Ennis D, Shmorak S, Jantscher-Krenn E & Yassour M. Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. Nat. Commun. 15, 894, 2024.
 

Kijner S, Ennis D, Shmorak S, Florentin A & Yassour M. CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat. Commun. 15, 105, 2024.
 

Bar O, Sudhof LS, Yockey LJ, Bergerat A, Moriel N, Andrews E, Ananthakrishnan AN, Xavier RJ, Yassour M & Mitchell CM. Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls. PLoS One 18, e0284709, 2023.

Hayashi A, Ruppo S, Heilbrun EE, Mazzoni C, Adar S, Yassour M, Rmaileh A A & Shaul Y D. GENI: A web server to identify gene set enrichments in tumor samples. Comput. Struct. Biotechnol. J. 21, 5531–5537, 2023.
 

Kennedy KM, de Goffau M C, … , Yassour M & Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613, 639–649, 2023. 
 

Vatanen T,... , Yassour M, … , Knip, M. & Xavier, R. J. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 185, 4921–4936.e15, 2022.

Martin VM, Virkud YV, Dahan E, Seay HL, Itzkovits D, Vlamakis H, Xavier R, Shreffler WG, Yuan Q & Yassour M. Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis. Microbiome. 2022 Sep.

Kijner S, Kolodny O, Yassour M. Human Milk Oligosaccharides and the Infant Gut Microbiome From an Ecological Perspective. Current Opinion in Microbiology. 2022 May 

Dahan E, Martin VM, Yassour M. EasyMap - an interactive web tool for evaluating and comparing associations of clinical variables and microbiome composition. Frontiers in Cellular and Infection Microbiology. 2022 May

Vorontsov O, Levitt L, Lilleri D, Vainer GW, Caplan O, Schreiber L, Arossa A, Spinillo A, Furione M, Alfi O, Oiknine-Djian E, Kupervaser M, Nevo Y, Elgavish S, Yassour M, Zavattoni M, Bdolah-Abram T, Baldanti F, Geal-Dor M, Zakay-Rones Z, Yanai N, Yagel S, Panet A, Wolf DG. Chemerin and galectin-3-binding protein are prognostic amniotic fluid biomarkers for congenital cytomegalovirus infection severity. The Journal of Clinical Investigation. 2022 Apr 19. 
 

Ennis D, Moriel N, Yassour M. Preemies going pro: How probiotic treatment matures the microbiome of extreme premature infants. Cell Host Microbe. 2022 May 11

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Kijner S, Cher A, Yassour M. The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides. Frontiers in Cellular and Infection Microbiology. 2022 Mar 18

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Vaishnav ED, de Boer CG, Molinet J, Yassour M, Fan L, Adiconis X, Thompson DA, Levin JZ, Cubillos FA, Regev A. The evolution, evolvability and engineering of gene regulatory DNA. Nature. 2022 Mar

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Moskovitz M, Nassar M, Moriel N, Cher A, Faibis S, Ram D, Zangen D, Yassour M, Steinberg D. Characterization of the Oral Microbiome Among Children With Type 1 Diabetes Compared With Healthy Children. Frontiers in Microbiology. 2021 Oct 29

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Barak N, Ben-Ami R, Sido T, Perri A, Shtoyer A, Rivkin M, Licht T, Peretz A, Magenheim J, Fogel I, Livneh A, Daitch Y, Oiknine-Djian E, Benedek G, Dor Y, Wolf D, Yassour M. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Science Translational Medicine. 2021 Feb 22.

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Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, Pochan S, Herman P, Carrigan M, Sharp K, Huttenhower C, Lander E, Vlamakis H, Xavier R, Yassour M. Delivery Mode Affects Stability of Early Infant Gut Microbiota. Cell Reports Medicine. 2020 Dec 22.
 

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, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol. 2019 Mar

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Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ. Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med. 2018 Nov

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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, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ. Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host Microbe. 2018 Jul

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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, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe. 2018 Jul

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Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D. SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies. Front Microbiol. 2018 Apr

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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, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 2017 Nov

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Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M; DIABIMMUNE Study Group, Xavier RJ. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016 Jun

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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; DIABIMMUNE Study Group, Xavier RJ. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016 May

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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
 

Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014

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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, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014 Mar

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Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug

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Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012 Feb

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Grabherr MG*, Haas BJ*, Yassour M*, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 May

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Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Comparative functional genomics of the fission yeasts. Science. 2011 May
 

Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol. 2010
 

Levin JZ*, Yassour M*, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010 Sep
 

Kim TS, Liu CL, Yassour M, Holik J, Friedman N, Buratowski S, Rando OJ. RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast. Genome Biol. 2010
 

Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010 Jan

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Yassour M*, Kaplan T*, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Ab-initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009 Mar

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Yassour M, Kaplan T, Jaimovich A, Friedman N. Nucleosome positioning fromtiling microarray data. Bioinformatics. 2008 Jul

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