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Aleksandar David Kostic, Ph.D.

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Biography
Broad Institute of MIT & Harvard, Cambridge, MAPostdoctoral Fellowship08/2016Microbiome-Immune Interfaces
Harvard University, Cambridge, MAPh.D.05/2013Biological & Biomedical Sciences
University of Toronto, Toronto, ONHon.B.Sc.05/2008Molecular Biology
2017 - 2022
Pathway to Stop Diabetes Initiator Award
2017 - 2019
Smith Family Awards Program for Excellence in Biomedical Research
2015 - 2016
Merck Fellow of the Helen Hay Whitney Foundation
2014 - 2016
The Lawrence H. Summers Postdoctoral Fellowship

Overview
Our research combines computational and experimental expertise to probe the relationship between the human microbiome and type 1 diabetes. We strive to generate a high-level understanding of how the molecular interactions between the immune system and our indigenous microbiome regulate human health. We have worked to characterize the developing infant gut microbiome in dense, longitudinal metagenomic analyses of birth cohorts at risk for type 1 diabetes, including mechanistic evidence by which the human microbiome may directly influence immune development and progression to type 1 diabetes. The ultimate goal of our lab is to develop new methods to diagnose and treat type 1 diabetes by deepening our understanding of the immunomodulatory effects of the diverse constituents of the symbiotic microbiota and their impact on autoimmunity.

Bibliographic
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. Ramanan D, Sefik E, Galván-Peña S, Wu M, Yang L, Yang Z, Kostic A, Golovkina TV, Kasper DL, Mathis D, Benoist C. An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint. Cell. 2020 Jun 11; 181(6):1276-1290.e13. PMID: 32402238.
    Citations:    
  2. Le Goallec A, Tierney BT, Luber JM, Cofer EM, Kostic AD, Patel CJ. A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type. PLoS Comput Biol. 2020 May; 16(5):e1007895. PMID: 32392251.
    Citations:    
  3. Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ. 2020; 8:e9001. PMID: 32337106.
    Citations:    
  4. Kostic AD. Reply to "Is physical performance (in mice) increased by Veillonella atypica or decreased by Lactobacillus bulgaricus?" J Sport Health Sci. 2020 May; 9(3):201-202. PMID: 32444144.
    Citations:    
  5. Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe. 2019 08 14; 26(2):283-295.e8. PMID: 31415755.
    Citations:    
  6. 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:    
  7. Scheiman J, Luber JM, Chavkin TA, MacDonald T, Tung A, Pham LD, Wibowo MC, Wurth RC, Punthambaker S, Tierney BT, Yang Z, Hattab MW, Avila-Pacheco J, Clish CB, Lessard S, Church GM, Kostic AD. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nat Med. 2019 07; 25(7):1104-1109. PMID: 31235964.
    Citations:    
  8. 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.
    Citations:    
  9. Luber JM, Kostic AD. A perfect storm: Genetics and anticommensal antibodies shore up type 1 diabetes. Sci Immunol. 2019 02 01; 4(32). PMID: 30709844.
    Citations:    Fields:    
  10. Jovanovic N, Mitrovic T, Cvetkovic VJ, Tošic S, Vitorovic J, Stamenkovic S, Nikolov V, Kostic A, Vidovic N, Krstic M, Jevtovic-Stoimenov T, Pavlovic D. The Impact of MGMT Promoter Methylation and Temozolomide Treatment in Serbian Patients with Primary Glioblastoma. Medicina (Kaunas). 2019 Feb 01; 55(2). PMID: 30717206.
    Citations:    
  11. Aguayo-Mazzucato C, Diaque P, Hernandez S, Rosas S, Kostic A, Caballero AE. Understanding the growing epidemic of type 2 diabetes in the Hispanic population living in the United States. Diabetes Metab Res Rev. 2019 02; 35(2):e3097. PMID: 30445663.
