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2024

1. Wang Z, Grosvenor L, Ray D, Ruczinski I, Beaty TH, Volk H, Ladd-Acosta C, Chatterjee N (2024).
   Estimation of direct and indirect polygenic effects and gene-environment interactions using polygenic scores in case-parent trio studies.
   medRxiv.
2. Grant-McAuley W, Morgenlander WR, Ruczinski I, Kammers K, Laeyendecker O, Hudelson SE, Thakar M, Piwowar-Manning E, Clarke W, Breaud A, Ayles H, Bock P, Moore A, Kosloff B, Shanaube K, Meehan SA, van Deventer A, Fidler S, Hayes R, Larman HB, Eshleman SH; HPTN 071 (PopART) Study Team (2024).
   Identification of antibody targets associated with lower HIV viral load and viremic control.
   PLoS One 19(9): e0305976.
3. Morgenlander WR, Chia WN, Parra B, Monaco DR, Ragan I, Pardo CA, Bowen R, Zhong D, Norris DE, Ruczinski I, Durbin A, Wang LF, Larman HB, Robinson ML (2024).
   Precision arbovirus serology with a pan-arbovirus peptidome.
   Nature Communications 15(1): 5833.
4. Berke SR, Kanchan K, Marazita ML, Tobin E, Ruczinski I (2024).
   Custom biomedical FAIR data analysis in the cloud using CAVATICA.
   medRxiv.
5. Szczesny B, Boorgula MP, Chavan S, Campbell M, Johnson RK, Kammers K, Thompson EE, Cox MS, Shankar G, Cox C, Morin A, Lorizio W, Daya M, Kelada SNP, Beaty TH, Doumatey AP, Cruz AA, Watson H, Naureckas ET, Giles BL, Arinola GA, Sogaolu O, Falade AG, Hansel NN, Yang IV, Olopade CO, Rotimi CN, Landis RC, Figueiredo CA, Altman MC, Kenny E, Ruczinski I, Liu AH, Ober C, Taub MA, Barnes KC, Mathias RA (2024).
   Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations.
   Nature Communications 15(1): 4546.
6. Keener R, Chhetri SB, Connelly CJ, Taub MA, Conomos MP, Weinstock J, Ni B, Strober B, Aslibekyan S, Auer PL, Barwick L, Becker LC, Blangero J, Bleecker ER, Brody JA, Cade BE, Celedon JC, Chang YC, Cupples LA, Custer B, Freedman BI, Gladwin MT, Heckbert SR, Hou L, Irvin MR, Isasi CR, Johnsen JM, Kenny EE, Kooperberg C, Minster RL, Naseri T, Viali S, Nekhai S, Pankratz N, Peyser PA, Taylor KD, Telen MJ, Wu B, Yanek LR, Yang IV, Albert C, Arnett DK, Ashley-Koch AE, Barnes KC, Bis JC, Blackwell TW, Boerwinkle E, Burchard EG, Carson AP, Chen Z, Chen YI, Darbar D, de Andrade M, Ellinor PT, Fornage M, Gelb BD, Gilliland FD, He J, Islam T, Kaab S, Kardia SLR, Kelly S, Konkle BA, Kumar R, Loos RJF, Martinez FD, McGarvey ST, Meyers DA, Mitchell BD, Montgomery CG, North KE, Palmer ND, Peralta JM, Raby BA, Redline S, Rich SS, Roden D, Rotter JI, Ruczinski I, Schwartz D, Sciurba F, Shoemaker MB, Silverman EK, Sinner MF, Smith NL, Smith AV, Tiwari HK, Vasan RS, Weiss ST, Williams LK, Zhang Y, Ziv E, Raffield LM, Reiner AP; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Hematology and Hemostasis Working Group; TOPMed Structural Variation Working Group; Arvanitis M, Greider CW, Mathias RA, Battle A (2024).
   Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes.
   Nature Communications 15(1): 4417.
7. Leroux A, Crainiceanu C, Zeger S, Taub M, Ansari B, Wager TD, Bayman E, Coffey C, Langefeld C, McCarthy R, Tsodikov A, Brummet C, Clauw DJ, Edwards RR, Lindquist MA; A2CPS Consortium incl Ruczinski I (2024).
   Statistical modeling of acute and chronic pain patient-reported outcomes obtained from ecological momentary assessment.
   Pain 65(9): 1955-1965.
8. Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB (2024).
   Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.
   Nature Communications 15(1): 1577.

   2023

9. Grant-McAuley W, Morgenlander W, Hudelson SE, Thakar M, Piwowar-Manning E, Clarke W, Breaud A, Blankson J, Wilson E, Ayles H, Bock P, Moore A, Kosloff B, Shanaube K, Meehan SA, van Deventer A, Fidler S, Hayes R, Ruczinski I, Kammers K, Laeyendecker O, Larman HB, Eshleman SH (2023).
   Comprehensive profiling of pre-infection antibodies identifies HIV targets associated with viremic control and viral load.
   Frontiers in Immunology 14: 1178520.
10. Berube S, Kobayashi T, Norris DE, Ruczinski I, Moss WJ, Wesolowski A, Louis TA (2023).
    Novel bioinformatic methods and machine learning approaches reveal candidate biomarkers of the intensity and timing of past exposure to Plasmodium falciparum.
    PLoS Global Public Health 3(8): e0001840.
11. Berube S, Kobayashi T, Wesolowski A, Norris DE, Ruczinski I, Moss WJ, Louis TA (2023).
    A Bayesian hierarchical model for signal extraction from protein microarrays.
    Statistics in Medicine 42(9): 1445-1460.
12. Huffaker MF, Kanchan K, Bahnson HT, Ruczinski I, Shankar G, Leung DYM, Baloh C, Du Toit G, Lack G, Nepom GT, Mathias RA (2023).
    Epidermal differentiation complex genetic variation in atopic dermatitis and peanut allergy.
    The Journal of Allergy and Clinical Immunology 151(4): 1137-1142.

    Consortium

13. Recto K, Kachroo P, Huan T, Van Den Berg D, Lee GY, Bui H, Lee DH, Gereige J, Yao C, Hwang SJ, Joehanes R, Weiss ST; NHLBI Trans-Omics in Precision Medicine (TOPMed) Consortium incl Ruczinski I, O'Connor GT, Levy D, DeMeo DL (2023).
    Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma.
    eBioMedicine 95: 104758.
14. Wong WJ, Emdin C, Bick AG, Zekavat SM, Niroula A, Pirruccello JP, Dichtel L, Griffin G, Uddin MM, Gibson CJ, Kovalcik V, Lin AE, McConkey ME, Vromman A, Sellar RS, Kim PG, Agrawal M, Weinstock J, Long MT, Yu B, Banerjee R, Nicholls RC, Dennis A, Kelly M, Loh PR, McCarroll S, Boerwinkle E, Vasan RS, Jaiswal S, Johnson AD, Chung RT, Corey K, Levy D, Ballantyne C; NHLBI TOPMed Hematology Working Group incl Ruczinski I, Ebert BL, Natarajan P (2023).
    Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis.
    Nature 616(7958): 747-754.
15. Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy A, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S (2023).
    Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis.
    Nature 616(7958): 755-763.
16. Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ (2023).
    Structural variation across 138,134 samples in the TOPMed consortium.
    biorXiv.
17. 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, Goering HH, 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 incl Ruczinski I, TOPMed Lipids Working Group, Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X (2023).
    Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies.
    Nature Genetics 55(1): 154-164.

    2022

18. Kanchan K, Shankar G, Huffaker MF, Bahnson HT, Chinthrajah RS, Sanda S, Manohar M, Ling H, Paschall JE, Toit GD, Ruczinski I, Togias A, Lack G, Nadeau KC, Jones SM, Nepom GT, Mathias RA (2022).
    HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success.
    Frontiers in Immunology 13: 941839.
19. Grant-McAuley W, Laeyendecker O, Monaco D, Chen A, Hudelson SE, Klock E, Brookmeyer R, Morrison D, Piwowar-Manning E, Morrison CS, Hayes R, Ayles H, Bock P, Kosloff B, Shanaube K, Mandla N, van Deventer A, Ruczinski I, Kammers K, Larman HB, Eshleman SH (2022).
    Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment.
    BMC Infectious Disease 22(1): 838.
20. Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I (2022).
    Detecting antibody reactivities in phage immuno-precipitation sequencing data.
    BMC Genomics 23(1): 654.
21. Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I (2022).
    Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER.
    Bioinformatics 38(19): 4647-9.
22. Angkeow JW, Monaco DR, Chen A, Venkataraman T, Jayaraman S, Valencia C, Sie BM, Liechti T, Farhadi PN, Funez-dePagnier G, Sherman-Baust CA, Wong MQ, Ruczinski I, Caturegli P, Sears CL, Simner PJ, Round JL, Duggal P, Laserson U, Steiner TS, Sen R, Lloyd TE, Roederer M, Mammen AL, Longman RS, Rider LG, Larman HB (2022).
    Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses.
    Immunity 55(6): 1051-1066.
23. Taub MA, Conomos MP, Keener R, Iyer KR, Weinstock JS, Yanek LR, Lane J, Miller-Fleming TW, Brody JA, Raffield LM, McHugh CP, Jain D, Gogarten SM, Laurie CA, Keramati A, Arvanitis M, Smith AV, Heavner B, Barwick L, Becker LC, Bis JC, Blangero J, Bleecker ER, Burchard EG, Celedon JC, Chang YPC, Custer B, Darbar D, de Las Fuentes L, DeMeo DL, Freedman BI, Garrett ME, Gladwin MT, Heckbert SR, Hidalgo BA, Irvin MR, Islam T, Johnson WC, Kaab S, Launer L, Lee J, Liu S, Moscati A, North KE, Peyser PA, Rafaels N, Seidman C, Weeks DE, Wen F, Wheeler MM, Williams LK, Yang IV, Zhao W, Aslibekyan S, Auer PL, Bowden DW, Cade BE, Chen Z, Cho MH, Cupples LA, Curran JE, Daya M, Deka R, Eng C, Fingerlin TE, Guo X, Hou L, Hwang SJ, Johnsen JM, Kenny EE, Levin AM, Liu C, Minster RL, Naseri T, Nouraie M, Reupena MS, Sabino EC, Smith JA, Smith NL, Su JL, Taylor JG, Telen MJ, Tiwari HK, Tracy RP, White MJ, Zhang Y, Wiggins KL, Weiss ST, Vasan RS, Taylor KD, Sinner MF, Silverman EK, Shoemaker MB, Sheu WH, Sciurba F, Schwartz DA, Rotter JI, Roden D, Redline S, Raby BA, Psaty BM, Peralta JM, Palmer ND, Nekhai S, Montgomery CG, Mitchell BD, Meyers DA, McGarvey ST; NHLBI CARE Network, Mak AC, Loos RJ, Kumar R, Kooperberg C, Konkle BA, Kelly S, Kardia SL, Kaplan R, He J, Gui H, Gilliland FD, Gelb BD, Fornage M, Ellinor PT, de Andrade M, Correa A, Chen YI, Boerwinkle E, Barnes KC, Ashley-Koch AE, Arnett DK; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Hematology and Hemostasis Working Group; TOPMed Structural Variation Working Group, Laurie CC, Abecasis G, Nickerson DA, Wilson JG, Rich SS, Levy D, Ruczinski I, Aviv A, Blackwell TW, Thornton T, O'Connell J, Cox NJ, Perry JA, Armanios M, Battle A, Pankratz N, Reiner AP, Mathias RA (2022).
    Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed.
    Cell Genomics 2(1): 100084.
24. Ngwa JS, Yanek LR, Kammers K, Kanchan K, Taub MA, Scharpf RB, Faraday N, Becker LC, Mathias RA, Ruczinski I (2022).
    Secondary analyses for genome-wide association studies using expression quantitative trait loci.
    Genetic Epidemiology 46: 170-181.
25. Berube S, Kobayashi T, Wesolowski A, Norris DE, Ruczinski I, Moss WJ, Louis TA (2022).
    A pre-processing pipeline to quantify, visualize and reduce technical variation in protein microarray studies.
    Proteomics 22(3): e2100033.
26. Kanchan K, Grinek S, Bahnson HT, Ruczinski I, Shankar G, Larson D, Du Toit G, Barnes KC, Sampson HA, Suarez-Farinas M, Lack G, Nepom GT, Cerosaletti K, Mathias RA (2022).
    HLA alleles and sustained peanut consumption promote IgG4 responses in subjects protected from peanut allergy.
    Journal of Clinical Investigation 132(1): e152070.

