THE LEE LAB | MGH/HMS/Broad
Computational Genomics and Medicine
Publications
2018 & Under Review
  • Zhu Z, Anttila V, Smoller JW, Lee PH.
    Statistical power and utility of meta-analysis methods for cross-phenotype genome-wide association studies.
    Under revision.

  • Lee PH, Wee BH, Lee C, Jung J, Daly M.
    Practical guides to the studies of de novo mutations using whole genome sequencing data.
    Under revision.

  • Zhu Z, Lee PH, Chaffin M, Chung W, Loh P-R, Lu Q, Christiani D, Liang L.
    Shared genetic architecture between asthma and allergic diseases: a genome-wide cross trait analysis of 112,000 individuals from UK Biobank.
    Nature Genetics Revision submitted.  [ Link ]

  • Chen C-Y, Lee PH, Castro VM, Minnier J, Murphy SN, Gainer V, Cai T, Jones I, Pato C, Landen M, Sklar P, Perlis RH, Smoller JW.
    Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records.
    Translational Psychiatry Accepted.  

  • Stahl EA, et al. 
    Genome-wide association study identifies 30 Loci Associated with Bipolar Disorder.
    Under Review. 

  • Satizabal CL, et al.
    Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide.
    Under Review. 
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        ​                      
2017
  • Hibar DP, Adams H, Jahanshad N, Chauhan G, Stein J, Hofer E, Renteria M, Bis J, Arias-Vasquez A, ..., Lee PH, et al. 
    Novel genetic loci associated with hippocampal volume, shape and subfields.
    Nature Communications 2017; 8:13624. [ Link ]

  • Charney AW, Ruderfer DM, Stahl EA, Moran JL, Chambert K, Belliveau RA, Forty L, Gordon-Smith K, Di Florio A, Lee PH, et al. 
    Evidence for genetic heterogeneity between clinical subtypes of bipolar disorder.
    Translational Psychiatry 2017; 7: e993. [ Link ]
 
  • The Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium; Anney RJL, Ripke S, Anttila V, Holmans P, Huang H, Klei L, Lee PH, Medland SE, Neale Ben, Robinson E, et al.
    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.
    Molecular Autism 2017; 8:21. [ Link ]
   
  • Anttila V, Bulik-Sullivan B, Finucane H, Bras J, Cavalleri G, Duncan L, Falcone G, Gormley P, Malik R, Oldham H, Ripke S, Walters R, Wei Z, Yu D, Lee PH, GCAN Consortium, IGAP Consoritum, IHGC Consortium, ILAE Consortium, et al.
    Analysis of shared heritability in common disorders of the brain. 
    Science Accepted. [ Link ]
    
  • Kim Y, Giusti-Rodriguez P, Crowley JJ, Nonneman RJ, Ryan AK, Quackenbush CR, Iglesias-Ussel M, Lee PH, Sun W, de Villena FD-M, Sullivan PF.
    Comparative genomic evidence for the involvement of schizophrenia risk genes in antipsychotic effects.
    Molecular Psychiatry 2017 May 30 Epub ahead of print. [ Link ]

  • Lee PH, Lee C, Ki X, Wee B, Dwivedi T, Daly M.
         Principles and methods of in-sillico prioritization of non-coding regulatory variants.
    Human Genetics 2017 Dec 29. Epub ahead of print. [ Link ]
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        ​                      
2016

  • Lee PH, Baker JT, Holmes AJ, Jahanshad N, Ge T, Jung J-Y, Cruz Y, Hibar DP, Faskowitz J, McMahon K, de Zubicaray G, Martin N, Wright M, Roffman J, Buckner R, Thompson P, Ongur D, Smoller JW.
    Partitioning heritability analysis reveals a shared genetic basis of brain anatomy and schizophrenia.
    Molecular Psychiatry 2016 Dec;21(12):1680-1689. [ Link ]
     
  • Song J, Bergen SE, Di Florio A, Karlsson R, Charney A, Ruderfer DM, Stahl EA; Members of the International Cohort Collection for Bipolar Disorder (ICCBD), Chambert KD, Moran JL, Gordon-Smith K, Forty L, Green EK, Jones I, Jones L, Scolnick EM, Sklar P, Smoller JW, Lichtenstein P, Hultman C, Craddock N, Landén M, Smoller JW, Perlis RH, Lee PH, Castro VM, Hoffnagle AG, Sklar P, Stahl EA, et al.
    Genome-wide association study identifies SESTD1 as a novel risk gene for lithium-responsive bipolar disorder.
    Molecular Psychiatry 2016 Sep; 21(9):1290-7. [ Link ] [PDF].

