMCID: PMC9132548.
    Citations: 8     Fields:    Translation:HumansCells
  8. Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell. 2022 02 03; 185(3):513-529.e21. PMID: 35120663; PMCID: PMC8896310.
    Citations: 3     Fields:    Translation:Cells
  9. 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, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol. 2021 11; 17(11):e1009442. PMID: 34784344; PMCID: PMC8714082.
    Citations: 80     Fields:    Translation:Humans
  10. Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA, Janson L, Huttenhower C. A statistical model for describing and simulating microbial community profiles. PLoS Comput Biol. 2021 09; 17(9):e1008913. PMID: 34516542; PMCID: PMC8491899.
    Citations: 7     Fields:    
  11. Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe. 2021 09 08; 29(9):1366-1377.e9. PMID: 34416161; PMCID: PMC9064000.
    Citations: 15     Fields:    Translation:HumansCells
  12. Zhang Y, Thompson KN, Huttenhower C, Franzosa EA. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics. 2021 07 12; 37(Suppl_1):i34-i41. PMID: 34252963; PMCID: PMC8275336.
    Citations: 5     Fields:    
  13. Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT. Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Genome Med. 2021 06 17; 13(1):102. PMID: 34140026; PMCID: PMC8212460.
    Citations: 8     Fields:    Translation:HumansPHPublic Health
  14. Zhang Y, Thompson KN, Branck T, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci. 2021 07 20; 4:279-311. PMID: 34465175.
    Citations: 8     Fields:    Translation:HumansCells
  15. 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, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021 05 04; 10. PMID: 33944776; PMCID: PMC8096432.
    Citations: 94     Fields:    Translation:HumansCells
  16. Wilkinson JE, Franzosa EA, Everett C, Li C, Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower C. A framework for microbiome science in public health. Nat Med. 2021 05; 27(5):766-774. PMID: 33820996.
    Citations: 9     Fields:    Translation:HumansPHPublic Health
  17. Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol. 2020 12 11; 21(1):301. PMID: 33308267.
    Citations: 2     Fields:    Translation:HumansCells
  18. Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C. Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe. 2021 01 13; 29(1):94-106.e4. PMID: 33217332; PMCID: PMC7813156.
    Citations: 4     Fields:    Translation:HumansCells
  19. Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020 08 13; 12(1):71. PMID: 32791981.
    Citations: 19     Fields:    Translation:HumansPHPublic Health
  20. 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, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129. PMID: 32103176; PMCID: PMC7252668.
    Citations: 86     Fields:    Translation:HumansAnimals
  21. 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, Vlamakis H, Xavier RJ. Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol. 2020 03; 5(3):486-497. PMID: 31959971; PMCID: PMC7047597.
    Citations: 16     Fields:    Translation:HumansAnimalsCells
  22. Thingholm LB, Rühlemann MC, Koch M, Fuqua B, Laucke G, Boehm R, Bang C, Franzosa EA, Hübenthal M, Rahnavard A, Frost F, Lloyd-Price J, Schirmer M, Lusis AJ, Vulpe CD, Lerch MM, Homuth G, Kacprowski T, Schmidt CO, Nöthlings U, Karlsen TH, Lieb W, Laudes M, Franke A, Huttenhower C. Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. Cell Host Microbe. 2019 08 14; 26(2):252-264.e10. PMID: 31399369.
    Citations: 73     Fields:    Translation:HumansAnimalsCells
  23. 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. Nat Commun. 2019 07 17; 10(1):3136. PMID: 31316056.
    Citations: 48     Fields:    Translation:Humans
  24. 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, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 05; 569(7758):655-662. PMID: 31142855; PMCID: PMC6650278.
    Citations: 524     Fields:    Translation:HumansAnimalsCells
  25. 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, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe. 2019 05 08; 25(5):668-680.e7. PMID: 31071294; PMCID: PMC6544385.
    Citations: 80     Fields:    Translation:AnimalsCells
  26. 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, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 May; 4(5):898. PMID: 30971771.
    Citations: 6     Fields:    
  27. 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 Campylobacter showae. Emerg Microbes Infect. 2019; 8(1):827-840. PMID: 31169073.