    Consortium

27. 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 incl Ruczinski I; TOPMed Lipids Working Group, Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X (2022).
    A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.
    Nature Methods 9(12): 1599-1611.
28. Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody JA, Cade BE, Chuang LM, Chung RH, Curran JE, de Las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, Kral BG, Lange L, Li X, Lisa M, Lubitz SA, Manichaikul AW, Michael P, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Reupena MS, Smith JA, Sun X, Taylor KD, Tracy RP, Tsai MY, Wang Z, Wang Y, Bao W, Wilkins JT, Yanek LR, Zhao W, Arnett DK, Blangero J, Boerwinkle E, Bowden DW, Chen YI, Correa A, Cupples LA, Dutcher SK, Ellinor PT, Fornage M, Gabriel S, Germer S, Gibbs R, He J, Kaplan RC, Kardia SLR, Kim R, Kooperberg C, Loos RJF, Viaud-Martinez KA, Mathias RA, McGarvey ST, Mitchell BD, Nickerson D, North KE, Psaty BM, Redline S, Reiner AP, Vasan RS, Rich SS, Willer C, Rotter JI, Rader DJ, Lin X; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Peloso GM, Natarajan P (2022).
    Whole genome sequence analysis of blood lipid levels in > 66,000 individuals.
    Nature Communications 13(1): 5995.
29. Tahir UA, Katz DH, Avila-Pachecho J, Bick AG, Pampana A, Robbins JM, Yu Z, Chen ZZ, Benson MD, Cruz DE, Ngo D, Deng S, Shi X, Zheng S, Eisman AS, Farrell L, Hall ME, Correa A, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Guo X, Yao J, Chen YI, Manichaikul AW, Ruberg FL, Blaner WS, Jain D; NHLBI Trans-Omics for Precision Medicine Consortium incl Ruczinski I, Bouchard C, Sarzynski MA, Rich SS, Rotter JI, Wang TJ, Wilson JG, Clish CB, Natarajan P, Gerszten RE (2022).
    Whole genome association study of the plasma metabolome identifies metabolites linked to cardiometabolic disease in black individuals.
    Nature Communications 3(1): 4923.
30. Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, Bartz TM, Kumar R, Li X, Yu B, Cade BE, Laurie CA, Sofer T, Ruczinski I, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Gabriel S, Gupta N, Dugan-Perez S, Cupples LA, Loehr LR, Jain D, Rotter JI, Wilson JG, Psaty BM, Fornage M, Morrison AC, Vasan RS, Washko G, Rich SS, O'Connor GT, Bleecker E, Kaplan RC, Kalhan R, Redline S, Gharib SA, Meyers D, Ortega V, Dupuis J, London SJ, Lappalainen T, Oelsner EC, Silverman EK, Barr RG, Thornton TA, Wheeler HE; TOPMed Lung Working Group, Cho MH, Im HK, Manichaikul A (2022).
    Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program.
    American Journal of Human Genetics 109(5): 857-870.
31. Wainschtein P, Jain D, Zheng Z; TOPMed Anthropometry Working Group; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Cupples LA, Shadyab AH, McKnight B, Shoemaker BM, Mitchell BD, Psaty BM, Kooperberg C, Liu CT, Albert CM, Roden D, Chasman DI, Darbar D, Lloyd-Jones DM, Arnett DK, Regan EA, Boerwinkle E, Rotter JI, O'Connell JR, Yanek LR, de Andrade M, Allison MA, McDonald MN, Chung MK, Fornage M, Chami N, Smith NL, Ellinor PT, Vasan RS, Mathias RA, Loos RJF, Rich SS, Lubitz SA, Heckbert SR, Redline S, Guo X, Chen Y-I, Laurie CA, Hernandez RD, McGarvey ST, Goddard ME, Laurie CC, North KE, Lange LA, Weir BS, Yengo L, Yang J, Visscher PM (2022).
    Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data.
    Nature Genetics 54(3): 263-273.
32. Katz DH, Tahir UA, Bick AG, Pampana A, Ngo D, Benson MD, Yu Z, Robbins JM, Chen ZZ, Cruz DE, Deng S, Farrell L, Sinha S, Schmaier AA, Shen D, Gao Y, Hall ME, Correa A, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Guo X, Yao J, Ida Chen YD, Manichaikul AW, Jain D, Bouchard C, Sarzynski MA, Rich SS, Rotter JI, Wang TJ, Wilson JG, Natarajan P, Gerszten RE; National Heart, Lung, and Blood Institute TOPMed (Trans-Omics for Precision Medicine) Consortium incl Ruczinski I (2022).
    Whole genome sequence analysis of the plasma proteome in black adults provides novel insights into cardiovascular disease.
    Circulation 145(5): 357-370.
33. Mason SE, Moreta-Martinez R, Labaki WW, Strand MJ, Regan EA, Bon J, San Jose Estepar R, Casaburi R, McDonald ML, Rossiter HB, Make B, Dransfield MT, Han MK, Young K, Curtis JL, Stringer K, Kinney G, Hokanson JE, San Jose Estepar R, Washko GR; COPDGene Investigators incl Ruczinski I (2022).
    Longitudinal association between muscle loss and mortality in ever smokers.
    Chest 161(4): 960-970.

    2021

34. Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schonherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, McLaren PJ, Raychaudhuri S (2021).
    A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.
    Nature Genetics 53(10): 1504-1516.
35. Daya M, Cox C, Acevedo N, Boorgula MP, Campbell M, Chavan S, Cho MH, David GL, Kachroo P, Lasky-Su J, Li X, McHugh CP, Qiao D, Rafaels N, Beck LA, Bleecker ER, Caraballo L, Cupples AL, Figueiredo CA, Gallo RL, Hanifin J, Hansel NN, Hata TR, Hersh CP, Knight-Madden J, Leung DYM, Guttman-Yassky E, Meyers DA, O'Connor G, Ober C, Ong PY, Ortega VE, Paller AS, Putcha N, Reed RM, Schneider LC, Silverman EK, Slifka MK, Spergel JM, Vasan RS, Viaud-Martinez KA, Watson H, Weiss ST; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Ruczinski I, Beaty TH, Mathias RA, Barnes KC (2021).
    Multi-ethnic genome-wide and HLA association study of total serum IgE.
    Journal of Allergy and Clinical Immunology 148(6): 1589-1595.
36. Kammers K, Chen A, Monaco DR, Hudelson SE, Grant-McAuley W, Moore RD, Alter G, Deeks SG, Morrison CS, Eller LA, Blankson JN, Laeyendecker O, Ruczinski I, Eshleman SH, Larman HB (2021).
    HIV antibody profiles in HIV controllers and persons with treatment-induced viral suppression.
    Frontiers in Immunology 12: 740395.
37. Cade BE, Lee J, Sofer T, Wang H, Zhang M, Chen H, Gharib SA, Gottlieb DJ, Guo X, Lane JM, Liang J, Lin X, Mei H, Patel SR, Purcell SM, Saxena R, Shah NA, Evans DS, Hanis CL, Hillman DR, Mukherjee S, Palmer LJ, Stone KL, Tranah GJ; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Abecasis GR, Boerwinkle EA, Correa A, Cupples LA, Kaplan RC, Nickerson DA, North KE, Psaty BM, Rotter JI, Rich SS, Tracy RP, Vasan RS, Wilson JG, Zhu X, Redline S; TOPMed Sleep Working Group (2021).
    Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program.
    Genome Medicine 13(1): 136.
38. Yang C, Hallmark B, Chai JC, O'Connor TD, Reynolds LM, Wood AC, Seeds M, Chen YI, 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 (2021).
    Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations.
    Communication Biology 4(1): 918.
39. Ray D, Venkataraghavan S, Zhang W, Leslie EJ, Hetmanski JB, Weinberg SM, Murray JC, Marazita ML, Ruczinski I, Taub MA, Beaty TH (2021).
    Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios.
    PLoS Genetics 17(7): e1009584.
40. Keramati AR, Chen MH, Rodriguez BAT, Yanek LR, Bhan A, Gaynor BJ, Ryan K, Brody JA, Zhong X, Wei Q; NHLBI Trans-Omics for Precision (TOPMed) Consortium, Kammers K, Kanchan K, Iyer K, Kowalski MH, Pitsillides AN, Cupples LA, Li B, Schlaeger TM, Shuldiner AR, O'Connell JR, Ruczinski I, Mitchell BD, Faraday N, Taub MA, Becker LC, Lewis JP, Mathias RA, Johnson AD (2021).
    Genome sequencing unveils a regulatory landscape of platelet reactivity.
    Nature Communications 12(1): 3626.
41. Sofer T, Zheng X, Laurie CA, Gogarten SM, Brody JA, Conomos MP, Bis JC, Thornton TA, Szpiro A, O'Connell JR, Lange EM, Gao Y, Cupples LA, Psaty BM; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Rice KM (2021).
    Variant-specific inflation factors for assessing population stratification at the phenotypic variance level.
    Nature Communications 12(1): 3506.
42. Zhang W, Venkataraghavan S, Hetmanski JB, Leslie EJ, Marazita ML, Feingold E, Weinberg SM, Ruczinski I, Taub MA, Scott AF, Ray D, Beaty TH (2021).
    Detecting gene-environment interaction for maternal exposures using case-parent trios ascertained through a case with non-syndromic orofacial cleft.
    Frontiers in Cell and Developmental Biology 9: 798.
43. Kasela S, Ortega VE, Martorella M, Garudadri S, Nguyen J, Ampleford E, Pasanen A, Nerella S, Buschur KL, Barjaktarevic IZ, Barr RG, Bleecker ER, Bowler RP, Comellas AP, Cooper CB, Couper DJ, Criner GJ, Curtis JL, Han MK, Hansel NN, Hoffman EA, Kaner RJ, Krishnan JA, Martinez FJ, McDonald MN, Meyers DA, Paine R 3rd, Peters SP, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Israel E, Jarjour NN, Levy BD, Li X, Moore WC, Wenzel SE, Zein J; NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS); NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I, Langelier C, Woodruff PG, Lappalainen T, Christenson SA (2021).
    Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium.
    Genome Medicine 13(1): 66.
44. Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung YJ, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf G, Montasser ME, Moon JY, Muzny D, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FF, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang YC, Chen YI, Choi WJ, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAV, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJ, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo JS, Smith AV, Tracy RP, Vasan RS, Kathiresan S, Cupples LA, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I; FinnGen, Peloso GM (2021).
    Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices.
    Nature Communications 12(1): 2182.
45. Chen A, Laeyendecker O, Eshleman SH, Monaco DR, Kammers K, Larman HB, Ruczinski I (2021).
    A top scoring pairs classifier for recent HIV infections.
    Statistics in Medicine 40(11): 2604-2612.
46. Morgenlander WR, Henson S, Monaco D, Chen A, Littlefield K, Bloch EM, Fujimura E, Ruczinski I, Crowley AR, Natarajan H, Butler SE, Weiner JA, Li MZ, Bonny TS, Benner SE, Balagopal A, Sullivan D, Shoham S, Quinn TC, Eshleman S, Casadevall A, Redd AD, Laeyendecker O, Ackerman ME, Pekosz A, Elledge SJ, Robinson M, Tobian AAR, Larman HB (2021).
    Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality.
    The Journal of Clinical Investigation 131(7): e146927.
47. Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR (2021).
    Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
    Nature 590(7845): 290-299.
48. Bin L, Malley C, Taylor P, PreethiBoorgula M, Chavan S, Daya M, Mathias M, Shankar G, Rafaels N, Vergara C, Potee J, Campbell M, Hanifin JM, Simpson E, Schneider LC, Gallo RL, Hata T, Paller AS, De Benedetto A, Beck LA, Ong PY, Guttman-Yassky E, Richers B, Baraghoshi D, Ruczinski I, Barnes K, Leung DYM, Mathias RA (2021).
    Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum.
    Allergy 76(8): 2510-2523.
49. Reiner AP, Raffield LM, Franceschini N, Auer PL, Lange EM, Nickerson DA, Zakai NA, Correa A, Olson N; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium incl Ruczinski I; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium (2021).
    Effect of sickle cell trait and APOL1 genotype on the association of soluble uPAR with kidney function measures in blacks.
    Clinical Journal of the American Society of Nephrology 6(2): 287-289.
50. Kammers K, Taub M, Rodriguez B, Yanek LR, Ruczinski I, Martin J, Kanchan K, Battle A, Cheng L, Wang ZZ, Johnson AD, Leek J, Faraday N, Becker L, Mathias R (2021).
    Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole genome and RNA sequencing.
    Blood 37(7): 959-968.

