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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Scharpf RB, Ting JC, Pevsner J, Ruczinski I (2007).
SNPchip: R Classes and Methods for SNP Array Data.
Bioinformatics, 23(5): 627-8.
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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.
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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.
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Dai J, Ruczinski I, LeBlanc M, Kooperberg C (2006).
Imputation Methods to Improve Inference in SNP Association Studies.
Genetic Epidemiology, 30(8): 690-702.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Kooperberg C, Ruczinski I (2005).
Identifying Interacting SNPs using Monte Carlo Logic Regression.
Genetic Epidemiology, 28(2): 157-70.
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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.
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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.
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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.
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Ruczinski I, Kooperberg C, LeBlanc M (2003).
Logic Regression.
Journal of Computational and Graphical Statistics, 12(3): 475-511.
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Bonneau R, Ruczinski I, Tsai J, Baker D (2002).
Contact Order and Ab Initio Protein Structure Prediction.
Protein Science, 11(8): 1937-44.
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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.
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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.
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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.
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Kooperberg C, Ruczinski I, LeBlanc M, Hsu L (2001).
Sequence Analysis using Logic Regression.
Genetic Epidemiology, 21 (S1): 626-31.
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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.
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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.
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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.
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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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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.
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Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D (1999).
Improved Recognition of Native-like Protein Structures using a Combination of Sequence-dependent and Sequence-independent Features of Proteins.
Proteins: Structure, Function and Genetics, 34(1): 82-95.
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