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Ani Manichaikul

Ani Manichaikul

Professor, Public Health Sciences

Primary Location
Box 800717
Primary Phone Number
216.12.
Email
[email protected]
Website
https://sites.google.com/view/animanichaikul/

Bio & Overview

My research lies in the areas of statistical genetics and genetic epidemiology with an emphasis on 1) analysis of genome-wide association studies in the multi-ethnic cohort studies, 2) gene-based analysis of rare variants, 3) quantitative trait mapping in experimental crosses, and 4) translational research efforts bridging mouse and human studies. I am actively involved in genome-wide association analysis of cardiovascular and pulmonary phenotypes performed through the Multi-Ethnic Study of Atherosclerosis (MESA). We are performing post-GWAS research, including gene-environment interaction studies, fine mapping studies, and candidate gene investigations with collaborators who are experts in animal models and in vitro studies of more focused genetic pathways. We are working actively on integrative 'omics combining genomic, transcriptomic, proteomic and other high-dimensional data sets from the NHLBI Trans-omics for Precision Medicine (TOPMed) project, the Genotype-Tissue Expression (GTEx) project, and others to identify causal genes and pathways influencing diseases of interest.

Academic Information

Department
Public Health Sciences
Academic Title
Associate Professor

Primary Education

  • PhD, undefinedJohns Hopkins University, 2008

Other Appointments

  • Assistant Professor, Biochemistry and Molecular Genetics
  • Postdoctoral Researcher, Biomedical Engineering

Other Affiliations

  • BIMS

Research Interests

Statistical Genetics, Genetic Epidemiology, Biostatistics, Network analysis

Research Disciplines

  • Biochemistry
  • Bioinformatics and Genomics
  • Computational Biology
  • Genetics

Research Opportunities

  • Biochemistry
  • Bioinformatics & Genomics
  • Computational Biology
  • Genetics