    2020

51. Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IY, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD; NHLBI Trans-Omics for Precision Medicine Consortium incl Ruczinski I, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P (2020).
    Inherited causes of clonal haematopoiesis in 97,691 whole genomes.
    Nature 586(7831): 763-768.
52. 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 (2020).
    Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants.
    Nature Communications 11(1): 5182.
53. Cristiano S, McKean D, Carey J, Bracci P, Brennan P, Chou M, Du M, Gallinger S, Goggins MG, Hassan MM, Hung RJ, Kurtz RC, Li D, Lu L, Neale R, Olson S, Petersen G, Rabe KG, Fu J, Risch H, Rosner GL, Ruczinski I, Klein AP, Scharpf RB (2020).
    Bayesian copy number detection and association in large-scale studies.
    BMC Cancer 20(1): 856.
54. Strand M, Austin E, Moll M, Pratte KA, Regan EA, Hayden LP, Bhatt SP, Boriek AM, Casaburi R, Silverman EK, Fortis S, Ruczinski I, Koegler H, Rossiter HB, Occhipinti M, Hanania NA, Gebrekristos HT, Lynch DA, Kunisaki KM, Young KA, Sieren JC, Ragland M, Hokanson JE, Lutz SM, Make BJ, Kinney GL, Cho MH, Pistolesi M, DeMeo DL, Sciurba FC, Comellas AP, Diaz AA, Barjaktarevic I, Bowler RP, Kanner RE, Peters SP, Ortega VE, Dransfield MT, Crapo JD (2020).
    A risk prediction model for mortality among smokers in the COPDGene study.
    Chronic Obstructive Pulmonary Diseases 7(4): 346-361.
55. 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 incl Ruczinski I; TOPMed Lipids Working Group, Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, Lin X (2020).
    Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale.
    Nature Genetics 52(9): 969-983.
56. Milne S, Li X, Hernandez Cordero AI, Yang CX, Cho MH, Beaty TH, Ruczinski I, Hansel NN, Bossé Y, Brandsma CA, Sin DD, Obeidat M (2020).
    Protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study.
    Thorax (11): 934-943.
57. Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muneton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ (2020).
    Genome-wide enrichment of de novo coding mutations in orofacial cleft trios.
    American Journal of Human Genetics S0002-9297(20) 30165-8.
58. Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA (2020).
    Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program.
    Stem Cell Research 46: 101803.
59. Sergeant S, Hallmark B, Mathias RA, Mustin TL, Ivester P, Bohannon ML, Ruczinski I, Johnstone L, Seeds MC, Chilton FH (2020).
    Prospective clinical trial examining the impact of genetic variation in FADS1 on the metabolism of linoleic acid and gamma-linolenic acid-containing botanical oils.
    The American Journal of Clinical Nutrition 111(5): 1068-1078.
60. Vince N, Limou S, Daya M, Morii W, Rafaels N, Geffard E, Douillard V, Walencik A, Boorgula MP, Chavan S, Vergara C, Ortega VE, Wilson JG, Lange LA, Watson H, Nicolae DL, Meyers DA, Hansel NN, Ford JG, Faruque MU, Bleecker ER, Campbell M, Beaty TH, Ruczinski I, Mathias RA, Taub MA, Ober C, Noguchi E, Barnes KC, Torgerson D, Gourraud PA; CAAPA (2020).
    Association of HLA-DRB1*09:01 with tIgE levels among African ancestry individuals with asthma.
    Journal of Allergy and Clinical Immunology S0091-6749(20)30098-1.
61. Ruczinski I, Kooperberg C, LeBlanc M (2020).
    A novel algorithmic approach to Bayesian logic regression - invited discussion.
    Bayesian Analysis, 15(1): 290-294.
62. Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedon JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zoellner S, O'Connell JR, Mitchell BD; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I; TOPMed Population Genetics Working Group, O'Connor TD (2020).
    De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population.
    Proceedings of the National Academy of Sciences 117(5): 2560-2569.
63. Hecker J, Ruczinski I, Cho MH, Silverman EK, Coull B, Lange C (2020).
    A flexible and nearly optimal sequential testing approach to randomized testing: QUICK-STOP.
    Genetic Epidemiology 44(2): 139-147.

    2019

64. Lowe KE, Regan EA, Anzueto A, Austin E, Austin JHM, Beaty TH, Benos PV, Benway CJ, Bhatt SP, Bleecker ER, Bodduluri S, Bon J, Boriek AM, Boueiz AR, Bowler RP, Budoff M, Casaburi R, Castaldi PJ, Charbonnier JP, Cho MH, Comellas A, Conrad D, Costa Davis C, Criner GJ, Curran-Everett D, Curtis JL, DeMeo DL, Diaz AA, Dransfield MT, Dy JG, Fawzy A, Fleming M, Flenaugh EL, Foreman MG, Fortis S, Gebrekristos H, Grant S, Grenier PA, Gu T, Gupta A, Han MK, Hanania NA, Hansel NN, Hayden LP, Hersh CP, Hobbs BD, Hoffman EA, Hogg JC, Hokanson JE, Hoth KF, Hsiao A, Humphries S, Jacobs K, Jacobson FL, Kazerooni EA, Kim V, Kim WJ, Kinney GL, Koegler H, Lutz SM, Lynch DA, MacIntye NR Jr, Make BJ, Marchetti N, Martinez FJ, Maselli DJ, Mathews AM, McCormack MC, McDonald MN, McEvoy CE, Moll M, Molye SS, Murray S, Nath H, Newell JD Jr, Occhipinti M, Paoletti M, Parekh T, Pistolesi M, Pratte KA, Putcha N, Ragland M, Reinhardt JM, Rennard SI, Rosiello RA, Ross JC, Rossiter HB, Ruczinski I, San Jose Estepar R, Sciurba FC, Sieren JC, Singh H, Soler X, Steiner RM, Strand MJ, Stringer WW, Tal-Singer R, Thomashow B, Vegas Sánchez-Ferrero G, Walsh JW, Wan ES, Washko GR, Michael Wells J, Wendt CH, Westney G, Wilson A, Wise RA, Yen A, Young K, Yun J, Silverman EK, Crapo JD (2019).
    COPDGene 2019: Redefining the diagnosis of chronic obstructive pulmonary disease.
    Chronic Obstructive Pulmonary Diseases 6(5): 384-399.
65. Kachroo P, Hecker J, Chawes BL, Ahluwalia TS, Cho MH, Qiao D, Kelly RS, Chu SH, Virkud YV, Huang M, Barnes KC, Burchard EG, Eng C, Hu D, Celedón JC, Daya M, Levin AM, Gui H, Williams LK, Forno E, Mak ACY, Avila L, Soto-Quiros ME, Cloutier MM, Acosta-Pérez E, Canino G, Bønnelykke K, Bisgaard H, Raby BA, Lange C, Weiss ST, Lasky-Su JA; National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium incl Ruczinski I (2019).
    Whole genome sequencing identifies CRISPLD2 as a lung function gene in children with asthma.
    Chest 156(6): 1068-1079.
66. Obeidat M, Faiz A, Li X, van den Berge M, Hansel NN, Joubert P, Hao K, Brandsma CA, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Paul Man SF, Pare PD, Sin DD (2019).
    The pharmacogenomics of inhaled corticosteroids and lung function decline in COPD.
    European Respiratory Journal 54(6) 1900521.
67. Boorgula MP, Taub MA, Rafaels N, Daya M, Campbell M, Chavan S, Shetty A, Cheadle C, Barkataki S, Fan J, David G, Beaty TH, Ruczinski I, Hanifin J, Schneider LC, Gallo RL, Paller AS, Beck LA, Leung DY, Mathias RA, Barnes KC (2019).
    Replicated methylation changes associated with eczema herpeticum and allergic response.
    Clinical Epigenetics 11(1): 122.
68. Eshleman SH, Laeyendecker O, Kammers K, Chen A, Sivay MV, Kottapalli S, Sie BM, Yuan T, Monaco DR, Mohan D, Wansley D, Kula T, Morrison C, Elledge SJ, Brookmeyer R, Ruczinski I, Larman HB (2019).
    Comprehensive profiling of HIV antibody evolution.
    Cell Reports 27(5): 1422-1433.
69. Harris DN, Ruczinski I, Yanek LR, Becker LC, Becker DM, Guio H, Cui T, Chilton FH, Mathias RA, O'Connor TD (2019).
    Evolution of hominin polyunsaturated fatty acid metabolism: from Africa to the new world.
    Genome Biology and Evolution 11(5): 1417-1430.
70. Winters A, Bahnson HT, Ruczinski I, Boorgula MP, Malley C, Keramati AR, Chavan S, Larson D, Cerosaletti K, Sayre PH, Plaut M, Du Toit G, Lack G, Barnes KC, Nepom GT, Mathias RA; Immune Tolerance Network LEAP Study Team (2019).
    The MALT1 locus and peanut avoidance in the risk for peanut allergy.
    Journal of Allergy and Clinical Immunology 143(6): 2326-2329.
71. Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC; CAAPA (2019).
    Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.
    Nature Communications 10(1): 880.
72. Tietz T, Selinski S, Golka K, Hengstler JG, Gripp S, Ickstadt K, Ruczinski I, Schwender H (2019).
    Identification of interactions of binary variables associated with survival time using survivalFS.
    Archives of Toxicology 93(3): 585-602.
73. Sherman T, Fu J, Scharpf RB, Bureau A, Ruczinski I (2019).
    Detection of rare disease variants in extended pedigrees using RVS.
    Bioinformatics 35(14): 2509-2511.
74. Wang AW, Avramopoulos D, Lori A, Mulle J, Conneely K, Powers A, Duncan E, Almli L, Massa N, McGrath J, Schwartz AC, Goes FS, Weng L, Wang R, Yolken R, Ruczinski I, Gillespie CF, Jovanovic T, Ressler K, Pulver AE, Pearce BD (2019).
    Genome-wide association study in two populations to determine genetic variants associated with Toxoplasma gondii infection and relationship to schizophrenia risk.
    Progress in Neuropsychopharmacology and Biological Psychiatry 92: 133-147.
75. Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL (2019).
    Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
    Nature Genetics 51(1): 30-35.
76. Bureau A, Begum F, Taub MA, Hetmanski J, Parker MM, Albacha-Hejazi H, Scott AF, Murray JC, Marazita ML, Bailey-Wilson JE, Beaty TH, Ruczinski I (2019).
    Inferring disease risk genes from sequencing data in multiplex pedigrees through sharing of rare variants.
    Genetic Epidemiology 43(1): 37-49.
77. Fu JM, Leslie EJ, Scott AF, Marazita ML, Beaty TH, Scharpf RB, Ruczinski I (2019).
    Detection of de novo copy number deletions from targeted sequencing of trios.
    Bioinformatics 35(4): 571-578.

    2018

78. Rosenthal EA, Shirts BH, Amendola LM, Horike-Pyne M, Robertson PD, Hisama FM, Bennett RL, Dorschner MO, Nickerson DA, Stanaway IB, Nassir R, Vickers KT, Li C, Grady WM, Peters U, Jarvik GP; NHLBI GO Exome Sequencing Project incl Ruczinski I (2018).
    Rare loss of function variants in candidate genes and risk of colorectal cancer.
    Human Genetics 137(10): 795-806.
79. Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S; NHLBI TOPMed Lipids Working Group incl Ruczinski I (2018).
    Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.
    Nature Communications 9(1): 3391.
80. Qiao D, Ameli A, Prokopenko D, Chen H, Kho AT, Parker MM, Morrow J, Hobbs BD, Liu Y, Beaty TH, Crapo JD, Barnes KC, Nickerson DA, Bamshad M, Hersh CP, Lomas DA, Agusti A, Make BJ, Calverley PMA, Donner CF, Wouters EF, Vestbo J, Paré PD, Levy RD, Rennard SI, Tal-Singer R, Spitz MR, Sharma A, Ruczinski I, Lange C, Silverman EK, Cho MH; NHLBI Exome Sequencing Project, University of Washington Center for Mendelian Genomics, Lung GO, COPDGene Investigators (2018).
    Whole exome sequencing analysis in severe chronic obstructive pulmonary disease.
    Human Molecular Genetics 27(21): 3801-3812.
81. Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Ramachandran VS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P; NHLBI TOPMed Lipids Working Group incl Ruczinski I (2018).
    Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.
    Nature Communications 9(1): 2606.
82. Sun X, Gao J, Jin P, Eng C, Burchard EG, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Wang F, Qin Z; CAAPA consortium (2018).
    Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files.
    Gigascience 7(6): giy052.
83. Obeidat M, Zhou G, Li X, Hansel NN, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Paré PD, Sin DD (2018).
    The genetics of smoking in individuals with chronic obstructive pulmonary disease.
    Respiratory Research 19(1): 59.
84. Reynolds LM, Howard TD, Ruczinski I, Kanchan K, Seeds MC, Mathias RA, Chilton FH (2018).
    Tissue-specific impact of FADS cluster variants on FADS1 and FADS2 gene expression.
    PLoS One 3(3): e0194610.
85. Parks S, Avramopoulos D, Mulle J, McGrath J, Wang R, Goes FS, Conneely K, Ruczinski I, Yolken R, Pulver AE, Pearce BD (2018).
    HLA typing using genome wide data reveals susceptibility types for infections in a psychiatric disease enriched sample.
    Brain, Behavior, and Immunity 70: 203-213.
86. Keramati AR, Yanek LR, Iyer K, Taub MA, Ruczinski I, Becker DM, Becker LC, Faraday N, Mathias RA (2018).
    Targeted deep sequencing of the PEAR1 locus for platelet aggregation in European and African American families.
    Platelets 19: 1-7.

