Research Overview

The Flannick Lab develops computational approaches to use human genetic and broader genomic data to understand or better treat human diseases, with a current focus on diabetes. Our research lies at the intersection of computer science, statistical genetics, and computational biology, and it includes the development of fundamental statistical methods and computational algorithms, large-scale exome sequence association analysis, and computational disease modeling. We are interested specifically in developing methods to quantify the phenotypic and molecular effects of coding mutations, so that they might be used to identify or prioritize novel therapeutic targets. We also have a commitment to make genetic data and tools more useful to communities who traditionally lack the means to access or interpret it.

Laboratory Projects

  1. Interpretation of coding mutations from large-scale exome sequence data:We are involved in international consortia to aggregate and analyze exome sequence data for associations with metabolic traits, with sample sizes currently exceeding 50,000 and expected to exceed hundreds of thousands in the next few years. Our goals are to develop methods to use these data to quantify the likelihood that molecular perturbations of hypothesized disease genes impact disease-relevant phenotypes.
  2. Using data from common diseases to understand rare diseases:Because of their higher prevalence, more genetic data is often available for common diseases than for rare diseases. We are interested to explore whether data collected and analyzed for a common disease can be used to better understand rare diseases with overlapping clinical symptoms.
  3. Knowledge portals for human genetic disease:Our group develops and maintains the Knowledge Portal Network, a series of portals that aggregate and disseminate genetic association for a range of common diseases. Our goals, over time, are to extend these portals to rare diseases as well.
  4. Disease modeling and data integration:We are interested in computational models of the human disease process and using a variety of ‘omic datasets to calibrate these models, both to understand the molecular and cellular mechanisms of disease associations and to classify diseases based on shared pathophysiology. Our work on the NCATS Biomedical Translator is a first step toward this goal.

About Jason Flannick

Jason Flannick is an Assistant Professor of Pediatrics at Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital, and an Associate Member of the Broad Institute of Harvard and MIT. Dr. Flannick obtained his PhD in Computer Science at Stanford University before training as a Postdoctoral Fellow in Human Genetics at Massachusetts Hospital and the Broad Institute. Dr. Flannick plays a leadership role in several national and international genetics and bioinformatics consortia, including the Accelerating Medicines Partnership for Type 2 Diabetes, a public/private partnership that funds his group to develop a public knowledge portal to make human genetic data broadly accessible to the global research community. Dr. Flannick’s research has spanned pure computer science, comparative genomics, and finally human genetics, with a current focus on using computational and statistical methods to impact human health.

Selected Publications

Fuchsberger C*, Flannick J*, Teslovich TM*, Mahajan A*, Agarwala V*, Gaulton KJ*, et al. The genetic architecture of type 2 diabetes. Nature. 2016;536(7614):41-7.

Flannick J, Florez JC. Type 2 diabetes: genetic data sharing to advance complex disease research. Nature Reviews Genetics. 2016;17(9):535-49.

Flannick J, Johansson S, Njolstad PR. Common and rare forms of diabetes mellitus: towards a continuum of diabetes subtypes. Nature Reviews Endocrinology. 2016;12(7):394-406.

Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N et al. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nature Genetics. 2014;46(4):357-63.

Flannick J*, Beer NL*, Bick AG, Agarwala V, Molnes J et al. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nature Genetics. 2013;45(11):1380-5.

Agarwala V*, Flannick J*, Sunyaev S, GoTD Consortium, Altshuler D. Evaluating empirical bounds on complex disease genetic architecture. Nature Genetics. 2013;45(12):1418-27.