PhD Programs

  • Biochemistry & Molecular Genetics
  • Computational Biology

Selected Publications

Manuscripts as senior or co-senior author

  1. Kim JS, Debban CL, Manichaikul A. Reply to Wang et al.: Causal Inference Considerations in Proteomic Biomarker Studies for Interstitial Lung Disease. Am J Respir Crit Care Med. 2026 Feb 4:aamag029. Online ahead of print.
  1. Hu X‡, Araujo DS, Khunsriraksakul C, Wang L, Sun Q, Wen J, Zhou L, Ekunwe L, Lange LA, Lange EM, Montgomery SB, Reiner AP, Aguet F, Ardlie KG, Lappalainen T, Gignoux CR, Burchard EG, , Taylor KD, Guo X, Rotter JI, Rich SS, Cornell E, Durda P, Tracy RP, Liu Y, Johnson WC, Papanicolaou GP, Perera MA, Cho MH, Liu DJ, Raffield LM, Li Y, TOPMed Multi-Omics Working Group, Wheeler HE, Im HK, Manichaikul A‡. Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies. Am J Hum Genet. 2026 Apr 2;113(4):828-841. 
  1. Kim W#, Hu X#, Kim K#, Chun S, Orchard P, Qiao D, Ruczinski I, Saferali A, Aguet F, Antonacci-Fulton L, Balte PP, Bartz TM, Anamika WJ , Zhou X , Duan J , Brody JA, Cade BE, Daviglus ML, Doddapaneni H, Dugan-Perez S, Dutcher SK, Frazer C, Gabriel SB, Gharib SA, Gupta N, Hobbs BD, Kasela S, Loehr LR, Metcalf GA, Muzny DM, Oelsner EC, Rasmussen-Torvik LJ, Sitlani CM, Smith J, Sofer T, Xu H, Yu B, Zhang D, Ziniti J, Barr RG, Carson AP, Fornage M, Hou L, Kalhan R, Kaplan R, Lappalainen T, London SJ, Morrison AC, O'Connor GT, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Silverman EK, Manichaikul A‡, Cho MH‡. Whole Genome Sequence Analysis of Pulmonary Function and COPD in 44,287 Multi-ancestry Participants. Genome Biol. 2026 Jan 15;27(1):28. 
  1. Kim JS, Debban CA, Guzman D, Salvatore M, Hannan RT, Zhang D, McGroder C, Podolanczuk AJ, Ma SF, Huang Y, Sturek JM, Rich SS, Rotter JI, Deo R, Dubin R, Pugashetti JV, Wang J, Han ML, Oldham JM, Noth I, Woodruff P, Ortega VE, Hoffman EA, Fanburg-Smith JC, Stelow EB, Moskaluk CA, Hoffman EA, Garcia CK, Bowler RP, Ganz P, Barr RG, Manichaikul A. Associations of High Attenuation Area-Related Proteomic Biomarkers with Fibrotic or Subpleural Interstitial Lung Abnormalities. Am J Respir Crit Care Med. 2025 Oct;211(10):1811-1822.
  1. Hu X‡, Webb-Robertson BM, Parikh HM, Nakayasu ES, Onengut-Gumuscu S, Chen WM, Frazer-Abel A, Metz TO, Rich SS, Rewers MJ, Manichaikul A‡. Genetic mapping of complement system proteins for islet autoimmunity in children with high risk of T1D. Commun Biol. 2025 Sep 26;8(1):1366. 
  1. Debban CL, Ambalavanan A, Ghosh A, Li Z, Buschur KL, Ma Y, George E, Pistenmaa C, Bertoni AG, Oelsner EC, Michos ED, Moraes TJ, Jacobs DR Jr, Christenson S, Bhatt SP, Kaner RJ, Simons E, Turvey SE, Vameghestahbanati M, Engert JC, Kirby M, Bourbeau J, Tan WC, Gabriel SB, Gupta N, Woodruff PG, Subbarao P, Ortega VE, Bleecker ER, Meyers DA, Rich SS, Hoffman EA, Barr RG, Cho MH, Bossé Y, Duan Q, Manichaikul A‡, Smith BM‡. Dysanapsis Genetic Risk Predicts Lung Function Across the Lifespan. Am J Respir Crit Care Med. 2024 Dec 15;210(12):1421-1431.
  1. Hu X, Kim JS, Saferali A, Huang Y, Ma SF, Bingham GC, Bonham CA, Flores C, Castaldi P, Hersh CP, Cho MH, Noth I, Manichaikul A*; IPF Survival GWAS Consortium. Transcriptome-Wide Association Study of Idiopathic Pulmonary Fibrosis Survival Identifies PTPN9 and SNRPB2. Am J Respir Crit Care Med. 2024 Sep 1;210(5):683-686. 
  1. Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A*. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep. 2023 Oct 17;13(1):17680.
  1. Yang C, Veenstra J, Bartz T, Pahl M, Hallmark B, Chen YI, Westra J, Steffen L, Brown C, Siscovick D, Tsai M, Wood A, Rich S, Smith C, O'Connor T, Mozaffarian D, Grant S, Chilton F, Tintle N, Lemaitre R, Manichaikul A*. Genome-Wide Association Studies and fine-mapping identify genomic loci for n-3 and n-6 Polyunsaturated Fatty Acids in Hispanic American and African American Cohorts. Commun Biol. 2023 Aug 16;6(1):852. 
  1. Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, ...[41 authors]..., Wheeler HE, TOPMed Lung Working Group, Cho MH, Im HK, Manichaikul A*. Polygenic transcriptome risk scores improve cross-ethnic portability for COPD and lung function in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. Am J Hum Genet. 2022 May 5;109(5):857-870.