    2017

87. Obeidat M, Li X, Burgess S, Zhou G, Fishbane N, Hansel NN, Bosse Y, Joubert P, Hao K, Nickle DC, van den Berge M, Timens W, Cho MH, Hobbs BD, de Jong K, Boezen M, Hung RJ, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Pare PD, Sin DD; International COPD Genetics Consortium, Lung eQTL Consortium, Lung Health Study (2017).
    Surfactant protein D is a causal risk factor for COPD: results of Mendelian randomisation.
    The European Respiratory Journal 50(5): 1700657.
88. Rahbar E, Ainsworth HC, Howard TD, Hawkins GA, Ruczinski I, Mathias R, Seeds MC, Sergeant S, Hixson JE, Herrington DM, Langefeld CD, Chilton FH (2017).
    Uncovering the DNA methylation landscape in key regulatory regions within the FADS cluster.
    PLoS One 12(9): e0180903.
89. Johnston HR, Hu YJ, Gao J, O'Connor TD, Abecasis GR, Wojcik GL, Gignoux CR, Gourraud PA, Lizee A, Hansen M, Genuario R, Bullis D, Lawley C, Kenny EE, Bustamante C, Beaty TH, Mathias RA, Barnes KC, Qin ZS; CAAPA Consortium incl Ruczinski I (2017).
    Identifying tagging SNPs for African specific genetic variation from the African diaspora genome.
    Scientific Reports 7:46398
90. Yu Y, Zuo X, He M, Gao J, Fu Y, Qin C, Meng L, Wang W, Song Y, Cheng Y, Zhou F, Chen G, Zheng X, Wang X, Liang B, Zhu Z, Fu X, Sheng Y, Hao J, Liu Z, Yan H, Mangold E, Ruczinski I, Liu J, Marazita ML, Ludwig KU, Beaty TH, Zhang X, Sun L, Bian Z (2017).
    Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity.
    Nature Communications 8:14364.
91. Qiao D, Lange C, Laird NM, Won S, Hersh CP, Morrow J, Hobbs BD, Lutz SM, Ruczinski I , Beaty TH, Silverman EK, Cho MH (2017).
    Gene-based segregation method for identifying rare variants in family-based sequencing studies.
    Genetic Epidemiology 41(4): 309-319.
92. Long X, Daya M, Zhao J, Rafaels N, Liang H, Potee J, Campbell M, Zhang B, Araujo MI, Oliveira RR, Mathias RA, Gao L, Ruczinski I, Georas SN, Vercelli D, Beaty TH, Barnes KC, Chen X, Chen Q (2017).
    The role of ST2 and ST2 genetic variants in schistosomiasis.
    Journal of Allergy and Clinical Immunology 140(5): 1416-1422.
93. Wain LV, Shrine N, Artigas MS, Erzurumluoglu AM, Noyvert B, Bossini-Castillo L, Obeidat M, Henry AP, Portelli MA, Hall RJ, Billington CK, Rimington TL, Fenech AG, John C, Blake T, Jackson VE, Allen RJ, Prins BP; Understanding Society Scientific Group, Campbell A, Porteous DJ, Jarvelin MR, Wielscher M, James AL, Hui J, Wareham NJ, Zhao JH, Wilson JF, Joshi PK, Stubbe B, Rawal R, Schulz H, Imboden M, Probst-Hensch NM, Karrasch S, Gieger C, Deary IJ, Harris SE, Marten J, Rudan I, Enroth S, Gyllensten U, Kerr SM, Polasek O, Kahonen M, Surakka I, Vitart V, Hayward C, Lehtimäki T, Raitakari OT, Evans DM, Henderson AJ, Pennell CE, Wang CA, Sly PD, Wan ES, Busch R, Hobbs BD, Litonjua AA, Sparrow DW, Gulsvik A, Bakke PS, Crapo JD, Beaty TH, Hansel NN, Mathias RA, Ruczinski I, Barnes KC, Bosse Y, Joubert P, van den Berge M, Brandsma CA, Paré PD, Sin DD, Nickle DC, Hao K, Gottesman O, Dewey FE, Bruse SE, Carey DJ, Kirchner HL; Geisinger-Regeneron DiscovEHR Collaboration, Jonsson S, Thorleifsson G, Jonsdottir I, Gislason T, Stefansson K, Schurmann C, Nadkarni G, Bottinger EP, Loos RJ, Walters RG, Chen Z, Millwood IY, Vaucher J, Kurmi OP, Li L, Hansell AL, Brightling C, Zeggini E, Cho MH, Silverman EK, Sayers I, Trynka G, Morris AP, Strachan DP, Hall IP, Tobin MD (2017).
    Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets.
    Nature Genetics 49(3): 416-425.
94. Kammers K, Taub MA, Ruczinski I, Martin J, Yanek LR, Frazee A, Gao Y, Hoyle D, Faraday N, Becker DM, Cheng L, Wang ZZ, Leek JT, Becker LC, Mathias RA (2017).
    Integrity of induced pluripotent stem cell (iPSC) derived megakaryocytes as assessed by genetic and transcriptomic analysis.
    PLoS One 12(1): e0167794.
95. Xiao Y, Taub MA, Ruczinski I, Begum F, Hetmanski JB, Schwender H, Leslie EJ, Koboldt DC, Murray JC, Marazita ML, Beaty TH (2017).
    Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios.
    Genetic Epidemiology 41(3): 244-250.
96. Fu J, Beaty TH, Scott AF, Hetmanski J, Parker MM, Wilson JE, Marazita ML, Mangold E, Albacha-Hejazi H, Murray JC, Bureau A, Carey J, Cristiano S, Ruczinski I, Scharpf RB (2017).
    Whole exome association of rare deletions in multiplex oral cleft families.
    Genetic Epidemiology 41(1): 61-69.

    2016

97. Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J; CAAPA, Barnes KC (2016).
    A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome.
    Nature Communications 7: 12522.
98. Kessler MD, Yerges-Armstrong L, Taub MA, Shetty AC, Maloney K, Jeng LJ, Ruczinski I, Levin AM, Williams LK, Beaty TH, Mathias RA, Barnes KC; Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), O'Connor TD (2016).
    Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.
    Nature Communications 7: 12521.
99. Begum F, Ruczinski I, Hokanson JE, Lutz SM, Parker MM, Cho MH, Hetmanski JB, Scharpf RB, Crapo JD, Silverman EK, Beaty TH (2016).
    Hemizygous deletion on chromosome 3p26.1 is associated with heavy smoking among African American subjects in the COPDGene study.
    PLoS One 11(10): e0164134.
100. Begum F, Ruczinski I, Li S, Silverman EK, Cho MH, Lynch DA, Curran-Everett D, Crapo J, Scharpf RB, Parker MM, Hetmanski JB, Beaty TH (2016).
     Identifying a deletion affecting total lung capacity among subjects in the COPDGene study cohort.
     Genetic Epidemiology 40(1): 81-8.
101. Sergeant S, Ruczinski I, Ivester P, Lee TC, Morgan TM, Nicklas BJ, Mathias RA, Chilton FH (2016).
     Impact of methods used to express levels of circulating fatty acids on the degree and direction of associations with blood lipids in humans.
     British Journal of Nutrition 115(2): 251-61.
102. Gao L, Emond MJ, Louie T, Cheadle C, Berger AE, Rafaels N, Vergara C, Kim Y, Taub MA, Ruczinski I, Mathai SC, Rich SS, Nickerson DA, Hummers LK, Bamshad MJ, Hassoun PM, Mathias RA; National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project, Barnes KC (2016).
     Identification of rare variants in ATP8B4 as a risk factor for systemic sclerosis by whole-exome sequencing.
     Arthritis Rheumatology 68(1): 191-200.

     2015

103. Gao L, Bin L, Rafaels NM, Huang L, Potee J, Ruczinski I, Beaty TH, Paller AS, Schneider LC, Gallo R, Hanifin JM, Beck LA, Geha RS, Mathias RA, Barnes KC, Leung DY (2015).
     Targeted deep sequencing identifies rare loss-of-function variants in IFNGR1 for risk of atopic dermatitis complicated by eczema herpeticum.
     Journal of Allergy and Clinical Immunology 136(6): 1591-600.
104. Lee SE, West KP Jr, Cole RN, Schulze KJ, Christian P, Wu LS, Yager JD, Groopman J, Ruczinski I (2015).
     Plasma proteome biomarkers of inflammation in school aged children in Nepal.
     PLoS One 10(12): e0144279.
105. Goes FS, McGrath J, Avramopoulos D, Wolyniec P, Pirooznia M, Ruczinski I, Nestadt G, Kenny EE, Vacic V, Peters I, Lencz T, Darvasi A, Mulle JG, Warren ST, Pulver AE (2015).
     Genome-wide association study of schizophrenia in Ashkenazi Jews.
     American Journal of Medical Genetics Part B 68(8): 649-59.
106. Long X, Chen Q, Zhao J, Rafaels N, Mathias P, Liang H, Potee J, Campbell M, Zhang B, Gao L, Georas SN, Vercelli D, Beaty TH, Ruczinski I, Mathias R, Barnes KC, Chen X (2015).
     An IL-13 promoter polymorphism associated with liver fibrosis in patients with schistosoma japonicum.
     PLoS One 10(8): e0135360.
107. Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT Jr, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS; National Heart, Lung, and Blood Institute Exome Sequencing Project incl Ruczinski I (2015).
     Rare and coding region genetic variants associated with risk of ischemic stroke: the NHLBI Exome Sequence Project.
     JAMA Neurology 72(7): 781-8.
108. Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I (2015).
     A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts.
     Birth Defects Research Part A: Clinical and Molecular Teratology 103(4): 276-83.
109. Kammers K, Cole RN, Tiengwe C, Ruczinski I (2015).
     Detecting significant changes in protein abundance.
     EuPA Open Proteomics 7: 11-19.
110. Avramopoulos D, Pearce BD, McGrath J, Wolyniec P, Wang R, Eckart N, Hatzimanolis A, Goes FS, Nestadt G, Mulle J, Coneely K, Hopkins M, Ruczinski I, Yolken R, Pulver AE (2015).
     Infection and inflammation in schizophrenia and bipolar disorder: a genome wide study for interactions with genetic variation.
     PLoS One 10(3): e0116696.
111. Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FW, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC (2015).
     Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci.
     American Journal of Human Genetics 96(3): 397-411.
112. Hansel NN, Pare PD, Rafaels N, Sin D, Sandford A, Daley D, Vergara C, Huang L, Elliott WM, Pascoe CD, Arsenault BA, Postma DS, Boezen HM, Bosse Y, van den Berge M, Hiemstra PS, Cho MH, Litonjua AA, Sparrow D, Ober C, Wise RA, Connett J, Neptune ER, Beaty TH, Ruczinski I, Mathias R, Barnes KC, on behalf of the Lung Health Study (2015).
     Genome wide association study identifies novel loci associated with airway responsiveness in COPD.
     American Journal of Respiratory Cell and Molecular Biology 53(2): 226-34.
113. Do R, Stitziel NO, Won HH, Jørgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL; NHLBI Exome Sequencing Project (incl Ruczinski I), Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Hovingh GK, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Cupples LA, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S (2015).
     Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction.
     Nature 518(7537): 102-6.
114. Dluzniewski PJ, Xu J, Ruczinski I, Isaacs WB, Platz EA (2015).
     Polymorphisms influencing prostate specific antigen concentration may bias genome-wide association studies on prostate cancer.
     Cancer Epidemiology, Biomarkers & Prevention 24(1): 88-93.

