Mingyao Li, PhD
| Office Location | 213, Blockley Hall |
| Office Phone | (215)746-3916 |
| mingyao@mail.med.upenn.edu | |
| Personal Website | https://dbe.med.upenn.edu/biostat-research/MingyaoLi |
Faculty Information | |
| CCEB Appointment | Senior Scholar, Biostatistics |
| Primary Faculty Appointment | Associate Professor of Biostatistics, University of Pennsylvania SOM |
Additional Positions
Member, Genomics and Computational Biology Graduate Group
Research Statement
I am a statistical geneticist motivated in my research to identify and characterize genes that determine human variation and diseases. My research program involves two synergistic components: a methodological component focused on developing novel statistical methods for gene mapping and an applied component focused on using statistical methods to map genes involved in complex traits. My current research involves analysis of high-throughput genetics data such as those generated from genome-wide association and next-generation sequencing studies. I am particularly interested in the analysis of admixed populations, RNA-sequencing data, and genetics of gene expression. My collaborative research includes studies of the genetics of cardiovascular disease and childhood obesity.
Courses Taught
BSTA787: Methods for Statistical Genetics in Complex Human Diseases (2007 Spring; 2008 Spring; 2010 Spring; 2011 Spring; 2012 fall)
Selected Publications
2012
- Vardhanabhuti S, Li M, Li H: A hierarchical Bayesian model for estimating and inferring differential isoform expression for multi-sample RNA-Seq data. Statistics in Biosciences: in press. [pdf]
2011
- Khetarpal SA, Edmondson AC, Raghavan A, Neeli H, Jin W, Badellino KO, Demissie S, Manning AK, DerOhannessian SL, Wolfe ML, Cupples LA, Li M, Kathiresan S, Rader DJ: Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol. PLoS Genetics 7:e1002392. [pdf]
- Chen HY, Li M: Improving power and robustness for detecting genetic association with extreme-value sampling design. Genetic Epidemiology 35:823-830. [pdf]
- The IBC 50K CAD Consortium: Large-scale gene-centric analysis identifies novel variants for coronary artery disease. PLoS Genetics 7:e1002260. [pdf]
- He J, Li H, Edmondson AC, Rader DJ, Li M *: A Gaussian copula approach for the analysis of secondary phenotypes in case-control genetic association studies. Biostatistics: in press. [pdf] (* corresponding author)
- Zhao J, Bradfield JP, Zhang H, Sleiman PM, Kim C, Glessner JT, Deliard S, Thomas KA, Frackelton EC, Li M, Chiavacci RM, Berkowitz RI, Hakonarson H, Grant SFA: Role of BMI-associated loci identified in GWAS meta-analyses in the context of common childhood obesity in European Americans. Obesity 19:2436-2439. [pdf]
- Wang K, Edmondson AC, Li M, Gao F, Qasim AN, Devaney JM, Burnett MS, Waterworth DM, Mooser V, Grant SF, Epstein SE, Reilly MP, Hakonarson H, Rader DJ: Pathway-wide association study implicates multiple sterol transport metablism genes in HDL cholesterol regulation. Frontiers in Genetics: in press. [pdf].
- Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WH, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL: Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. American Journal of Human Genetics 89:368-381. [pdf]
- Rushefski M, Aplenc R, Meyer N, Li M, Feng R, Lanken PN, Gallop R, Bellamy S, Localio RA, Feinstein SI, Fisher AB, Albelda SM, Christie JD: Novel variants in the PRDX6 gene and the risk of acute lung injury following major trauma. BMC Medical Genetics 12:77. [pdf]
- Wild PS, Zeller T, Schillert A, Szymczak S, Sinning CR, Deiseroth A, Schnabel RB, Lubos E, Keller T, Eleftheriadis MS, Bickel C, Rupprecht HJ, Wilde S, Rossmann H, Diemert P, Cupples LA, Perret C, Erdmann J, Stark K, Kleber ME, Epstein SE, Voight BF, Kuulaasma K, Li M, Schafer AS, Klopp N, Braund PS, Sager HB, Demissie S, Proust C, Konig IR, Wichmann HE, Reinhard W, Hoffmann MM, Virtamo J, Burnett MS, Siscovick D, Wiklund PG, Qu L, El Mokthari NE, Thompson JR, Peters A, Smith AV, Yon E, Baumert J, Hengstenberg C, Marz W, Amouyel P, Devaney J, Schwartz SM, Saarela O, Mehta NN, Rubin D, Silander K, Hall AS, Ferrieres J, Harris TB, Melander O, Kee F, Hakonarson H, Schrezenmeir J, Gudnason V, Elosua R, Arveiler D, Evans A, Rader DJ, Illig T, Schreiber S, Bis JC, Altshuler D, Kavousi M, Witteman JC, Uitterlinden AG, Hofman A, Folsom AR, Barbalic M, Boerwinkle E, Kathiresan S, Reilly MP, O'Donnell CJ, Samani NJ, Schunkert H, Cambien F, Lackner KJ, Tiret L, Salomaa V, Munzel T, Ziegler A, Blankenberg S: A genome-wide association study identifies LIPA as a susceptibility gene for coronary artery disease. Circulation Cardiovascular Genetics 4:403-412. [pdf]
