Ingo's Publications

Publications

Click here for all PubMed abstracts. Supplementary material for some of the manuscripts is here.

Published Journal Articles [ 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 and earlier ]

Forthcoming Journal Articles and Book Chapters

Louis TA, Ruczinski I (2009).
Efficient evaluation of ranking procedures when the number of units is large, with application to SNP identification.
Biometrical Journal (to appear).

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 (2009).
A genome-wide association study on african-ancestry populations identifies novel asthma genes.
Journal of Allergy and Clinical Immunology (to appear).

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 (2009).
Common variants in DENND1B associate with pediatric asthma.
New England Journal of Medicine (to appear).

Scharpf RB, Ruczinski I (2009).
R Classes and Methods for SNP Array Data.
Bioinformatics in Clinical OMICs Research, Humana Press (to appear).

Ruczinski I, Kooperberg C (2009).
Logic Regression.
Encyclopedia of Medical Decision Making (to appear).

Published Journal Articles and Book Chapters

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, Li\'egeois 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.

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): 553-63.

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.

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.

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.

	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, Li\'egeois 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.
	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): 553-63.
	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.
	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.
	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.