     2014

115. Neumann C, Taub MA, Younkin SG, Beaty TH, Ruczinski I, Schwender H (2014).
     Analytic power and sample size calculation for the genotypic transmission/disequilibrium test in case-parent trio studies.
     Biometrical Journal 56(6):1076-92.
116. Golozar A, Beaty TH, Gravitt PE, Ruczinski I, Qiao YL, Fan JH, Ding T, Tang ZZ, Etemadi A, Hu N, Hyland PL, Wang L, Wang C, Dawsey SM, Freedman ND, Abnet CC, Goldstein AM, Taylor PR (2014).
     Oesophageal squamous cell carcinoma in high-risk Chinese populations: possible role for vascular epithelial growth factor A.
     European Journal Of Cancer 50(16): 2855-65.
117. Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, O'Donnell CJ, Rich SS, Nickerson DA; NHLBI Exome Sequencing Project (incl Ruczinski I), Bamshad MJ (2014).
     Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results.
     American Journal of Human Genetics 95(2): 183-93.
118. Schwender H, Li Q, Neumann C, Taub MA, Younkin SG, Berger P, Scharpf RB, Beaty TH, Ruczinski I (2014).
     Detecting disease variants in case-parent trio studies using the Bioconductor software package trio.
     Genetic Epidemiology 38(6): 516-22.
119. Scharpf RB, Mireles L, Yang Q, Kottgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox CS, Coresh J, Kao WH (2014).
     Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.
     BMC Genetics 15(1): 81.
120. Bureau A, Parker MM, Ruczinski I, Taub MA, Marazita ML, Murray JC, Mangold E, Noethen MM, Ludwig KU, Hetmanski JB, Bailey-Wilson JE, Cropp CD, Li Q, Szymczak S, Albacha-Hejazi H, Alqosayer K, Field LL, Wu-Chou YH, Doheny KF, Ling H, Scott AF, Beaty TH (2014).
     Whole exome sequencing of distant relatives in multiplex families implicates rare variants in candidate genes for oral clefts.
     Genetics 197(3): 1039-1044.
121. Tang W, Kowgier M, Loth DW, Soler Artigas M, Joubert BR, Hodge E, Gharib SA, Smith AV, Ruczinski I, Gudnason V, Mathias RA, Harris TB, Hansel NN, Launer LJ, Barnes KC, Hansen JG, Albrecht E, Aldrich MC, Allerhand M, Barr RG, Brusselle GG, Couper DJ, Curjuric I, Davies G, Deary IJ, Dupuis J, Fall T, Foy M, Franceschini N, Gao W, Glaeser S, Gu X, Hancock DB, Heinrich J, Hofman A, Imboden M, Ingelsson E, James A, Karrasch S, Koch B, Kritchevsky SB, Kumar A, Lahousse L, Li G, Lind L, Lindgren C, Liu Y, Lohman K, Lumley T, McArdle WL, Meibohm B, Morris AP, Morrison AC, Musk B, North KE, Palmer LJ, Probst-Hensch NM, Psaty BM, Rivadeneira F, Rotter JI, Schulz H, Smith LJ, Sood A, Starr JM, Strachan DP, Teumer A, Uitterlinden AG, Voelzke H, Voorman A, Wain LV, Wells MT, Wilk JB, Williams OD, Heckbert SR, Stricker BH, London SJ, Fornage M, Tobin MD, O Connor GT, Hall IP, Cassano PA (2014).
     Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.
     PLoS One 9(7): e100776.
122. Bureau A, Younkin S, Parker MM, Bailey-Wilson JE, Marazita ML, Murray JC, Mangold E, Albacha-Hejazi H, Beaty TH, Ruczinski I (2014).
     Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
     Bioinformatics 30(15): 2189-96.
123. Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I (2014).
     A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.
     BMC Genetics 15(1): 24.
124. Wu T, Schwender H, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Parker MM, Wang P, Murray T, Taub M, Li S, Redett RJ, Fallin MD, Liang KY, Wu-Chou YH, Chong SS, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Jee SH, Scott AF, Beaty TH (2014).
     Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate.
     PLoS One 9(2): e88088.
125. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang ZZ, Bizon C, Lange EM, Smith JD, Turner EH, Jun G, Kang HM, Peloso G, Auer P, Li KP, Flannick J, Zhang J, Fuchsberger C, Gaulton K, Lindgren C, Locke A, Manning A, Sim X, Rivas MA, Holmen OL, Gottesman O, Lu Y, Ruderfer D, Stahl EA, Duan Q, Li Y, Durda P, Jiao S, Isaacs A, Hofman A, Bis JC, Correa A, Griswold ME, Jakobsdottir J, Smith AV, Schreiner PJ, Feitosa MF, Zhang Q, Huffman JE, Crosby J, Wassel CL, Do R, Franceschini N, Martin LW, Robinson JG, Assimes TL, Crosslin DR, Rosenthal EA, Tsai M, Rieder MJ, Farlow DN, Folsom AR, Lumley T, Fox ER, Carlson CS, Peters U, Jackson RD, van Duijn CM, Uitterlinden AG, Levy D, Rotter JI, Taylor HA, Gudnason V Jr, Siscovick DS, Fornage M, Borecki IB, Hayward C, Rudan I, Chen YE, Bottinger EP, Loos RJ, Saetrom P, Hveem K, Boehnke M, Groop L, McCarthy M, Meitinger T, Ballantyne CM, Gabriel SB, O'Donnell CJ, Post WS, North KE, Reiner AP, Boerwinkle E, Psaty BM, Altshuler D, Kathiresan S, Lin DY, Jarvik GP, Cupples LA, Kooperberg C, Wilson JG, Nickerson DA, Abecasis GR, Rich SS, Tracy RP, Willer CJ; NHLBI Grand Opportunity Exome Sequencing Project incl Ruczinski I (2014).
     Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol.
     American Journal of Human Genetics 94(2): 233-45.
126. Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, Ioannidis JP, Peters U, Robinson JG, Sucheston LE, Wang D, Sotoodehnia N, Rotter JI, Psaty BM, Jackson RD, Herrington DM, O'Donnell CJ, Reiner AP, Rich SS, Rieder MJ, Bamshad MJ, Nickerson DA; NHLBI GO Exome Sequencing Project incl Ruczinski I (2014).
     Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset.
     Human Molecular Genetics 23(8): 1957-63.

     2013

127. Taub MA, Schwender HR, Younkin SG, Louis TA, Ruczinski I (2013).
     On multi-marker tests for association in case-control studies.
     Frontiers in Statistical Genetics and Methodology 4:252, 1-12.
128. Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, Nickerson DA; NHLBI GO Exome Sequencing Project (incl Ruczinski I), Wijsman EM, Jarvik GP (2013).
     Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia.
     American Journal of Human Genetics 93(6): 1035-45.
129. Stephens SH, Hartz SM, Hoft NR, Saccone NL, Corley RC, Hewitt JK, Hopfer CJ, Breslau N, Coon H, Chen X, Ducci F, Dueker N, Franceschini N, Frank J, Han Y, Hansel NN, Jiang C, Korhonen T, Lind PA, Liu J, Lyytikainen LP, Michel M, Shaffer JR, Short SE, Sun J, Teumer A, Thompson JR, Vogelzangs N, Vink JM, Wenzlaff A, Wheeler W, Yang BZ, Aggen SH, Balmforth AJ, Baumeister SE, Beaty TH, Benjamin DJ, Bergen AW, Broms U, Cesarini D, Chatterjee N, Chen J, Cheng YC, Cichon S, Couper D, Cucca F, Dick D, Foroud T, Furberg H, Giegling I, Gillespie NA, Gu F, Hall AS, Hallfors J, Han S, Hartmann AM, Heikkila K, Hickie IB, Hottenga JJ, Jousilahti P, Kaakinen M, Kahonen M, Koellinger PD, Kittner S, Konte B, Landi MT, Laatikainen T, Leppert M, Levy SM, Mathias RA, McNeil DW, Medland SE, Montgomery GW, Murray T, Nauck M, North KE, Pare PD, Pergadia M, Ruczinski I, Salomaa V, Viikari J, Willemsen G, Barnes KC, Boerwinkle E, Boomsma DI, Caporaso N, Edenberg HJ, Francks C, Gelernter J, Grabe HJ, Hops H, Jarvelin MR, Johannesson M, Kendler KS, Lehtimaki T, Magnusson PK, Marazita ML, Marchini J, Mitchell BD, Noethen MM, Penninx BW, Raitakari O, Rietschel M, Rujescu D, Samani NJ, Schwartz AG, Shete S, Spitz M, Swan GE, Voelzke H, Veijola J, Wei Q, Amos C, Cannon DS, Grucza R, Hatsukami D, Heath A, Johnson EO, Kaprio J, Madden P, Martin NG, Stevens VL, Weiss RB, Kraft P, Bierut LJ, Ehringer MA (2013).
     Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.
     Genetic Epidemiology 37(8): 846-59.
130. Cole RN, Ruczinski I, Schulze K, Christian P, Herbrich S, Wu L, Devine LR, O'Meally RN, Shrestha S, Boronina TN, Yager JD, Groopman J, West KP (2013).
     The plasma proteome identifies expected and novel proteins correlated with micronutrient status in undernourished Nepalese children.
     The Journal of Nutrition 143(10): 1540-8.
131. Beaty TH, Taub MA, Scott AF, Murray JC, Marazita ML, Schwender H, Parker MM, Hetmanski JB, Balakrishnan P, Mansilla MA, Mangold E, Ludwig KU, Noethen MM, Rubini M, Elcioglu N, Ruczinski I (2013).
     Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study.
     Human Genetics 132(7): 771-81.
132. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP; NHLBI Exome Sequencing Project incl Ruczinski I (2013).
     Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project.
     Blood 122(4): 590-7.
133. Guo DC, Regalado E, Casteel DE, Santos-Cortez RL, Gong L, Kim JJ, Dyack S, Horne SG, Chang G, Jondeau G, Boileau C, Coselli JS, Li Z, Leal SM, Shendure J, Rieder MJ, Bamshad MJ, Nickerson DA; GenTAC Registry Consortium; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project (incl Ruczinski I), Kim C, Milewicz DM (2013).
     Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections.
     American Journal of Human Genetics 93(2): 398-404.
134. O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E; NHLBI GO Exome Sequencing Project; ESP Population Genetics, Statistical Analysis Working Group (incl Ruczinski I), Leal SM, Akey JM (2013).
     Fine-scale patterns of population stratification confound rare variant association tests.
     PLoS One 8(7): e65834.
135. Li Q, Schwender H, Louis TA, Fallin MD, Ruczinski I (2013).
     Efficient simulation of epistatic interactions in case-parent trios.
     Human Heredity 75(1): 12-22.
136. May DH, Navarro SL, Ruczinski I, Hogan J, Ogata Y, Schwarz Y, Levy L, Holzman T, McIntosh MW, Lampe JW (2013).
     Metabolomic profiling of urine: response to a randomised, controlled feeding study of select fruits and vegetables, and application to an observational study.
     British Journal of Nutrition 9: 1-11.
137. Vergara C, Murray T, Rafaels N, Lewis R, Campbell M, Foster C, Gao L, Faruque M, Oliveira RR, Carvalho E, Araujo MI, Cruz AA, Watson H, Mercado D, Knight-Madden J, Ruczinski I, Dunston G, Ford J, Caraballo L, Beaty TH, Mathias RA, Barnes KC (2013).
     African ancestry is a risk factor for asthma and high total IgE levels in African Admixed populations.
     Genetic Epidemiology 37(4): 393-401.
138. Omoumi A, Wang Z, Yeow V, Wu-Chou YH, Chen PK, Ruczinski I, Cheng J, Cheah FS, Lee CG, Beaty TH, Chong SS (2013).
     Fetal polymorphisms at the ABCB1-transporter gene locus are associated with susceptibility to non-syndromic oral cleft malformations.
     European Journal of Human Genetics 12: 1436-41.
139. Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE; National Heart, Lung, and Blood Institute GO Exome Sequencing Project (incl Ruczinski I) and the Exome Sequencing Project Family Studies Project Team (2013).
     Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy.
     Circulation: Cardiovascular Genetics 6(2): 144-53.
140. Herbrich SM, Cole RN, West KP, Schulze K, Yager JD, Groopman JD, Christian P, Wu L, O'Meally RN, May DH, McIntosh MW, Ruczinski I (2013).
     Statistical inference from multiple iTRAQ experiments without using common reference standards.
     Journal of Proteome Research 12(2): 594-604.
141. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project (incl Ruczinski I), Akey JM (2013).
     Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
     Nature 493(7431): 216-20.
142. Patel PJ, Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Wu T, Murray T, Rose M, Redett RJ, Jin SC, Lie RT, Wu-Chou YH, Wang H, Ye X, Yeow V, Chong S, Jee SH, Shi B, Scott AF (2013).
     X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts.
     European Journal of Oral Science 121(2): 63-68.
143. Hansel NN, Ruczinski I, Rafaels N, Sin DD, Daley D, Malinina A, Huang L, Sandford A, Murray T, Kim Y, Vergara C, Heckbert SR, Psaty BM, Li G, Elliott WM, Aminuddin F, Dupuis J, O'Connor GT, Doheny K, Scott AF, Boezen HM, Postma DS, Smolonska J, Zanen P, Mohamed Hoesein FA, de Koning HJ, Crystal RG, Tanaka T, Ferrucci L, Silverman E, Wan E, Vestbo J, Lomas DA, Connett J, Wise RA, Neptune ER, Mathias RA, Pare PD, Beaty TH, Barnes KC (2013).
     Genome-wide study identifies two loci associated with lung function decline in mild to moderate COPD.
     Human Genetics 132(1): 79-90.
144. Wang H, Zhang T, Wu T, Hetmanski JB, Ruczinski I, Schwender H, Murray T, Fallin MD, Redett RJ, Raymond GV, Jin SC, Wu-Chou YH, Chen PK, Yeow V, Chong SS, Cheah FS, Jee SH, Jabs EW, Liang KY, Scott A, Beaty TH (2013).
     The FGF & FGFR gene family and risk of cleft lip with/without cleft palate.
     The Cleft Palate-Craniofacial Journal 50(1): 96-103.
145. Alberg AJ, Jorgensen TJ, Ruczinski I, Wheless L, Yao Shugart Y, Berthier Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Kao WH, Francis L, Alani RM, Smith MW, Strickland PT (2013).
     DNA repair gene variants in relation to overall cancer risk: a population-based study.
     Carcinogenesis 34(1): 86-92.

