Johns Hopkins Medicine

About

What We Do

Modern genetics involves the decoding of biological information encoded in organismal genomes and how this DNA code specifies phenotypes, be they biochemical or organismal. Genetics is also concerned with elucidating how various biological processes maintain or alter this code, its mechanism of transmission across generations and its evolution. Human genetics is the specific study of these questions in humans, studies that raise new challenges both because we cannot design genetic crosses as we do in model organisms but also because we can study phenotypes unique to humans, such as mental illness. A particular focus of human genetics is to understand the molecular basis of human disease and, thus, disease pathophysiology.

Our laboratory focuses on the formulation, development and application of genetic, genomic, and computational technologies and perspectives for discovery of genes and mechanisms in a variety of complex (non-Mendelian) human diseases. Specifically, we use a variety of human patients, their families and animal models of these disorders to infer the genetic characteristics of two developmental disorders of neuronal function (Hirschsprung disease, autism) and two late age-at-onset cardiovascular disorders (hypertension, sudden cardiac death). These disorders represent the extremes of genetic action, provide us with different models of non-Mendelian inheritance and articulate the importance of gene regulatory networks in human disease.

Common human diseases, be they birth defects, diabetes, cardiovascular disease, infectious disease, psychiatric illness or neurodegenerative disease, are familial and arise from a combination of genetic and environmental factors. The familial nature of most diseases suggests an underlying genetic susceptibility, but environmental, stochastic and epigenetic factors are also critical. Additional genetic hallmarks of complex disorders are that the underlying mutations are neither necessary nor sufficient for the development of disease, and that these mutations are common in the general population. Current genomic technologies, using the human genomic sequence, comparative sequence from many other vertebrates, a genome-wide map of polymorphic sites and emerging genome-wide maps of functional elements are all critical elements of this genetic dissection and the tools of our trade.

Our overall goals are to develop a paradigm for the genetics of common disease and to assess how genomic information can be used in modern clinical medicine in the era of personalized medicine.

Lab Members

Lab Gallery

Aravinda Chakravarti

Lab Alumni

Undergraduate Students

  • Patricia Viola (2015)
  • Prakash Chakraborty (2014)
  • Linda Xu (2013-2014)
  • Kameko Karasaki (2013-2014)
  • Ashley Gelata (2014)
  • Yun Ling (2012-2013)
  • Sayar Karmakar (2012)
  • Soudeep Deb (2011)
  • Christina Valerio (2010-2011)
  • Gaurav Dhar (2010)
  • Kinjal Basu (2010)
  • Kemi Abolade (2009-2010)
  • Saurabh Vyas (2009-2010)
  • Jaclyn Lim (2008-2009)
  • Carolyn Purington (2008)
  • Naiara Barbosa (2008)
  • Ada Davidoff (2008)
  • Parichoy Pal Chowdhury (2008)
  • Abhinash Saika (2007-2008)

MS Students

  • Kameko Karasaki (2016)
  • Vatsal Agarwal (2013)
  • Anne Kirwan (2012)
  • Jacqueline Wentworth (2011)
  • Audrey Lynn (1993)
  • Jennifer Scott (1993)
  • Laura Lasher (1991)
  • Sarah Shaw (1989)
  • Tara K. Cox (1988)
  • Susan A. Slaugenhaupt (1988)
  • Thomas R. Marino (1985)
  • Judith A. Badner (1984)
  • Kenneth H. Buetow (1983)
  • Nancy J. Wahl (1983)

High School Students

  • Arjun Rao (2011)
  • Eskender McCoy (2010)
  • Fady Hijji (2008-2009)
  • Laura Pisano (2008-2009)
  • John Rodgers (2007)
  • Kelly Beym (2007)
  • Erika Yeung (2006-2007)
  • Abena Bruce (2006)
  • Ijeoma Eboh (2006)

Research

Research in my laboratory focuses on the human genetics of complex traits and disease and the use of computational and animal models of human disease. Our studies cover three broad areas, as outlined below. Specifically, we are developing the principles and methods to do genetics ‘by sequence not breeding.’ The combination of whole genome studies (using genetic markers, sequencing or expression) and phenotypic analyses of patients, their family members and controls, can now allow the detailed dissection of both rare and common complex disorders into their component genes. Hypotheses of transmission and disease mechanism can then be studied using animal models (zebrafish and mouse). We are specifically interested in developing gene regulatory networks by cell types, that is groups of functionally interacting genes and their encoded proteins, as a basis for the multigenic action and interactions in complex traits.

Hirschsprung Disease Study

An Overview

Publications

  • All trainees are highlighted.
  • Dr. Chakravarti’s full publication list can be found here.
2017
  • Nandakumar P, Tin A, Grove ML, Ma J, Boerwinkle E, Coresh J, Chakravarti A: MicroRNAs in the miR-17 and miR-15 families are downregulated in chronic kidney disease with hypertension. PLoS One 12(8):e0176734, 2017. PMID 28771472.

  • Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, O’Reilly PF, Cabrera CP, Warren HR, Rose LM, Verwoert GC, Hottenga JJ, Strawbridge RJ, Esko T, Arking DE, Hwang SJ, Guo X, Kutalik Z, Trompet S, Shrine N, Teumer A, Ried JS, Bis JC, Smith AV, Amin N, Nolte IM, Lyytikäinen LP, Mahajan A, Wareham NJ, Hofer E, Joshi PK, Kristiansson K, Traglia M, Havulinna AS, Goel A, Nalls MA, Sõber S, Vuckovic D, Luan J, Del Greco M F, Ayers KL, Marrugat J, Ruggiero D, Lopez LM, Niiranen T, Enroth S, Jackson AU, Nelson CP, Huffman JE, Zhang W, Marten J, Gandin I, Harris SE, Zemunik T, Lu Y, Evangelou E, Shah N, de Borst MH, Mangino M, Prins BP, Campbell A, Li-Gao R, Chauhan G, Oldmeadow C, Abecasis G, Abedi M, Barbieri CM, Barnes MR, Batini C, Beilby J, Blake T, Boehnke M, Bottinger EP, Braund PS, Brown M, Brumat M, Campbell H, Chambers JC, Cocca M, Collins F, Connell J, Cordell HJ, Damman JJ, Davies G, de Geus EJ, de Mutsert R, Deelen J, Demirkale Y, Doney ASF, Dörr M, Farrall M, Ferreira T, Frånberg M, Gao H, Giedraitis V, Gieger C, Giulianini F, Gow AJ, Hamsten A, Harris TB, Hofman A, Holliday EG, Hui J, Jarvelin MR, Johansson Å, Johnson AD, Jousilahti P, Jula A, Kähönen M, Kathiresan S, Khaw KT, Kolcic I, Koskinen S, Langenberg C, Larson M, Launer LJ, Lehne B, Liewald DCM, Lin L, Lind L, Mach F, Mamasoula C, Menni C, Mifsud B, Milaneschi Y, Morgan A, Morris AD, Morrison AC, Munson PJ, Nandakumar P, Nguyen QT, Nutile T, Oldehinkel AJ, Oostra BA, Org E, Padmanabhan S, Palotie A, Paré G, Pattie A, Penninx BWJH, Poulter N, Pramstaller PP, Raitakari OT, Ren M, Rice K, Ridker PM, Riese H, Ripatti S, Robino A, Rotter JI, Rudan I, Saba Y, Saint Pierre A, Sala CF, Sarin AP, Schmidt R, Scott R, Seelen MA, Shields DC, Siscovick D, Sorice R, Stanton A, Stott DJ, Sundström J, Swertz M, Taylor KD, Thom S, Tzoulaki I, Tzourio C, Uitterlinden AG, Völker U, Vollenweider P, Wild S, Willemsen G, Wright AF, Yao J, Thériault S, Conen D, Attia J, Sever P, Debette S, Mook-Kanamori DO, Zeggini E, Spector TD, van der Harst P, Palmer CNA, Vergnaud AC, Loos RJF, Polasek O, Starr JM, Girotto G, Hayward C, Kooner JS, Lindgren CM, Vitart V, Samani NJ, Tuomilehto J, Gyllensten U, Knekt P, Deary IJ, Ciullo M, Elosua R, Keavney BD, Hicks AA, Scott RA, Gasparini P, Laan M, Liu Y, Watkins H, Hartman CA, Salomaa V, Toniolo D, Perola M, Wilson JF, Schmidt H, Zhao JH, Lehtimäki T, van Duijn CM, Gudnason V, Psaty BM, Peters A, Rettig R, James A, Jukema JW, Strachan DP, Palmas W, Metspalu A, Ingelsson E, Boomsma DI, Franco OH, Bochud M, Newton-Cheh C, Munroe PB, Elliott P, Chasman DI, Chakravarti A, Knight J, Morris AP, Levy D, Tobin MD, Snieder H, Caulfield MJ, Ehret GB: Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney. Hypertension pii: HYPERTENSIONAHA.117.09438, 2017. PMID 28739976.

  • Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium: Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia. Mol Autism 8:21, 2017. PMID 28540026. PMC5441062.

  • Weiner DJ, Wigdor EM, Ripke S, Walters RK, Kosmicki JA, Grove J, Samocha KE, Goldstein JI, Okbay A, Bybjerg-Grauholm J, Werge T, Hougaard DM, Taylor J; iPSYCH-Broad Autism Group; Psychiatric Genomics Consortium Autism Group, Skuse D, Devlin B, Anney R, Sanders SJ, Bishop S, Mortensen PB, Børglum AD, Smith GD, Daly MJ, Robinson EB: Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nat Genet 49(7):978-985, 2017. PMID 28504703.

  • Liang J, Le TH, Edwards DRV, Tayo BO, Gaulton KJ, Smith JA, Lu Y, Jensen RA, Chen G, Yanek LR, Schwander K, Tajuddin SM, Sofer T, Kim W, Kayima J, McKenzie CA, Fox E, Nalls MA, Young JH, Sun YV, Lane JM, Cechova S, Zhou J, Tang H, Fornage M, Musani SK, Wang H, Lee J, Adeyemo A, Dreisbach AW, Forrester T, Chu PL, Cappola A, Evans MK, Morrison AC, Martin LW, Wiggins KL, Hui Q, Zhao W, Jackson RD, Ware EB, Faul JD, Reiner AP, Bray M, Denny JC, Mosley TH, Palmas W, Guo X, Papanicolaou GJ, Penman AD, Polak JF, Rice K, Taylor KD, Boerwinkle E, Bottinger EP, Liu K, Risch N, Hunt SC, Kooperberg C, Zonderman AB, Laurie CC, Becker DM, Cai J, Loos RJF, Psaty BM, Weir DR, Kardia SLR, Arnett DK, Won S, Edwards TL, Redline S, Cooper RS, Rao DC, Rotter JI, Rotimi C, Levy D, Chakravarti A, Zhu X, Franceschini N: Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. PLoS Genet 13(5):e1006728, 2017. PMID 28498854. PMC5446189.