    Citations:    Fields:    
  12. Hamada T, Zhang X, Mima K, Bullman S, Sukawa Y, Nowak JA, Kosumi K, Masugi Y, Twombly TS, Cao Y, Song M, Liu L, da Silva A, Shi Y, Gu M, Li W, Koh H, Nosho K, Inamura K, Keum N, Wu K, Meyerhardt JA, Kostic AD, Huttenhower C, Garrett WS, Meyerson M, Giovannucci EL, Chan AT, Fuchs CS, Nishihara R, Giannakis M, Ogino S. Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status. Cancer Immunol Res. 2018 11; 6(11):1327-1336. PMID: 30228205.
    Citations:    Fields:    
  13. Luber JM, Tierney BT, Cofer EM, Patel CJ, Kostic AD. Aether: leveraging linear programming for optimal cloud computing in genomics. Bioinformatics. 2018 05 01; 34(9):1565-1567. PMID: 29228186.
    Citations: 1     Fields:    
  14. Orengo JM, Radin AR, Kamat V, Badithe A, Ben LH, Bennett BL, Zhong S, Birchard D, Limnander A, Rafique A, Bautista J, Kostic A, Newell D, Duan X, Franklin MC, Olson W, Huang T, Gandhi NA, Lipsich L, Stahl N, Papadopoulos NJ, Murphy AJ, Yancopoulos GD. Treating cat allergy with monoclonal IgG antibodies that bind allergen and prevent IgE engagement. Nat Commun. 2018 04 12; 9(1):1421. PMID: 29650949.
    Citations:    
  15. Fujisaka S, Avila-Pacheco J, Soto M, Kostic A, Dreyfuss JM, Pan H, Ussar S, Altindis E, Li N, Bry L, Clish CB, Kahn CR. Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites. Cell Rep. 2018 03 13; 22(11):3072-3086. PMID: 29539432.
    Citations: 1     Fields:    
  16. Fang C, Zhong H, Lin Y, Chen B, Han M, Ren H, Lu H, Luber JM, Xia M, Li W, Stein S, Xu X, Zhang W, Drmanac R, Wang J, Yang H, Hammarström L, Kostic AD, Kristiansen K, Li J. Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. Gigascience. 2018 03 01; 7(3):1-8. PMID: 29293960.
    Citations: 3     Fields:    Translation:HumansCells
  17. Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T, Hämäläinen AM, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A. 2017 07 25; 114(30):E6166-E6175. PMID: 28696303.
    Citations: 13     Fields:    Translation:HumansCells
  18. Mehta RS, Nishihara R, Cao Y, Song M, Mima K, Qian ZR, Nowak JA, Kosumi K, Hamada T, Masugi Y, Bullman S, Drew DA, Kostic AD, Fung TT, Garrett WS, Huttenhower C, Wu K, Meyerhardt JA, Zhang X, Willett WC, Giovannucci EL, Fuchs CS, Chan AT, Ogino S. Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue. JAMA Oncol. 2017 Jul 01; 3(7):921-927. PMID: 28125762.
    Citations: 20     Fields:    Translation:HumansCells
  19. Luber JM, Kostic AD. Gut Microbiota: Small Molecules Modulate Host Cellular Functions. Curr Biol. 2017 04 24; 27(8):R307-R310. PMID: 28441565.
    Citations: 1     Fields:    
  20. Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ. A Microbiome Foundation for the Study of Crohn's Disease. Cell Host Microbe. 2017 Mar 08; 21(3):301-304. PMID: 28279336.
    Citations: 6     Fields:    Translation:Humans
  21. Bullman S, Meyerson M, Kostic AD. Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease. Annu Rev Pathol. 2017 Jan 24; 12:217-244. PMID: 27959634.
    Citations: 1     Fields:    Translation:HumansAnimals
  22. Mima K, Cao Y, Chan AT, Qian ZR, Nowak JA, Masugi Y, Shi Y, Song M, da Silva A, Gu M, Li W, Hamada T, Kosumi K, Hanyuda A, Liu L, Kostic AD, Giannakis M, Bullman S, Brennan CA, Milner DA, Baba H, Garraway LA, Meyerhardt JA, Garrett WS, Huttenhower C, Meyerson M, Giovannucci EL, Fuchs CS, Nishihara R, Ogino S. Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location. Clin Transl Gastroenterol. 2016 Nov 03; 7(11):e200. PMID: 27811909.