  • Sebat J, Marshall C, Howrigan D, Merico D, Thiruvahindrapuram B, Wu W, Greer D, ...,  Lee PH, et al.
    A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects.
    Nature Genetics 2016 Nov 21. [Epub ahead of print]  [ Link ].
 
  • Ge T, Reuter M, Winkler AM, Lee PH, Holmes AJ, Tirrell L, Roffman JL, Buckner RL, Smoller JW, Sabuncu MR. 
    Multidimensional heritability analysis of neuroanatomical shape.
    Nature Communications 2016 Nov;7:13291. [ Link ]
 
  • Franke B, Stein J, Ripke S, Anttila V, Hibar D, van Hulzen K, Arias-Vasquez A, Smoller JW, Nichols TE, Neale MC, McIntosh AM,
    Lee PH, McMahon, Meyer-Lindenberg, Mattheisen, Andreassen, Bruber, Sachdev, Roiz-Santianez, Saykin, Ehrlich, Mather, et al.
    Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept. 
    Nature Neuroscience 2016 Mar; 19(3):420-31 [ Link ] [ PDF ].
 
  • Germine L, Robinson EB, Smoller JW, Calkins ME, Moore TM, Hakonarson H, Daly MJ, Lee PH, Holmes AJ, Buckner RL, Gur RC, Gur RE. 
    Polygenic risk for schizophrenia is associated with differences in social cognition across development. 
    Translational Psychiatry 2016 Oct; 6(10):e924. [ Link ]
 
  • Adams H, Hibar DP, Chouraki V, Stein JL, Nyquist P, Renteria ME, Trompet S, Arias-Vasquez A, Seshadri S, ..., Lee PH, et al. 
    Novel genetic loci underlying human intracranial volume identified through genome-wide association. 
    Nature Neuroscience 2016 Oct. [Epub ahead of print]  [ Link ].
      
  • Gormley  P, Anttila  V, Winsvold  BS, Palta P, Esko  T, Pers  TH, Farh  K-H, Cuenca-Leon  E, Muona  M, ..., Lee PH, et al.
    Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. 
    Nature Genetics 2016 Aug; 48(8):855-66 [ Link ] [ PDF ].

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        ​                      
2015 
 
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  • Thompson PM, Andreassen OA, Arias-Vasquez A, Bearden CE, Boedhoe PS, Brouwer RM, Buckner RL, Buitelaar JK, Bulaeva KB, Cannon DM, Cohen RA, Conrod PJ, Dale AM, Deary IJ, Dennis EL, de Reus MA, Desrivieres S, Dima D, Donohoe G, Fisher SE, Fouche JP, Francks C, Frangou S, Franke B, Ganjgahi H, Garavan H, Glahn DC, Grabe HJ, Guadalupe T, Gutman BA, Hashimoto R, Hibar DP, Holland D, Hoogman M, Pol HE, Hosten N, Jahanshad N, Kelly S, Kochunov P, Kremen WS, Lee PH, Mackey S, Martin NG, et al. 
    ENIGMA and the individual: predicting factors that affect the brain in 35 Countries worldwide.
    Neuroimage 2015 Dec 4. pii: S1053-8119(15)01081-2. [ Link ] [ PDF ]
 
 
 
    
 
2014
  • Pearson-Fuhrhop K, Dunn EC, Mortero S, Devan WJ, Falcone GJ, Lee PH, Holmes AJ, Hollinshead MO, Roffman JL, Smoller JW, Rosand J, Cramer SC.
      Dopamine genetic risk score predicts depressive symptoms in healthy adults and adults with depression.
       PLoS ONE 2014; 9(5): e93772. [ Link ] [ PDF ] 
 