- Li M*, Wang IX*, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG: Widespread RNA and DNA sequence differences in the human transcriptome. Science 33:53-58. (* co-first authors) [pdf]
- Chikkagoudar S *, Wang K, Li M *: GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores. BMC Research Notes 4:158. [pdf] [website] (* corresponding authors)
- Kanetsky PA, Mitra N, Vardhanabhuti S, Vaughn DJ, Li M, Ciosek SL, Letrero R, D'Andrea K, Vaddi M, Doody DR, Weaver J, Chen C, Starr JR, Hakonarson H, Rader DJ, Godwin AK, Reilly MP, Schwartz SM, Nathanson KL: A second independent locus within DMRT1 is associated with testicular germ cell tumor susceptibility. Human Molecular Genetics 20:3109-3117. [pdf]
- Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WH, Ruczinski I, Fornage M, Siscovick DS, Zhu X, Larkin E, Lange LA, Cupples LA, Yang Q, Akylbekova EL, Musani SK, Divers J, Mychaleckyj J, Li M, Papanicolaou GJ, Millikan RC, Ambrosone CB , John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante SJ, Bandera EV, Ingles SA, Press MF, Chanock SJ, Derming SL, Rodriguez-Gil JL, Palmer CD, Buxbaum S, Ekunwe L, Hirschhorn JN, Henderson BE, Myers S, Haiman CA, Reich D, Patterson N, Wilson JG, Price AL: Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS Genetics 7:e1001371. [pdf]
- Toung JM, Morley M, Li M, Cheung VC: RNA-Sequence analysis of human B-cells. Genome Research 21:991-998. [pdf]
- Shah R, Hinkle CC, Ferguson JF, Mehta NN, Li M, Qu L, Lu Y, Putt ME, Ahima RS, Reilly MP: Fractalkine is a novel human adipochemokine associated with type 2 diabetes. Diabetes 60:1512-1518. [pdf]
- Mehta NN, Li M, William D, Khera A, DerOhannessian S, Qu L, Ferguson J, McLaughlin C, Shaikh LH, Shah R, Patel P, He J, Stylianou I, Hakonarson H, Rader DJ, Reilly MP: The novel atherosclerosis locus at 10q11 regulates plasma CXCL12 levels. European Heart Journal 32:963-971. [pdf]
- Schunkert H, Konig IR, Kathiresan S, Reilly MP, Assimes TL, Holm H, Preuss M, Stewart AF, Barbalic M, Gieger C, Absher D, Aherrahrou Z, Allayee H, Altshuler D, Anand SS, Andersen K, Anderson JL, Ardissino D, Ball SG, Balmforth AJ, Barnes TA, Becker DM, Becker LC, Berger K, Bis JC, Boekholdt SM, Boerwinkle E, Braund PS, Brown MJ, Burnett MS, Buysschaert I; Cardiogenics, Carlquist JF, Chen L, Cichon S, Codd V, Davies RW, Dedoussis G, Dehghan A, Demissie S, Devaney JM, Diemert P, Do R, Doering A, Eifert S, Mokhtari NE, Ellis SG, Elosua R, Engert JC, Epstein SE, de Faire U, Fischer M, Folsom AR, Freyer J, Gigante B, Girelli D, Gretarsdottir S, Gudnason V, Gulcher JR, Halperin E, Hammond N, Hazen SL, Hofman A, Horne BD, Illig T, Iribarren C, Jones GT, Jukema JW, Kaiser MA, Kaplan LM, Kastelein JJ, Khaw KT, Knowles JW, Kolovou G, Kong A, Laaksonen R, Lambrechts D, Leander K, Lettre G, Li M, Lieb W, Loley C, Lotery AJ, Mannucci PM, Maouche S, Martinelli N, McKeown PP, Meisinger C, Meitinger T, Melander O, Merlini PA, Mooser V, Morgan T, Muhleisen TW, Muhlestein JB, Munzel T, Musunuru K, Nahrstaedt J, Nelson CP, Nothen MM, Olivieri O, Patel RS, Patterson CC, Peters A, Peyvandi F, Qu L, Quyyumi AA, Rader DJ, Rallidis LS, Rice C, Rosendaal FR, Rubin D, Salomaa V, Sampietro ML, Sandhu MS, Schadt E, Schafer A, Schillert A, Schreiber S, Schrezenmeir J, Schwartz SM, Siscovick DS, Sivananthan M, Sivapalaratnam S, Smith A, Smith TB, Snoep JD, Soranzo N, Spertus JA, Stark K, Stirrups K, Stoll M, Tang WH, Tennstedt S, Thorgeirsson G, Thorleifsson G, Tomaszewski M, Uitterlinden AG, van Rij AM, Voight BF, Wareham NJ, Wells GA, Wichmann HE, Wild PS, Willenborg C, Witteman JC, Wright BJ, Ye S, Zeller T, Ziegler A, Cambien F, Goodall AH, Cupples LA, Quertermous T, Marz W, Hengstenberg C, Blankenberg S, Ouwehand WH, Hall AS, Deloukas P, Thompson JR, Stefansson K, Roberts R, Thorsteinsdottir U, O'Donnell CJ, McPherson R, Erdmann J; the CARDIoGRAM Consortium, Samani NJ: Large-scale association analysis identifies 13 new loci for coronary artery disease. Nature Genetics 43:333-338. [pdf]