Researcher Services

PUBLICATIONS

Publications powered by Harvard Catalyst Profiles

  1. Gusarova V, O'Dushlaine C, Teslovich TM, Benotti PN, Mirshahi T, Gottesman O, Van Hout CV, Murray MF, Mahajan A, Nielsen JB, Fritsche L, Wulff AB, Gudbjartsson DF, Sjögren M, Emdin CA, Scott RA, Lee WJ, Small A, Kwee LC, Dwivedi OP, Prasad RB, Bruse S, Lopez AE, Penn J, Marcketta A, Leader JB, Still CD, Kirchner HL, Mirshahi UL, Wardeh AH, Hartle CM, Habegger L, Fetterolf SN, Tusie-Luna T, Morris AP, Holm H, Steinthorsdottir V, Sulem P, Thorsteinsdottir U, Rotter JI, Chuang LM, Damrauer S, Birtwell D, Brummett CM, Khera AV, Natarajan P, Orho-Melander M, Flannick J, Lotta LA, Willer CJ, Holmen OL, Ritchie MD, Ledbetter DH, Murphy AJ, Borecki IB, Reid JG, Overton JD, Hansson O, Groop L, Shah SH, Kraus WE, Rader DJ, Chen YI, Hveem K, Wareham NJ, Kathiresan S, Melander O, Stefansson K, Nordestgaard BG, Tybjærg-Hansen A, Abecasis GR, Altshuler D, Florez JC, Boehnke M, McCarthy MI, Yancopoulos GD, Carey DJ, Shuldiner AR, Baras A, Dewey FE, Gromada J. Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes. Nat Commun. 2018 Jun 13; 9(1):2252. View abstract
  2. Ganna A, Satterstrom FK, Zekavat SM, Das I, Kurki MI, Churchhouse C, Alfoldi J, Martin AR, Havulinna AS, Byrnes A, Thompson WK, Nielsen PR, Karczewski KJ, Saarentaus E, Rivas MA, Gupta N, Pietiläinen O, Emdin CA, Lescai F, Bybjerg-Grauholm J, Flannick J, Mercader JM, Udler M, Laakso M, Salomaa V, Hultman C, Ripatti S, Hämäläinen E, Moilanen JS, Körkkö J, Kuismin O, Nordentoft M, Hougaard DM, Mors O, Werge T, Mortensen PB, MacArthur D, Daly MJ, Sullivan PF, Locke AE, Palotie A, Børglum AD, Kathiresan S, Neale BM. Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum. Am J Hum Genet. 2018 Jun 07; 102(6):1204-1211. View abstract
  3. Bonàs-Guarch S, Guindo-Martínez M, Miguel-Escalada I, Grarup N, Sebastian D, Rodriguez-Fos E, Sánchez F, Planas-Fèlix M, Cortes-Sánchez P, González S, Timshel P, Pers TH, Morgan CC, Moran I, Atla G, González JR, Puiggros M, Martí J, Andersson EA, Díaz C, Badia RM, Udler M, Leong A, Kaur V, Flannick J, Jørgensen T, Linneberg A, Jørgensen ME, Witte DR, Christensen C, Brandslund I, Appel EV, Scott RA, Luan J, Langenberg C, Wareham NJ, Pedersen O, Zorzano A, Florez JC, Hansen T, Ferrer J, Mercader JM, Torrents D. Publisher Correction: Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes. Nat Commun. 2018 May 30; 9(1):2162. View abstract
  4. Mahajan A, Wessel J, Willems SM, Zhao W, Robertson NR, Chu AY, Gan W, Kitajima H, Taliun D, Rayner NW, Guo X, Lu Y, Li M, Jensen RA, Hu Y, Huo S, Lohman KK, Zhang W, Cook JP, Prins BP, Flannick J, Grarup N, Trubetskoy VV, Kravic J, Kim YJ, Rybin DV, Yaghootkar H, Müller-Nurasyid M, Meidtner K, Li-Gao R, Varga TV, Marten J, Li J, Smith AV, An P, Ligthart S, Gustafsson S, Malerba G, Demirkan A, Tajes JF, Steinthorsdottir V, Wuttke M, Lecoeur C, Preuss M, Bielak LF, Graff M, Highland HM, Justice AE, Liu DJ, Marouli E, Peloso GM, Warren HR, Afaq S, Afzal S, Ahlqvist E, Almgren P, Amin N, Bang LB, Bertoni AG, Bombieri C, Bork-Jensen J, Brandslund I, Brody JA, Burtt NP, Canouil M, Chen YI, Cho YS, Christensen C, Eastwood SV, Eckardt KU, Fischer K, Gambaro G, Giedraitis V, Grove ML, de Haan HG, Hackinger S, Hai Y, Han S, Tybjærg-Hansen