  • He KY, Wang H, Cade BE, Nandakumar P, Giri A, Ware EB, Haessler J, Liang J, Smith JA, Franceschini N, Le TH, Kooperberg C, Edwards TL, Kardia SL, Lin X, Chakravarti A, Redline S, Zhu X: Rare variants in fox-1 homolog A (RBFOX1) are associated with lower blood pressure. PLoS Genet 13(3):e1006678, 2017. PMID 28346479. PMC5386302.

  • Kapoor A, Auer DR, Lee D, Chatterjee S, Chakravarti A: Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development. Hum Mol Genet , 2017. PMID 28334784.

  • Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, Le TL, Lui VC, Luzón-Toro B, Matera I, Ngan ES, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CS, van den Hout MC, van der Linde HC, van Ham TJ, van IJcken WF, Verheij JB, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PK, Garcia-Barceló MM, Hofstra RM: Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biol 18(1):48, 2017. PMID 28274275. PMC5343413.

  • Nandakumar P, Lee D, Richard MA, Tekola-Ayele F, Tayo BO, Ware E, Sung YJ, Salako B, Ogunniyi A, Gu CC, Grove ML, Fornage M, Kardia S, Rotima C, Cooper RS, Morrison AC, Ehret G, Chakravarti A: Rare coding variants associated with blood pressure variation in 15914 individuals of African ancestry. J Hypertens , 2017. PMID 28234671.

  • Hoffmann TJ, Ehret GB, Nandakumar P, Ranatunga D, Schaefer C, Kwok P-Y, Iribarren C, Chakravarti A, Risch N: Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. Nat Genet 49(1):54-64, 2017. PMID 27841878. PMC5370207.

2016
  • Tang C S-m, Gui H, Kapoor A, Kim J-H, Luzon-Toro B, Pelet A, Burzynski G, Lantieri F, So M-t, Berrios C, Doo Shin H, Fernandez RM, Le T-L, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Guillermo A, Amiel J, Seo J-M, Kim D-Y, Oh J-T, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim H-Y, Sham PC, Tam PKH, Garcia-Barcelo M-M: Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet pii: ddw333, 2016. PMID 27702942.

  • Franceschini N, Carty CL, Lu Y, Tao R, Sung YJ, Manichaikul A, Haessler J, Fornage M, Schwander K, Zubair N, Bien S, Hindorff LA, Guo X, Bielinski SJ, Ehret G, Kaufman JD, Rich SS, Carlson CS, Bottinger EP, North KE, Rao DC, Chakravarti A, Barrett PQ, Loos RJ, Buyske S, Kooperberg C: Variant Discovery and Fine Mapping of Genetic Loci Associated with Blood Pressure Traits in Hispanics and African Americans. PLoS One 11(10):e0164132, 2016. PMID 27736895. PMC5063457.

  • Chatterjee S, Kapoor A, Akiyama JA, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio LA, Chakravarti A: Enhancer variants synergistically drive dysregulation of the RET gene regulatory network in Hirschsprung disease. Cell 167:355-368, 2016. PMID 27693352. PMC5113733.

  • Ehret GB, Ferreira T, Chasman DI, Jackson AU, Schmidt EM, Johnson T, Thorleifsson G, Luan J, Donnelly LA, Kanoni S, Petersen AK, Pihur V, Strawbridge RJ, Shungin D, Hughes MF, Meirelles O, Kaakinen M, Bouatia-Naji N, Kristiansson K, Shah S, Kleber ME, Guo X, Lyytikäinen LP, Fava C, Eriksson N, Nolte IM, Magnusson PK, Salfati EL, Rallidis LS, Theusch E, Smith AJ, Folkersen L, Witkowska K, Pers TH, Joehanes R, Kim SK, Lataniotis L, Jansen R, Johnson AD, Warren H, Kim YJ, Zhao W, Wu Y, Tayo BO, Bochud M; CHARGE-EchoGen Consortium; CHARGE-HF Consortium; Wellcome Trust Case Control Consortium, Absher D, Adair LS, Amin N, Arking DE, Axelsson T, Baldassarre D, Balkau B, Bandinelli S, Barnes MR, Barroso I, Bevan S, Bis JC, Bjornsdottir G, Boehnke M, Boerwinkle E, Bonnycastle LL, Boomsma DI, Bornstein SR, Brown MJ, Burnier M, Cabrera CP, Chambers JC, Chang IS, Cheng CY, Chines PS, Chung RH, Collins FS, Connell JM, Döring A, Dallongeville J, Danesh J, de Faire U, Delgado G, Dominiczak AF, Doney AS, Drenos F, Edkins S, Eicher JD, Elosua R, Enroth S, Erdmann J, Eriksson P, Esko T, Evangelou E, Evans A, Fall T, Farrall M, Felix JF, Ferrières J, Ferrucci L, Fornage M, Forrester T, Franceschini N, Franco OH, Franco-Cereceda A, Fraser RM, Ganesh SK, Gao H, Gertow K, Gianfagna F, Gigante B, Giulianini F, Goel A, Goodall AH, Goodarzi MO, Gorski M, Gräßler J, Groves CJ, Gudnason V, Gyllensten U, Hallmans G, Hartikainen AL, Hassinen M, Havulinna AS, Hayward C, Hercberg S, Herzig KH, Hicks AA, Hingorani AD, Hirschhorn JN, Hofman A, Holmen J, Holmen OL, Hottenga JJ, Howard P, Hsiung CA, Hunt SC, Ikram MA, Illig T, Iribarren C, Jensen RA, Kähönen M, Kang HM, Kathiresan S, Keating BJ, Khaw KT, Kim YK, Kim E, Kivimaki M, Klopp N, Kolovou G, Komulainen P, Kooner JS, Kosova G, Krauss RM, Kuh D, Kutalik Z, Kuusisto J, Kvaløy K, Lakka TA, Lee NR, Lee IT, Lee WJ, Levy D, Li X, Liang KW, Lin H, Lin L, Lindström J, Lobbens S, Männistö S, Müller G, Müller-Nurasyid M, Mach F, Markus HS, Marouli E, McCarthy MI, McKenzie CA, Meneton P, Menni C, Metspalu A, Mijatovic V, Moilanen L, Montasser ME, Morris AD, Morrison AC, Mulas A, Nagaraja R, Narisu N, Nikus K, O’Donnell CJ, O’Reilly PF, Ong KK, Paccaud F, Palmer CD, Parsa A, Pedersen NL, Penninx BW, Perola M, Peters A, Poulter N, Pramstaller PP, Psaty BM, Quertermous T, Rao DC, Rasheed A, Rayner NW, Renström F, Rettig R, Rice KM, Roberts R, Rose LM, Rossouw J, Samani NJ, Sanna S, Saramies J, Schunkert H, Sebert S, Sheu WH, Shin YA, Sim X, Smit JH, Smith AV, Sosa MX, Spector TD, Stančáková A, Stanton AV, Stirrups KE, Stringham HM, Sundstrom J, Swift AJ, Syvänen AC, Tai ES, Tanaka T, Tarasov KV, Teumer A, Thorsteinsdottir U, Tobin MD, Tremoli E, Uitterlinden AG, Uusitupa M, Vaez A, Vaidya D, van Duijn CM, van Iperen EP, Vasan RS, Verwoert GC, Virtamo J, Vitart V, Voight BF, Vollenweider P, Wagner A, Wain LV, Wareham NJ, Watkins H, Weder AB, Westra HJ, Wilks R, Wilsgaard T, Wilson JF, Wong TY, Yang TP, Yao J, Yengo L, Zhang W, Zhao JH, Zhu X, Bovet P, Cooper RS, Mohlke KL, Saleheen D, Lee JY, Elliott P, Gierman HJ, Willer CJ, Franke L, Hovingh GK, Taylor KD, Dedoussis G, Sever P, Wong A, Lind L, Assimes TL, Njølstad I, Schwarz PE, Langenberg C, Snieder H, Caulfield MJ, Melander O, Laakso M, Saltevo J, Rauramaa R, Tuomilehto J, Ingelsson E, Lehtimäki T, Hveem K, Palmas W, März W, Kumari M, Salomaa V, Chen YI, Rotter JI, Froguel P, Jarvelin MR, Lakatta EG, Kuulasmaa K, Franks PW, Hamsten A, Wichmann HE, Palmer CN, Stefansson K, Ridker PM, Loos RJ, Chakravarti A, Deloukas P, Morris AP, Newton- Cheh C, Munroe PB: The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals. Nature Genetics 48:1171-1184, 2016. PMID 27618452. PMC5042863.

  • Liu C, Kraja AT, Smith JA, Brody JA, Franceschini N, Bis JC, Rice K, Morrison AC, Lu Y, Weiss S, Guo X, Palmas W, Martin LW, Chen YI, Surendran P, Drenos F, Cook JP, Auer PL, Chu AY, Giri A, Zhao W, Jakobsdottir J, Lin LA, Stafford JM, Amin N, Mei H, Yao J, Voorman A; CHD Exome+ Consortium; ExomeBP Consortium; GoT2DGenes Consortium; T2D-GENES Consortium, Larson MG, Grove ML, Smith AV, Hwang SJ, Chen H, Huan T, Kosova G, Stitziel NO, Kathiresan S, Samani N, Schunkert H, Deloukas P; Myocardial Infarction Genetics and CARDIoGRAM Exome Consortia, Li M, Fuchsberger C, Pattaro C, Gorski M; CKDGen Consortium, Kooperberg C, Papanicolaou GJ, Rossouw JE, Faul JD, Kardia SL, Bouchard C, Raffel LJ, Uitterlinden AG, Franco OH, Vasan RS, O’Donnell CJ, Taylor KD, Liu K, Bottinger EP, Gottesman O, Daw EW, Giulianini F, Ganesh S, Salfati E, Harris TB, Launer LJ, Dörr M, Felix SB, Rettig R, Völzke H, Kim E, Lee WJ, Lee IT, Sheu WH, Tsosie KS, Edwards DR, Liu Y, Correa A, Weir DR, Völker U, Ridker PM, Boerwinkle E, Gudnason V, Reiner AP, van Duijn CM, Borecki IB, Edwards TL, Chakravarti A, Rotter JI, Psaty BM, Loos RJ, Fornage M, Ehret GB, Newton-Cheh C, Levy D, Chasman DI: Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. Nat Genet 48:1162-1170, 2016. PMID 27618448.

  • Kapoor A, Bakshy K, Xu L, Nandakumar P, Lee D, Boerwinkle E, Grove ML, Arking DE, Chakravarti A: Rare coding TTN variants are associated with electrocardiographic QT interval in the general population. Sci Reports 6:28356, 2016. PMID 27321809. PMC4913250.

  • Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L: The Genome Project – Write. Science 353:126-127, 2016. PMID 27256881.

  • Khayat M, Tilghman JM, Chervinsky I, Zalman L, Chakravarti A, Shalev S: A PIGN Mutation Responsible for Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome 1 (MCAHS1) in an Israeli-Arab Family. Amer J Med Genet Part A 170:176-182, 2016. PMID 26364997.