  2. Yang C, Hallmark, B, Chai JC, O’Connor TD, Reynolds LM, Wood AC, Seeds M, Chen YDI, Steffen LM, Tsai MY, Kaplan RC, Daviglus ML, Mandarino LJ, Fretts AM, Lemaitre RN, Coletta DK, Blomquist SA, Johnstone LM, Tontsch C, Qi Q, Ruczinski I, Rich SS, Mathias RA, Chilton FH, Manichaikul A*. Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations. Commun Biol. 2021 Jul 28;4(1):918.
  1. Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O'Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lung Working Group, Cho MH‡*, Manichaikul A‡*. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun. 2020 Oct 14;11(1):5182.  
  1. Wyss AB#, Sofer T#, Lee MK#, Terzikhan N#, Nguyen JN#, Lahousse L#, Latourelle JC, Smith AB, Bartz TM, Feitosa MF, Gao W, Ahluwalia TS, Tang, W Oldmeadow C, Duan Q, de Jong K, Wojczynski MK, Wang XQ, Noordam R, … [56 authors] …, Kim WJ, Attia JR, Lange L, Boezen HM, Thyagarajan B, Rich SS, Mook-Kanamori DO, Horta BL, Uitterlinden AG, Sin DD, Im HK, Cho MH, Brusselle GG‡, Gharib SA‡, Dupuis J‡, Manichaikul A‡, London SJ‡. Multiethnic meta-analysis identifies new loci for pulmonary function. Nat Commun. 2018 Jul 30;9(1):2976. 

  

Manuscripts as first or co-first author

  1.  Manichaikul A, Lin H, Kang C, Yang C, Rich SS, Taylor KD, Guo X, Rotter JI, Craig Johnson W, Cornell E, Tracy RP, Peter Durda J, Liu Y, Vasan RS, Adrienne Cupples L, Gerszten RE, Clish CB, Jain D, Conomos MP, Blackwell T, Papanicolaou GJ, Rodriguez A. Lymphocyte activation gene-3-associated protein networks are associated with HDL-cholesterol and mortality in the Trans-omics for Precision Medicine program. Commun Biol. 2022 May 2;5(1):362.

  2. Manichaikul A, Peres LC, Wang XQ, Barnard ME, Chyn D, Sheng X, Du Z, Tyrer J, Dennis J, Schwartz AG, Cote ML, Peters E, Moorman PG, Bondy M, Barnholtz-Sloan JS, Terry P, Alberg AJ, Bandera EV, Funkhouser E, Wu AH, Pearce CL, Pike M, Setiawan VW, Haiman CA; African American Breast Cancer Consortium (AABC); African Ancestry Prostate Cancer Consortium (AAPC), Palmer JR, LeMarchand L, Wilkens LR, Berchuck A, Doherty JA, Modugno F, Ness R, Moysich K, Karlan BY, Whittemore AS, McGuire V, Sieh W, Lawrenson K, Gayther S, Sellers TA, Pharoah P, Schildkraut JM; African American Cancer Epidemiology Study (AACES) and the Ovarian Cancer Association Consortium (OCAC). Identification of novel epithelial ovarian cancer loci in women of African ancestry. Int J Cancer. 2020 Jun 1;146(11):2987-2998.

  3. Manichaikul A, Wang XQ, Li L, Erdmann J, Lettre G, Bis JC, Waterworth D, Cushman M, Jenny NS, Post WS, Palmas W, Tsai MY, Wallentin L, White H, Schunkert H, O'Donnell CJ, Herrington DM, Rich SS, O'Donoghue ML, Rodriguez A. Lp-PLA2, scavenger receptor class B type I gene (SCARB1) rs10846744 variant, and cardiovascular disease. PLoS One. 2018 Oct 5;13(10):e0204352.

  4. Manichaikul A, Nguyen JN. Genetic studies as a tool for identifying novel potential targets for treatment of COPD. Eur Respir J. 2017 Nov 30;50(5).

  5. Manichaikul A*, Wang XQ, Sun L, Dupuis J, Borczuk AC, Nguyen JN, Raghu G, Hoffman EA, Onengut-Gumuscu S, Farber EA, Kaufman JD, Rabinowitz D, Stukovsky KDH, Kawut SM, Hunninghake GM, Washko GR, O'Connor GT, Rich SS, Barr RG, Lederer DJ. Genome-wide association study of subclinical interstitial lung disease in MESA. Respir Res. 2017 May 18;18(1):97.

  6. Manichaikul A, Sun L, Borczuk AC, Onengut-Gumuscu S, Farber EA, Mathai SK, Zhang W, Raghu G, Kaufman JD, Hinckley-Stukovsky KD, Kawut SM, Jelic S, Liu W, Fingerlin TE, Schwartz DA, Sell JL, Rich SS, Barr RG, Lederer DJ. Plasma Soluble Receptor for Advanced Glycation End Products in Idiopathic Pulmonary Fibrosis. Ann Am Thorac Soc. 2017 May;14(5):628-635. 