A, Hivert MF, Isomaa B, Jäger S, Jørgensen ME, Jørgensen T, Käräjämäki A, Kim BJ, Kim SS, Koistinen HA, Kovacs P, Kriebel J, Kronenberg F, Läll K, Lange LA, Lee JJ, Lehne B, Li H, Lin KH, Linneberg A, Liu CT, Liu J, Loh M, Mägi R, Mamakou V, McKean-Cowdin R, Nadkarni G, Neville M, Nielsen SF, Ntalla I, Peyser PA, Rathmann W, Rice K, Rich SS, Rode L, Rolandsson O, Schönherr S, Selvin E, Small KS, Stancáková A, Surendran P, Taylor KD, Teslovich TM, Thorand B, Thorleifsson G, Tin A, Tönjes A, Varbo A, Witte DR, Wood AR, Yajnik P, Yao J, Yengo L, Young R, Amouyel P, Boeing H, Boerwinkle E, Bottinger EP, Chowdhury R, Collins FS, Dedoussis G, Dehghan A, Deloukas P, Ferrario MM, Ferrières J, Florez JC, Frossard P, Gudnason V, Harris TB, Heckbert SR, Howson JMM, Ingelsson M, Kathiresan S, Kee F, Kuusisto J, Langenberg C, Launer LJ, Lindgren CM, Männistö S, Meitinger T, Melander O, Mohlke KL, Moitry M, Morris AD, Murray AD, de Mutsert R, Orho-Melander M, Owen KR, Perola M, Peters A, Province MA, Rasheed A, Ridker PM, Rivadineira F, Rosendaal FR, Rosengren AH, Salomaa V, Sheu WH, Sladek R, Smith BH, Strauch K, Uitterlinden AG, Varma R, Willer CJ, Blüher M, Butterworth AS, Chambers JC, Chasman DI, Danesh J, van Duijn C, Dupuis J, Franco OH, Franks PW, Froguel P, Grallert H, Groop L, Han BG, Hansen T, Hattersley AT, Hayward C, Ingelsson E, Kardia SLR, Karpe F, Kooner JS, Köttgen A, Kuulasmaa K, Laakso M, Lin X, Lind L, Liu Y, Loos RJF, Marchini J, Metspalu A, Mook-Kanamori D, Nordestgaard BG, Palmer CNA, Pankow JS, Pedersen O, Psaty BM, Rauramaa R, Sattar N, Schulze MB, Soranzo N, Spector TD, Stefansson K, Stumvoll M, Thorsteinsdottir U, Tuomi T, Tuomilehto J, Wareham NJ, Wilson JG, Zeggini E, Scott RA, Barroso I, Frayling TM, Goodarzi MO, Meigs JB, Boehnke M, Saleheen D, Morris AP, Rotter JI, McCarthy MI. Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes. Nat Genet. 2018 Apr; 50(4):559-571. View abstract
  5. Merino J, Leong A, Liu CT, Porneala B, Walford GA, von Grotthuss M, Wang TJ, Flannick J, Dupuis J, Levy D, Gerszten RE, Florez JC, Meigs JB. Metabolomics insights into early type 2 diabetes pathogenesis and detection in individuals with normal fasting glucose. Diabetologia. 2018 06; 61(6):1315-1324. View abstract
  6. Kayatekin C, Amasino A, Gaglia G, Flannick J, Bonner JM, Fanning S, Narayan P, Barrasa MI, Pincus D, Landgraf D, Nelson J, Hesse WR, Costanzo M, Myers CL, Boone C, Florez JC, Lindquist S. Translocon Declogger Ste24 Protects against IAPP Oligomer-Induced Proteotoxicity. Cell. 2018 Mar 22; 173(1):62-73.e9. View abstract
  7. Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stancáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Sci Data. 2018 Jan 23; 5:180002. View abstract
  8. Bonàs-Guarch S, Guindo-Martínez M, Miguel-Escalada I, Grarup N, Sebastian D, Rodriguez-Fos E, Sánchez F, Planas-Fèlix M, Cortes-Sánchez P, González S, Timshel P, Pers TH, Morgan CC, Moran I, Atla G, González JR, Puiggros M, Martí J, Andersson EA, Díaz C, Badia RM, Udler M, Leong A, Kaur V, Flannick J, Jørgensen T, Linneberg A, Jørgensen ME, Witte DR, Christensen C, Brandslund I, Appel EV, Scott RA, Luan J, Langenberg C, Wareham NJ, Pedersen O, Zorzano A, Florez JC, Hansen T, Ferrer J, Mercader JM, Torrents D. Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes. Nat Commun. 2018 01 22; 9(1):321. View abstract