  • Rose A, Shah A, Venturini G, Krishna A, Chakravarti A, Rivolta C, Bhattacharya S: Transcription-al regulation of PRPF31 gene expression by MSR1 repeat elements causes incomplete penetrance in retinitis pigmentosa. Sci Reports 6:19450, 2016. PMID 26781568. PMC4725990.

  • Yu B, Pulit SL, Hwang SJ, Brody JA, Amin N, Auer PL, Bis JC, Boerwinkle E, Burke GL, Chakravarti A, Correa A, Dreisbach AW, Franco OH, Ehret GB, Franceschini N, Hofman A, Lin DY, Metcalf GA, Musani SK, Muzny D, Palmas W, Raffel L, Reiner A, Rice K, Rotter JI, Veeraraghavan N, Fox E, Guo X, North KE, Gibbs RA, van Duijn CM, Psaty BM, Levy D, Newton-Cheh C, Morrison AC; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium; National Heart, Lung, and Blood Institute GO Exome Sequencing Project: Rare Exome Sequence Variants in CLCN6 Reduce Blood Pressure Levels and Hypertension Risk. Circ Cardiovasc Genet 9:64-70, 2016. PMID 26658788. PMC4771070.

2015
  • Chong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, Harrell TM, McMillin MJ, Wiszniewski W, Gambin T, Coban Akdemir ZH, Doheny K, Scott AF, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer PD, Ling H, Hetrick K, Watkins L, Patterson KE, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton VR, Tabor HK, Leal SM, Gunel M, Mane S, Gibbs RA, Boerwinkle E, Hamosh A, Shendure J, Lupski JR, Lifton RP, Valle D, Nickerson DA; Centers for Mendelian Genomics, Bamshad MJ: The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Amer J Hum Genet 97:199-215, 2015. PMID 26166479. PMC4573249.

  • Manolio TA, Abramowicz M, Al-Mulla F, Anderson W, Balling R, Berger AC, Bleyl S, Chakravarti A, Chantratita W, Chisholm RL, W Dissanayake VH, Dunn M, Dzau VJ, Han BG, Hubbard T, Kolbe A, Korf B, Kubo M, Lasko P, Leego E, Mahasirimongkol S, Majumdar PP, Matthijs G, McLeod HL, Metspalu A, Meulien P, Miyano S, Naparstek Y, O’Rourke PP, Patrinos GP, Rehm HL, Relling MV, Rennert G, Rodriguez LL, Roden DM, Shuldiner AR, Sinha S, Tan P, Ulfendahl M, Ward R, Williams MS, L Wong JE, Green ED, Ginsburg GS: Global implementation of genomic medicine: We are not alone. Sci Transl Med 7:290ps13, 2015. PMID 26041702. PMC4898888.

  • Swaminathan M, Oron AP, Chatterjee S, Piper H, Cope-Yokoyama S, Chakravarti A, Kapur RP: Intestinal neuronal dysplasia-like submucosal ganglion cell hyperplasia at the proximal margins of Hirschsprung disease resections. Ped Dev Pathol 18:466-476, 2015. PMID 26699691. PMC4809533.

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CHARGE Consortium; DIAGRAM Consortium; GLGC Consortium; Global-BPGen Consortium; ICBP Consortium; MAGIC Consortium, Chakravarti A, Clegg DJ, Cupples LA, Gordon- Larsen P, Jaquish CE, Rao DC, Abecasis GR, Assimes TL, Barroso I, Berndt SI, Boehnke M, Deloukas P, Fox CS, Groop LC, Hunter DJ, Ingelsson E, Kaplan RC, McCarthy MI, Mohlke KL, O’Connell JR, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Hirschhorn JN, Lindgren CM, Heid IM, North KE, Borecki IB, Kutalik Z, Loos RJ: The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. 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  • Cornish TC, Chakravarti A, Kapoor A, Halushka MK: HPASubC: A suite of tools for user subclassification of human protein atlas tissue images. J Pathol Inform 6:36, 2015. PMID 26167380. PMC4485190.

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  • Jiang Q, Arnold S, Heanue T, Kilambi KP, Doan B, Kapoor A, Ling AY, Soca MX, Guy M, Jiang Q, Burzynski G, Wesy K, Bessling S, Griseri P, Amiel J, Fernandez RM, Verheij JBGM, Hofstra RMW, Borrego S, Lyonnet S, Ceccherini I, Gray JJ, Pachnis V, McCallion AS, Chakravarti A: Functional loss of Semaphorin 3C/ Semaphorin 3D and epistatic interaction with RET are critical to Hirschsprung disease liability. Amer J Hum Genet 96:581-596, 2015. PMID 25839327. PMC4385176.

2014
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  • Gunadi, Kapoor A, Ling AY, Rochadi, Makhmudi A, Herini ES, Sosa MX, Chatterjee S, Chakravarti A: Effects of RET and NRG1 polymorphisms in Indonesian patients with Hirschsprung disease. J Pediatric Surg 49:1614-1618, 2014. PMID 25475805. PMC4258000.

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  • Wang YJ, Tayo BO, Bandyopadhyay A, Wang H, Feng T, Franceschini N, Tang H, Gao J, Sung YJ; COGENT BP consortium, Elston RC, Williams SM, Cooper RS, Mu TW, Zhu X: The association of the vanin-1 N131S variant with blood pressure is mediated by endoplasmic reticulum-associated degradation and loss of function. PLoS Genet 10:e1004641, 2014. PMID 25233454. PMC4169380.

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Electronic Medical Records and Genomics (eMERGE) Consortium; MIGen Consortium; PAGE Consortium; LifeLines Cohort Study, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PI, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hayes MG, Hui J, Hunter DJ, Hveem K, Jukema JW, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, März W, Melbye M, Moebus S, Munroe PB, Njølstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Pérusse L, Peters U, Powell JE, Power C, Quertermous T, Rauramaa R, Reinmaa E, Ridker PM, Rivadeneira F, Rotter JI, Saaristo TE, Saleheen D, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Strauch K, Stumvoll M, Tuomilehto J, Uusitupa M, van der Harst P, Völzke H, Walker M, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Zanen P, Deloukas P, Heid IM, Lindgren CM, Mohlke KL, Speliotes EK, Thorsteinsdottir U, Barroso I, Fox CS, North KE, Strachan DP, Beckmann JS, Berndt SI, Boehnke M, Borecki IB, McCarthy MI, Metspalu A, Stefansson K, Uitterlinden AG, van Duijn CM, Franke L, Willer CJ, Price AL, Lettre G, Loos RJ, Weedon MN, Ingelsson E, O’Connell JR, Abecasis GR, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM: Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 46:1173-1186, 2014. PMID 25282103. PMC4250049.

  • Hoggart CJ, Venturini G, Mangino M, Gomez F, Ascari G, Zhao JH, Teumer A, Winkler TW, Tšernikova N, Luan J, Mihailov E, Ehret GB, Zhang W, Lamparter D, Esko T, Macé A, Rüeger S, Bochud PY, Barcella M, Dauvilliers Y, Benyamin B, Evans DM, Hayward C, Lopez MF, Franke L, Russo A, Heid IM, Salvi E, Vendantam S, Arking DE, Boerwinkle E, Chambers JC, Fiorito G, Grallert H, Guarrera S, Homuth G, Huffman JE, Porteous D; Generation Scotland Consortium; LifeLines Cohort study; GIANT Consortium, Moradpour D, Iranzo A, Hebebrand J, Kemp JP, Lammers GJ, Aubert V, Heim MH, Martin NG, Montgomery GW, Peraita-Adrados R, Santamaria J, Negro F, Schmidt CO, Scott RA, Spector TD, Strauch K, Völzke H, Wareham NJ, Yuan W, Bell JT, Chakravarti A, Kooner JS, Peters A, Matullo G, Wallaschofski H, Whitfield JB, Paccaud F, Vollenweider P, Bergmann S, Beckmann JS, Tafti M, Hastie ND, Cusi D, Bochud M, Frayling TM, Metspalu A, Jarvelin MR, Scherag A, Smith GD, Borecki IB, Rousson V, Hirschhorn JN, Rivolta C, Loos RJ, Kutalik Z: Novel Approach Identifies SNPs in SLC2A10 and KCNK9 with Evidence for Parent-of-Origin Effect on Body Mass Index. PLoS Genetics 10(7):e1004508, 2014. PMID 25078964. PMC4117451.

2013
  • Ganesh SK, Arnett DK, Assimes TL, Basson CT, Chakravarti A, Ellinor PT, Engler MB, Goldmuntz E, Herrington DM, Hershberger RE, Hong Y, Johnson JA, Kittner SJ, McDermott DA, Meschia JF, Mestroni L, O’Donnell CJ, Psaty BM, Vasan RS, Ruel M, Shen W-K, Terzic A, Waldman SA; on behalf of the American Heart Association Council on Functional Genomics and Translational Biology, Council on Epidemiology and Prevention, Council on Basic Cardiovascular Sciences, Council on Cardiovascular Disease in the Young, Council on Cardiovascular Surgery and Anesthesia, Council on Clinical Cardiology, Council on Cardiovascular and Stroke Nursing, and Stroke Council: Genetics and genomics for the prevention and treatment of cardiovascular disease: update: a scientific statement from the American Heart Association. Circulation 128:2813–2851, 2013. PMID 24297835.

  • Fernández RM, Bleda M, Luzón-Toro B, García-Alonso L, Arnold S, Sribudiani Y, Besmond C, Lantieri F, Doan B, Ceccherini I, Lyonnet S, Hofstra RM, Chakravarti A, Antiñolo G, Dopazo J, Borrego S: Pathways systematically associated to Hirschsprung’s disease. Orphanet J Rare Dis 8:187, 2013. PMID 24289864. PMC3879038.

