I. Ruczinski

Holger Schwender, Ingo Ruczinski, Alan F. Scott, 2013, The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association.

A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts.

T. Beaty, R. Scharpf, I. Ruczinski, 2015, Birth defects research. Part A, Clinical and molecular teratology.

Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.

Ingo Ruczinski, Jonathan Pevsner, Giovanni Parmigiani, 2008, The annals of applied statistics.

Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program

Chad A. Cowan, K. Frazer, J. Knowles, 2020, Stem cell research.

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations

E. Boerwinkle, R. Scharpf, A. Chakravarti, 2014, BMC Genetics.

Assessing DNA copy numbers in large scale studies using genomic arrays

R. Scharpf, I. Ruczinski, 2010 .

Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and ϕ values

I. Ruczinski, K. Plaxco, 2009, Proteins.

Cross-platform Comparison of Two Pancreatic Cancer Phenotypes

G. Parmigiani, L. Cope, R. Scharpf, 2010, Cancer informatics.

Genome-wide association study of asthma in individuals of African ancestry reveals novel asthma susceptibility loci

Zachary A. Szpiech, Zhaohui S. Qin, Francisco M. De La Vega, 2017, bioRxiv.

Protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study

M. Obeidat, Y. Bossé, T. Beaty, 2020, Thorax.

The protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study

M. Obeidat, Y. Bossé, T. Beaty, 2019, bioRxiv.

Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole genome and RNA sequencing.

Andrew D. Johnson, J. Leek, A. Battle, 2020, Blood.

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Ivana V. Yang, Zhaohui S. Qin, Andrew D. Johnson, 2018, Nature Communications.

Multiple loci associated with indices of renal function and chronic kidney disease

Yurii S. Aulchenko, Ingo Ruczinski, Qiong Yang, 2009, Nature Genetics.

Targeted deep sequencing of the PEAR1 locus for platelet aggregation in European and African American families

I. Ruczinski, M. Taub, L. Becker, 2019, Platelets.

Nonmelanoma skin cancer and risk for subsequent malignancy.

I. Ruczinski, A. Alberg, K. Helzlsouer, 2008, Journal of the National Cancer Institute.

Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses.

Priya D. Duggal, A. Mammen, I. Ruczinski, 2022, Immunity.

Alcohol dehydrogenase genetic polymorphisms, low-to-moderate alcohol consumption, and risk of breast cancer.

I. Ruczinski, R. Crum, S. Berndt, 2007, Alcoholism, clinical and experimental research.

Efficient Evaluation of Ranking Procedures when the Number of Units is Large, with Application to SNP Identification

T. Louis, I. Ruczinski, 2010, Biometrical journal. Biometrische Zeitschrift.

e-Control Study Matched on Cigarette Smoking

I. Ruczinski, Y. Shugart, A. Alberg, 2010 .

Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios.

T. Beaty, D. Cutler, M. Epstein, 2020, American journal of human genetics.

A top scoring pairs classifier for recent HIV infections

I. Ruczinski, O. Laeyendecker, H. B. Larman, 2021, Statistics in medicine.

The Association between Skin Characteristics and Skin Cancer Prevention Behaviors

I. Ruczinski, A. Alberg, N. Liégeois, 2009, Cancer Epidemiology, Biomarkers & Prevention.

X- linked markers in DMD associated with oral clefts

R. T. Lie, T. Beaty, Hong Wang, 2013 .

X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts.

R. T. Lie, T. Beaty, I. Ruczinski, 2013, European journal of oral sciences.

Identification of interactions of binary variables associated with survival time using survivalFS

Holger Schwender, Ingo Ruczinski, Jan G Hengstler, 2019, Archives of Toxicology.

Erratum: Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci (American Journal of Human Genetics (2012) 90 (410-425))

Suzette J. Bielinski, Christian Gieger, Ingo Ruczinski, 2012 .

Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort

Ingo Ruczinski, Edwin K Silverman, Douglas Curran-Everett, 2016, Genetic epidemiology.

Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies

Ingo Ruczinski, Giovanni Parmigiani, Cristian Pattaro, 2008, BMC Genomics.

A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4

Holger Schwender, Ingo Ruczinski, Jacqueline B Hetmanski, 2010, Nature Genetics.