- Lettre G, Palmer CD, Young T, Ejebe KG, Allayee H, Benjamin EJ, Bennett F, Bowden DW, Chakravarti A, Dreisbach A, Farlow DN, Folsom AR, Fornage M, Forrester T, Fox E, Haiman CA, Hartiala J, Harris TB, Hazen SL, Heckbert SR, Henderson BE, Hirschhorn JN, Keating BJ, Kritchevsky SB, Larkin E, Li M, Rudock ME, McKenzie CA, Meigs JB, Meng YA, Mosley TH, Newman AB, Newton-Cheh CH, Paltoo DN, Papanicolaou GJ, Patterson N, Post WS, Psaty BM, Qasim AN, Qu L, Rader DJ, Redline S, Reilly MP, Reiner AP, Rich SS, Rotter JI, Liu Y, Shrader P, Siscovick DS, Tang WH, Taylor HA, Tracy RP, Vasan RS, Waters KM, Wilks R, Wilson JG, Fabsitz RR, Gabriel SB, Kathiresan S, Boerwinkle E: Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe project. PLoS Genetics 7:e1001300. [pdf]
- Meyer NJ, Li M, Feng R, Bradfield J, Gallop R, Bellamy S, Fuchs BD, Lanken PN, Albelda SM, Rushefski M, Aplenc R, Abramova E, Atochina-Vasserman EN, Beers MF, Calfee CS, Cohen MJ, Pittet JF, Christiani DC, O'Keefe GE, Ware LB, May AK, Wurfel MM, Hakonarson H, Christie JD: ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma angiopoietin-2 isoform ratio. American Journal of Respiratory and Critical Care Medicine 183:1344-1353. [pdf]
- Lanktree MB, Guo Y, Murtaza M, Glessner JT, Bailey SD, Onland-Moret NC, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson CP, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow JS, Shah S, Taylor K, Barnard J, Peters BJ, Maloney CM, Lobmeyer MT, Stanton A, Zafarmand MH, Romaine SP, Mehta A, van Iperen EP, Gong Y, Price TS, Smith EN, Kim CE, Li YR, Asselbergs FW, Atwood LD, Bailey KM, Bhatt D, Bauer F, Behr ER, Bhangale T, Boer JM, Boehm BO, Bradfield JP, Brown M, Braund PS, Burton PR, Carty C, Chandrupatla HR, Chen W, Connell J, Dalgeorgou C, Boer A, Drenos F, Elbers CC, Fang JC, Fox CS, Frackelton EC, Fuchs B, Furlong CE, Gibson Q, Gieger C, Goel A, Grobbee DE, Hastie C, Howard PJ, Huang GH, Johnson WC, Li Q, Kleber ME, Klein BE, Klein R, Kooperberg C, Ky B, Lacroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch FD, Meyer NJ, Monda KL, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse SJ, Otieno FG, Patel SR, Putt ME, Rodriguez S, Safa RN, Sawyer DB, Schreiner PJ, Simpson C, Sivapalaratnam S, Srinivasan SR, Suver C, Swergold G, Sweitzer NK, Thomas KA, Thorand B, Timpson NJ, Tischfield S, Tobin M, Tomaszweski M, Verschuren WM, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda JM, Clarke R, Balmforth AJ, Danesh J, Day IN, Schork NJ, de Bakker PI, Delles C, Duggan D, Hingorani AD, Hirschhorn JN, Hofker MH, Humphries SE, Kivimaki M, Lawlor DA, Kottke-Marchant K, Mega JL, Mitchell BD, Morrow DA, Palmen J, Redline S, Shields DC, Shuldiner AR, Sleiman PM, Smith GD, Farrall M, Jamshidi Y, Christiani DC, Casas JP, Hall AS, Doevendans PA, Christie JD, Berenson GS, Murray SS, Illig T, Dorn GW 2nd, Cappola TP, Boerwinkle E, Sever P, Rader DJ, Reilly MP, Caulfield M, Talmud PJ, Topol E, Engert JC, Wang K, Dominiczak A, Hamsten A, Curtis SP, Silverstein RL, Lange LA, Sabatine MS, Trip M, Saleheen D, Peden JF, Cruickshanks KJ, Marz W, O'Connell JR, Klungel OH, Wijmenga C, Maitland-van der Zee AH, Schadt EE, Johnson JA, Jarvik GP, Papanicolaou GJ; Hugh Watkins on behalf of PROCARDIS, Grant SF, Munroe PB, North KE, Samani NJ, Koenig W, Gaunt TR, Anand SS, van der Schouw YT; Meena Kumari on behalf of the Whitehall II Study and the WHII 50K Group, Soranzo N, Fitzgerald GA, Reiner A, Hegele RA, Hakonarson H, Keating BJ: Meta-analysis of dense genecentric association studies reveals common and uncommon variants associated with height. American Journal of Human Genetics 88:6-18. [pdf]
- Cappola TP, Matkovich S, Wang W, van Booven D, Li M, Wang X, Qu L, Sweitzer N, Fang J, Reilly MP, Hakonarson H, Nerbonne J, Dorn G II: A loss-of-function DNA sequence variant in CLCNKA implicates the cardio-renal axis in inter-individual heart failure risk variation. Proceedings of the National Academy of Sciences 108:2056-2061. [pdf]
- Wang X, Zhu X, Qin H, Cooper R, Ewens E, Li C*, Li M*: Adjustment for local ancestry in genetic association analysis of admixed populations. Bioinformatics 27:670-677. [pdf] (* corresponding authors)