  • Thompson PM, Stein JL, Medland SE, Hibar DP, Vasquez AA, Renteria ME, Toro R, Jahanshad N, Schumann G, Franke B, Wright MJ, Martin NG, Agartz I, Alda M, Alhusaini S, et al.  
      The ENIGMA consortium: large-scale collaborative analyses of neuroimaging and genetic data.
       Brain Imaging Behav 2014; 8(2):153-182. [ Link ] [ PDF ]
   
  • Schizophrenia Working Group of the Psychaitric Genomics Consortium; Ripke S, Neale BM, Corvin A, Walters JT, Farh KH, Holmans PA, Lee PH, Bulik-Sullivan B, Collier DA, Huang H, Pers TH, Agartz I, Agerbo E, Albus M, et al.  
       Nature 2014; 511(7510):421-427. [ Link ] [ PDF ]
 
  • Bergen SE, O’Dushlaine CT, Lee PH, Fanous AH, Ruderfer DM, Ripke S, International Schizophrenia Consortium, Swedish Schizophrenia Consortium, Sullivan PF, Smoller JW, Purcell SM, Corvin A.
       Schizophr Res 2014; 154(1-3):48-53. [ Link ] [ PDF ]
 
  • Duncan LE, Holmans PA, Lee PH, O’Dushlaine CT, Kirby AW, Smoller JW, Ongur D, Cohen BM.
       PLoS One 2014; 9(2):e89441. [ Link ] [ PDF ]
 
       Schizophr Bull 2014; 40(6):1263-1271. [ Link ] [ PDF ]
 
2013
  • SanGiovanni JP, Lee PH.
      AMD-associated genes encoding MAPK pathway constituents are identified by interval-based enrichment analysis.
       PLoS ONE 2013; 8(8):e71239. [ Link ] [ PDF ]
 
       Am J Med Genet B Neuropsychiatr Genet 2013; 162B(8):779-788. [ Link ] [ PDF ]
   
  • Lee SH, Ripke S, Neale BM, Faraone SV, Purcell SM, Perlis RH, Mowry BJ, Thapar A, Goddard ME, Witte JS, Absher D, Agartz I, et al. 
       Nat Genet 2013; 45(9):984-994. [ Link ] [ PDF ]
 
  • Smoller JW, Ripke S, Lee PH (*I ran cross disorder modeling, pathway analysis, and brain eQTL enrichment analyses in this study), Neale B, Nurnberger JI, Santangelo S, Sullivan PF, Perlis RH, Purcell SM, Fanous A, et al.
      Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
       Lancet 2013; 381(9875):1371-1379. [ Link ] [ PDF ]
 
  • Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW.
       Nat Rev Genet 2013; 14(7):483-495. [ Link ] [ PDF ] 
2012
  • Holmes A*, Lee PH* (co-first author; I led whole genome data analysis in this collaborative neuroimaging genomics study), Hollinshead M, Bakst L, Roffman JL, Smoller JW, Buckner RL.
       Individual differences in amygdala-medial prefrontal anatomy link negative affect, impaired social functioning, and
       polygenic depression risk.
       J Neurosci 2012; 32(50): 18087-18100. [ Link ] [ PDF ]   
 
  • Lee PH, Perlis RH, Jung JY, Byrne EM, Rueckert E, Siburian R, Haddad S, Mayerfeld CE, Heath AC, Pergadia ML, Madden PA, Boomsma DI, Penninx BW, Sklar P, Martin NG, Wray NR, Purcell SM, Smoller JW.
      Multi-locus genome-wide association analysis supports the role of glutamatergic synaptic transmission in the
      etiology of major depressive disorder.
       Transl Psychiatry 2012; 2:e184. [ Link ] [ PDF ]
   
  • Hall MH, Smoller JW, Cook NR, Schulze K, Lee PH, Taylor G, Bramon E, Coleman MJ, Murray RM, Salisbury DF, Levy DL.
       Psychiatry Res 2012; 200(2-3):272-280. [ Link ] [ PDF ]
 