  7. Manichaikul A, Rich SS, Allison MA, Guagliardo NA, Bayliss DA, Carey RM, Barrett PQ. KCNK3 Variants Are Associated With Hyperaldosteronism and Hypertension. Hypertension. 2016 Aug;68(2):356-64.

  8. Manichaikul A, Wang XQ, Zhao W, Wojczynski MK, Siebenthall K, Stamatoyannopoulos JA, Saleheen D, Borecki IB, Reilly MP, Rich SS, Bornfeldt KE. Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis. J Lipid Res. 2016 Mar;57(3):433-42.

  9. Manichaikul A, Wang XQ, Musani S, Herrington D, Post WS, Wilson JG, Rich SS, Rodriguez A. Association of the lipoprotein receptor SCARB1 common missense variant rs4238001 with incident coronary heart disease. PLOS One. 2015 May 20;10(5):e0125497.

  10. Chen W#, Brehm JM#, Manichaikul A#, Cho MH, Boutaoui N, Yan Q, Burkart KM, Enright PL, Rotter JI, Petersen H, Leng S, Obeidat M, Bossé Y, Brandsma CA, Hao K, Rich SS, Powell R, Avila L, Soto-Quiros M, Silverman EK, Tesfaigzi Y, Barr RG, Celedón JC. A genome-wide association study of chronic obstructive pulmonary disease in Hispanics. Ann Am Thorac Soc. 2015 Mar;12(3):340-8.

  11. Guan W#, Steffen BT#, Lemaitre RN#, Wu JH#, Tanaka T#, Manichaikul A#, Foy M#, Rich SS, Wang L, Nettleton JA, Tang W, Gu X, Bandinelli S, King IB, McKnight B, Psaty BM, Siscovick D, Djousse L, Ida Chen YD, Ferrucci L‡, Fornage M‡, Mozafarrian D‡, Tsai MY‡, Steffen LM‡*. Genome-wide association study of plasma n6 polyunsaturated Fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium. Circ Cardiovasc Genet. 2014 Jun;7(3):321-331.

  12. Manichaikul A, Rich SS, Perry H, Yeboah J, Law M, Davis M, Parker M, Ragosta M, Connelly JJ, McNamara CA, Taylor AM. A functionally significant polymorphism in ID3 is associated with human coronary pathology. PLOS One. 2014 Mar 6;9(3):e90222.

  13. Manichaikul A, Hoffman EA, Smolonska J, Gao W, Cho MH, Baumhauer H, Budoff M, Austin JH, Washko GR, Carr JJ, Kaufman JD, Pottinger T, Powell CA, Wijmenga C, Zanen P, Groen HJ, Postma DS, Wanner A, Rouhani FN, Brantly ML, Powell R, Smith BM, Rabinowitz D, Raffel LJ, Hinckley Stukovsky KD, Crapo JD, Beaty TH, Hokanson JE, Silverman EK, Dupuis J, O'Connor GT, Boezen HM, Rich SS‡, Barr RG‡*. Genome-wide study of percent emphysema on computed tomography in the general population. The Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study. Am J Respir Crit Care Med. 2014 Feb 15;189(4):408-18.

  14. Hancock DB#, Artigas MS#, Gharib SA#, Henry A#, Manichaikul A#, Ramasamy A#, Loth DW#, … [ 73 authors] …, Gudnason V, Boezen HM, Barr RG, Cassano PA‡, Strachan DP‡, Fornage M‡, Hall IP‡, Dupuis J‡, Tobin MD‡*, London SJ‡*. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PLoS Genet. 2012;8(12):e1003098.

  15. Wilk JB#*, Shrine NR#, Loehr LR#, Zhao JH#, Manichaikul A#, Lopez LM#, Smith AV#, … [67 authors] …, Gharib SA, Hall IP, O'Connor GT, Tobin MD, Stricker BH. Genome-Wide Association Studies Identify CHRNA5/3 and HTR4 in the Development of Airflow Obstruction. Am J Respir Crit Care Med. 2012 Oct 1;186(7):622-32.