- Edmondson AC, Braund PS, Stylianou IM, Khera AV, Nelson CP, Wolfe ML, DerOhannessian SL, Keating BJ, Qu L, He J, Tobin MD, Tomaszewski M, Baumert J, Klopp N, Doring A, Thorand B, Li M, Reilly MP, Koenig W, Samani NJ, Rader DJ: Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterol. Circulation Cardiovascular Genetics 4:145-155. [pdf]
- Zhao J, Bradfield JP, Li M, Zhang H, Mentch FD, Wang K, Sleiman PM, Kim CE, Glessner JT, Frackelton EC, Chiavacci RM, Berkowitz RI, Zemel BS, Hakonarson H, Grant SFA: BMD-associated variation at the Osterix locus is correlated with childhood obesity in females. Obesity 19:1311-1314. [pdf]
- Reilly M*, Li M*, He J, Ferguson JF, Stylianou IM, Mehta NN, Burnett MS, Devaney JM, Knouff CW, Thompson JR, Horne BD, Stewart AF, Assimes TL, Wild PS, Allayee H, Linsel-Nitschke P, Patel RS, Myocardial Infarction Genetics Consortium, Wellcome Trust Case Control Consortium, Martinelli N, Girelli D, Quyyumi AA, Anderson JL, Erdmann J, Hall AS, Schunkert H, Quertermous T, Blankenberg S, Hazen SL, Roberts R, Kathiresan S, Samani NJ, Epstein SE, Rader DJ: Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. The Lancet 377:383-392. (*co-first authors) [pdf]
2010
- Wang K, Li M, Hakonarson H: Analysis of biological pathways in genome-wide association studies. Nature Review Genetics 11:843-854. [pdf]
- Li Y, Byrnes AE, Li M: Rare Variants, WHaIT: Weighted Haplotype and Imputation-based Tests. American Journal of Human Genetics 87:728-735. [pdf]
- Zhao J, Schug JJ, Li M, Kaestner KH, Grant SFA: Disease-associated loci are significantly over-represented among genes bound by TCF7L2 in vivo. Diabetologia 53: 2340-2346.
- Soranzo N, Sanna S, Wheeler E, Gieger C, Radke D, Dupuis J, Bouatia-Naji N, Langenberg C, Prokopenko I, Stolerman E, Sandhu MS, Heeney MM, Devaney JM, Reilly MP, Ricketts SL, Stewart AF, Voight BF, Willenborg C, Wright B, Altshuler D, Arking D, Balkau B, Barnes D, Boerwinkle E, Bhm B, Bonnefond A, Bonnycastle LL, Boomsma DI, Bornstein SR, Bottcher Y, Bumpstead S, Burnett-Miller MS, Campbell H, Cao A, Chambers J, Clark R, Collins FS, Coresh J, de Geus EJ, Dei M, Deloukas P, Doring A, Egan JM, Elosua R, Ferrucci L, Forouhi N, Fox CS, Franklin C, Franzosi MG, Gallina S, Goel A, Graessler J, Grallert H, Greinacher A, Hadley D, Hall A, Hamsten A, Hayward C, Heath S, Herder C, Homuth G, Hottenga JJ, Hunter-Merrill R, Illig T, Jackson AU, Jula A, Kleber M, Knouff CW, Kong A, Kooner J, Kottgen A, Kovacs P, Krohn K, Kuhnel B, Kuusisto J, Laakso M, Lathrop M, Lecoeur C, Li M, Loos RJ, Luan J, Lyssenko V, Magi R, Magnusson PK, Mlarstig A, Mangino M, Martnez-Larrad MT, Marz W, McArdle WL, McPherson R, Meisinger C, Meitinger T, Melander O, Mohlke KL, Mooser VE, Morken MA, Narisu N, Nathan DM, Nauck M, O'Donnell C, Oexle K, Olla N, Pankow JS, Payne F, Peden JF, Pedersen NL, Peltonen L, Perola M, Polasek O, Porcu E, Rader DJ, Rathmann W, Ripatti S, Rocheleau G, Roden M, Rudan I, Salomaa V, Saxena R, Schlessinger D, Schunkert H, Schwarz P, Seedorf U, Selvin E, Serrano-Rios M, Shrader P, Silveira A, Siscovick D, Song K, Spector TD, Stefansson K, Steinthorsdottir V, Strachan DP, Strawbridge R, Stumvoll M, Surakka I, Swift AJ, Tanaka T, Teumer A, Thorleifsson G, Thorsteinsdottir U, Tonjes A, Usala G, Vitart V, Volzke H, Wallaschofski H, Waterworth DM, Watkins H, Wichmann HE, Wild SH, Willemsen G, Williams GH, Wilson JF, Winkelmann J, Wright AF; WTCCC, Zabena C, Zhao JH, Epstein SE, Erdmann J, Hakonarson HH, Kathiresan S, Khaw KT, Roberts R, Samani NJ, Fleming MD, Sladek R, Abecasis G, Boehnke M, Froguel P, Groop L, McCarthy MI, Kao WH, Florez JC, Uda M, Wareham NJ, Barroso I, Meigs JB: Common variants at 10 genomic loci influence hemoglobin A1C levels via glycemic and nonglycemic pathways. Diabetes 59:3229-3239. [pdf]
- Assimes TL, Holm H, Kathiresan S, Reilly MP, Thorleifsson G, Voight BF, Erdmann J, Willenborg C, Vaidya D, Xie C, Patterson CC, Morgan TM, Burnett MS, Li M, ..., Rader DJ, Elosua R, Engert JC, Anand SS, Hall AS, Ziegler A, O'Donnell CJ, Spertus JA, Siscovick D, Schwartz SM, Becker D, Thorsteinsdottir U, Stefansson K, Schunkert H, Samani NJ, Quertermous T: Lack of Association between the Trp719Arg polymorphism in kinesin-like protein-6 and coronary artery disease in 19 case-control studies. Journal of American College of Cardiology 56:1552-1563 [pdf].