  • Global Lipids Genetics Consortium, Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Gustafsson S, Kanoni S, Ganna A, Chen J, Buchkovich ML, Mora S, Beckmann JS, Bragg- Gresham JL, Chang HY, Demirkan A, Den Hertog HM, Do R, Donnelly LA, Ehret GB, Esko T, Feitosa MF, Ferreira T, Fischer K, Fontanillas P, Fraser RM, Freitag DF, Gurdasani D, Heikkilä K, Hyppönen E, Isaacs A, Jackson AU, Johansson A, Johnson T, Kaakinen M, Kettunen J, Kleber ME, Li X, Luan J, Lyytikäinen LP, Magnusson PK, Mangino M, Mihailov E, Montasser ME, Müller-Nurasyid M, Nolte IM, O’Connell JR, Palmer CD, Perola M, Petersen AK, Sanna S, Saxena R, Service SK, Shah S, Shungin D, Sidore C, Song C, Strawbridge RJ, Surakka I, Tanaka T, Teslovich TM, Thorleifsson G, Van den Herik EG, Voight BF, Volcik KA, Waite LL, Wong A, Wu Y, Zhang W, Absher D, Asiki G, Barroso I, Been LF, Bolton JL, Bonnycastle LL, Brambilla P, Burnett MS, Cesana G, Dimitriou M, Doney AS, Döring A, Elliott P, Epstein SE, Eyjolfsson GI, Gigante B, Goodarzi MO, Grallert H, Gravito ML, Groves CJ, Hallmans G, Hartikainen AL, Hayward C, Hernandez D, Hicks AA, Holm H, Hung YJ, Illig T, Jones MR, Kaleebu P, Kastelein JJ, Khaw KT, Kim E, Klopp N, Komulainen P, Kumari M, Langenberg C, Lehtimäki T, Lin SY, Lindström J, Loos RJ, Mach F, McArdle WL, Meisinger C, Mitchell BD, Müller G, Nagaraja R, Narisu N, Nieminen TV, Nsubuga RN, Olafsson I, Ong KK, Palotie A, Papamarkou T, Pomilla C, Pouta A, Rader DJ, Reilly MP, Ridker PM, Rivadeneira F, Rudan I, Ruokonen A, Samani N, Scharnagl H, Seeley J, Silander K, Stancáková A, Stirrups K, Swift AJ, Tiret L, Uitterlinden AG, van Pelt LJ, Vedantam S, Wainwright N, Wijmenga C, Wild SH, Willemsen G, Wilsgaard T, Wilson JF, Young EH, Zhao JH, Adair LS, Arveiler D, Assimes TL, Bandinelli S, Bennett F, Bochud M, Boehm BO, Boomsma DI, Borecki IB, Bornstein SR, Bovet P, Burnier M, Campbell H, Chakravarti A, Chambers JC, Chen YD, Collins FS, Cooper RS, Danesh J, Dedoussis G, de Faire U, Feranil AB, Ferrières J, Ferrucci L, Freimer NB, Gieger C, Groop LC, Gudnason V, Gyllensten U, Hamsten A, Harris TB, Hingorani A, Hirschhorn JN, Hofman A, Hovingh GK, Hsiung CA, Humphries SE, Hunt SC, Hveem K, Iribarren C, Järvelin MR, Jula A, Kähönen M, Kaprio J, Kesäniemi A, Kivimaki M, Kooner JS, Koudstaal PJ, Krauss RM, Kuh D, Kuusisto J, Kyvik KO, Laakso M, Lakka TA, Lind L, Lindgren CM, Martin NG, März W, McCarthy MI, McKenzie CA, Meneton P, Metspalu A, Moilanen L, Morris AD, Munroe PB, Njølstad I, Pedersen NL, Power C, Pramstaller PP, Price JF, Psaty BM, Quertermous T, Rauramaa R, Saleheen D, Salomaa V, Sanghera DK, Saramies J, Schwarz PE, Sheu WH, Shuldiner AR, Siegbahn A, Spector TD, Stefansson K, Strachan DP, Tayo BO, Tremoli E, Tuomilehto J, Uusitupa M, van Duijn CM, Vollenweider P, Wallentin L, Wareham NJ, Whitfield JB, Wolffenbuttel BH, Ordovas JM, Boerwinkle E, Palmer CN, Thorsteinsdottir U, Chasman DI, Rotter JI, Franks PW, Ripatti S, Cupples LA, Sandhu MS, Rich SS, Boehnke M, Deloukas P, Kathiresan S, Mohlke KL, Ingelsson E, Abecasis GR: Discovery and refinement of loci associated with lipid levels. Nat Genet 45:1274-1283, 2013. PMID 24097068. PMC3838666.

  • Do R, Willer CJ, Schmidt EM, Sengupta S, Gao C, Peloso GM, Gustafsson S, Kanoni S, Ganna A, Chen J, Buchkovich ML, Mora S, Beckmann JS, Bragg-Gresham JL, Chang HY, Demirkan A, Den Hertog HM, Donnelly LA, Ehret GB, Esko T, Feitosa MF, Ferreira T, Fischer K, Fontanillas P, Fraser RM, Freitag DF, Gurdasani D, Heikkilä K, Hyppönen E, Isaacs A, Jackson AU, Johansson A, Johnson T, Kaakinen M, Kettunen J, Kleber ME, Li X, Luan J, Lyytikäinen LP, Magnusson PK, Mangino M, Mihailov E, Montasser ME, Müller-Nurasyid M, Nolte IM, O’Connell JR, Palmer CD, Perola M, Petersen AK, Sanna S, Saxena R, Service SK, Shah S, Shungin D, Sidore C, Song C, Strawbridge RJ, Surakka I, Tanaka T, Teslovich TM, Thorleifsson G, Van den Herik EG, Voight BF, Volcik KA, Waite LL, Wong A, Wu Y, Zhang W, Absher D, Asiki G, Barroso I, Been LF, Bolton JL, Bonnycastle LL, Brambilla P, Burnett MS, Cesana G, Dimitriou M, Doney AS, Döring A, Elliott P, Epstein SE, Eyjolfsson GI, Gigante B, Goodarzi MO, Grallert H, Gravito ML, Groves CJ, Hallmans G, Hartikainen AL, Hayward C, Hernandez D, Hicks AA, Holm H, Hung YJ, Illig T, Jones MR, Kaleebu P, Kastelein JJ, Khaw KT, Kim E, Klopp N, Komulainen P, Kumari M, Langenberg C, Lehtimäki T, Lin SY, Lindström J, Loos RJ, Mach F, McArdle WL, Meisinger C, Mitchell BD, Müller G, Nagaraja R, Narisu N, Nieminen TV, Nsubuga RN, Olafsson I, Ong KK, Palotie A, Papamarkou T, Pomilla C, Pouta A, Rader DJ, Reilly MP, Ridker PM, Rivadeneira F, Rudan I, Ruokonen A, Samani N, Scharnagl H, Seeley J, Silander K, Stančáková A, Stirrups K, Swift AJ, Tiret L, Uitterlinden AG, van Pelt LJ, Vedantam S, Wainwright N, Wijmenga C, Wild SH, Willemsen G, Wilsgaard T, Wilson JF, Young EH, Zhao JH, Adair LS, Arveiler D, Assimes TL, Bandinelli S, Bennett F, Bochud M, Boehm BO, Boomsma DI, Borecki IB, Bornstein SR, Bovet P, Burnier M, Campbell H, Chakravarti A, Chambers JC, Chen YD, Collins FS, Cooper RS, Danesh J, Dedoussis G, de Faire U, Feranil AB, Ferrières J, Ferrucci L, Freimer NB, Gieger C, Groop LC, Gudnason V, Gyllensten U, Hamsten A, Harris TB, Hingorani A, Hirschhorn JN, Hofman A, Hovingh GK, Hsiung CA, Humphries SE, Hunt SC, Hveem K, Iribarren C, Järvelin MR, Jula A, Kähönen M, Kaprio J, Kesäniemi A, Kivimaki M, Kooner JS, Koudstaal PJ, Krauss RM, Kuh D, Kuusisto J, Kyvik KO, Laakso M, Lakka TA, Lind L, Lindgren CM, Martin NG, März W, McCarthy MI, McKenzie CA, Meneton P, Metspalu A, Moilanen L, Morris AD, Munroe PB, Njølstad I, Pedersen NL, Power C, Pramstaller PP, Price JF, Psaty BM, Quertermous T, Rauramaa R, Saleheen D, Salomaa V, Sanghera DK, Saramies J, Schwarz PE, Sheu WH, Shuldiner AR, Siegbahn A, Spector TD, Stefansson K, Strachan DP, Tayo BO, Tremoli E, Tuomilehto J, Uusitupa M, van Duijn CM, Vollenweider P, Wallentin L, Wareham NJ, Whitfield JB, Wolffenbuttel BH, Altshuler D, Ordovas JM, Boerwinkle E, Palmer CN, Thorsteinsdottir U, Chasman DI, Rotter JI, Franks PW, Ripatti S, Cupples LA, Sandhu MS, Rich SS, Boehnke M, Deloukas P, Mohlke KL, Ingelsson E, Abecasis GR, Daly MJ, Neale BM, Kathiresan S.: Polymorphisms associated with plasma triglycerides and risk for coronary artery disease. Nat Genet 45:1345-1352, 2013. PMID 24097064. PMC3904346.

  • Sampath S, Bhat S, Gupta S, O’Connor A, Sosa MX, West AB, Arking DE, Chakravarti A: Defining the contribution of CNTNAP2 to autism susceptibility. PLoS One 8:e77906, 2013. PMID 24147096. PMC3798378.

  • Prasad MK, Bhalla K, Pan ZH, O’Connell JR, Weder AR, Chakravarti A, Tian B, Chang Y-P C: A polymorphic 3’UTR element in ATP1B1 regulates alternative polyadenylation and is associated with blood pressure. PLoS One 8:e76290, 2013. PMID 24098465. PMC3788127.

  • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M: Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342:1235587, 2013. PMID 24092746. PMC3947637.

  • Pistis G, Okonkwo SU, Traglia M, Sala C, Shin SY, Masciullo C, Buetti I, Massacane R, Mangino M, Thein SL, Spector TD, Ganesh S; CHARGE Consortium Hematology Working, Pirastu N, Gasparini P, Soranzo N, Camaschella C, Hart D, Green MR, Toniolo D: Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans. PLoS One 8:e69206, 2013. PMID 23935956. PMC3729833.

  • Franceschini N, Fox E, Zhang Z, Edwards TL, Nalls MA, Sung YJ, Tayo BO, Sun YV, Gottesman O, Adeyemo A, Johnson AD, Young JH, Rice K, Duan Q, Chen F, Li Y, Tang H, Fornage M, Keene KL, Andrews JS, Smith JA, Faul JD, Guangfa Z, Guo W, Liu Y, Murray SS, Musani SK, Srinivasan S, Velez Edwards DR, Wang H, Becker LC, Bovet P, Bochud M, Broeckel U, Burnier M, Carty C, Chasman DI, Ehret G, Chen WM, Chen G, Chen W, Ding J, Dreisbach AW, Evans MK, Guo X, Garcia ME, Jensen R, Keller MF, Lettre G, Lotay V, Martin LW, Moore JH, Morrison AC, Mosley TH, Ogunniyi A, Palmas W, Papanicolaou G, Penman A, Polak JF, Ridker PM, Salako B, Singleton AB, Shriner D, Taylor KD, Vasan R, Wiggins K, Williams SM, Yanek LR, Zhao W, Zonderman AB, Becker DM, Berenson G, Boerwinkle E, Bottinger E, Cushman M, Eaton C, Nyberg F, Heiss G, Hirschhron JN, Howard VJ, Karczewsk KJ, Lanktree MB, Liu K, Liu Y, Loos R, Margolis K, Snyder M; the Asian Genetic Epidemiology Network Consortium, Psaty BM, Schork NJ, Weir DR, Rotimi CN, Sale MM, Harris T, Kardia SL, Hunt SC, Arnett D, Redline S, Cooper RS, Risch NJ, Rao DC, Rotter JI, Chakravarti A, Reiner AP, Levy D, Keating BJ, Zhu X: Genome-wide Association Analysis of Blood-Pressure Traits in African-Ancestry Individuals Reveals Common Associated Genes in African and Non-African Populations. Am J Hum Genet 93(3):545-554, 2013. PMID 23972371. PMC3769920.

  • Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee SH, Ripke S, Neale BM, Faraone SV, Purcell SM, Perlis RH, Mowry BJ, Thapar A, Goddard ME, Witte JS, Absher D, Agartz I, Akil H, Amin F, Andreassen OA, Anjorin A, Anney R, Anttila V, Arking DE, Asherson P, Azevedo MH, Backlund L, Badner JA, Bailey AJ, Banaschewski T, Barchas JD, Barnes MR, Barrett TB, Bass N, Battaglia A, Bauer M, Bayés M, Bellivier F, Bergen SE, Berrettini W, Betancur C, Bettecken T, Biederman J, Binder EB, Black DW, Blackwood DH, Bloss CS, Boehnke M, Boomsma DI, Breen G, Breuer R, Bruggeman R, Cormican P, Buccola NG, Buitelaar JK, Bunney WE, Buxbaum JD, Byerley WF, Byrne EM, Caesar S, Cahn W, Cantor RM, Casas M, Chakravarti A, Chambert K, Choudhury K, Cichon S, Cloninger CR, Collier DA, Cook EH, Coon H, Cormand B, Corvin A, Coryell WH, Craig DW, Craig IW, Crosbie J, Cuccaro ML, Curtis D, Czamara D, Datta S, Dawson G, Day R, De Geus EJ, Degenhardt F, Djurovic S, Donohoe GJ, Doyle AE, Duan J, Dudbridge F, Duketis E, Ebstein RP, Edenberg HJ, Elia J, Ennis S, Etain B, Fanous A, Farmer AE, Ferrier IN, Flickinger M, Fombonne E, Foroud T, Frank J, Franke B, Fraser C, Freedman R, Freimer NB, Freitag CM, Friedl M, Frisén L, Gallagher L, Gejman PV, Georgieva L, Gershon ES, Geschwind DH, Giegling I, Gill M, Gordon SD, Gordon-Smith K, Green EK, Greenwood TA, Grice DE, Gross M, Grozeva D, Guan W, Gurling H, De Haan L, Haines JL, Hakonarson H, Hallmayer J, Hamilton SP, Hamshere ML, Hansen TF, Hartmann AM, Hautzinger M, Heath AC, Henders AK, Herms S, Hickie IB, Hipolito M, Hoefels S, Holmans PA, Holsboer F, Hoogendijk WJ, Hottenga JJ, Hultman CM, Hus V, Ingason A, Ising M, Jamain S, Jones EG, Jones I, Jones L, Tzeng JY, Kähler AK, Kahn RS, Kandaswamy R, Keller MC, Kennedy JL, Kenny E, Kent L, Kim Y, Kirov GK, Klauck SM, Klei L, Knowles JA, Kohli MA, Koller DL, Konte B, Korszun A, Krabbendam L, Krasucki R, Kuntsi J, Kwan P, Landén M, Långström N, Lathrop M, Lawrence J, Lawson WB, Leboyer M, Ledbetter DH, Lee PH, Lencz T, Lesch KP, Levinson DF, Lewis CM, Li J, Lichtenstein P, Lieberman JA, Lin DY, Linszen DH, Liu C, Lohoff FW, Loo SK, Lord C, Lowe JK, Lucae S, Macintyre DJ, Madden PA, Maestrini E, Magnusson PK, Mahon PB, Maier W, Malhotra AK, Mane SM, Martin CL, Martin NG, Mattheisen M, Matthews K, Mattingsdal M, McCarroll SA, McGhee KA, McGough JJ, McGrath PJ, McGuffin P, McInnis MG, McIntosh A, McKinney R, McLean AW, McMahon FJ, McMahon WM, McQuillin A, Medeiros H, Medland SE, Meier S, Melle I, Meng F, Meyer J, Middeldorp CM, Middleton L, Milanova V, Miranda A, Monaco AP, Montgomery GW, Moran JL, Moreno-De-Luca D, Morken G, Morris DW, Morrow EM, Moskvina V, Muglia P, Mühleisen TW, Muir WJ, Müller-Myhsok B, Murtha M, Myers RM, Myin-Germeys I, Neale MC, Nelson SF, Nievergelt CM, Nikolov I, Nimgaonkar V, Nolen WA, Nöthen MM, Nurnberger JI, Nwulia EA, Nyholt DR, O’Dushlaine C, Oades RD, Olincy A, Oliveira G, Olsen L, Ophoff RA, Osby U, Owen MJ, Palotie A, Parr JR, Paterson AD, Pato CN, Pato MT, Penninx BW, Pergadia ML, Pericak-Vance MA, Pickard BS, Pimm J, Piven J, Posthuma D, Potash JB, Poustka F, Propping P, Puri V, Quested DJ, Quinn EM, Ramos-Quiroga JA, Rasmussen HB, Raychaudhuri S, Rehnström K, Reif A, Ribasés M, Rice JP, Rietschel M, Roeder K, Roeyers H, Rossin L, Rothenberger A, Rouleau G, Ruderfer D, Rujescu D, Sanders AR, Sanders SJ, Santangelo SL, Sergeant JA, Schachar R, Schalling M, Schatzberg AF, Scheftner WA, Schellenberg GD, Scherer SW, Schork NJ, Schulze TG, Schumacher J, Schwarz M, Scolnick E, Scott LJ, Shi J, Shilling PD, Shyn SI, Silverman JM, Slager SL, Smalley SL, Smit JH, Smith EN, Sonuga-Barke EJ, St Clair D, State M, Steffens M, Steinhausen HC, Strauss JS, Strohmaier J, Stroup TS, Sutcliffe JS, Szatmari P, Szelinger S, Thirumalai S, Thompson RC, Todorov AA, Tozzi F, Treutlein J, Uhr M, van den Oord EJ, Van Grootheest G, Van Os J, Vicente AM, Vieland VJ, Vincent JB, Visscher PM, Walsh CA, Wassink TH, Watson SJ, Weissman MM, Werge T, Wienker TF, Wijsman EM, Willemsen G, Williams N, Willsey AJ, Witt SH, Xu W, Young AH, Yu TW, Zammit S, Zandi PP, Zhang P, Zitman FG, Zöllner S; International Inflammatory Bowel Disease Genetics Consortium (IIBDGC), Devlin B, Kelsoe JR, Sklar P, Daly MJ, O’Donovan MC, Craddock N, Sullivan PF, Smoller JW, Kendler KS, Wray NR.: Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet 45:984-994, 2013. PMID 23933821. PMC3800159.

2012
  • Sosa M, Sivakumar IKA, Maragh S, Veeramachanen V, Hariharan R, Parulekar M, Fredrikson KM, Harkins TT, Lin J, Feldman A, Tata P, Ehret G, Chakravarti A: Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency. PLoS Comp Biol 8:e1002737, 2012. PMID 23133345. PMC3486893.

  • 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes. Nature 491:55-65, 2012. PMID 23128226. PMC3498066.

  • Ellinor PT, Lunetta KL, Albert CM, Glazer NL, Ritchie MD, Smith AV, Arking DE, Müller- Nurasyid M, Krijthe BP, Lubitz SA, Bis JC, Chung MK, Dörr M, Ozaki K, Roberts JD, Smith JG, Pfeufer A, Sinner MF, Lohman K, Ding J, Smith NL, Smith JD, Rienstra M, Rice KM, Van Wagoner DR, Magnani JW, Wakili R, Clauss S, Rotter JI, Steinbeck G, Launer LJ, Davies RW, Borkovich M, Harris TB, Lin H, Völker U, Völzke H, Milan DJ, Hofman A, Boerwinkle E, Chen LY, Soliman EZ, Voight BF, Li G, Chakravarti A, Kubo M, Tedrow UB, Rose LM, Ridker PM, Conen D, Tsunoda T, Furukawa T, Sotoodehnia N, Xu S, Kamatani N, Levy D, Nakamura Y, Parvez B, Mahida S, Furie KL, Rosand J, Muhammad R, Psaty BM, Meitinger T, Perz S, Wichmann HE, Witteman JC, Kao WH, Kathiresan S, Roden DM, Uitterlinden AG, Rivadeneira F, McKnight B, Sjögren M, Newman AB, Liu Y, Gollob MH, Melander O, Tanaka T, Stricker BH, Felix SB, Alonso A, Darbar D, Barnard J, Chasman DI, Heckbert SR, Benjamin EJ, Gudnason V, Kääb S: Meta-analysis identifies six new susceptibility loci for atrial fibrillation. Nat Genet 44:670-675, 2012. PMID 22544366. PMC3366038.

  • Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium: The 1000 Genomes Project: data management and community access. Nat Methods 9:459-462, 2012. PMID 22543379. PMC3340611.

  • Jiang Q, Turner T, Sosa M, Rakha A, Arnold S, Chakravarti A: Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer. Hum Mutat 33:281-289, 2012. PMID 21898659. PMC3240684.

  • Amin N, Byrne E, Johnson J, Chenevix-Trench G, Walter S, Nolte IM; kConFab Investigators, Vink JM, Rawal R, Mangino M, Teumer A, Keers JC, Verwoert G, Baumeister S, Biffar R, Petersmann A, Dahmen N, Doering A, Isaacs A, Broer L, Wray NR, Montgomery GW, Levy D, Psaty BM, Gudnason V, Chakravarti A, Sulem P, Gudbjartsson DF, Kiemeney LA, Thorsteinsdottir U, Stefansson K, van Rooij FJ, Aulchenko YS, Hottenga JJ, Rivadeneira FR, Hofman A, Uitterlinden AG, Hammond CJ, Shin SY, Ikram A, Witteman JC, Janssens AC, Snieder H, Tiemeier H, Wolfenbuttel BH, Oostra BA, Heath AC, Wichmann E, Spector TD, Grabe HJ, Boomsma DI, Martin NG, van Duijn CM: Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM. Mol Psych 17:1116-1129, 2012. PMID 21876539. PMC3482684.

2011
  • Won J-H, Ehret G, Chakravarti A, Olshen RA: SNPs and other features as they predispose to complex disease: genome-wide predictive analysis of quantitative phenotypes for hypertension. PLoS One 6:e27891, 2011. PMID 22140480. PMC3227593.

  • Benke KS, Carlson MC, Doan BQ, Walston JD, Xue QL, Reiner AP, Fried LP, Arking DE, Chakravarti A, Fallin MD: The association of genetic variants in interleukin-1 genes with cognition: Findings from the cardiovascular health study. Exptl Geront 46:1010-1019, 2011. PMID 21968104. PMC3689225.

  • Chakravarti A: Widespread promiscuous genetic information transfer from DNA to RNA. Circ Res 109:1202-1203, 2011. PMID 22076505.

  • Turner T, Pihur V, Chakravarti A: Quantifying and modeling birth order effects in autism. PLoS One 6:e26418, 2011. PMID 22039484. PMC3198479.

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  • Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project: The functional spectrum of low-frequency coding variation. Genome Biol 12:R84, 2011. PMID 21917140. PMC3308047.

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group: The variant call format and VCFtools. Bioinformatics 27:2156-2158, 2011. PMID 21653522. PMC3137218.