  16. Manichaikul A, Naj AC, Herrington D, Post W, Rich SS, Rodriguez A. Association of SCARB1 variants with subclinical atherosclerosis and incident cardiovascular disease: the Multi-ethnic study of atherosclerosis. Arterioscler Thromb Vasc Biol. 2012 Aug;32(8):1991-9.

  17. Manichaikul A*, Palmas W, Rodriguez CJ, Peralta CA, Divers J, Guo X, Chen WM, Wong Q, Williams K, Kerr KF, Taylor KD, Tsai MY, Goodarzi MO, Sale MM, Diez-Roux AV, Rich SS, Rotter JI, Mychaleckyj JC. Population structure of Hispanics in the United States: the Multi-ethnic study of atherosclerosis. PLoS Genet. 2012;8(4):e1002640.

  18. Manichaikul A, Chen WM, Williams K, Wong Q, Sale MM, Pankow JS, Tsai MY, Rotter JI, Rich SS, Mychaleckyj JC*. Analysis of family- and population-based samples in cohort genome-wide association studies. Hum Genet. 2012 Feb;131(2):275-87.

  19. Manichaikul A, Wang Q, Shi YL, Zhang Z, Leitinger N, Shi W. Characterization of Ath29, a major mouse atherosclerosis susceptibility locus, and identification of Rcn2 as a novel regulator of cytokine expression. Am J Physiol Heart Circ Physiol. 2011 Aug 2;7:518.

  20. Lemaitre RN#, Tanaka T#, Tang W#, Manichaikul A#, Foy M#, Kabagambe EK, Nettleton JA, King IB, Weng LC, Bhattacharya S, Bandinelli S, Bis JC, Rich SS, Jacobs DR Jr, Cherubini A, McKnight B, Liang S, Gu X, Rice K, Laurie CC, Lumley T, Browning BL, Psaty BM, Chen YD, Friedlander Y, Djousse L, Wu JH, Siscovick DS, Uitterlinden AG, Arnett DK, Ferrucci L, Fornage M, Tsai MY, Mozaffarian D, Steffen LM. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from th

  21. Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. Robust relationship inference in genome-wide association studies. 2010 Nov 15;26(22):2867-73.

  22. Manichaikul A#, Ghamsari L#, Hom EF#, Lin C#, Murray RR#, Chang RL#, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods. 2009 Aug;6(8):589-92.

  23. Manichaikul A*, Broman KW. Binary trait mapping in experimental crosses with selective genotyping. 2009 Jul;182(3):863-74.

  24. Manichaikul A, Moon JY, Sen S, Yandell BS, Broman KW*. A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. 2009 Mar;181(3):1077-86.

  25. Manichaikul A, Palmer AA, Sen S, Broman KW. Significance thresholds for quantitative trait locus mapping under selective genotyping. 2007 Nov;177(3):1963-6.

  26. Manichaikul A, Dupuis J, Sen S, Broman KW*. Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus. 2006 Sep;174(1):481-9.

 