     2012

146. Scharpf RB, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I (2012).
     Fast detection of de novo copy number variants from SNP arrays for case-parent trios.
     BMC Bioinformatics 13(1): 330.
147. Mathias RA, Fu W, Akey JM, Ainsworth HC, Torgerson DG, Ruczinski I, Sergeant S, Barnes KC, Chilton FH (2012).
     Adaptive evolution of the FADS gene cluster within Africa.
     PLoS One 7(9): e44926.
148. Ruczinski I, Jorgensen T, Yao Shugart Y, Berthier Schaad Y, Kessing B, Hoffman-Bolton J, Helzlsouer K, Kao WH, Wheless L, Francis L, Alani R, Strickland P, Smith M, Alberg A (2012).
     A population-based study of DNA repair gene variants in relation to nonmelanoma skin cancer as a marker of a cancer-prone phenotype.
     Carcinogenesis 33(9): 1692-8.
149. Ludwig KU, Mangold E, Herms S, Nowak S, Reutter H, Paul A, Becker J, Herberz R, Alchawa T, Nasser E, Boehmer AC, Mattheisen M, Alblas MA, Barth S, Kluck N, Lauster C, Braumann B, Reich RH, Hemprich A, Poetzsch S, Blaumeiser B, Daratsianos N, Kreusch T, Murray JC, Marazita ML, Ruczinski I, Scott AF, Beaty TH, Kramer FJ, Wienker TF, Steegers-Theunissen RP, Rubini M, Mossey PA, Hoffmann P, Lange C, Cichon S, Propping P, Knapp M, Noethen MM (2012).
     Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
     Nature Genetics 44(9): 968-71.
150. Boileau C, Guo DC, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, d'Indy H, Braverman AC, Grandchamp B, Kwartler CS, Gouya L, Santos-Cortez RL, Abifadel M, Leal SM, Muti C, Shendure J, Gross MS, Rieder MJ, Vahanian A, Nickerson DA, Michel JB; National Heart, Lung, and Blood Institute (NHLBI) Go Exome Sequencing Project (incl Ruczinski I), Jondeau G, Milewicz DM (2012).
     TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome.
     Nature Genetics 44(8): 916-21.
151. Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC; National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project (incl Ruczinski I); Lung GO, Gibson RL, Bamshad MJ (2012).
     Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis..
     Nature Genetics 44(8): 886-9.
152. Jorgensen TJ, Ruczinski I, Shugart YY, Wheless L, Berthier-Schaud Y, Kessing B, Hoffman-Bolton J, Helzlsouer KJ, Linda Kao WH, Francis L, Alani R, Strickland PT, Smith MW, Alberg AJ (2012).
     A population-based study of hedgehog pathway gene variants in relation to the dual risk of contracting both basal cell carcinoma plus another cancer.
     Cancer Epidemiology 36(5): e288-93.
153. Schwender H, Taub MA, Beaty TH, Marazita ML, Ruczinski I (2012).
     Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimation.
     Biometrics 68(3): 766-73.
154. Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS (2012).
     Detectable clonal mosaicism from birth to old age and its relationship to cancer.
     Nature Genetics 44(6): 642-50.
155. Hartz SM, Short SE, Saccone NL, Culverhouse R, Chen L, Schwantes-An TH, Coon H, Han Y, Stephens SH, Sun J, Chen X, Ducci F, Dueker N, Franceschini N, Frank J, Geller F, Gubjartsson D, Hansel NN, Jiang C, Keskitalo-Vuokko K, Liu Z, Lyytikainen LP, Michel M, Rawal R, Rosenberger A, Scheet P, Shaffer JR, Teumer A, Thompson JR, Vink JM, Vogelzangs N, Wenzlaff AS, Wheeler W, Xiao X, Yang BZ, Aggen SH, Balmforth AJ, Baumeister SE, Beaty T, Bennett S, Bergen AW, Boyd HA, Broms U, Campbell H, Chatterjee N, Chen J, Cheng YC, Cichon S, Couper D, Cucca F, Dick DM, Foroud T, Furberg H, Giegling I, Gu F, Hall AS, Hallfors J, Han S, Hartmann AM, Hayward C, Heikkila K, Hewitt JK, Hottenga JJ, Jensen MK, Jousilahti P, Kaakinen M, Kittner SJ, Konte B, Korhonen T, Landi MT, Laatikainen T, Leppert M, Levy SM, Mathias RA, McNeil DW, Medland SE, Montgomery GW, Muley T, Murray T, Nauck M, North K, Pergadia M, Polasek O, Ramos EM, Ripatti S, Risch A, Ruczinski I, Rudan I, Salomaa V, Schlessinger D, Styrkarsdottir U, Terracciano A, Uda M, Willemsen G, Wu X, Abecasis G, Barnes K, Bickeboeller H, Boerwinkle E, Boomsma DI, Caporaso N, Duan J, Edenberg HJ, Francks C, Gejman PV, Gelernter J, Grabe HJ, Hops H, Jarvelin MR, Viikari J, Kaehoenen M, Kendler KS, Lehtimaki T, Levinson DF, Marazita ML, Marchini J, Melbye M, Mitchell BD, Murray JC, Noethen MM, Penninx BW, Raitakari O, Rietschel M, Rujescu D, Samani NJ, Sanders AR, Schwartz AG, Shete S, Shi J, Spitz M, Stefansson K, Swan GE, Thorgeirsson T, Voelzke H, Wei Q, Wichmann HE, Amos CI, Breslau N, Cannon DS, Ehringer M, Grucza R, Hatsukami D, Heath A, Johnson EO, Kaprio J, Madden P, Martin NG, Stevens VL, Stitzel JA, Weiss RB, Kraft P, Bierut LJ (2012).
     Increased genetic vulnerability to smoking at CHRNA5 in early-onset smokers.
     Archives of General Psychiatry 69(8): 854-60.
156. Taub M, Schwender H, Beaty TH, Louis TA, Ruczinski I (2012).
     Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions.
     Genetic Epidemiology 36(3): 244-52.
157. Chen Q, Wang H, Hetmanski JB, Zhang T, Ruczinski I, Schwender H, Liang KY, Fallin MD, Redett RJ, Raymond GV, Wu Chou YH, Chen PK, Yeow V, Chong SS, Cheah FS, Jabs EW, Scott AF, Beaty TH (2012).
     BMP4 was associated with NSCL/P in an Asian population.
     PLoS One 7(4): e35347.
158. Murray T, Taub MA, Ruczinski I, Scott AF, Hetmanski JB, Schwender H, Patel P, Zhang TX, Munger RG, Wilcox AJ, Ye X, Wang H, Wu T, Wu-Chou YH, Shi B, Jee SH, Chong S, Yeow V, Murray JC, Marazita ML, Beaty TH (2012).
     Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and Europeans.
     Genetic Epidemiology 36(4): 392-9.
159. Zhang TX, Beaty TH, Ruczinski I (2012).
     Candidate pathway based analysis for cleft lip with or without cleft palate.
     Statistical Applications in Genetics and Molecular Biology 11(2): Article 10.
160. Wang H, Hetmanski JB, Ruczinski I, Liang KY, Fallin MD, Redett RJ, Raymond GV, Chou YH, Chen PK, Yeow V, Chong SS, Cheah FSh, Jabs EW, Scott AF, Beaty TH (2012).
     ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population.
     Chinese Medical Journal 125(3): 476-480.
161. Shi M, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Wu T, Murray T, Redett RJ, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Yeow V, Chong SS, Shi B, Christensen K, Scott AF, Patel P, Cheah F, Beaty TH (2012).
     Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
     American Journal of Medical Genetics 8A(4): 784-94.
162. Scholl PF, Cole RN, Ruczinski I, Gucek M, Diez R, Rennie A, Nathasingh C, Schulze K, Christian P, Yager JD, Groopman JD, West KP Jr (2012).
     Maternal serum proteome changes between the first and third trimester of pregnancy in rural southern Nepal.
     Placenta 33(5): 424-32.
163. Wheless L, Kistner-Griffin E, Jorgensen TJ, Ruczinski I, Berthier-Schaad Y, Kessing B, Hoffman-Bolton J, Francis L, Shugart YY, Strickland PT, Kao WH, Alani RM, Smith MW, Alberg AJ (2012).
     A community-based study of nucleotide excision repair polymorphisms in relation to the risk of non-melanoma skin cancer.
     Journal of Investigative Dermatology 132(5): 1354-62.
164. Saxena R, Elbers CC, Guo Y, Peter I, Gaunt TR, Mega JL, Lanktree MB, Tare A, Castillo BA, Li YR, Johnson T, Bruinenberg M, Gilbert-Diamond D, Rajagopalan R, Voight BF, Balasubramanyam A, Barnard J, Bauer F, Baumert J, Bhangale T, Böhm BO, Braund PS, Burton PR, Chandrupatla HR, Clarke R, Cooper-DeHoff RM, Crook ED, Davey-Smith G, Day IN, de Boer A, de Groot MC, Drenos F, Ferguson J, Fox CS, Furlong CE, Gibson Q, Gieger C, Gilhuijs-Pederson LA, Glessner JT, Goel A, Gong Y, Grant SF, Grobbee DE, Hastie C, Humphries SE, Kim CE, Kivimaki M, Kleber M, Meisinger C, Kumari M, Langaee TY, Lawlor DA, Li M, Lobmeyer MT, Maitland-van der Zee AH, Meijs MF, Molony CM, Morrow DA, Murugesan G, Musani SK, Nelson CP, Newhouse SJ, O'Connell JR, Padmanabhan S, Palmen J, Patel SR, Pepine CJ, Pettinger M, Price TS, Rafelt S, Ranchalis J, Rasheed A, Rosenthal E, Ruczinski I, Shah S, Shen H, Silbernagel G, Smith EN, Spijkerman AW, Stanton A, Steffes MW, Thorand B, Trip M, van der Harst P, van der A DL, van Iperen EP, van Setten J, van Vliet-Ostaptchouk JV, Verweij N, Wolffenbuttel BH, Young T, Zafarmand MH, Zmuda JM; Look AHEAD Research Group; DIAGRAM consortium, Boehnke M, Altshuler D, McCarthy M, Kao WH, Pankow JS, Cappola TP, Sever P, Poulter N, Caulfield M, Dominiczak A, Shields DC, Bhatt DL, Zhang L, Curtis SP, Danesh J, Casas JP, van der Schouw YT, Onland-Moret NC, Doevendans PA, Dorn GW 2nd, Farrall M, FitzGerald GA, Hamsten A, Hegele R, Hingorani AD, Hofker MH, Huggins GS, Illig T, Jarvik GP, Johnson JA, Klungel OH, Knowler WC, Koenig W, März W, Meigs JB, Melander O, Munroe PB, Mitchell BD, Bielinski SJ, Rader DJ, Reilly MP, Rich SS, Rotter JI, Saleheen D, Samani NJ, Schadt EE, Shuldiner AR, Silverstein R, Kottke-Marchant K, Talmud PJ, Watkins H, Asselbergs FW, de Bakker PI, McCaffery J, Wijmenga C, Sabatine MS, Wilson JG, Reiner A, Bowden DW, Hakonarson H, Siscovick DS, Keating BJ(2012).
     Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.
     American Journal of Human Genetics 90(3): 410-25.
165. Wu T, Fallin MD, Shi M, Ruczinski I, Liang KY, Hetmanski JB, Wang H, Ingersoll RG, Huang S, Ye X, Wu-Chou YH, Chen PK, Jabs EW, Shi B, Redett R, Scott AF, Murray JC, Marazita ML, Munger RG, Beaty TH (2012).
     Evidence of gene-environment interaction for the RUNX2 gene and environmental tobacco smoke in controlling the risk of cleft lip with/without cleft palate.
     Birth Defects Research 94(2): 76-83.