  • Lee PH, O’Dushlaine C, Thomas B, Purcell SM.
       Bioinformatics 2012; 28(13):1797-1799. [ Link ] [ PDF ]      
 
  • Bergen SE, O'Dushlaine CT, Ripke S, Lee PH, Ruderfer DM, Akterin S, Moran JL, Chambert KD, Handsaker RE, Backlund L, Ösby U, McCarroll S, Landen M, Scolnick EM, Magnusson PK, Lichtenstein P, Hultman CM, Purcell SM, Sklar P, Sullivan PF.
       Mol Psychiatry 2012; 17(9):880-889. [ Link ] [ PDF ]
 
  • Stein JL, Medland SE, Vasquez AA, Hibar DP, Senstad RE, Winkler AM, Toro R, Appel K, Bartecek R, Bergmann Ø, Bernard M, Brown AA, Cannon DM, Chakravarty MM, Christoforou A, Domin M, Grimm O, Hollinshead M, Holmes AJ, Homuth G, Hottenga JJ, Langan C, Lopez LM, Hansell NK, Hwang KS, Kim S, Laje G, Lee PH, et al.
       Nat Genet 2012; 44(5):552-561. [ Link ] [ PDF ]
 
  • Willour VL, Seifuddin F, Mahon PB, Jancic D, Pirooznia M, Steele J, Schweizer B, Goes FS, Mondimore FM, Mackinnon DF; Bipolar Genome Study Consortium, Perlis RH, Lee PH, Huang J, Kelsoe JR, Shilling PD, Rietschel M, Nöthen M, Cichon S, Gurling H, Purcell S, Smoller JW, Craddock N, DePaulo JR Jr, Schulze TG, McMahon FJ, Zandi PP, Potash JB.
       Mol Psychiatry 2012; 17(4): 433-444. [ Link ] [ PDF ]
 
  • Sabuncu M, Buckner R, Smoller JW, Lee PH, Fischl B, Sperling R; Alzheimer’s Disease Neuroimaging Initiative.
       Cereb Cortex 2012; 22(11):2653-2661. [ Link ] [ PDF ]
 
 
2011
 
  • Lee PH, Bergen SE, Perlis RH, Sullivan PF, Sklar P, Smoller JW, Purcell SM.
      Modifiers and subtype-specific analyses in whole-genome association studies: a likelihood framework.
       Hum Hered 2011; 72(1):10-20. [ Link ] [ PDF ]
   
  • Middeldorp CM, de Moor MH, McGrath LM, Gordon SD, Blackwood DH, Costa PT, Terracciano A, Krueger RF, de Geus EJ, Nyholt DR, Tanaka T, Esko T, Madden PA, Derringer J, Amin N, Willemsen G, Hottenga JJ, Distel MA, Uda M, Sanna S, Spinhoven P, Hartman CA, Ripke S, Sullivan PF, Realo A, Allik J, Heath AC, Pergadia ML, Agrawal A, Lin P, Grucza RA, Widen E, Cousminer DL, Eriksson JG, Palotie A, Barnett JH, Lee PH, Luciano M, et al.
      The genetic association between personality traits and major depression or bipolar disorder. A polygenic score
      analysis using genome-wide association data.
       Trans Psychiatry 2011; 1:e50. [ Link ] [ PDF ]
 
  • Psychiatric GWAS Consortium Bipolar Disorder Working Group; Sklar P, Ripke S, Scott LJ, Andreassen OA, Cichon S, Craddock N, Edenberg HJ Jr, Nurnberger JI, Rietschel M, Blackwood D, Corvin A, Flickinger M, Guan W, Mattingsdal M, McQuillen A, et al.
      Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
       Nat Genet 2011; 43(10):977-983. [ Link ] [ PDF ]
   
  • Yu Y, Bhangale T, Fagerness J, Ripke S, Thorleifsson G, Tan PL, Souied EH, Richardson AJ, Merriam JE, Buitendijk GH, Reynolds R, Raychaudhuri S, Chin KA, Sobrin L, Evangelou E, Lee PH, Lee AY, Leveziel N, Zack DJ, Campochiaro B, Campochiaro P, Smith RT, Barlle GR, Guymer RH, et al.
       Hum Mol Genet 2011; 20(18):3699-3709. [ Link ] [ PDF ]
 