  9. Crawford KM, Gallego-Fabrega C, Kourkoulis C, Miyares L, Marini S, Flannick J, Burtt NP, von Grotthuss M, Alexander B, Costanzo MC, Vaishnav NH, Malik R, Hall JL, Chong M, Rosand J, Falcone GJ. Cerebrovascular Disease Knowledge Portal: An Open-Access Data Resource to Accelerate Genomic Discoveries in Stroke. Stroke. 2018 02; 49(2):470-475. View abstract
  10. Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stancáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JC, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Sci Data. 2017 12 19; 4:170179. View abstract
  11. Noh HJ, Tang R, Flannick J, O'Dushlaine C, Swofford R, Howrigan D, Genereux DP, Johnson J, van Grootheest G, Grünblatt E, Andersson E, Djurfeldt DR, Patel PD, Koltookian M, M Hultman C, Pato MT, Pato CN, Rasmussen SA, Jenike MA, Hanna GL, Stewart SE, Knowles JA, Ruhrmann S, Grabe HJ, Wagner M, Rück C, Mathews CA, Walitza S, Cath DC, Feng G, Karlsson EK, Lindblad-Toh K. Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive-compulsive disorder. Nat Commun. 2017 10 17; 8(1):774. View abstract
  12. Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukiainen T, Huerta-Chagoya A, Moreno-Macías H, Jablonski KA, Hanson RL, Walford GA, Moran I, Chen L, Agarwala V, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Rodríguez-Torres M, Segura-Kato Y, García-Ortiz H, Centeno-Cruz F, Barajas-Olmos F, Caulkins L, Puppala S, Fontanillas P, Williams AL, Bonàs-Guarch S, Hartl C, Ripke S, Tooley K, Lane J, Zerrweck C, Martínez-Hernández A, Córdova EJ, Mendoza-Caamal E, Contreras-Cubas C, González-Villalpando ME, Cruz-Bautista I, Muñoz-Hernández L, Gómez-Velasco D, Alvirde U, Henderson BE, Wilkens LR, Le Marchand L, Arellano-Campos O, Riba L, Harden M, Gabriel S, Abboud HE, Cortes ML, Revilla-Monsalve C, Islas-Andrade S, Soberon X, Curran JE, Jenkinson CP, DeFronzo RA, Lehman DM, Hanis CL, Bell GI, Boehnke M, Blangero J, Duggirala R, Saxena R, MacArthur D, Ferrer J, McCarroll SA, Torrents D, Knowler WC, Baier LJ, Burtt N, González-Villalpando C, Haiman CA, Aguilar-Salinas CA, Tusié-Luna T, Flannick J, Jacobs SBR, Orozco L, Altshuler D, Florez JC. A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. Diabetes. 2017 11; 66(11):2903-2914. View abstract
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  33. Ito K, Bick AG, Flannick J, Friedman DJ, Genovese G, Parfenov MG, Depalma SR, Gupta N, Gabriel SB, Taylor HA, Fox ER, Newton-Cheh C, Kathiresan S, Hirschhorn JN, Altshuler DM, Pollak MR, Wilson JG, Seidman JG, Seidman C. Increased burden of cardiovascular disease in carriers of APOL1 genetic variants. Circ Res. 2014 Feb 28; 114(5):845-50. View abstract
  34. Agarwala V, Flannick J, Sunyaev S, Altshuler D. Evaluating empirical bounds on complex disease genetic architecture. Nat Genet. 2013 Dec; 45(12):1418-27. View abstract
  35. Flannick J, Beer NL, Bick AG, Agarwala V, Molnes J, Gupta N, Burtt NP, Florez JC, Meigs JB, Taylor H, Lyssenko V, Irgens H, Fox E, Burslem F, Johansson S, Brosnan MJ, Trimmer JK, Newton-Cheh C, Tuomi T, Molven A, Wilson JG, O'Donnell CJ, Kathiresan S, Hirschhorn JN, Njølstad PR, Rolph T, Seidman JG, Gabriel S, Cox DR, Seidman CE, Groop L, Altshuler D. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nat Genet. 2013 Nov; 45(11):1380-5. View abstract
