Publications

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[ 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 and earlier ]


    2014

  1. 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 (to appear).
  2. 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 (to appear).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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, Sætrom 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.
  11. 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

  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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

  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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

  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. Schwender H, Ruczinski I, Ickstadt K (2011).
    Testing SNPs and sets of SNPs for importance in association studies.
    Biostatistics 12(1): 18-32.
  63. 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

  64. 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
  65. 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.
  66. Schwender H, Ruczinski I (2010).
    Logic regression and its extensions.
    Advances in Genetics 72: 25-45.
  67. Scientists for Reproducible Research (2010).
    Disclose all data in publications.
    Nature 467: 401.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. Scharpf RB, Ruczinski I (2010).
    R classes and methods for SNP array data.
    Methods in Molecular Biology 593: 67-79.
  79. 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

  80. 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.
  81. 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.
  82. 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.
  83. 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.
  84. Ruczinski I, Kooperberg C (2009).
    Logic Regression.
    Encyclopedia of Medical Decision Making, Sage Publications, 678-81.
  85. 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.
  86. 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.
  87. 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.
  88. 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.
  89. 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

  90. 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.
  91. 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.
  92. 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.
  93. 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.
  94. 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.
  95. 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

  96. 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.
  97. Scharpf RB, Ting JC, Pevsner J, Ruczinski I (2007).
    SNPchip: R Classes and Methods for SNP Array Data.
    Bioinformatics, 23(5): 627-8.
  98. 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.
  99. 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.
  100. Dai J, Ruczinski I, LeBlanc M, Kooperberg C (2006).
    Imputation Methods to Improve Inference in SNP Association Studies.
    Genetic Epidemiology, 30(8): 690-702.
  101. 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.
  102. 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.
  103. 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.
  104. 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.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. Kooperberg C, Ruczinski I (2005).
    Identifying Interacting SNPs using Monte Carlo Logic Regression.
    Genetic Epidemiology, 28(2): 157-70.
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    Exploring Interactions in High Dimensional Genomic Data: An Overview of Logic Regression, With Applications.
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    Random-Coil Behavior and the Dimensions of Chemically Unfolded Proteins.
    Proceedings of the National Academy of Sciences, 101(34): 12491-6.
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    Journal of Computational and Graphical Statistics, 12(3): 475-511.
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    Protein Science, 11(8): 1937-44.
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    Distributions of Beta Sheets in Proteins with Application to Structure Prediction.
    Proteins: Structure, Function and Genetics, 48: 85-97.
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    Journal of Molecular Biology, 316: 225-33.
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    Rosetta in CASP4: Progress in Ab Initio Protein Structure Prediction.
    Proteins: Structure, Function and Genetics, 45(S5): 119-26.
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    Genetic Epidemiology, 21 (S1): 626-31.
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    Biochemistry, 39(37): 11177-83.
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    Journal of Molecular Biology, 298: 303-12.
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    Proteins: Structure, Function and Genetics, 37 (S3): 171-76.
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    Nature Structural Biology, 6: 1016-24.
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    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.