    Citations: 3     Fields:    Translation:HumansCells
  28. 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, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 02; 4(2):293-305. PMID: 30531976; PMCID: PMC6342642.
    Citations: 349     Fields:    Translation:Humans
  29. 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. Nat Methods. 2018 11; 15(11):962-968. PMID: 30377376; PMCID: PMC6235447.
    Citations: 415     Fields:    Translation:HumansCells
  30. 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, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018 10; 562(7728):589-594. PMID: 30356183; PMCID: PMC6296767.
    Citations: 208     Fields:    Translation:HumansAnimalsCells
  31. 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, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Cell Host Microbe. 2018 10 10; 24(4):600-610.e4. PMID: 30308161; PMCID: PMC6277984.
    Citations: 60     Fields:    Translation:HumansCells
  32. McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018 04 01; 34(7):1235-1237. PMID: 29194469; PMCID: PMC6030947.
    Citations: 78     Fields:    
  33. Lai PS, Kolde R, Franzosa EA, Gaffin JM, Baxi SN, Sheehan WJ, Gold DR, Gevers D, Xavier RJ, Phipatanakul W. The classroom microbiome and asthma morbidity in children attending 3 inner-city schools. J Allergy Clin Immunol. 2018 06; 141(6):2311-2313. PMID: 29518428; PMCID: PMC5994187.
    Citations: 8     Fields:    Translation:HumansPHPublic Health
  34. 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 Med. 2018 01 29; 10(1):6. PMID: 29378630.
    Citations: 53     Fields:    Translation:Humans
  35. 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, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018 03; 3(3):337-346. PMID: 29311644.
    Citations: 145     Fields:    Translation:HumansCells
  36. 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. Sci Rep. 2017 12 15; 7(1):17686. PMID: 29247187.
    Citations: 38     Fields:    Translation:HumansCells
  37. Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol. 2017 11 30; 18(1):228. PMID: 29187204; PMCID: PMC5708111.
    Citations: 61     Fields:    Translation:HumansAnimals
  38. 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. 2017 11 09; 551(7679):256. PMID: 29022944.
    Citations: 9     Fields:    
  39. 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. 2017 10 05; 550(7674):61-66. PMID: 28953883; PMCID: PMC5831082.
    Citations: 372     Fields:    Translation:Humans
  40. 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. 2017 Jul-Aug; 2(4). PMID: 28808691; PMCID: PMC5547758.
    Citations: 5     
  41. 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, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ. Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host Microbe. 2017 Jul 12; 22(1):25-37.e6. PMID: 28704649; PMCID: PMC5672633.
    Citations: 184     Fields:    Translation:HumansAnimalsCells
  42. 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 LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016 12 15; 167(7):1897. PMID: 27984736.
    Citations: 77     Fields:    
  43. Hill JH, Franzosa EA, Huttenhower C, Guillemin K. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife. 2016 12 13; 5. PMID: 27960075.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  44. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016 11 03; 167(4):1125-1136.e8. PMID: 27814509; PMCID: PMC5131922.
    Citations: 272     Fields:    Translation:HumansAnimalsCells
  45. Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwer C, Koenen H, Joosten I, Xavier RJ, Wijmenga C. Understanding human immune function using the resources from the Human Functional Genomics Project. Nat Med. 2016 08 04; 22(8):831-3. PMID: 27490433.
    Citations: 28     Fields:    Translation:Humans
  46. 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. Sci Transl Med. 2016 06 15; 8(343):343ra81. PMID: 27306663; PMCID: PMC5032909.
    Citations: 333     Fields:    Translation:HumansCells
  47. 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, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, Xavier RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 Jun 02; 165(6):1551. PMID: 27259157.
    Citations: 83     Fields:    
  48. 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, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, Xavier RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 May 05; 165(4):842-53. PMID: 27133167.
    Citations: 373     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  49. 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 Med. 2016 Feb 17; 8(1):17. PMID: 26884067.
    Citations: 85     Fields:    Translation:HumansCells
  50. Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PLoS Comput Biol. 2015 Dec; 11(12):e1004557. PMID: 26682918; PMCID: PMC4684307.
    Citations: 105     Fields:    Translation:Humans
  51. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015 Oct; 12(10):902-3. PMID: 26418763.