- Haas EJ, Zaoutis TE, Prasad P, Li M, Coffin SE: Risk factors and outcomes for vancomycin-resistant enterococcus bloodstream infection in children. Infection Control Hospital Epidemiology: in press [pdf].
- Song PX, Li M, Yuan Y: Rejoinder to "Joint regression analysis for discrete longitudinal data" By Madsen and Fang. Biometrics 67:1175-1176. [pdf]
- Shen H, Bielak LF, Ferguson JF, Streeten EA, Yerges-Armstrong LM, Liu J, Post W, O'Connell JR, Hixson JE, Kardia SL, Sun YV, Jhun MA, Wang X, Mehta NN, Li M, Koller DL, Hakonarson H, Keating BJ, Rader DJ, Shuldiner AR, Peyser PA, Reilly MP, Mitchell BD: Association of the vitamin D metabolism gene CYP24A1 with coronary artery calcification. Arteriosclerosis Thrombosis Vascular Biology 30:2648-2654 [pdf].
- Qin H, Morris N, Kang SJ, Li M, Tayo B, Lyon H, Hirschhorn J, Cooper RS, Zhu X: Interrogating local population structure for fine mapping in genome-wide association studies. Bioinformatics 26:2961-2968 [pdf].
- Glessner J, Bradfield JP, Wang K, Takahashi N, Zhang H, Sleiman PM, Mentch FD, Kim CE, Hou C, Thomas KA, Garris ML, Deliard S, Frackelton EC, Otieno FG, Zhao J, Chiavacci RM, Li M, Buxbaum JD, Berkowitz RI, Hakonarson H, Grant SFA: Genome-wide copy number variation study reveals loci impacted only in childhood obesity. American Journal of Human Genetics 87:661-666 [pdf].
- He J, Wang K, Edmondson A, Rader DJ, Li C, Li M *: Gene-based interaction analysis by incorporating external linkage disequilibrium information. European Journal of Human Genetics 19:164-172 [pdf] (* corresponding author).
- Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ, Johansen CT, Fouchier SW, Isaacs A, Peloso GM, Barbalic M, Ricketts SL, Bis JC, Aulchenko YS, Thorleifsson G, Feitosa MF, Chambers J, Orho-Melander M, Melander O, Johnson T, Li X, Guo X, Li M, Shin Cho Y, Jin Go M, Jin Kim Y, Lee JY, Park T, Kim K, Sim X, Twee-Hee Ong R, Croteau-Chonka DC, Lange LA, Smith JD, Song K, Hua Zhao J, Yuan X, Luan J, Lamina C, Ziegler A, Zhang W, Zee RY, Wright AF, Witteman JC, Wilson JF, Willemsen G, Wichmann HE, Whitfield JB, Waterworth DM, Wareham NJ, Waeber G, Vollenweider P, Voight BF, Vitart V, Uitterlinden AG, Uda M, Tuomilehto J, Thompson JR, Tanaka T, Surakka I, Stringham HM, Spector TD, Soranzo N, Smit JH, Sinisalo J, Silander K, Sijbrands EJ, Scuteri A, Scott J, Schlessinger D, Sanna S, Salomaa V, Saharinen J, Sabatti C, Ruokonen A, Rudan I, Rose LM, Roberts R, Rieder M, Psaty BM, Pramstaller PP, Pichler I, Perola M, Penninx BW, Pedersen NL, Pattaro C, Parker AN, Pare G, Oostra BA, O'Donnell CJ, Nieminen MS, Nickerson DA, Montgomery GW, Meitinger T, McPherson R, McCarthy MI, McArdle W, Masson D, Martin NG, Marroni F, Mangino M, Magnusson PK, Lucas G, Luben R, Loos RJ, Lokki ML, Lettre G, Langenberg C, Launer LJ, Lakatta EG, Laaksonen R, Kyvik KO, Kronenberg F, Konig IR, Khaw KT, Kaprio J, Kaplan LM, Johansson A, Jarvelin MR, Janssens AC, Ingelsson E, Igl W, Kees Hovingh G, Hottenga JJ, Hofman A, Hicks AA, Hengstenberg C, Heid IM, Hayward C, Havulinna AS, Hastie ND, Harris TB, Haritunians T, Hall AS, Gyllensten U, Guiducci C, Groop LC, Gonzalez E, Gieger C, Freimer NB, Ferrucci L, Erdmann J, Elliott P, Ejebe KG, Doring A, Dominiczak AF, Demissie S, Deloukas P, de Geus EJ, de Faire U, Crawford G, Collins FS, Chen YD, Caulfield MJ, Campbell H, Burtt NP, Bonnycastle LL, Boomsma DI, Boekholdt SM, Bergman RN, Barroso I, Bandinelli S, Ballantyne CM, Assimes TL, Quertermous T, Altshuler D, Seielstad M, Wong TY, Tai ES, Feranil AB, Kuzawa CW, Adair LS, Taylor HA Jr, Borecki IB, Gabriel SB, Wilson JG, Holm H, Thorsteinsdottir U, Gudnason V, Krauss RM, Mohlke KL, Ordovas JM, Munroe PB, Kooner JS, Tall AR, Hegele RA, Kastelein JJ, Schadt EE, Rotter JI, Boerwinkle E, Strachan DP, Mooser V, Stefansson K, Reilly MP, Samani NJ, Schunkert H, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, van Duijn CM, Peltonen L, Abecasis GR, Boehnke M, Kathiresan S: Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466:707-713. [pdf]
- Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38:e164. [pdf]