    Citations: 20     
  23. Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016 07 13; 8(1):75. PMID: 27412252.
    Citations: 21     Fields:    Translation:HumansCells
  24. 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: 20     Fields:    
  25. 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: 83     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  26. Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, Giovannucci EL, Garraway LA, Freeman GJ, Dranoff G, Garrett WS, Huttenhower C, Meyerson M, Meyerhardt JA, Chan AT, Fuchs CS, Ogino S. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut. 2016 12; 65(12):1973-1980. PMID: 26311717.
    Citations: 71     Fields:    Translation:HumansCells
  27. Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS, Ogino S. Fusobacterium nucleatum and T Cells in Colorectal Carcinoma. JAMA Oncol. 2015 Aug; 1(5):653-61. PMID: 26181352.
    Citations: 68     Fields:    Translation:HumansCells
  28. Wlodarska M, Kostic AD, Xavier RJ. An integrative view of microbiome-host interactions in inflammatory bowel diseases. Cell Host Microbe. 2015 May 13; 17(5):577-91. PMID: 25974300.
    Citations: 41     Fields:    Translation:Humans
  29. 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.
    Citations: 149     Fields:    Translation:Humans
  30. Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014 Jun 19; 40(6):843-54. PMID: 24950204.
    Citations: 72     Fields:    Translation:HumansAnimals
  31. 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 12; 15(3):382-392. PMID: 24629344.
    Citations: 418     Fields:    Translation:HumansCells
  32. Pulloor NK, Nair S, McCaffrey K, Kostic AD, Bist P, Weaver JD, Riley AM, Tyagi R, Uchil PD, York JD, Snyder SH, García-Sastre A, Potter BV, Lin R, Shears SB, Xavier RJ, Krishnan MN. Human genome-wide RNAi screen identifies an essential role for inositol pyrophosphates in Type-I interferon response. PLoS Pathog. 2014 Feb; 10(2):e1003981. PMID: 24586175.
    Citations: 21     Fields:    Translation:HumansCells
  33. Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology. 2014 May; 146(6):1489-99. PMID: 24560869.
    Citations: 230     Fields:    Translation:HumansAnimalsCells
  34. Kostic AD, Chun E, Meyerson M, Garrett WS. Microbes and inflammation in colorectal cancer. Cancer Immunol Res. 2013 Sep; 1(3):150-7. PMID: 24777677.
    Citations: 12     Fields:    Translation:Humans
  35. Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, El-Omar EM, Brenner D, Fuchs CS, Meyerson M, Garrett WS. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013 Aug 14; 14(2):207-15. PMID: 23954159.
    Citations: 264     Fields:    Translation:HumansAnimalsCells
  36. Kostic AD, Howitt MR, Garrett WS. Exploring host-microbiota interactions in animal models and humans. Genes Dev. 2013 Apr 01; 27(7):701-18. PMID: 23592793.
    Citations: 71     Fields:    Translation:HumansAnimals
  37. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25. PMID: 23257362.
    Citations: 137     Fields:    Translation:HumansCTClinical Trials
  38. 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, Garrett WS, Meyerson M. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012 Feb; 22(2):292-8. PMID: 22009990.
    Citations: 389     Fields:    Translation:HumansCells
  39. Sealey DC, Kostic AD, LeBel C, Pryde F, Harrington L. The TPR-containing domain within Est1 homologs exhibits species-specific roles in telomerase interaction and telomere length homeostasis. BMC Mol Biol. 2011 Oct 18; 12:45. PMID: 22011238.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  40. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortés ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio RC, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR. The mutational landscape of head and neck squamous cell carcinoma. Science. 2011 Aug 26; 333(6046):1157-60. PMID: 21798893.
    Citations: 739     Fields:    Translation:HumansAnimalsCells
  41. Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011 May; 29(5):393-6. PMID: 21552235.
    Citations: 87     Fields:    Translation:HumansCells
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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.