Detecting Gene-Environment Interaction for Maternal Exposures Using Case-Parent Trios Ascertained Through a Case With Non-Syndromic Orofacial Cleft

T. Beaty, I. Ruczinski, M. Taub, 2021, Frontiers in Cell and Developmental Biology.

Pleiotropy method identifies genetic overlap between orofacial clefts at multiple loci from GWAS of multi-ethnic trios

T. Beaty, I. Ruczinski, M. Taub, 2020, medRxiv.

Evidence for SNP‐SNP interaction identified through targeted sequencing of cleft case‐parent trios

T. Beaty, D. Koboldt, I. Ruczinski, 2017, Genetic epidemiology.

Genome wide study of maternal and parent‐of‐origin effects on the etiology of orofacial clefts

R. T. Lie, T. Beaty, I. Ruczinski, 2012, American journal of medical genetics. Part A.

Web-based Supplementary Materials for ” Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation ” by

T. Beaty, I. Ruczinski, M. Taub, 2011 .

A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA 4

Hong Wang, Holger Schwender, Ingo Ruczinski, 2010 .

Detection of SNP‐SNP interactions in trios of parents with schizophrenic children

Ingo Ruczinski, Thomas A Louis, Kung-Yee Liang, 2010, Genetic epidemiology.

Improved Analysis of Phage ImmunoPrecipitation Sequencing (PhIP-Seq) Data Using a Z-score Algorithm

Ingo Ruczinski, Uri Laserson, Divya Mohan, 2018, bioRxiv.

Evidence for gene-environment interaction in a genome wide study of isolated, non-syndromic cleft palate

Holger Schwender, Ingo Ruczinski, Alan F. Scott, 2011 .

Whole exome association of rare deletions in multiplex oral cleft families

Ingo Ruczinski, Alexandre Bureau, Hasan Albacha-Hejazi, 2017, Genetic epidemiology.

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk

Holger Schwender, Ingo Ruczinski, Alan F Scott, 2014, BMC Genetics.

Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci.

Ingo Ruczinski, Qunyuan Zhang, Ferdouse Begum, 2015, American journal of human genetics.

Metabolomic profiling of urine: response to a randomised, controlled feeding study of select fruits and vegetables, and application to an observational study

Ingo Ruczinski, Johanna W Lampe, Damon H May, 2013, British Journal of Nutrition.

Hypothesis-driven candidate gene association studies: practical design and analytical considerations.

Ingo Ruczinski, Anthony J Alberg, Yin Yao Shugart, 2009, American journal of epidemiology.

Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal

Ingo Ruczinski, Keith P. West, James D. Yager, 2015, PloS one.

Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene.

Ingo Ruczinski, Christoph Lange, James W Baurley, 2009, American journal of human genetics.

Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.

Xiaofeng Zhu, Ingo Ruczinski, Swapan Mallick, 2011, American journal of human genetics.

COPDGene® 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease.

Nicola A Hanania, Jennifer G. Dy, Raúl San José Estépar, 2019, Chronic obstructive pulmonary diseases.

Examining Markers in 8q24 to Explain Differences in Evidence for Association With Cleft Lip With/Without Cleft Palate Between Asians and Europeans

Holger Schwender, Ingo Ruczinski, Tao Wu, 2012, Genetic epidemiology.

Evidence of gene–environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate

Ingo Ruczinski, Alan F. Scott, Terri H. Beaty, 2010, Human Genetics.

Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate

Ingo Ruczinski, Terri H. Beaty, T. Beaty, 2012, Statistical applications in genetics and molecular biology.

ciferous Vegetable Intake and Lung Cancer Risk : A Nested B & P e-Control Study Matched on Cigarette Smoking

I. Ruczinski, Y. Shugart, A. Alberg, 2010 .

Genome-Wide Association Study Identification of Novel Loci Associated with Airway Responsiveness in Chronic Obstructive Pulmonary Disease.

Y. Bossé, D. Postma, P. Paré, 2014, American journal of respiratory cell and molecular biology.

A genome-wide association study on African-ancestry populations for asthma.

L. Liang, G. Abecasis, H. Hakonarson, 2010, The Journal of allergy and clinical immunology.

Methods for the accurate estimation of confidence intervals on protein folding φ‐values

I. Ruczinski, K. Plaxco, T. Sosnick, 2006, Protein science : a publication of the Protein Society.

Detectable clonal mosaicism from birth to old age and its relationship to cancer

Ingo Ruczinski, Li-e Wang, William L. Lowe, 2012, Nature Genetics.

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Ryan D. Hernandez, May E. Montasser, Min A. Jhun, 2018, Nature Communications.

Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER

R. Scharpf, I. Ruczinski, H. B. Larman, 2022, Bioinform..

Whole exome sequencing analysis in severe chronic obstructive pulmonary disease

Michael Bamshad, Ingo Ruczinski, Christoph Lange, 2018, Human molecular genetics.

Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment

R. Brookmeyer, I. Ruczinski, C. Morrison, 2022, BMC Infectious Diseases.

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Ryan D. Hernandez, S. Salzberg, Z. Qin, 2019, Nature Communications.

TSLP polymorphisms are associated with asthma in a sex‐specific fashion

I. Ruczinski, E. Israel, G. O'Connor, 2010, Allergy.

Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

Andrew D. Johnson, May E. Montasser, Nicholette D. Palmer, 2022, Nature Genetics.

Fast detection of de novo copy number variants from SNP arrays for case-parent trios

T. Beaty, R. Scharpf, I. Ruczinski, 2012, BMC Bioinformatics.

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

Zachary A. Szpiech, Zhaohui S. Qin, Francisco M. De La Vega, 2016, Nature Communications.

Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

Andrew D. Johnson, Benjamin D. Heavner, Michael E. Hall, 2022, Nature Communications.

Genome sequencing unveils a regulatory landscape of platelet reactivity

Benjamin D. Heavner, May E. Montasser, Nicholette D. Palmer, 2019, Nature Communications.

Detecting Significant Changes in Protein Abundance.

Ingo Ruczinski, Kai Kammers, R. Cole, 2015, EuPA open proteomics.

Two complex genotypes relevant to the kynurenine pathway and melanotropin function show association with schizophrenia and bipolar disorder

Peter N. Murakami, I. Ruczinski, R. Ross, 2009, Schizophrenia Research.

A Random Forest Classifier Uses Antibody Responses to Plasmodium Antigens to Reveal Candidate Biomarkers of the Intensity and Timing of Past Exposure to Plasmodium falciparum

T. Louis, I. Ruczinski, A. Wesolowski, 2022, bioRxiv.

Confirming genes influencing risk to cleft lip with/without cleft palate in a case–parent trio study

I. Ruczinski, M. Taub, A. F. Scott, 2013, Human Genetics.

Structural variation across 138,134 samples in the TOPMed consortium

Mark J. P. Chaisson, Nicholette D. Palmer, M. Fornage, 2023, bioRxiv.

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children with asthma.

Ivana V. Yang, Andrew D. Johnson, Ryan D. Hernandez, 2019, Chest.

Detecting Disease Variants in Case‐Parent Trio Studies Using the Bioconductor Software Package trio

Holger Schwender, Ingo Ruczinski, Qing Li, 2014, Genetic epidemiology.

Fetal polymorphisms at the ABCB1-transporter gene locus are associated with susceptibility to non-syndromic oral cleft malformations

T. Beaty, I. Ruczinski, S. Chong, 2013, European Journal of Human Genetics.

Rapid Testing of SNPs and Gene–Environment Interactions in Case–Parent Trio Data Based on Exact Analytic Parameter Estimation

Holger Schwender, Ingo Ruczinski, Margaret A Taub, 2012, Biometrics.

BMP4 Was Associated with NSCL/P in an Asian Population

T. Beaty, I. Ruczinski, E. Jabs, 2012, PloS one.

ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population.

T. Beaty, I. Ruczinski, E. Jabs, 2012, Chinese medical journal.

Detection of de novo copy number deletions from targeted sequencing of trios

Ingo Ruczinski, Jack M. Fu, Elizabeth J. Leslie, 2018, bioRxiv.

Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity

T. Beaty, I. Ruczinski, Liangdan Sun, 2017, Nature Communications.

Associations of Classic Kaposi Sarcoma with Common Variants in Genes that Modulate Host Immunity

J. Goedert, S. Chanock, D. Fallin, 2006, Cancer Epidemiology Biomarkers & Prevention.

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

Andrew D. Johnson, Ryan D. Hernandez, May E. Montasser, 2022, Nature Genetics.

Differential parental transmission of markers in RUNX2 among cleft case‐parent trios from four populations

T. Beaty, I. Ruczinski, E. Jabs, 2008, Genetic epidemiology.

Genome‐wide association study of schizophrenia in Ashkenazi Jews

Vladimir Vacic, Ingo Ruczinski, Mehdi Pirooznia, 2015, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

Lack of Association Between the Trp 719 Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control

Alexander F. Wilson, A. F. Wilson, D. Absher, 2017 .

Lack of association between the Trp719Arg polymorphism in kinesin-like protein-6 and coronary artery disease in 19 case-control studies.

Alexander F. Wilson, A. F. Wilson, Benjamin J. Wright, 2010, Journal of the American College of Cardiology.

P Lack of Association Between the Trp 719 Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies

Alexander F. Wilson, A. F. Wilson, D. Absher, 2010 .

Recombination rates in admixed individuals identified by ancestry-based inference

Ingo Ruczinski, John Novembre, Sharon L R Kardia, 2011, Nature Genetics.

