Click here for all PubMed abstracts.

Published Journal Articles [ 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 and earlier ]

Forthcoming Journal Articles and Book Chapters

• Schwender H, Beaty TH, Marazita ML, Ruczinski I (2011).
  Testing SNPs in case-parent trio data based on exact analytic parameter estimations.
  Biometrics (to appear).

• Wang H, Wu T, Hetmanski JB, Ruczinski I, Schwender H, Liang KY, Murray T, Fallin MD, Redett RA, Raymond G, Jin SC, Wu-Chou YH, Chen PK, Yeow V, Park BY, Chong SS, Cheah F, Jee SH, Ingersoll RG, Jabs EW, Scott AF, Beaty TH (2011).
  The FGF & FGFR gene family and risk of cleft lip with/without cleft palate.
  The Cleft Palate-Craniofacial Journal (to appear).

• Zhang TX, Beaty TH, Ruczinski I (2011).
  Candidate pathway based analysis for cleft lip with or without cleft palate.
  Statistical Applications in Genetics and Molecular Biology (to appear).

Published Journal Articles and Book Chapters

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• Schwender H, Ruczinski I, Ickstadt K (2011).
  Testing SNPs and sets of SNPs for importance in association studies.
  Biostatistics 12(1): 18-32.

• 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.

• Louis TA, Li Q, Carvalho B, Fallin MD, Irizarry RA, Louis TA Ruczinski I (2010).
  Association tests that accommodate genotyping errors [ with discussion ]
  Bayesian Statistics 9: 393-420

• 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.

• Schwender H, Ruczinski I (2010).
  Logic regression and extensions.
  Advances in Genetics 72: 25-45.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• Scharpf RB, Ruczinski I (2010).
  R Classes and Methods for SNP Array Data.
  Methods in Molecular Biology 593: 67-79.

• 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.

• 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.

• 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.

• 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.

• 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.

• Ruczinski I, Kooperberg C (2009).
  Logic Regression.
  Encyclopedia of Medical Decision Making, Sage Publications, 678-81.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• Scharpf RB, Ting JC, Pevsner J, Ruczinski I (2007).
  SNPchip: R Classes and Methods for SNP Array Data.
  Bioinformatics, 23(5): 627-8.

• 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.

• 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.

• Dai J, Ruczinski I, LeBlanc M, Kooperberg C (2006).
  Imputation Methods to Improve Inference in SNP Association Studies.
  Genetic Epidemiology, 30(8): 690-702.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• Kooperberg C, Ruczinski I (2005).
  Identifying Interacting SNPs using Monte Carlo Logic Regression.
  Genetic Epidemiology, 28(2): 157-70.

• 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.

• 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.

• 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.

• Ruczinski I, Kooperberg C, LeBlanc M (2003).
  Logic Regression.
  Journal of Computational and Graphical Statistics, 12(3): 475-511.

• Bonneau R, Ruczinski I, Tsai J, Baker D (2002).
  Contact Order and Ab Initio Protein Structure Prediction.
  Protein Science, 11(8): 1937-44.

• 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.

• 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.

• 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.

• Kooperberg C, Ruczinski I, LeBlanc M, Hsu L (2001).
  Sequence Analysis using Logic Regression.
  Genetic Epidemiology, 21 (S1): 626-31.

• 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.

• 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.

• 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.

• 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.

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