     2011

166. 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 (2011).
     Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.
     American Journal of Human Genetics 89(3): 368-81.
167. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedón JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF Jr, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ; Mexico City Childhood Asthma Study (MCAAS), Gilliland FD; Children's Health Study (CHS) and HARBORS study, Burchard EG; Genetics of Asthma in Latino Americans (GALA) Study, Study of Genes-Environment and Admixture in Latino Americans (GALA2) and Study of African Americans, Asthma, Genes & Environments (SAGE), Martinez FD; Childhood Asthma Research and Education (CARE) Network, Weiss ST; Childhood Asthma Management Program (CAMP), Williams LK; Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE), Barnes KC; Genetic Research on Asthma in African Diaspora (GRAAD) Study, Ober C, Nicolae DL (2011).
     Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.
     Nature Genetics 43(9): 887-92.
168. Faraday N, Yanek L, Yang XP, Mathias R, Herrera-Galeano E, Suktitipat B, Qayyum R, Johnson AD, Chen MH, Tofler GH, Ruczinski I, Friedman AD, Gylfason A, Thorsteinsdottir U, Bray PF, O'Donnell CJ, Becker DM, Becker LC (2011).
     Identification of a specific intronic PEAR1 gene variant associated with greater platelet aggregability and protein expression.
     Blood 118(12): 3367-75.
169. Wegmann D, Kessner D, Veeramah K, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Becker LC, Ruczinski I, Beaty TH, Kardia SL, Meyers D, Barnes KC, Becker DM, Freimer N, Novembre J (2011).
     Recombination rates in admixed individuals revealed by ancestry-based inference.
     Nature Genetics 43(9): 847-53.
170. Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Murray T, Redett RJ, Fallin MD, Liang KY, Wu T, Patel PJ, Jin SC, Zhang TX, Schwender H, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Lie RT, Jee SH, Christensen K, Doheny K, Pugh EW, Ling H, Scott AF (2011).
     Evidence for gene-environment interaction in a genome wide study of isolated, non-syndromic cleft palate.
     Genetic Epidemiology 35(6): 469-78.
171. Mathias RA, Sergeant S, Ruczinski I, Torgerson DG, Hugenschmidt C, Kubala M, Vaidya D, Suktitipat B, Ziegler JT, Ivester P, Case D, Yanek L, Freedman B, Rudock ME, Barnes KC, Langefeld C, Becker LC, Bowden DW, Becker DM, Chilton FH (2011).
     The impact of FADS genetic variants on omega-6 polyunsaturated fatty acid metabolism in African Americans.
     BMC Genetics 12(1): 50.
172. 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, Deming 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 (2011).
     Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium.
     PLoS Genetics 7(4):e1001371.
173. Scharpf RB, Irizarry RA, Ritchie M, Carvalho B, Ruczinski I (2011).
     Using the R package crlmm for genotyping and copy number estimation.
     Journal of Statistical Software 40(12): 1-32.
174. Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf RB, Jie C, Hao H, Hetrick K, Jedlicka A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, Irizarry RA (2011).
     Performance assessment of copy number microarray platforms using a spike-in experiment.
     Bioinformatics 27(8): 1052-60.
175. Kral BG, Mathias RA, Suktitipat B, Ruczinski I, Vaidya D, Yanek LR, Quyyumi AA, Patel RS, Zafari AM, Vaccarino V, Hauser ER, Kraus WE, Becker LC, Becker DM (2011).
     A common variant in the CDKN2B gene on chromosome 9p21 protects against coronary artery disease in Americans of African ancestry.
     Journal of Human Genetics 56(3): 224-9.
176. Schwender H, Bowers K, Fallin MD, Ruczinski I (2011).
     Importance measures for epistatic interactions in case-parent trios.
     Annals of Human Genetics 75(1): 122-32.
177. Schwender H, Ruczinski I, Ickstadt K (2011).
     Testing SNPs and sets of SNPs for importance in association studies.
     Biostatistics 12(1): 18-32.
178. Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA (2011).
     A multilevel model to address batch effects in copy number estimation using SNP arrays.
     Biostatistics 12(1): 33-50.

     2010

179. Louis TA, Li Q, Carvalho B, Fallin MD, Irizarry RA, Ruczinski I (2010).
     Association tests that accommodate genotyping errors [ with discussion ]
     Bayesian Statistics 9: 393-420
180. Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Lakkar S, Garrett-Mayer E, Parmigiani G (2010).
     Cross-platform comparison of two pancreatic cancer phenotypes.
     Cancer Informatics 9: 257-64.
181. Schwender H, Ruczinski I (2010).
     Logic regression and its extensions.
     Advances in Genetics 72: 25-45.
182. Scientists for Reproducible Research (2010).
     Disclose all data in publications.
     Nature 467: 401.
183. 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, Hlatky MA, Knowles JW, Thompson JR, Absher D, Iribarren C, Go A, Fortmann SP, Sidney S, Risch N, Tang H, Myers RM, Berger K, Stoll M, Shah SH, Thorgeirsson G, Andersen K, Havulinna AS, Herrera JE, Faraday N, Kim Y, Kral BG, Mathias RA, Ruczinski I, Suktitipat B, Wilson AF, Yanek LR, Becker LC, Linsel-Nitschke P, Lieb W, Konig IR, Hengstenberg C, Fischer M, Stark K, Reinhard W, Winogradow J, Grassl M, Grosshennig A, Preuss M, Schreiber S, Wichmann HE, Meisinger C, Yee J, Friedlander Y, Do R, Meigs JB, Williams G, Nathan DM, Macrae CA, Qu L, Wilensky RL, Matthai WH Jr, Qasim AN, Hakonarson H, Pichard AD, Kent KM, Satler L, Lindsay JM, Waksman R, Knouff CW, Waterworth DM, Walker MC, Mooser VE, Marrugat J, Lucas G, Subirana I, Sala J, Ramos R, Martinelli N, Olivieri O, Trabetti E, Malerba G, Pignatti PF, Guiducci C, Mirel D, Parkin M, Hirschhorn JN, Asselta R, Duga S, Musunuru K, Daly MJ, Purcell S, Eifert S, Braund PS, Wright BJ, Balmforth AJ, Ball SG; Myocardial Infarction Genetics Consortium; Wellcome Trust Case Control Consortium, Cardiogenics, Ouwehand WH, Deloukas P, Scholz M, Cambien F, Huge A, Scheffold T, Salomaa V, Girelli D, Granger CB, Peltonen L, McKeown PP, Altshuler D, Melander O, Devaney JM, Epstein SE, 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 (2010).
     Lack of association between the Trp719Arg polymorphism in kinesin-like protein 6 and coronary artery disease in 19 case-control studies.
     Journal of the American College of Cardiology 56(19): 1552-63.
184. Lam TK, Ruczinski I, Helzlsouer K, Shugart YY, Caulfield LE, Alberg AJ (2010).
     Cruciferous vegetable intake and lung cancer risk: a nested case-control study matched on cigarette smoking.
     Cancer Epidemiology Biomarkers and Prevention 19(10): 2534-40.
185. Wu T, Liang KY, Hetmanski JB, Ruczinski I, Fallin MD, Ingersoll RG, Wang H, Huang S, Ye X, Wu-Chou Y, Chen PK, Jabs EW, Shi B, Redett R, Scott AF, Beaty TH (2010).
     Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate.
     Human Genetics 28(4): 401-10.
186. Murray T, Beaty T, Mathias R, Rafaels N, Faraque M, Watson H, Ruczinski I, Dunston G, Barnes KC (2010).
     African and non-African admixture components in African Americans and an African Caribbean population.
     Genetic Epidemiology 34(6): 561-8.
187. Li Q, Fallin MD, Louis TA, Lasseter VK, McGrath JA, Avramopoulos D, Wolyniec PS, Valle D, Liang KY, Pulver AE, Ruczinski I (2010).
     Detection of SNP-SNP interactions in trios of parents with schizophrenic children.
     Genetic Epidemiology 34(5): 396-406.
188. Hunninghake GM, Soto-Quiros ME, Avila L, Kim HP, Lasky-Su J, Rafaels N, Ruczinski I, Beaty TH, Mathias RA, Barnes KC, Wilk JB, O'Connor GT, Gauderman WJ, Baurley JW, Gilliland F, Liang C, Sylvia JS, Klanderman BJ, Sharma SS, Himes BE, Bossley C, Israel E, Raby BA, Bush A, Choi AM, Weiss ST, Celedon JC (2010).
     TSLP polymorphisms are associated with asthma in a sex-specific fashion.
     Allergy 65(12): 1566-75.
189. Mathias RA, Kim Y, Sung H, Yanek LR, Hererra-Galeano JE, Ruczinski I, Wilson AF, Faraday N, Becker LC, Becker DM, Mantese VJ (2010).
     A combined genome-wide linkage and association approach to find susceptibility loci for platelet function phenotypes in Caucasian and African American families with coronary artery disease.
     BMC Medical Genomics 3(1): 22.
190. Beaty TH, Hetmanski JB, Murray JC, Marazita ML, Munger RG, Ruczinski I, Liang KY, Wu T, Murray T, Fallin MD, Redett RA, Raymond G, Schwender H, Jin SJ, Rose M, Cooper ME, Dunnwald M, Mansilla MA, Leslie E, Bullard S, Lidral A, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox A, Lie RT, Jabs EW, Wu-Chou YH, Wang H, Ye X, , Huang S, Yeow V, Chong SS, Jee SH, Shi B, Christensen K, Doheny K, Pugh EW, Ling H, Castilla EE, Czeizel AE, Ma L, Field LL, Brody L, Pangilinan F, Mills JL, Molloy AM, Kirke PN, Scott JM, Arcos-Burgos M, Scott AF (2010).
     A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4.
     Nature Genetics 42(6): 525-9.
191. Louis TA, Ruczinski I (2010).
     Efficient evaluation of ranking procedures when the number of units is large, with application to SNP identification.
     Biometrical Journal 52(1): 34-49.
192. Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA, Wang K, Rafaels NM, Michel S, Bonnelykke K, Zhang H, Kim CE, Frackelton EC, Glessner JT, Hou C, Otieno FG, Santa E, Thomas K, Smith RM, Glaberson WR, Garris M, Chiavacci RM, Beaty TH, Ruczinski I, Orange J, Allen J, Spergel JM, Grundmeier R, Mathias RA, Christie JD, von Mutius E, Cookson WO, Kabesch M, Moffatt MF, Grunstein MM, Barnes KC, Devoto M, Magnusson M, Li H, Struan FA, Grant SF, Bisgaard H, Hakonarson H (2010).
     Variants of DENND1B associated with asthma in children.
     New England Journal of Medicine 362(1): 36-44.
193. Scharpf RB, Ruczinski I (2010).
     R classes and methods for SNP array data.
     Methods in Molecular Biology 593: 67-79.
194. Mathias RA, Grant AV, Rafaels R, Hand T, Gao L, Vergara C, Tsai YJ, Yang M, Campbell M, Foster C, Gao P, Togias A, Hansel N, Diette G, Adkinson NF, Liu M, Faruque M, Dunston GM, Watson H, Bracken MB, Hoh J, Maul P, Maul T, Murray T, Hetmanski JB, Ashworth R, Ongaco C, Hendricks K, Doheney K, Pugh E, Scott AF, Kabesch M, Liang L, Abecasis G, Moffatt MF, Cookson WO, Ruczinski I, Beaty TH, Barnes KC (2010).
     A genome-wide association study on African-ancestry populations for asthma.
     Journal of Allergy and Clinical Immunology 25(2): 336-346.

