Publications
Aether: Leveraging Linear Programming For Optimal Cloud Computing In Genomics
JM Luber, BT Tierney, EM Cofer, CJ Patel, AD Kostic2017
An integrative view of microbiome-host interactions in inflammatory bowel diseases
M Wlodarska, AD Kostic, RJ Xavier • Cell Host & Microbe 17 (5), 577-5912015
RS Mehta, R Nishihara, Y Cao, M Song, K Mima, ... • JAMA Oncology 3 (7), 921-927
2017
KA Shaw, M Bertha, T Hofmekler, P Chopra, T Vatanen, A Srivatsa, J Prince, A Kumar, C Sauer, ME Zwick, GA Satten, AD Kostic, JG Mulle, RJ Xavier, S Kugathasan • Genome Medicine 8 (1), 75
2016
Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease
S Bullman, ML Meyerson, AD Kostic • Annual Review of Pathology: Mechanisms of Disease 12 (1)2017
Exploring host-microbiota interactions in animal models and humans
AD Kostic, MR Howitt, WS Garrett • Genes & Development 27, 701-7182013
K Mima, Y Sukawa, R Nishihara, ZR Qian, M Yamauchi, K Inamura, SA Kim, A Masuda, JA Nowak, K Nosho, AD Kostic, M Giannakis, H Watanabe, S Bullman, DA Milner, CC Harris, E Giovannucci, LA Garraway, GJ Freeman, G Dranoff, AT Chan, WS Garrett, C Huttenhower, CS Fuchs, S Ogino • JAMA Oncology 1 (5), 653-661
2015
Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location
K Mima, Y Cao, AT Chan, ZR Qian, JA Nowak, Y Masugi, Y Shi, M Song, A da Silva, M Gu, W Li, T Hamada, K Kosumi, A H, L Liu, AD Kostic, M Giannakis, S Bullman, CA Brennan, DA Milner, H Baba, LA Garraway, JA Meyerhardt, WS Garrett, C Huttenhower, M Meyerson, EL Giovannucci, CS Fuchs, R Nishihara, S Ogino • Clinical and Translational Gastroenterology 7, 2002016
Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis
K Mima, R Nishihara, ZR Qian, Y Cao, Y Sukawa, JA Nowak, J Yang, R Dou, Y Masugi, M Song, AD Kostic, M Giannakis, S Bullman, DA Milner, H Baba, EL Giovannucci, LA Garraway, GJ Freeman, G Dranoff, WS Garrett, C Huttenhower, M Meyerson, JA Meyerhardt, AT Chan, CS Fuchs, S Ogino • Gut 65, 1973-19802015
AD Kostic, E Chun, L Robertson, JN Glickman, CA Gallini, M Michaud, TE Clancy, DC Chung, P Lochhead, GL Hold, EM El-Omar, D Brenner, CS Fuchs, M Meyerson, WS Garrett • Cell Host & Microbe 14 (2), 207-215
2013
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
AD Kostic, D Gevers, CS Pedamallu, M Michaud, F Duke, AM Earl, AI Ojesina, J Jung, AJ Bass, J Tabernero, Baselga J, C Liu, RA Shivdasani, S Ogino, BW Birren, C Huttenhower, WS Garrett, M Meyerson • Genome Research 22 (2), 292-2982012
Gut Microbiota: Small Molecules Modulate Host Cellular Functions
JM Luber, AD Kostic • Current Biology 27 (8), R307 - R3102017
NK Pulloor, S Nair, AD Kostic, P Bist, JD Weaver, AM Riley, R Tyagi, PD Uchil, JD York, SH Snyder, A Garcia-Sastre, BVL Potter, R Lin, SB Shears, RJ Xavier, MN Krishnan • PLoS Pathog 10 (2), e1003981
2014
Inflammatory bowel disease as a model for translating the microbiome
C Huttenhower, AD Kostic, RJ Xavier • Immunity 40 (6), 843-8542014
AD Kostic, WS Garrett • EMBO Reports 13 (6), 478-480
2012
AD Kostic, E Chun, M Meyerson, WS Garrett • Cancer Immunology Research 1 (3), 150-157