  • Tomas M, …, Arking DE, et al: Polymorphisms in the NOS1AP gene modulate QT interval duration and risk of arrhythmias in the Long QT syndrome (LQTS). J Amer Coll Cardiol 55:2745-2752, 2010. PMID 20538168.

  • Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, The 1000 Genomes Project: Variation in genome-wide mutation rates within and between human families. Nat Genet 43:712-714, 2011. PMID 21666693. PMC3322360.

2010
  • Sotoodehnia N, Isaacs A, de Bakker PI, Dörr M, Newton-Cheh C, Nolte IM, van der Harst P, Müller M, Eijgelsheim M, Alonso A, Hicks AA, Padmanabhan S, Hayward C, Smith AV, Polasek O, Giovannone S, Fu J, Magnani JW, Marciante KD, Pfeufer A, Gharib SA, Teumer A, Li M, Bis JC, Rivadeneira F, Aspelund T, Köttgen A, Johnson T, Rice K, Sie MP, Wang YA, Klopp N, Fuchsberger C, Wild SH, Mateo Leach I, Estrada K, Völker U, Wright AF, Asselbergs FW, Qu J, Chakravarti A, Sinner MF, Kors JA, Petersmann A, Harris TB, Soliman EZ, Munroe PB, Psaty BM, Oostra BA, Cupples LA, Perz S, de Boer RA, Uitterlinden AG, Völzke H, Spector TD, Liu FY, Boerwinkle E, Dominiczak AF, Rotter JI, van Herpen G, Levy D, Wichmann HE, van Gilst WH, Witteman JC, Kroemer HK, Kao WH, Heckbert SR, Meitinger T, Hofman A, Campbell H, Folsom AR, van Veldhuisen DJ, Schwienbacher C, O’Donnell CJ, Volpato CB, Caulfield MJ, Connell JM, Launer L, Lu X, Franke L, Fehrmann RS, te Meerman G, Groen HJ, Weersma RK, van den Berg LH, Wijmenga C, Ophoff RA, Navis G, Rudan I, Snieder H, Wilson JF, Pramstaller PP, Siscovick DS, Wang TJ, Gudnason V, van Duijn CM, Felix SB, Fishman GI, Jamshidi Y, Stricker BH, Samani NJ, Kääb S, Arking DE: Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet 42:1068-1076, 2010. PMID 21076409. PMC3338195.

  • Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn  L, Shendure J, The 1000 Genomes Project Consortium, Eichler EE: Diversity of human copy number variation and multicopy genes. Science 330:641-646, 2010. PMID 21030649. PMC3020103.

  • The 1000 Genomes Project Consortium: A map of human genome variation from population- scale sequencing. Nature 467:1061-1073, 2010. PMID 20981092. PMC3042601.

  • Fradin D, Cheslack-Postava K, Ladd-Acosta C, Newschaffer C, Chakravarti A, Arking DE, Feinberg A, Fallin MD: Parent-Of-Origin Effects in Autism Identified Through Genome-Wide Linkage Analysis of 16,000 SNPs. PLoS One 5:e12513, 2010. PMID 20824079. PMC2932694.

  • Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry R: A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics 12:33-50, 2010. PMID 20625178. PMC3006124.

  • Meyer TE, Verwoert GC, Hwang SJ, Glazer NL, Smith AV, van Rooij FJ, Ehret GB, Boerwinkle E, Felix JF, Leak TS, Harris TB, Yang Q, Dehghan A, Aspelund T, Katz R, Homuth G, Kocher T, Rettig R, Ried JS, Gieger C, Prucha H, Pfeufer A, Meitinger T, Coresh J, Hofman A, Sarnak MJ, Chen YD, Uitterlinden AG, Chakravarti A, Psaty BM, van Duijn CM, Kao WH, Witteman JC, Gudnason V, Siscovick DS, Fox CS, Köttgen A; Genetic Factors for Osteoporosis Consortium; Meta Analysis of Glucose and Insulin Related Traits Consortium: Genome-wide association studies of serum magnesium, potassium and sodium concentrations identify six novel loci influencing serum magnesium levels. PLoS Genet 6: e1001045, 2010. PMID 20700443. PMC2916845.

  • Moore AZ, Biggs M, Matteini A, O’Conner A, McGuire S, Beamer B, Fallin D, Fried L, Walston J, Chakravarti A, Arking D: Polymorphisms in the mitochondrial DNA control region and frailty in older adults. PLoS One 5:e11069, 2010. PMID 20548781. PMC2883558.

  • Emison E, International Hirschsprung Disease Consortium, Chakravarti A: Differential contributions of mutations across the allelic spectrum of RET to multifactorial Hirschsprung disease liability. Amer J Hum Genet 87:60-74, 2010. PMID 20598273. PMC2896767.

  • Arking DE, Reinier K, Post W, Jui J, Hilton G, O’Connor A, Prineas RJ, Boerwinkle E,Psaty BM, Tomaselli GF, Rea T, Sotoodehnia N, Siscovick DS, Burke GL, Marban E, Spooner PM, Chakravarti A, Chugh SS: Genome-Wide Association Study Identifies GPC5 as a Novel Genetic Locus Protective against Sudden Cardiac Arrest. PLoS One 5:e9879, 2010. PMID 20360844. PMC2845611.

  • Chakravarti A: PRINCIPIA GENETICA: Our Future Science. Amer J Hum Genet 86:302-308, 2010. PMC2833370.

2009
  • Kucharska-Newton AM, Couper DJ, Pankow JS, Prineas RJ, Rea TD, Sotoodehnia N, Chakravarti A, Folsom AR, Siscovick DS, Rosamond WD: Hemostasis, inflammation and fatal and non-fatal coronary heart disease: long-term follow-up of the Atherosclerosis Risk in Communities (ARIC) cohort. Arterio Thromb Vasc Biol 29:2182-2190, 2009. PMID 19797708. PMC3057473.

  • Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM: Finding the missing heritability of complex diseases. Nature 461:747- 753, 2009. PMID 19812666. PMC2831613.

  • Ganesh SK, Zakai NA, van Rooij FJ, Soranzo N, Smith AV, Nalls MA, Chen MH, Kottgen A, Glazer NL, Dehghan A, Kuhnel B, Aspelund T, Yang Q, Tanaka T, Jaffe A, Bis JC, Verwoert GC, Teumer A, Fox CS, Guralnik JM, Ehret GB, Rice K, Felix JF, Rendon A, Eiriksdottir G, Levy D, Patel KV, Boerwinkle E, Rotter JI, Hofman A, Sambrook JG, Hernandez DG, Zheng G, Bandinelli S, Singleton AB, Coresh J, Lumley T, Uitterlinden AG, Vangils JM, Launer LJ, Cupples LA, Oostra BA, Zwaginga JJ, Ouwehand WH, Thein SL, Meisinger C, Deloukas P, Nauck M, Spector TD, Gieger C, Gudnason V, van Duijn CM, Psaty BM, Ferrucci L, Chakravarti A, Greinacher A, O’Donnell CJ, Witteman JC, Furth S, Cushman M, Harris TB, Lin JP: Multiple loci influence erythrocyte phenotypes in the CHARGE consortium. Nature Genet 41:1191-1198, 2009. PMID 19862010. PMC2778265.

  • Arking DE, Chakravarti A: Understanding cardiovascular disease through the lens of genome wide association studies. Trends Genet 25:387-394, 2009. PMID 19716196.

  • Weiss L, Arking DE, The Gene Discovery Project of Johns Hopkins and the Autism Consortium: A genome-wide linkage and association scan reveals novel genes for autism. Nature 461:802-808, 2009. PMID 19812673. PMC2772655.

  • Milan DJ, Kim AM, Winterfield JR, Jones IL, Pfeufer A, Sanna S, Arking DE, Amsterdam AH, Sabeh KM, Mably JD, Rosenbaum DS, Peterson RT, Chakravarti A, Kääb S, Roden DM, MacRae CA: A drug-sensitized zebrafish screen identifies multiple genes, including GINS3, as regulators of myocardial repolarization. Circulation 120:553-559, 2009. PMID 19652097. PMC2771327.

  • Ehret GE, O’Connor AA, Weder A, Cooper RS, Chakravarti A: Follow-up of a major linkage peak on chromosome 1 reveals multiple QTLs associated with essential hypertension: The GenNet study. Eur J Hum Genet 17:1650-1657, 2009. PMID 19536175. PMC2783544.

  • Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T, Aulchenko Y, Lumley T, Köttgen A, Vasan RS, Rivadeneira F, Eiriksdottir G,Guo X, Arking DE, Mitchell GF, Mattace-Raso FU, Smith AV, Taylor K, Scharpf RB, Hwang SJ, Sijbrands EJ, Bis J, Harris TB, Ganesh SK, O’Donnell CJ, Hofman A, Rotter JI, Coresh J, Benjamin EJ, Uitterlinden AG, Heiss G, Fox CS, Witteman JC, Boerwinkle E, Wang TJ, Gudnason V, Larson MG, Chakravarti A, Psaty BM, van Duijn CM: Genome-wide Association Study of Blood Pressure and Hypertension. Nat Genet 41:677-687, 2009. PMID 19430479. PMC2998712.

  • Joe B, Saad Y, Dhindaw S, Lee NH, Frank BC, Achinike OH, Luu TV, Gopalakrishnan K, Toland EJ, Farms P, Yerga-Woolwine S, Manickavasagam E, Rapp JP, Garrett MR, Coe D, Apte SS, Rankinen T, Pérusse L, Ehret GB, Ganesh SK, Cooper RS, O’Connor A, Rice T, Weder AB, Chakravarti A, Rao DC, Bouchard C: Positional identification of variants of ADAMTS16 linked to inherited hypertension. Hum Mol Genet 18:2825-2838, 2009. PMID 19423552. PMC2706685.

  • Franceschini N, North KE, Arnett D, Pankow JS, Chung JH, Baird L, Leppert MF, Eckfeldt JH, Boerwinkle E, Gu CC, Lewis CE, Myers RH, Turner ST, Weder A, Kao WH, Mosley TH, Chakravarti A, Kramer H, Zhang J, Hunt SC: The Association of Cell Cycle Checkpoint 2 Variants and Kidney Function: Findings of the Family Blood Pressure Program and the Atherosclerosis Risk in Communities Study. Amer J Hypertension 22:552-558, 2009. PMID 19265784. PMC2727134.

2008
  • Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA: Estimating Genome- Wide Copy Number Using Allele-Specific Mixture Models. J Comput Biol 15:857-866, 2008. PMID 18707534. PMC2612042.

  • Ehret GB, Morrison AC, O’Connor AA, Grove ML, Baird L, Schwander K, Weder A, Cooper RS, Rao DC, Hunt SC, Boerwinkle E, Chakravarti A: Replication of the Wellcome Trust genome-wide association study of essential hypertension: the Family Blood Pressure Program. Eur J Hum Genet 16:1507-1511, 2008. PMID 18523456. PMC2585612.

  • Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA: Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol 9(4):R63, 2008. PMID 18387188. PMC2643934.