    Citations: 714     Fields:    Translation:HumansCells
  52. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):E2930-8. PMID: 25964341; PMCID: PMC4460507.
    Citations: 158     Fields:    Translation:Humans
  53. 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. Nat Rev Microbiol. 2015 Jun; 13(6):360-72. PMID: 25915636; PMCID: PMC4800835.
    Citations: 195     Fields:    Translation:Humans
  54. 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. 2015; 3:e791. PMID: 26157642; PMCID: PMC4493686.
    Citations: 9     
  55. 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. 2015 Mar 11; 17(3):385-391. PMID: 25732063; PMCID: PMC4369771.
    Citations: 131     Fields:    Translation:Animals
  56. 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, Ilonen J, Virtanen SM, Clish CB, Orešic M, Huttenhower C, Knip M, Xavier RJ. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015 Feb 11; 17(2):260-73. PMID: 25662751; PMCID: PMC4689191.
    Citations: 411     Fields:    Translation:Humans
  57. Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. A proteome-scale map of the human interactome network. Cell. 2014 Nov 20; 159(5):1212-1226. PMID: 25416956; PMCID: PMC4266588.
    Citations: 552     Fields:    Translation:HumansAnimals
  58. 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. 2014 Oct 09; 159(2):227-30. PMID: 25303518.
    Citations: 33     Fields:    Translation:HumansAnimals
  59. 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. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):E2329-38. PMID: 24843156.
    Citations: 270     Fields:    Translation:HumansCells
  60. Garamszegi S, Franzosa EA, Xia Y. Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PLoS Pathog. 2013; 9(12):e1003778. PMID: 24339775.
    Citations: 21     Fields:    Translation:HumansCells
  61. 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 Med. 2013; 5(7):65. PMID: 23906180.
    Citations: 24     Fields:    
  62. Linghu B, Franzosa EA, Xia Y. Construction of functional linkage gene networks by data integration. Methods Mol Biol. 2013; 939:215-32. PMID: 23192549.
    Citations: 4     Fields:    Translation:Humans
  63. Franzosa EA, Xue R, Xia Y. Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. Genome Biol Evol. 2013; 5(4):734-44. PMID: 23512408.
    Citations: 7     Fields:    Translation:AnimalsCells
  64. Franzosa EA, Garamszegi S, Xia Y. Toward a three-dimensional view of protein networks between species. Front Microbiol. 2012; 3:428. PMID: 23267356.
    Citations: 14     
  65. Franzosa EA, Xia Y. Independent effects of protein core size and expression on residue-level structure-evolution relationships. PLoS One. 2012; 7(10):e46602. PMID: 23056364.
    Citations: 10     Fields:    
  66. Franzosa EA, Xia Y. Structural models for host-pathogen protein-protein interactions: assessing coverage and bias. Pac Symp Biocomput. 2012; 287-98. PMID: 22174284.
    Citations: 6     Fields:    Translation:HumansCells
  67. Franzosa EA, Albanèse V, Frydman J, Xia Y, McClellan AJ. Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PLoS One. 2011; 6(11):e28211. PMID: 22140548.
    Citations: 18     Fields:    Translation:AnimalsCells
  68. Franzosa EA, Xia Y. Structural principles within the human-virus protein-protein interaction network. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10538-43. PMID: 21680884.
    Citations: 57     Fields:    Translation:HumansCells
  69. Wang Y, Franzosa EA, Zhang XS, Xia Y. Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res. 2010 Oct; 38(18):5959-69. PMID: 20466810.
    Citations: 8     Fields:    
  70. Franzosa EA, Xia Y. Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol. 2009 Oct; 26(10):2387-95. PMID: 19597162.
    Citations: 85     Fields:    Translation:Animals
  71. Xia Y, Franzosa EA, Gerstein MB. Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput Biol. 2009 Jun; 5(6):e1000413. PMID: 19521505.
    Citations: 35     Fields:    Translation:Cells
  72. Franzosa E, Linghu B, Xia Y. Computational reconstruction of protein-protein interaction networks: algorithms and issues. Methods Mol Biol. 2009; 541:89-100. PMID: 19381528.
    Citations: 4     Fields:    Translation:Animals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.