2013
PathSeq: software to identify or discover microbes by deep sequencing of human tissue
AD Kostic, AI Ojesina, CS Pedamallu, J Jung, RG Verhaak, G Getz, M Meyerson • Nature Biotechnology 29 (5), 393-3962011
Prognostically relevant gene signatures of high-grade serous ovarian carcinoma
RGW Verhaak, P Tamayo, JY Yang, D Hubbard, H Zhang, CJ Creighton, S Fereday, M Lawrence, SL Carter, CH Mermel, AD Kostic, D Etemadmoghadam, G Saskena, K Cibulski, S Duraisamy, K Levanon, C Sougnez, A Tsherniak, S Gomez, R Onofrio, S Gabriel, L Chin, N Zhang, PT Spellman, Y Zhang, R Akbani, KA Hoadley, A Kahn, M Köbel, D Huntsman, RA Soslow, A Defazio, MJ Birrer, JW Gray, JN Weinstein, DD Bowtell, R Drapkin, JP Mesirov, G Getz, DA Levine, M Meyerson • The Journal of Clinical Investigation 123 (1), 517-5252013
Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome
AS Bhatt, SS Freeman, AF Herrera, CS Pedamallu, D Gevers, F Duke, J Jung, M Michaud, BJ Walker, S Young, AM Earl, AD Kostic, AI Ojesina, R Hasserjian, KK Ballen, YB Chen, G Hobbs, JH Antin, RJ Soiffer, LR Baden, WS Garrett, JL Hornick, FM Marty, M Meyerson • New England Journal of Medicine 369 (6), 517-5282013
AD Kostic, D Gevers, H Siljander, T Vatanen, T Hyötyläinen, AM Hämäläinen, A Peet, V Tillmann, P Pöhö, I Mattila, H Lähdesmäki, EA Franzosa, O Vaarala, M de Goffau, H Harmsen, J Ilonen, SM Virtanen, CB Clish, M Orešič, C Huttenhower, M Knip, RJ Xavier • Cell Host & Microbe 17 (2), 260-273
2015
The microbiome in inflammatory bowel disease: current status and the future ahead
AD Kostic, RJ Xavier, D Gevers • Gastroenterology 146 (6), 1489-14992014
The mutational landscape of head and neck squamous cell carcinoma
N Stransky, AM Egloff, AD Tward, AD Kostic, K Cibulskis, A Sivachenko, GV Kryukov, MS Lawrence, C Sougnez, A McKenna, E Shefler, AH Ramos, P Stojanov, SL Carter, D Voet, ML Cortés, D Auclair, MF Berger, G Saksena, C Guiducci, RC Onofrio, M Parkin, M Romkes, JL Weissfeld, RR Seethala, L Wang, C Rangel-Escareño, JC Fernandez-Lopez, A Hidalgo-Miranda, J Melendez-Zajgla, W Winckler, K Ardlie, SB Gabriel, M Meyerson, ES Lander, G Getz, TR Golub, LA Garraway, JR Grandis • Science 333 (6046), 1157-11602011
DCF Sealey, AD Kostic, C LeBel, F Pryde, L Harrington • BMC Molecular Biology 12 (1), 1
2011
D Gevers, S Kugathasan, LA Denson, Y Vázquez-Baeza, W Van Treuren, B Ren, E Schwager, D Knights, SJ Song, M Yassour, XC Morgan, AD Kostic, C Luo, A Gonzalez, D McDonald, Y Haberman, T Walters, S Baker, J Rosh, M Stephens, M Heyman, J Markowitz, R Baldassano, A Griffiths, F Sylvester, D Mack, S Kim, W Crandall, J Hyams, C Huttenhower, R Knight, RJ Xavier • Cell Host & Microbe 15 (3), 382-392
2014
Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans
T Vatanen, AD Kostic, E d'Hennezel, H Siljander, EA Franzosa, M Yassour, R Kolde, H Vlamakis, TD Arthur, AM Hämäläinen, A Peet, V Tillmann, R Uibo, S Mokurov, N Dorshakova, J Ilonen, SM Virtanen, SJ Szabo, JA Porter, H Lähdesmäki, C Huttenhower, D Gevers, TW Cullen, M Knip, RJ Xavier • Cell 165 (4), 842-8532016