- Raychaudhuri S, Ripke S, Li M, Neale BM, Fagerness J, Reynolds R, Sobrin L, Swaroop A, Abecasis G, Seddon JM, Daly MJ: Association of CFHR1-CFHR3 deletion and a CFH SNP to age-related macular degeneration are not independent. Nature Genetics 42:553-555. [pdf]
- Zhao J*, Li M*, Bradfield JP, Zhang H, Mentch FD, Wang K, Sleiman PM, Kim CE, Glessner JT, Hou C, Keating BJ, Thomas KA, Garris ML, Deliard S, Frackelton EC, Otieno FG, Chiavacci RM, Berkowitz RI, Hakonarson H, Grant SF: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. BMC Medical Genetics 11:96. [pdf] (* co-first authors)
- Liu JZ, Tozzi F, ..., Li M, ..., Marchini J: Meta analysis and imputation refines the association of 15q25 with smoking quantity. Nature Genetics 42:436-440. [pdf]
- CARDIoGRAM Consortium: Design of the Coronary ARtery DIsease Genome-wide Replication And Meta-Analysis (CARDIoGRAM) Study: A genome-wide association meta-analysis involving more than 22,000 cases and 60,000 controls. Circulation Cardiovascular Genetics 3:475-483 [pdf].
- Li M, Reilly MP, Rader DJ, Wang L-S: Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinformatics 26:798-806. [pdf]
- Cappola TP, Li M, He J, Ky B, Gilmore J, Qu L, Keating B, Reilly MP, Glessner J, Frackelton E, Hakonarson H, Syed F, Hindes A, Matkovich SJ, Cresci S, Dorn GW: Common variants in HSPB7 and FRMD4B associated with advanced heart failure. Circulation Cardiovascular Genetics 3:147-154.[pdf]
- Zhao J, Bradfield JP, Zhang H, Annaiah K, Wang K, Kim CE, Glessner JT, Frackelton EC, Otieno FG, Doran J, Thomas KA, Garris M, Hou C, Chiavacci RM, Li M, Berkowitz RI, Hakonarson H, Grant SFA. Examination of all type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMI. Diabetes 59:751-755.[pdf]
2009
- Soranzo N, Spector TD, Mangino M, Khnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, ..., Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C. A meta-analysis of eight hematological parameters identifies 22 associatedloci and extensive disease pleiotropy on chromosome 12q24. Nature Genetics 41:1182-1190. [pdf]
- Zhao J, Li M, Bradfield JP, Wang K, Zhang H, Sleiman P, Kim CE, Annaiah K, Glaberson W, Glessner JT, Otieno GF, Thomas KA, Garris M, Hou C, Frackelton EC, Chiavacci RM, Berkowitz RI, Hakonarson H, Grant SF. Examination of type 2 diabetes loci implicates CDKAL1 as a birth weight gene. Diabetes 58:2414-2418. [pdf]
- Bucan M, Abrahams BS, Wang K, Glessner J, Herman EI, Sonnenblick LI, Reteuro AIA, Imielinski M, Hadley D, Bradfield JP, Kim C, Gidaya NB, Yurcaba L, Hutman T, Sigman M, Lajonchere C, Kustanovich V, Singleton A, Kim J, Li M, Cantor RM, Grant SFA, Geschwind DH, Hakonarson H: Genome-wide analysis of exonic deletions identify novel autism susceptibility genes. PLoS Genetics 5: e1000536. [pdf]
- Brown RJ, Edmondson AC, Griffon N, Hill TB, Fuki IV, Badellino KO, Li M, Wolfe ML, Reilly MP, Rader DJ: A naturally occurring variant of endothelial lipase associated with elevated HDL exhibits impaired synthesis. Journal of Lipids Research 50:1910-1916. [pdf]
- Zhao J, Bradfield JP, Li M, Wang K, Zhang H, Kim CE, Annaiah K, Glessner JT, Thomas KA, Garris M, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Chiavacci RM, Berkowitz RI, Hakonarson H, Grant SFA: The role of obesity-associated loci identified in genome wide association studies in the determination of pediatric BMI. Obesity 17:2254-2257. [pdf]
- Kanetsky P, Mitra N, Vardhanabhuti S, Li M, Vaughn D, Letrero R, Ciosek S, Doody D, Smith L, Weaver J, Albano A, Chen C, Starr J, Rader DJ, Godwin AK, Reilly M, Hakonarson H, Schwartz S, Nathanson K: Common variation in KITLG and at 5q31.3 proximate to SPRY4 predispose to testicular germ cell cancer. Nature Genetics 41:811-815. [pdf]
- Wang K, Zhang H, Kugathasan S, Annese V, Bradfield J, Russell RK, Sleiman PMA, Imielinski M, Glessner J, Hou C, Wilson DC, Walters T, Kim C, Cucchiara S, Frackelton EC, Limbergen JV, Guthery S, Denson L, Piccoli D, Li M, Dubinsky M, Silverberg M, Griffiths A, Grant SFA, Sansangi J, Baldassano R, Hakonarson H: Diverse genome-wide association studies associate the IL12 pathway with Crohn's disease. American Journal of Human Genetics 84: 399-405. [pdf]