  • Belmonte Mahon P, Pirooznia M, Goes FS, Seifuddin F, Steele J, Lee PH, Huang J, Hamshere ML; Bipolar Genome Study (BiGS) Consortium, The Wellcome Trust Case Control Consortium Bipolar Disorder Group, Depaulo JR Jr, Kelsoe JR, Rietschel M, Nothen M, Cichon S, Gurling H, Purcell S, Smoller JW, Craddock N, Schulze TG, McMahon FJ, Potash JB, Zandi PP.
       Am J Med Genet B Neuropsychiatr Genet B 2011; 156B(3): 370-378. [ Link ] [ PDF ]
 
 
 
2010
  • Huang J, Perlis R, Lee PH, Rush AJ, Fava M, Sachs GS, Lieberman J, Hamilton SP, Sullivan P, Sklar P, Purcell S, and Smoller JW.
       Cross-disorder genomewide analysis of schizophrenia, bipolar disorder and depression.
       Am J Psychiatry 2010; 167(10):1254-1263. [ Link ] [ PDF ]
   
  • Lee PH, Jung J-Y, and Shatkay H.
       Functionally informative tag SNP Selection using a pareto-optimal approach: playing the game of life.
       Adv Exp Med Biol 2010; 680:173-180. [ Link ] [ PDF ]
2009 and before
  
  • Lee PH, Shatkay H.
       Bioinformatics 2009; 25(8):1048-1055. [ Link ] [ PDF ]
    
  • Lee PH, Shatkay H.
       Nucleic Acids Res 2008; 36(Database-Issue): d820-824. [ Link ] [ PDF ]
 
  • Lee PH, Shatkay H.
       In the Proc. of the American Medical Informatics Association Annual Symposium (AMIA'08), November 8-12, 2008.
       Washington DC,
       USA; pp. 667-671. [ Link ] [ PDF ]
 
  • Lee PH, Shatkay H. 
       Machine Learning in Bioinformatics, John Wiley & Sons, Y-Q Zhang, J.C. Rajapakse (Ed) 2008 p367-388.
 
  • Lee PH, Shatkay H.
       Springer Lecture Notes in Computer Science. 2007; 4645:61-72. [ Link ] [ PDF ]
 
  • Shen JJ, Lee PH, Holden JJ, Shatkay H.
       In the Proc. of the American Medical Informatics Association Annual Symposium (AMIA'07), November 10-14, 2007.
       Chicago, IL, USA;
       pp. 666-670. [ Link ] [ PDF ]    
 
  • Lee PH, Shatkay H.
       Bioinformatics 2006; 22(14):e211-e219. [ Link ] [ PDF ]
 
  • Jung J-Y, Lee PH.
       In the Proc. of the Int. Joint Conf. on Neural Networks (IJCNN'06), July 16-21, 2006. Vancouver, BC, Canada; pp. 2303-2307. 
       [ Link ] [ PDF ]
 
  • Lee PH, Lee D.
       Bioinformatics 2005; 21(11):2739-2747. [ Link ] [ PDF ]
 
  • Lee PH, Nam H, Lee D, Lee K-H.
       In the Proc. of the Korean Fuzzy Logic and Intelligent Systems Conference (KFIS'04), April 30-May 1, 2004. Kunsan, Korea;
       pp. 129-138.
 
  • Na D, Lee PH, Lee S, Lee D, Lee K-H, Bae M.
      EBIS: bio-data integration middle-ware system.
       In the Proc. of the Korea Information Science Conference (KISS'03) May 3, 2003. Kangleung, Korea; pp. 198-213 (in Korean).
   
  • Lee S, Lee PH, Na D, Lee D, Lee K-H, Bae M.
       In the Proc. of the 4th International Symposium on Advanced Intelligent Systems (ISIS'03), Sep 25-28, 2003. Jeju, Korea;
       pp. 230-242.
 
  • Lee PH, Lee D, Lee K-H.
       In the Proc. of the Korea Bioinformatics Conference (KSBI'03), Oct 3-4, Daejeon, Korea; pp.12-21.