Selected Collaborative manuscripts 

  1. Van Buren E, Zhang Y, Li X, Selvaraj MS, Li Z, Zhou H, Palmer ND, Arnett DK, Blangero J, Boerwinkle E, Cade BE, Carlson JC, Carson AP, Chen YI, Curran J, Duggirala R, Fornage M, Franceschini N, Graff M, Gu C, Guo X, He J, Heard-Cosa N, Hou L, Hung YJ, Kalyani RR, Kardia SLR, Kenny E, Kooperberg C, Kral BG, Lange L, Levy D, Li C, Liu S, Lloyd-Jones D, Loos RJF, Manichaikul AW, Martin LW, Mathias R, Minster RL, Mitchell BD, Mychaleckyj JC, Naseri T, North K, O'Connell J, Perry JA, Peyser PA, Psaty BM, Raffield LM, Vasan RS, Redline S, Reiner AP, Rich SS, Smith JA, Spitzer B, Tang H, Taylor KD, Tracy R, Viali S, Yanek L, Zhao W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Rotter JI, Peloso GM, Natarajan P, Lin X. cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions. Nat Methods. 2026 Feb;23(2):338-349. 
  1. Hou K, Ding Y, Xu Z, Wu Y, Bhattacharya A, Mester R, Belbin GM, Buyske S, Conti DV, Darst BF, Fornage M, Gignoux C, Guo X, Haiman C, Kenny EE, Kim M, Kooperberg C, Lange L, Manichaikul A, North KE, Peters U, Rasmussen-Torvik LJ, Rich SS, Rotter JI, Wheeler HE, Wojcik GL, Zhou Y, Sankararaman S, Pasaniuc B. Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals. Nat Genet. 2023 Apr;55(4):549-558.
  1. Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MS, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group; Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X. Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nat Genet. 2023 Jan;55(1):154-164. 
  1. Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X. A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods. 2022 Dec;19(12):1599-1611.
  1. Liang Y, Pividori M, Manichaikul A, Palmer AA, Cox NJ, Wheeler HE, Im HK. Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries. Genome Biol. 2022 Jan 13;23(1):23.
  1. Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O'Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group, Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, Lin X. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nat Genet. 2020 Sep;52(9):969-983. 
  1. Nicholas JC, Katz DH, Tahir UA, Debban CL, Aguet F, Blackwell T, Bowler RP, Broadaway KA, Chen J, Clish CB, Coresh J, Cornell E, Cruz DE, Deo R, Doyle MF, Durda P, Ekunwe L, Floyd JS, Gill D, Guo X, Hoogeveen RC, Johnson C, Lange LA, Li Y, Manning A, Meigs JB, Mi MY, Mychaleckyj JC, Olson NC, Pratte KA, Psaty BM, Reiner AP, Ruan P, Sevilla-Gonzalez M, Shah AM, Sun Q, Tracy RP, Wen J, Wood AC, Wilson JG, Young KL, Yu B, Rooney MR, Manichaikul A, Dubin R, Mohlke KL, Rich SS, Rotter JI, Ganz P, Gerszten RE, Taylor KD, Raffield LM. Cross-ancestry comparison of aptamer and antibody protein measures. Nat Commun. 2026 Jan 22;17(1):1054.

  2.  Cruz DE, Deng S, Tahir UA, Chen ZZ, Benson MD, Tuftin B, Chen J, Farrell L, Shen D, Meyer M, Lange E, Gao Y, Hall ME, Tracy RP, Rich SS, Taylor K, Manichaikul A, Rotter JI, Sofer T, Wilson JG, Gerszten RE, Raffield LM; National Heart, Lung, and Blood Institute TOPMed (Trans-Omics for Precision Medicine) Consortium. Admixture-mapping analysis reveals genetic determinants of the human plasma proteome. HGG Adv. 2026 Jan 15;7(1):100529.

  3. Borda V, Loesch DP, Guo B, Laboulaye R, Veliz-Otani D, French JN, Leal TP, Gogarten SM, Ikpe S, Gouveia MH, Mendes M, Abecasis GR, Alvim I, Arboleda-Bustos CE, Arboleda G, Arboleda H, Barreto ML, Barwick L, Bezzera MA, Blangero J, Borges V, Caceres O, Cai J, Chana-Cuevas P, Chen Z, Custer B, Dean M, Dinardo C, Domingos I, Duggirala R, Dieguez E, Fernandez W, Ferraz HB, Gilliland F, Guio H, Horta B, Curran JE, Johnsen JM, Kaplan RC, Kelly S, Kenny EE, Konkle BA, Kooperberg C, Lescano A, Lima-Costa MF, Loos RJF, Manichaikul A, Meyers DA, Naslavsky MS, Nickerson DA, North KE, Padilla C, Preuss M, Raggio V, Reiner AP, Rich SS, Rieder CR, Rienstra M, Rotter JI, Rundek T, Sacco RL, Sanchez C, Sankaran VG, Santos-Lobato BL, Schumacher-Schuh AF, Scliar MO, Silverman EK, Sofer T, Lasky-Su J, Tumas V, Weiss ST; Latin American Research Consortium on the Genetics of Parkinson’s Disease (LARGE-PD); National Institute of Neurological Disorders and Stroke (NINDS) Stroke Genetics Network (SiGN) Consortium; Trans-Omics for Precision Medicine (TOPMed) Population Genetics Working Group; Mata IF, Hernandez RD, Tarazona-Santos E, O'Connor TD. Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas. Cell Genom. 2024 Nov 13;4(11):100692.