  • Tan AC, Fan J-B, Karikari C, Bibikova M, Garcia EW, Zhou L, Barker D, Serre D, Feldmann G, Hruban RH, Klein AP, Goggins M, Couch FJ, Hudson TJ, Winslow RL, Maitra A, Chakravarti A: Allele-specific expression in the germline of patients with familial pancreatic cancer: An unbiased approach to cancer gene discovery. Cancer Biol Therapy 7:135-144, 2008. PMID 18059179. PMC4104667.

  • Weiss LA, Shen Y, Korn JM, Arking DE, Miller DT, Ferreira MAR, Green T, Platt OS, Ruderfer DM, Tanzi1 RE, Walsh CA, Investigators of the Autism Consortium, Chakravarti A, Santangelo SL, Gusella JF, Sklar P, Wu B-L, Daly MJ: A recurrent genetic cause of autism: microdeletion at 16p11.2. New Engl J Med 358:667-675, 2008. PMID 18184952.

  • Arking DE, Cutler DJ, Brune CW, Teslovich TM, Kristen West, Ikeda M, Rea A, Guy M, Lin S, Cook EH Jr., Chakravarti A: A common genetic variant in neurexin-superfamily member CNTNAP2 exhibits a parent-of-origin association with autism. Amer J Hum Genet 82:160-164, 2008. PMID 18179894.

  • Amiel J, Sproat-Emison E, Garcia-Barceo M, Lantieri F, Burzynski G, Borrego S, Pelet A, Arnold S, Miao X, Griseri P, Brooks AS, Antinolo G, De Pontual L, Clement-Ziza M, Munnich A, Kashuk C, West K, Wong KK, Lyonnet S, Chakravarti A, Tam PK, Ceccherini I, Hofstra RM, Fernandez R. Hirschsprung disease: associated syndromes and genetics. J Med Genet 45:1-14, 2008. PMID 17965226.

2007
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  • Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N: Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture. PLoS Genet 3:e119, 2007. PMID 17658953. PMC1925129.

  • Wen G, Wessel J, Zhou W, Ehret GB, Rao F, Stridsberg M, Mahata S, Gent PM, Das M, Cooper RS, Chakravarti A, Zhou H, Schork NJ, O’Connor DT, Hamilton BA: An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension. Hum Mol Genet 16:1752-1764, 2007. PMID 17584765. PMC2695823.

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2006
  • Blackman SM, Deering-Brose R, McWilliams R, Naughton K, Coleman B, Lai T, Algire M, Beck S, Hoover-Fong J, Hamosh A, Fallin MD, West K, Arking DE, Chakravarti A, Cutler D, Cutting GR and the CF Twin and Sibling Study: Relative contribution of genetic and non-genetic modifiers to intestinal obstruction in cystic fibrosis. Gastroenterology 131:1030-1039, 2006. PMID 17030173. PMC1764617.

  • Bibikova M, Chudin E, Wu B, Zhou L, Garcia EW, Liu Y, Shin S, Plaia TW, Auerbach JM, Arking DE, Gonzalez R, Crook J, Davidson B, Schulz TC, Robins A, Khanna A, Sartipy P, Hyllner J, Vanguri P, Savant-Bhonsale S, Smith AK, Chakravarti A, Maitra A, Rao M, Barker DL, Loring JF, Fan JB: Human embryonic stem cells have a unique epigenetic signature. Genome Res 16:1075-1083, 2006. PMID 16899657. PMC1557765.

  • Calhoun ES, Hucl T, Gallmeier E, West KM, Arking DE, Maitra A, Iacobuzio-Donahue CA, Chakravarti A, Hruban RH, Kern SE: Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer Without Matched Normals Using High-density SNP Arrays. Cancer Res 66:7920-7928, 2006. PMID 16912165.

  • Arking DE, Pfeufer A, Post W, Kao WHL, Ikeda M, West K, Kashuk C, Akyol M, Perz S, Jalilzadeh S, Illig T, Wichmann HE, Marban E, Kaab S, Spooner PM, Meitinger T, Chakravarti A: A common genetic variant in the nNOS regulator CAPON modulates cardiac repolarization (QT interval). Nat Genet 38:644-651, 2006. PMID 16648850.

  • Arking DE, Walston J, Fallin D, Li T, Beamer B, Xue QL, Fried LP, Chakravarti A: Variation in the ciliary neurotrophic factor gene and muscle strength in older Caucasian women. J Amer Geriat Soc 54:823-826, 2006. PMID 16696750.

  • Laramie JM, Wilk JB, Hunt SC, Ellison RC, Chakravarti A, Boerwinkle E, Myers RH: Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program. BMC Med Genet 7:17, 2006. PMID 16509988. PMC1413518.

  • Chang YP, Kim JD, Schwander K, Rao DC, Miller MB, Weder AB, Cooper RS, Schork NJ, Province MA, Morrison AC, Kardia SL, Quertermous T, Chakravarti A: The impact of data quality on the identification of complex disease genes: experience from the Family Blood Pressure Program. Eur J Hum Genet 14:469-477, 2006. PMID 16493446.

  • Zlotogora J, Carrasquillo MM, Barges S, Shalev SA, Hujerat Y, Chakravarti A: High incidence of deafness from three frequent connexin 26 mutations in an isolated community. Genet Testing 10:40-43, 2006. PMID 16545002.

2005
  • Young JH, Chang Y-PC, Kim J, Chretien J-P, Klag MJ, Levine MA, Ruff CB, Chakravarti A: Differential susceptibility to hypertension is due to selection during the Out-of-Africa expansion. PloS Genet 1:731-738, 2005. PMID 16429165. PMC1342636.

  • Gu CC, Chang Y-P C, Hunt S, Schwander K, Arnett D, Djousse L, Heiss G, Oberman A, Lalouel J- M, Province M, Chakravarti A, Rao DC: Haplotype Association Analysis of AGT Variants with Hypertension-related Traits: The HyperGEN Study. Hum Hered 60:164-176, 2005. PMID 16352906.

  • Grice E, Rochelle ES, Green ED, Chakravarti A, McCallion AS: Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer. Hum Mol Genet 14:3837-3845, 2005. PMID 16269442.

  • Armanios M, Chen J-L, Chang Y-P, Brodsky RA, Hawkins A, Griffin CA, Eshleman J, Cohen AR, Chakravarti A, Hamosh A, Greider C: Haploinsufficiency of hTERT Leads to Anticipation in Autosomal Dominant Dyskeratosis Congenita. Proc Natl Acad Sci (USA) 102:15960-15964, 2005. PMID 16247010. PMC1276104.

  • Rasmussen-Torvik LJ, North KE, Gu CC, Lewis CE, Wilk JB, Chakravarti A, Chang Y-P C, Miller MB, Li N, Devereux RB, Arnett DK: A population association study of angiotensinogen polymorphisms and haplotypes with left ventricular phenotypes. Hypertension 46:1294-1299, 2005. PMID 16286570.

  • The International HapMap Consortium: A Haplotype Map of the Human Genome. Nature 437:1299-1320, 2005. PMID 16255080. PMC1880871.

  • Maitra A, Arking DE, Shivapurkar N, Ikeda M, Stastny V, Kassauei K, Sui G, Cutler DJ, Ying Liu, Brimble SN, Noaksson K, Hyllner J, Schulz TC, Zeng X, Freed WJ, Colman A, Sartipy P, Matsui S-I, Carpenter M, Gazdar AF, Rao M, Chakravarti A: Genomic Alterations in Cultured Human Embryonic Stem Cells. Nat Genet 37:1099-1103, 2005. PMID 16142235.

  • Zlotogora J, Hujerat Y, Zalman L, Barges S, Filon D, Koren A, Shalev SA, Chakravarti A: Origin and Expansion of Four Different Beta Globin Mutations in a Single Arab Village. Amer J Hum Biol 17:659-661, 2005. PMID 16136542.

  • Mitchell AA, Chakravarti A, Cutler DJ: On the probability that a novel variant is a disease- causing mutation. Genome Res 15:960-966, 2005. PMID 15965029. PMC1172040.

  • Kashuk CS, Stone EA, Grice EA, Portnoy ME, Green ED, Sidow A, Chakravarti A, McCallion A: Genotype: Phenotype correlation in Hirschsprung disease illuminated by comparative RET protein sequence analysis. Proc Natl Acad Sci (USA) 102:8949-8954, 2005. PMID 15956201.

2004
  • Lin S, Chakravarti A, Cutler DJ: Exhaustive allelic disequilibrium tests are a new approach to genome-wide association studies. Nat Genet 36:1181-1188, 2004. PMID 15502828.

  • Lin S, Chakravarti A, Cutler DJ: Haplotype and Missing Data Inference in Nuclear Families. Genome Res 14:1624-32, 2004. PMID 15256514. PMC509272.

  • The International HapMap Consortium: Integrating Ethics and Science in the International HapMap Project. Nat Rev Genet 5:467-475, 2004. PMID 15153999. PMC2271136.

  • Maitra A, Cohen Y, Gillespie SED, Shah N, Sidransky D, Chakravarti A: The Human MitoChip: A high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res 14:812-819, 2004. PMID 15123581. PMC479107.

  • Mitchell AA, Zwick ME, Chakravarti A, Cutler DJ: Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns. Bioinformatics 20:1022-1032, 2004. PMID 14764571.

  • Arking DE, Chugh SS, Chakravarti A, Spooner PM: Genomics in Sudden Cardiac Death. Circ Rev 94:712-723, 2004. PMID 15059941.

  • Hong HK, Chakravarti A, Takahashi J: The gene for soluble NSF attachment protein α (α-SNAP) is mutated in hydrocephalus with hop gait mice. Proc Natl Acad Sci (USA) 101:1748-1753, 2004. PMID 14755058. PMC341847.

  • Xu Z, Kerstann KF, Sherman SL, Chakravarti A, Feingold E: A Trisomic Transmission Disequilibrium Test. Genet Epid 26:125-131, 2004. PMID 14748012.

  • Barkley RA, Chakravarti A, Cooper RS, Ellison RC, Hunt SC, Province MA, Turner ST, Weder AB, Boerwinkle E; Family Blood Pressure Program: Positional identification of hypertension susceptibility genes on chromosome 2. Hypertension 43:477-482, 2004. PMID 14732741.

2003
  • McCallion AS, Sproat-Emison EE, Kashuk CS, Bush RT, Kenton M, Carrasquillo MM, Jones KW, Kennedy GC, Portnoy M, Green E, Chakravarti A: Genomic variation in multigenic traits: Hirschsprung disease. Cold Spring Harbor Symp Quant Biol LXVIII 373-381, 2003. PMID 15338639.

  • Faden RR, Dawson L, Bateman-House AS, Mueller Agnew D, Bok H, Brock DW, Chakravarti A, Greene M, Hansen JA, King PA, O’Brien SJ, Sachs DH, Schill KE, Siegel A, Solter D, Suter SM, Verfaillie CM, Walters LB, Gearhart JD: Public Stem Cell Banks: Considerations of Justice in Stem Cell Research and Therapy. Hastings Center Report 33:13-27,2003. PMID 14983554.