     2009

195. Gallicchio L, Chang H, Christo DK, Thuita L, Huang HY, Strickland P, Ruczinski I, Hoffman SC, Helzlsouer KJ (2009).
     Single nucleotide polymorphisms in obesity-related genes and all-cause and cause-specific mortality: a prospective cohort study.
     BMC Medical Genetics 10(1): 103.
196. Jorgensen TJ, Ruczinski I, Kessing B, Smith MW, Shugart YY, Alberg AJ (2009).
     Hypothesis-driven candidate gene association studies: practical design and analytical considerations.
     American Journal of Epidemiology 170(8): 986-93.
197. Wheless L, Ruczinski I, Alani R, Clipp S, Hoffman-Bolton J, Jorgensen TJ, Liegeois NJ, Strickland PT, Alberg AJ (2009).
     The association between skin characteristics and skin cancer prevention behaviors.
     Cancer Epidemiology, Biomarkers, and Prevention 18(10): 2613-9.
198. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S (2009).
     Sensitive detection of chromosomal segments of distinct ancestry in admixed populations.
     PLoS Genetics 5(6): e1000519.
199. Ruczinski I, Kooperberg C (2009).
     Logic Regression.
     Encyclopedia of Medical Decision Making, Sage Publications, 678-81.
200. Miller CL, Murakami P, Ruczinski I, Ross RG, Sinkus M, Sullivan B, Leonard S (2009).
     Two complex genotypes relevant to the kynurenine pathway and melanotropin function show association with schizophrenia and bipolar disorder.
     Schizophrenia Research 113(2-3): 259-67.
201. Köttgen A, Glazer NL, Dehghan A, Hwang SJ, Katz R, Li M, Yang Q, Gudnason V, Launer LJ, Harris TB, Smith AV, Arking DE, Astor BC, Boerwinkle E, Ehret GB, Ruczinski I, Scharpf RB, Chen YI, de Boer IH, Haritunians T, Lumley T, Sarnak M, Siscovick D, Benjamin EJ, Levy D, Upadhyay A, Aulchenko YS, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, Chasman DI, Parle P, Ridker PM, Kao WH, Witteman JC, Coresh J, Shlipak MG, Fox CS (2009).
     Multiple loci associated with indices of renal function and chronic kidney disease.
     Nature Genetics 41(6): 712-7.
202. Himes BE, Hunninghake GM, Baurley JW, Rafaels NM, Sleiman P, Strachan DP, Wilk JB, Willis-Owen SA, Klanderman B, Lasky-Su J, Lazarus R, Murphy AJ, Soto-Quiros ME, Avila L, Beaty T, Mathias RA, Ruczinski I, Barnes KC, Celedon JC, Cookson WO, Gauderman WJ, Gilliland FD, Hakonarson H, Lange C, Moffatt MF, O'Connor GT, Raby BA, Silverman EK, Weiss ST (2009).
     Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene.
     The American Journal of Human Genetics 84: 581-93.
203. Lam TK, Ruczinski I, Helzlsouer K, Shugart YY, Li KE, Clipp S, Alberg AJ (2009).
     Copy number variants of GSTM1 and GSTT1 in relation to lung cancer risk in a prospective cohort study.
     Annals of Epidemiology 19(8): 546-52.
204. Ruczinski I, Plaxco KW (2009).
     Some Recommendations for the Practitioner to Improve the Precision of Experimentally Determined Protein Folding Rates and Φ Values.
     Proteins: Structure, Function, and Bioinformatics 74(2): 461-74.

     2008

205. Schulze KJ, Christian P, Ruczinski I, Ray AL, Nath A, Wu LS, Semba RD (2008).
     Hepcidin and Iron Status among Pregnant Women in Bangladesh.
     Asia Pacific Journal of Clinical Nutrition 17(3): 451-6.
206. Pattaro C, Ruczinski I, Fallin DM, Parmigiani G (2008).
     Haplotype Block Partitioning as a Tool for Dimensionality Reduction in SNP Association Studies.
     BMC Genomics 9(1): 405.
207. Chen J, Ruczinski I, Jorgensen TJ, Yenokyan G, Yao Y, Alani R, Liegeois NJ, Hoffman SC, Hoffman-Bolton J, Strickland PT, Helzlsouer KJ, Alberg AJ (2008).
     Nonmelanoma Skin Cancer as a Marker of Risk for Subsequent Malignancy: A Community-based Prospective Cohort Study.
     Journal of the National Cancer Institute 100(17): 1215-22.
208. Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I (2008).
     Hidden Markov Models for the Assessment of Chromosomal Alterations using High-throughput SNP Arrays.
     The Annals of Applied Statistics, 2(2): 687-713.
209. Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Park BY, Jee SH, Jabs EW, Redett R, Jung E, Ruczinski I, Scott AF, Beaty TH (2008).
     Differential Parental Transmission of Markers in RUNX2 among Cleft Case-parent Trios from Four Populations.
     Genetic Epidemiology 32(6): 505-12.
210. Gallicchio L, Chang H, Christo DK, Thuita L, Huang HY, Strickland P, Ruczinski I, Hoffman SC, Helzlsouer KJ (2008).
     Single Nucleotide Polymorphisms in Imflammation-related Genes and Mortality in a Community-based Cohort in Washington County, Maryland.
     American Journal of Epidemiology, 167(7): 807-13.

     2007 and earlier

211. Ting JC, Roberson ED, Miller N, Lysholm-Bernacchi A, Stephan DA, Capone GT, Ruczinski I, Thomas GH, Pevsner J (2007).
     Visualization of Uniparental Inheritance, Mendelian Inconsistencies, Deletions and Parent of Origin Effects in Single Nucleotide Polymorphism Trio Data with SNPtrio.
     Human Mutation, 28(12): 1225-35.
212. Scharpf RB, Ting JC, Pevsner J, Ruczinski I (2007).
     SNPchip: R Classes and Methods for SNP Array Data.
     Bioinformatics, 23(5): 627-8.
213. Visvanathan K, Crum RM, Strickland PT, You X, Ruczinski I, Berndt S, Alberg AJ, Hoffman SC, Comstock GW, Bell DA, Helzlsouer KJ (2007).
     Alcohol Dehydrogenase Genetic Polymorphisms, Low-to-moderate Alcohol Consumption and Risk of Breast Cancer.
     Alcoholism: Clinical and Experimental Research, 31(3): 467-76.
214. Jorgensen J, Visvanathan K, Ruczinski I, Thuita L, Helzlsouer KJ (2007).
     Breast Cancer Risk is Not Associated with Polymorphic Forms of Xeroderma Pigmentosum Genes in a Cohort of Women from Washington County, Maryland.
     Breast Cancer Research and Treatment, 101(1):65-71.
215. Dai J, Ruczinski I, LeBlanc M, Kooperberg C (2006).
     Imputation Methods to Improve Inference in SNP Association Studies.
     Genetic Epidemiology, 30(8): 690-702.
216. Ruczinski I, Sosnick TR, Plaxco KW (2006).
     Methods for the Accurate Estimation of Confidence Intervals on Protein Folding Φ Values.
     Protein Science, 15(10): 2257-64.
217. Brown EE, Fallin D, Ruczinski I, Hutchinson A, Staats B, Vitale F, Lauria C, Serraino D, Rezza G, Mbisa G, Whitby D, Messina A, Goedert JJ, Chanock SJ (2006).
     Associations of Classic Kaposi Sarcoma with Common Variants in Genes that Modulate Host Immunity.
     Cancer Epidemiology, Biomarkers and Prevention, 15(5): 926-34.
218. De Los Rios MA, Muralidhara BK, Wildes D, Sosnick TR, Marqusee S, Wittung-Stafshede P, Plaxco KW, Ruczinski I (2006).
     On the Precision of Experimentally Determined Protein Folding Rates and Φ-Values.
     Protein Science, 15(3): 553-6.
219. Ting JC, Ye Y, Thomas GH, Ruczinski I, Pevsner J (2006).
     Analysis and Visualization of Chromosomal Abnormalities in SNP Data with SNPscan.
     BMC Bioinformatics, 7(1):25.
220. Brewster AM, Jorgensen TJ, Ruczinski I, Huang HY, Hoffman S, Thuita L, Newschaffer C, Lunn RM, Bell D, Helzlsouer KJ (2006).
     Polymorphisms of the DNA Repair Genes XPD (Lys751Gln) and XRCC1 (Arg399Gln and Arg194Trp): Relationship to Breast Cancer Risk and Familial Predisposition to Breast Cancer.
     Breast Cancer Research and Treatment, 95(1): 73-80.
221. Mao R, Wang X, Spitznagel Jr EL, Frelin LP, Ting JC, Ding H, Kim J, Ruczinski I, Downey TJ, Pevsner J (2005).
     Primary and Secondary Transcriptional Effects in the Developing Human Down Syndrome Brain and Heart.
     Genome Biology, 6(13): R107.
222. McCarney ER, Werner JH, Bernstein SL, Ruczinski I, Makarov DE, Goodwin PM, Plaxco KW (2005).
     Site-specific Dimensions Across a Highly Denatured Protein; A Single Molecule Study.
     Journal of Molecular Biology, 352(3): 672-82.
223. Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT, Hedberg L, Horng JC, Bona D, Miller EJ, Vallee-Belisle A, Main ER, Bemporad F, Qiu L, Teilum K, Vu ND, Edwards AM, Ruczinski I, Poulsen FM, Kragelund BB, Michnick SW, Chiti F, Bai Y, Hagen SJ, Serrano L, Oliveberg M, Raleigh DP, Wittung-Stafshede P, Radford SE, Jackson SE, Sosnick TR, Marqusee S, Davidson AR, Plaxco KW (2005).
     Protein Folding: Defining a Standard Set of Experimental Conditions and a Preliminary Kinetic Data Set of Two-State Proteins.
     Protein Science, 14(3): 602-16.
224. Kooperberg C, Ruczinski I (2005).
     Identifying Interacting SNPs using Monte Carlo Logic Regression.
     Genetic Epidemiology, 28(2): 157-70.
225. Ruczinski I, Kooperberg C, LeBlanc M (2004).
     Exploring Interactions in High Dimensional Genomic Data: An Overview of Logic Regression, With Applications.
     Journal of Multivariate Analysis, 90: 178-95.
226. Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW (2004).
     Random-Coil Behavior and the Dimensions of Chemically Unfolded Proteins.
     Proceedings of the National Academy of Sciences, 101(34): 12491-6.
227. Ruczinski I, Kooperberg C, LeBlanc M (2003).
     Logic Regression - Methods and Software.
     Nonlinear Estimation and Classification, Lecture Notes in Statistics, Vol 171, Springer-Verlag, 333-44.
228. Ruczinski I, Kooperberg C, LeBlanc M (2003).
     Logic Regression.
     Journal of Computational and Graphical Statistics, 12(3): 475-511.
229. Bonneau R, Ruczinski I, Tsai J, Baker D (2002).
     Contact Order and Ab Initio Protein Structure Prediction.
     Protein Science, 11(8): 1937-44.
230. Ruczinski I, Kooperberg C, Bonneau R, Baker D (2002).
     Distributions of Beta Sheets in Proteins with Application to Structure Prediction.
     Proteins: Structure, Function and Genetics, 48: 85-97.
231. Larson S, Ruczinski I, Davidson AR, Baker D, Plaxco KW (2002).
     Residues Participating in the Folding Nucleus do Not Exhibit Preferential Evolutionary Conservation.
     Journal of Molecular Biology, 316: 225-33.
232. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss C, Baker D (2001).
     Rosetta in CASP4: Progress in Ab Initio Protein Structure Prediction.
     Proteins: Structure, Function and Genetics, 45(S5): 119-26.
233. Kooperberg C, Ruczinski I, LeBlanc M, Hsu L (2001).
     Sequence Analysis using Logic Regression.
     Genetic Epidemiology, 21 (S1): 626-31.
234. Bonneau R, Tsai J, Ruczinski I, Baker D (2001).
     Functional Inferences from Blind Ab Initio Protein Structure Predictions.
     Journal of Structural Biology, 134(2-3): 186-90.
235. Plaxco KW, Simons KT, Ruczinski I, Baker D (2000).
     Topology, Stability, Sequence, and Length: Defining the Determinants of Two-State Protein Folding Kinetics.
     Biochemistry, 39(37): 11177-83.
236. Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D (2000).
     Evolutionary Conservation in Protein Folding Kinetics.
     Journal of Molecular Biology, 298: 303-12.
237. Simons KT, Bonneau R, Ruczinski I, Baker D (1999).
     Ab Initio Protein Structure Prediction of CASP III Targets Using ROSETTA.
     Proteins: Structure, Function and Genetics, 37 (S3): 171-76.
238. Riddle DS, Grantcharova VP, Santiago J, Alm E, Ruczinski I, Baker D (1999).
     Experiment and Theory Highlight Role of Native State Topology in SH3 Folding.
     Nature Structural Biology, 6: 1016-24.
239. Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D (1999).
     Improved Recognition of Native-like Protein Structures using a Combination of Sequence-dependent and Sequence-independent Features of Proteins.
     Proteins: Structure, Function and Genetics, 34(1): 82-95.

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