  4. Tahir UA, Barber JL, Cruz DE, Kars ME, Deng S, Tuftin B, Gillman MG, Benson MD, Robbins JM, Chen ZZ, Rao P, Katz DH, Farrell L, Sofer T, Hall ME, Ekunwe L, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Guo X, Chen YI, Manichaikul AW, Jain D; NHLBI Trans-Omics for Precision Medicine Consortium; Wang TJ, Reiner AP, Natarajan P, Itan Y, Rich SS, Rotter JI, Wilson JG, Raffield LM, Gerszten RE. Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans. J Clin Invest. 2024 Sep 24;134(21):e181802.

  5. Zhang J, Moll M, Debban CL, Hobbs BD, Rijhwani H, Washko GR, Celli BR, Silverman EK, Bakke P, Oelsner EC, Barr RG, Agustí A, Faner R, Bruselle GG, Humphries SM, Lynch DA, Dupuis J, Manichaikul AW, O'Connor GT, Cho MH. BMI-Related Genetic Factors and COPD Imaging Phenotypes. Ann Am Thorac Soc. 2026 Feb 21:aaoag007. Online ahead of print.

  6.  Chiles JW 3rd, Rocco A, Srinivasasainagendra V, Rossiter HB, Casaburi R, Thalacker-Mercer A, Wells JM, Wan ES, Silverman EK, Cho MH, Hersh CP, Psaty BM, Gharib SA, Gao Y, O'Connor GT, Lange LA, Rich SS, Manichaikul AW, Barr RG, Ortega VE, Meyers DA, Smith AV, Tiwari HK, McDonald MN. Whole Genome Sequence Analysis of Weight Loss in 16 972 Participants With COPD Reveals Novel Risk Loci in DRAIC and RFX3. J Cachexia Sarcopenia Muscle. 2026 Jun;17(3):e70293.

  7. Waliullah ASM, Nguyen TA, Dziegielewska B, Zhang J, Qiu K, Tran ML, Nguyen NN, Wang L, Pan A, Nong M, Segovia N, Li Y, Zhang Y, Ummarino S, Nguyen TM, Manichaikul A, Ghosh P, Mohi G, Goldfarb AN, Craig JW, Tenen DG, Trinh BQ. The C/EBPα-(PU.1-LOUP) regulatory circuit regulates monocyte/macrophage development and immune functions. Blood. 2026 Apr 23;147(17):1970-1983.

  8. Patchen BK, Zhang J, Gaddis N, Bartz TM, Chen J, Debban C, Leonard H, Nguyen NQH, Seo J, Tern C, Allen R, DeMeo DL, Fornage M, Melbourne C, Minto M, Moll M, O'Connor GT, Pottinger T, Psaty BM, Rich SS, Rotter JI, Silverman EK, Stratford J, Zhang C, Barr RG, Cho MH, Gharib SA, Manichaikul A, North K, Oelsner EC, Simonsick EM, Tobin MD, Yu B, Choi SH, Dupuis J, Cassano PA, Hancock DB. Multi-ancestry genome-wide association study and meta-analysis of lung function decline. Respir Res. 2026 Feb 28;27(1):110.

  9. Zhang C, Konigsberg IR, He Y, Zhang J, Chikowore T, Feldman WB, Hu X, Ding Y, Pasaniuc B, Chang D, Chen Q, Lasky-Su JA, Hecker J, Tobin MD, Chen J, Kalra S, Pratte KA, Im HK, Wan ES, Manichaikul A, Silverman EK, Bowler RP, Lange LA, Ortega VE, Martin AR, Cho MH, Moll MR. Multi-trait polygenic scores for COPD and COPD exacerbations implicate druggable proteins. JCI Insight. 2026 Feb 19;11(7):e199951.