  • The International HapMap Consortium: The International HapMap Project. Nature 426:789-796, 2003. PMID 14685227.

  • Dawson L, Bateman-House AS, Mueller Agnew D, Bok H, Brock DW, Chakravarti A, Greene M, King PA, O’Brien SJ, Sachs DH, Schill KE, Siegel A, Solter D, Suter SM, Verfaillie CM, Walters LB, Gearhart JD, Faden RR: Safety issues in cell-based intervention trials. Fertility & Sterility 80:1077-1085, 2003. PMID 14907552.

  • Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK et al.: Development of a Human Protein Reference Database as an initial platform for approaching systems biology in humans. Genome Res 13:2363-2371, 2003. PMID 14525934. PMC403728.

  • Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Bektrom-Sternberg SM et al.: Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788- 793, 2003. PMID 12917688.

  • Zhu X, Chang Y-P C, Yan D, Weder A, Cooper R, Luke A, Donghui K, Chakravarti A: Associations between Hypertension and Genes in the Renin-Angiotensin System. Hypertension 41:1027-1034,2003. PMID 12695419.

  • Weder AB, Delgado MC, Zhu X, Gleiberman L, Kan D, Chakravarti A: Erythrocyte Sodium- Lithium Countertransport and Blood Pressure: A Genome-Wide Linkage Study. Hypertension 41:842-846,2003. PMID 12624006.

  • McCallion AS, Stames E, Conlon RA, Chakravarti A: Phenotype variation in two-locus mouse models of Hirschsprung disease: Tissue-specific interaction between Ret and Ednrb. Proc Natl Acad Sci (USA) 100:1826-1831, 2003. PMID 12574515. PMC149918.

  • Mitchell AA, Cutler DJ, Chakravarti A: Undetected Genotyping Errors Cause Apparent Over- Transmission of Common Alleles in the Transmission Disequilibrium Test. Amer J Hum Genet 72:598-610, 2003. PMID 12587097. PMC1180236.

2002
  • Merikangas K, Chakravarti A, Moldin S, Araj H, Blangero J, Burmeister M, Crabbe J, Depaulo J, Foulks E, Freimer N, Koretz D, Lichtenstein W, Mignot E, Reiss A, Risch N, Takahashi JS: Future of genetics of mood disorders research. Biol Psych 52:457-477, 2002. PMID 12361664.

  • Lin S, Cutler DJ, Zwick ME, Chakravarti A: Haplotype inference in random population samples. Amer J Hum Genet 71:1129-1137, 2002. PMID 12386835. PMC385088.

  • Carrasquillo MM, McCallion AS, Puffenberger EG, Kashuk CS, Nouri N, Chakravarti A: Genome- wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease. Nat Genet 32:237-244, 2002. PMID 12355085.

  • Marshall DG, Meier-Ruge WA, Chakravarti A, Langer JC: Chronic constipation due to Hirschsprung’s disease and desmosis coli in a single family. Pediat Surg Intl 18:110-114, 2002. PMID 11956774.

  • Christian SL, McDonough J, Liu C-Y, Shaikh S, Vlamakis V, Badner JA,Chakravarti A, Gershon ES: An evaluation of the assembly of a ~15 Mb region on Human Chromosome 13q32-q33 linked to Bipolar Disorder and Schizophrenia. Genomics 79:635-656, 2002. PMID 11991713.

  • Nath SK, Chakravarti A, Chen C-H, Cooper R, Weder A, Schork NJ: Segregation analysis of blood pressure and body mass index in a rural U.S. community. Hum Biol 74:11-23, 2002. PMID 11931572.

  • Bolk Gabriel S, Salomon R, Pelet A, Angrist M, Amiel J, Attie-Bitach T, Olson JM, Hofstra R, Buys C, Steffann J, Munnich A, Lyonnet S, Chakravarti A: Splitting a multigenic disease: segregation at three loci explains sibling recurrence risk in Hirschsprung disease. Nat Genet 31:89-93, 2002. PMID 11953745.

  • Blagoev B, Nielsen MM, Angrist M, Chakravarti A, Pandey A: Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene 284:161-168, 2002. PMID 11891057.

  • Weese-Mayer DE, Bolk S, Silvestri JM, Chakravarti A: Idiopathic Congenital Central Hypoventilation Syndrome: Evaluation of Brain-Derived Neurotrophic Factor Genomic DNA Sequence Variation. Amer J Med Genet 107:306-310, 2002. PMID 11840487.

  • Zhu X, Cooper RS, Luke A, Chen G, Wu X, Chakravarti A, Weder AB: A genome-wide scan for obesity in African Americans. Diabetes 51:541-544, 2002. PMID 11812767.

2001
  • Green ED, Chakravarti A: The Human Genome Sequence Expedition: Views from the “Base Camp”. Genome Res 11:645-651, 2001. PMID 11337462.

  • Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C, Mathews DJ, Shah NA, Eichler EE, Warrington JA, Chakravarti A: High-throughput variation detection and genotyping using microarrays. Genome Res 11:1913-1925, 2001. PMID 11691856. PMC311146.

  • Wiesner GL, Platzer P, Buxbaum S, Lewis S, MacMillen M, Olechnowicz J, Willis J, Chakravarti A, Elston RC, Markowitz SD: Absence of colon neoplasia susceptibility variants at the human COX2 locus. J Natl Cancer Inst 18:635-639, 2001. PMID 11309440.

  • Mathews DJ, Kashuk C, Brightwell G, Eichler EE, Chakravarti A: Sequence variation within the fragile X locus. Genome Res 11:1382-1391, 2001. PMID 11483579. PMC311115.

  • Hong H-K, Noveroske JK, Headon DJ, Liu T, Sy M-S, Justice MJ, Chakravarti A: The winged helix/forkhead transcription factor Foxq1 regulates differentiation of hair in satin mice. Genesis 29:163-171, 2001. PMID 11309849.

2000
  • Schork NJ, Chakravarti A, Thiel B, Fornage M, Jacob HJ, Cai R, Rotimi CN, Cooper RS, Weder AB: Lack of association between a biallelic polymorphism in the Adducin gene and blood pressure in Whites and African Americans. Amer J Hypertension 13:693-698, 2000. PMID 10912755.

  • Province MA, Boerwinkle E, Chakravarti A, Cooper R, Fornage M, Leppert M, Risch N, Ranade K: Lack of association of the angiotensinogen-6 polymorphism with blood pressure levels in the comprehensive NHLBI Family Blood Pressure Program. J Hypertension 18:867-76, 2000. PMID 10930184.

  • Schork NJ, Nath SK, Fallin D, Chakravarti A: Linkage disequilibrium analysis of bi-allelic markers, human quantitative trait loci, and threshold-defined cases and controls. Amer J Hum Genet 67:1208-1218, 2000. PMID 11032785. PMC1288563.

  • Zwick ME, Cutler DJ, Chakravarti A: Patterns of Genetic Variation in Mendelian and Complex Traits. Annu Rev Genomics Hum Genet 1:387-407, 2000. PMID 11701635.

  • Lynn A, Peterson MB, Kashuk C, Cox DR, Antonarakis SE, Chakravarti A: Patterns of Meiotic Recombination on the Long Arm of Human Chromosome 21. Genome Res 10:1319-1332, 2000. PMID 10984450.

  • Fan J-B, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz R, Lockhart DJ, Chakravarti A: Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 10:853-860, 2000. PMID 10854416. PMC 310915.

  • Zaragoza MV, Surti U, Redline RW, Millie E, Chakravarti A, Hassold TJ: Parental Origin and Phenotype of Triploidy in Spontaneous Abortions: Predominance of Diandry and Association with the Partial Hydatidiform Mole. Amer J Hum Genet 66:1807-1820, 2000. PMID 10801385. PMC1378061.

  • Bailey JA, Carrel L, Chakravarti A, Eichler EE: Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis. Proc Natl Acad Sci (USA) 97:6634-6639, 2000. PMID 10841562. PMC18684.

  • Bolk S, Pelet A, Hofstra R, Angrist M, Salomon R, Croaker D, Buys C, Lyonnet S, Chakravarti A: Multigenic inheritance of Hirschsprung disease: requirements of a new 9q31 locus and RET for phenotypic expression. Proc Natl Acad Sci (USA) 97:268-273, 2000. PMID 10618407. PMC26652.

How to apply

FOR PROSPECTIVE GRADUATE STUDENTS, POSTDOCTORAL FELLOWS AND OTHER TRAINEES….

I am always in the search for scientifically enthusiastic graduate students and postdoctoral fellows to join my laboratory. I find my laboratory exciting precisely because of my trainees who bring new perspectives, questions and ideas…and, of course, new interests and new personalities! Over the past 37 years, and ever since I have been a preceptor in one or more graduate and post-graduate training programs, I have been fortunate to recruit a large number (~70) of talented trainees who have taught me just as much as we have been able to teach them.

My laboratory is focused on the fundamentals of human genetics, particularly as it relates to the understanding of human disease. Our current research is focused on two disorders of the nervous system where disease onset is early (Hirschsprung disease, autism) and two disorders of the cardiovascular system where disease onset is late (sudden cardiac death, hypertension). This breadth emphasizes the gamut of human genetic mechanisms. I expect that human genetic diseases are the photographic ‘negatives’ from which the ‘positives’ of normal physiology will emerge. To do so, we successfully use both experimental and computational approaches in human genetics and genomics, as well as use model organisms to test mechanistic hypotheses emerging from gene discovery.

My philosophy has been to let trainees choose what they want to study within the confines of the broad interests and grant support of the laboratory. I do not force any of them, graduate students or postdoctoral fellows, to focus on a particular question, but do help and guide them to the major scientific questions of the day; rather, I expect my trainees to learn to think independently but to work collaboratively because this is what they will need to do when they start their careers. Nevertheless, I work with all of my trainees very closely and expect them to gain expertise in both experimental and computational approaches, and contribute to the scientific life of the lab.

Mine is not a very large lab nor one where high-throughput technologies dominate but one where genetic arguments and genetic perspectives are central: we use the tools, both small and large, necessary for answering the question at hand. For any potential PhD trainee interested in our research you will have to gain admission in either the Johns Hopkins School of Medicine Human Genetics & Molecular Biology Training Program or the Bloomberg School of Public Health Biostatistics Training Program; postdoctoral fellows should write to me directly at least 9 months prior to an expected start. For any trainee, a visit to the lab is always a good idea.

My lab also hosts visiting international undergraduate students in the summer, and any Hopkins undergraduate throughout the year through a practicum. For all such students, research work in my lab can be taken for academic credit. We also host exceptional high school students who have a deep interest in human genetics.

Aravinda Chakravarti

Principal Investigator

Email

CONTACT

Center for Complex Disease Genomics
McKusick-Nathans Inst. of Genetic Medicine
Johns Hopkins University School of Medicine
Edward D. Miller Research Building, suite 579
733 N. Broadway
Baltimore, MD 21205 USA

Tel: (410)-502-7525 Fax:(410)-502-7544

Administrative Coordinator: Ms. Ann Vukelich
Lab Manager: Dallas Auer

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