  36. Liu L, Sabo A, Neale BM, Nagaswamy U, Stevens C, Lim E, Bodea CA, Muzny D, Reid JG, Banks E, Coon H, Depristo M, Dinh H, Fennel T, Flannick J, Gabriel S, Garimella K, Gross S, Hawes A, Lewis L, Makarov V, Maguire J, Newsham I, Poplin R, Ripke S, Shakir K, Samocha KE, Wu Y, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Schellenberg GD, Sutcliffe JS, Daly MJ, Gibbs RA, Roeder K. Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls. PLoS Genet. 2013 Apr; 9(4):e1003443. View abstract
  37. Lim ET, Raychaudhuri S, Sanders SJ, Stevens C, Sabo A, MacArthur DG, Neale BM, Kirby A, Ruderfer DM, Fromer M, Lek M, Liu L, Flannick J, Ripke S, Nagaswamy U, Muzny D, Reid JG, Hawes A, Newsham I, Wu Y, Lewis L, Dinh H, Gross S, Wang LS, Lin CF, Valladares O, Gabriel SB, dePristo M, Altshuler DM, Purcell SM, State MW, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Daly MJ. Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron. 2013 Jan 23; 77(2):235-42. View abstract
  38. Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer JM, Alfredsson L, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch KA, Gregersen PK, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, Plenge RM. Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis. Am J Hum Genet. 2013 Jan 10; 92(1):15-27. View abstract
  39. Bick AG, Flannick J, Ito K, Cheng S, Vasan RS, Parfenov MG, Herman DS, DePalma SR, Gupta N, Gabriel SB, Funke BH, Rehm HL, Benjamin EJ, Aragam J, Taylor HA, Fox ER, Newton-Cheh C, Kathiresan S, O'Donnell CJ, Wilson JG, Altshuler DM, Hirschhorn JN, Seidman JG, Seidman C. Burden of rare sarcomere gene variants in the Framingham and Jackson Heart Study cohorts. Am J Hum Genet. 2012 Sep 07; 91(3):513-9. View abstract
  40. Flannick J, Korn JM, Fontanillas P, Grant GB, Banks E, Depristo MA, Altshuler D. Efficiency and power as a function of sequence coverage, SNP array density, and imputation. PLoS Comput Biol. 2012; 8(7):e1002604. View abstract
  41. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 Apr 04; 485(7397):242-5. View abstract
  42. Jimenez NL, Flannick J, Yahyavi M, Li J, Bardakjian T, Tonkin L, Schneider A, Sherr EH, Slavotinek AM. Targeted 'next-generation' sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations. BMC Med Genet. 2011 Dec 28; 12:172. View abstract
  43. Srinivasan BS, Evans EA, Flannick J, Patterson AS, Chang CC, Pham T, Young S, Kaushal A, Lee J, Jacobson JL, Patrizio P. A universal carrier test for the long tail of Mendelian disease. Reprod Biomed Online. 2010 Oct; 21(4):537-51. View abstract
  44. Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. J Comput Biol. 2009 Aug; 16(8):1001-22. View abstract
  45. Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, Crosson S. Genetic and computational identification of a conserved bacterial metabolic module. PLoS Genet. 2008 Dec; 4(12):e1000310. View abstract
  46. Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Brief Bioinform. 2007 Sep; 8(5):318-32. View abstract
  47. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Res. 2006 Sep; 16(9):1169-81. View abstract
  48. Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Res. 2005; 33(14):4563-77. View abstract