- Edmonson AC, Brown RJ, Kathiresan S, Cupples LA, Demissie S, Manning A, Jensen M, Rimm EB, Wang J, Wolfe ML, DerOhannessian S, Li M, Reilly M, Evens D, Hegele RA, Rader DJ: Loss-of-function variants in endothelial lipase are a cause of elevanted high density lipoprotein cholesterol in humans. Journal of Clinical Investigation 119:1042-1050. [pdf]
- Kathiresan S, Voight BF, Purcell S, Musunuru K, Ardissino D, Mannucci PM, Anand S, Engert JC, Samani NJ, Schunkert H, Erdmann J, Reilly MP, Rader DJ, Morgan T, Spertus JA, Stoll M, Girelli D, McKeown PP, Patterson CC, Siscovick DS, O'Donnell CJ, Elosua R, Peltonen L, Salomaa V, Schwartz SM, Melander O, Altshuler D, Ardissino D, Merlini PA, Berzuini C, Bernardinelli L, Peyvandi F, Tubaro M, Celli P, Ferrario M, Fetiveau R, Marziliano N, Casari G, Galli M, Ribichini F, Rossi M, Bernardi F, Zonzin P, Piazza A, Mannucci PM, Schwartz SM, Siscovick DS, Yee J, Friedlander Y, Elosua R, Marrugat J, Lucas G, Subirana I, Sala J, Ramos R, Kathiresan S, Meigs JB, Williams G, Nathan DM, MacRae CA, O'Donnell CJ, Salomaa V, Havulinna AS, Peltonen L, Melander O, Berglund G, Voight BF, Kathiresan S, Hirschhorn JN, Asselta R, Duga S, Spreafico M, Musunuru K, Daly MJ, Purcell S, Voight BF, Purcell S, Nemesh J, Korn JM, McCarroll SA, Schwartz SM, Yee J, Kathiresan S, Lucas G, Subirana I, Elosua R, Surti A, Guiducci C, Gianniny L, Mirel D, Parkin M, Burtt N, Gabriel SB, Samani NJ, Thompson JR, Braund PS, Wright BJ, Balmforth AJ, Ball SG, Hall AS; Wellcome Trust Case Control Consortium, Schunkert H, Erdmann J, Linsel-Nitschke P, Lieb W, Ziegler A, Konig I, Hengstenberg C, Fischer M, Stark K, Grosshennig A, Preuss M, Wichmann HE, Schreiber S, Schunkert H, Samani NJ, Erdmann J, Ouwehand W, Hengstenberg C, Deloukas P, Scholz M, Cambien F, Reilly MP, Li M, Chen Z, Wilensky R, Matthai W, Qasim A, Hakonarson HH, Devaney J, Burnett MS, Pichard AD, Kent KM, Satler L, Lindsay JM, Waksman R, Knouff CW, Waterworth DM, Walker MC, Mooser V, Epstein SE, Rader DJ, Scheffold T, Berger K, Stoll M, Huge A, Girelli D, Martinelli N, Olivieri O, Corrocher R, Morgan T, Spertus JA, McKeown P, Patterson CC, Schunkert H, Erdmann E, Linsel-Nitschke P, Lieb W, Ziegler A, Konig IR, Hengstenberg C, Fischer M, Stark K, Grosshennig A, Preuss M, Wichmann HE, Schreiber S, H�lm H, Thorleifsson G, Thorsteinsdottir U, Stefansson K, Engert JC, Do R, Xie C, Anand S, Kathiresan S, Ardissino D, Mannucci PM, Siscovick D, O'Donnell CJ, Samani NJ, Melander O, Elosua R, Peltonen L, Salomaa V, Schwartz SM, Altshuler D: Genome-wide association of early-onset myocardial infarction with common single nucleotide polymorphisms, common copy number variants, and rare copy number variants. Nature Genetics 41:334-341. [pdf]
- Grant SFA, Bradfield JP, Zhang H, Wang K, Kim CE, Annaiah K, Santa E, Glessner JT, Thomas K, Garris M, Frackelton EC, Otieno FG, Shane JL, Smith RM,Imielinski M, Chiavacci RM, Li M, Berkowitz RI, Hakonarson H: Association of MC4R with childhood obesity in European Americans does not extend to African ancestry. Obesity 17:1461-1465. [pdf]
- Li M, Abecasis GR: Linkage analysis of qualitative traits. Handbook on analyzing human genetic data. Springer Verlag. [pdf]
2008
- Li M, Wang K, Grant SFA, Hakonarson H, Li C: ATOM: A powerful gene-based association test by combining optimally weighted markers. Bioinformatics 25:497-503. [pdf]
- Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA: Concept, Design and Implementation of a cardiovascular gene-centric 50K SNP array for large-scale genomic association studies. PLoS ONE v3:e3583. [pdf]
- Wang K *, Chen Z, Tadesse MG, Glessner J, Grant SFA, Hakonarson H, Bucan M, Li M *: Modeling genetic inheritance of copy number variations. Nucleic Acids Research 36:e138. [pdf] (* corresponding author)
- Grant SFA, Li M, Bradfield JP, Kim CE, Annaiah K, Santa E, Glessner JT, Casalunovo T, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Eckert AW, Imielinski M, Chiavacci RM, Berkowitz RI, Hakonarson H: Association of HMGA2 gene variation with height in specific pediatric age categories. Genomics Insights 1:13-16.[pdf]
- Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K: Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Research 36:e126. [pdf] [suppl material]
- Ewens W, Li M, Spielman RS: A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker. PLoS Genetics 4:e1000180.[pdf]
- Wei Z, Li M, Rebbeck T, Li H: U-statistics-based tests for multiple genes in genetic association studies. Annals of Human Genetics 72:821-833. [pdf]
- Becker DJ, Gordon RY, Morris P, Yorko J, Gordon YJ, Li M, Iqbal N: Simvastatin versus therapeutic lifestyle changes and supplements: a randomized primary prevention trial. Mayo Clinic Proceedings 83:758-764.[pdf]
- Li M, Li C: Assessing departure from Hardy-Weinberg equilibrium in the presence of disease association. Genetic Epidemiology 32:589-599. [pdf]
- Grant SFA, Li M, Bradfield J, Kim C, Annaiah K, Santa E, Glessner J, Casalunovo T, Frackelton E, Otieno F, Shaner J, Smith R, Imielinski M, Eckert A, Chiavacci R, Berkowitz R, Hakonarson H: Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP. PLoS ONE v3:e1746. [pdf]
- Song P-XK, Li M, Yuan Y: Joint regression analysis of correlated data using Gaussian copulas. Biometrics 65:60-68. [pdf]
- Vorovich E, Chuai S, Li M, Averna J, Marwin V, Wolfe D, Reilly MP, Cappola TP: Comparison of MMP-9 and BNP as clinical biomarkers in chronic heart failure. American Heart Journal 155:992-997 [pdf]
- Christie JD, Ma SF, Aplenc R, Li M, Lanken PN, Fuchs B, Albelda SM, Flores C, Garcia JGN: Variation in the MYLK gene is associated with development of acute lung injury following major trauma. Critical Care Medicine 36:2794-2800.[pdf]
- Li C, Li M, Long J, Cai Q, Zheng W: Evaluating cost efficiency of SNP chips in genome-wide association studies. Genetic Epidemiology 32:387-395. [pdf]
- Li M, Li C, Guan W: Evaluation of coverage variation of SNP chips for genome-wide association studies. European Journal of Human Genetics 16:635-643. [pdf] [suppl Figure] [suppl Table]
- Ewens W, Li M: Comments on the entropy-based transmission/disequilibrium test. Human Genetics 123: 97-100. [pdf]
2007
- Li C, Li M: GWAsimulator: a rapid whole-genome simulation program. Bioinformatics 24:140-142. [pdf] [web]
- Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 17:1665-1674. [pdf] [web]
- Wang K, Li M, Bucan M: Pathway based approaches for analysis of genome-wide association studies. American Journal of Human Genetics 81:1278-1283. [pdf]
- Li C *, Li M *, Lange EM, Watanabe RM: Prioritized subset analysis: improving power in genome-wide association studies. Human Heredity 65:129-141 (*co-first author). [pdf]
2006
- Wei Z, Li M *: Genome-wide linkage and association analysis of rheumatoid arthritis in a Canadian population. BMC Proceedings 1:S19. [pdf] (* corresponding author)
- Li M, Atmaca-Sonmez P, Othman M, Branham KEH, Wade MS, Li Y, Liang L, Zareparsi S, Swaroop A, Abecasis GR: CFH Haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration. Nature Genetics 38:1049-1054. [pdf]
- Li M, Boehnke M, Abecasis GR, Song P-XK: Quantitative trait linkage analysis using Gaussian copulas. Genetics 173:2317-2327. [pdf]
2005
- Li M, Boehnke M, Abecasis GR: Efficient study designs for test of genetic association using sibship data and unrelated cases and controls. American Journal of Human Genetics 78:778-792. [pdf] [web]
- Zareparsi S, Branham KEH, Li M, Klein RJ, Ott J, Hoh J, Abecasis GR, Swaroop A: Stong association of Y402H variation in complement factor H at 1q32 with susceptibility for age-related macular degeneration. American Journal of Human Genetics 77:149-153. [pdf]
- Li M, Boehnke M, Abecasis GR: Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal. American Journal of Human Genetics 76:934-949. [pdf] [web]
- Zareparsi S, Buraczynski M, Branham KEH, Shah S, Eng D, Li M, Pawar H, Yashar BM, Moroi S, Lichter PR, Petty HR, Richards JE, Abecasis GR, Elner VM, Swaroop A: Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration. Human Molecular Genetics 14:1449-1455. [pdf]