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World

I. Ruczinski, L. Becker, D. Becker, 2017, bioRxiv.

A Common Variant in the CDKN2B Gene on Chromosome 9p21 Protects Against Coronary Artery Disease in Americans of African Ancestry

W. Kraus, I. Ruczinski, A. Quyyumi, 2011, Journal of Human Genetics.

A Common Variant in the CDKN 2 B Gene on Chromosome 9 p 21 Protects Against Coronary Artery Disease in Americans of African Ancestry : CDKN 2 B Gene Variant and CAD in African Americans

W. Kraus, I. Ruczinski, A. Quyyumi, 2022 .

DNA repair gene variants in relation to overall cancer risk: a population-based study.

I. Ruczinski, Y. Shugart, A. Alberg, 2013, Carcinogenesis.

A population-based study of DNA repair gene variants in relation to non-melanoma skin cancer as a marker of a cancer-prone phenotype.

I. Ruczinski, Y. Shugart, A. Alberg, 2012, Carcinogenesis.

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives

Ingo Ruczinski, Alexandre Bureau, Hasan Albacha-Hejazi, 2014, Bioinform..

Performance assessment of copy number microarray platforms using a spike-in experiment

Ingo Ruczinski, Jonathan Pevsner, Rafael A. Irizarry, 2011, Bioinform..

Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program.

Sina A. Gharib, M. Fornage, S. Redline, 2022, American journal of human genetics.

Meta-analysis of Genome-wide Association Studies of Asthma In Ethnically Diverse North American Populations

Ryan D. Hernandez, Christopher R. Gignoux, L. Liang, 2011, Nature Genetics.

HLA typing using genome wide data reveals susceptibility types for infections in a psychiatric disease enriched sample

I. Ruczinski, K. Conneely, D. Avramopoulos, 2018, Brain, Behavior, and Immunity.

Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed

Ivana V. Yang, Benjamin D. Heavner, Nicholette D. Palmer, 2022, Cell genomics.

Evolutionary conservation in protein folding kinetics.

Stefan M. Larson, D Baker, D. Baker, 2000, Journal of molecular biology.

Distinct Loci in the CHRNA5/CHRNA3/CHRNB4 Gene Cluster Are Associated With Onset of Regular Smoking

Sarah H. Stephens, Sarah M. Hartz, M. Jarvelin, 2013, Genetic epidemiology.

A HIDDEN MARKOV MODEL FOR JOINT ESTIMATION OF GENOTYPE AND COPY NUMBER IN HIGH-THROUGHPUT SNP CHIPS

Ingo Ruczinski, Giovanni Parmigiani, Robert B. Scharpf, 2007 .

Hepcidin and iron status among pregnant women in Bangladesh.

I. Ruczinski, A. Nath, R. Semba, 2008, Asia Pacific journal of clinical nutrition.

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Ivana V. Yang, Sebastian M. Armasu, Andrew D. Johnson, 2020, Nature.

HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success

G. Toit, I. Ruczinski, J. Paschall, 2022, Frontiers in Immunology.

Polymorphisms of the DNA repair genes XPD (Lys751Gln) and XRCC1 (Arg399Gln and Arg194Trp): relationship to breast cancer risk and familial predisposition to breast cancer

I. Ruczinski, D. Bell, K. Helzlsouer, 2005, Breast Cancer Research and Treatment.

An IL-13 Promoter Polymorphism Associated with Liver Fibrosis in Patients with Schistosoma japonicum

T. Beaty, I. Ruczinski, K. Barnes, 2015, PloS one.

Coding de novo mutations identified by WGS reveal novel orofacial cleft genes

T. Beaty, D. Cutler, M. Epstein, 2020, bioRxiv.

Incorporating Genotype Uncertainties Into the Genotypic TDT for Main Effects and Gene‐Environment Interactions

Holger Schwender, Ingo Ruczinski, Thomas A Louis, 2012, Genetic epidemiology.

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS

Ingo Ruczinski, Rafael A. Irizarry, Robert B. Scharpf, 2009 .

Single nucleotide polymorphisms in obesity-related genes and all-cause and cause-specific mortality: a prospective cohort study

I. Ruczinski, K. Helzlsouer, P. Strickland, 2009, BMC Medical Genetics.

Amerind ancestry predicts the impact of FADS genetic variation on omega-3 PUFA deficiency, cardiometabolic and inflammatory risk in Hispanic populations

I. Ruczinski, L. Mandarino, S. Rich, 2021, medRxiv.

Association of HLA-DRB1*09:01 with tIgE levels among African ancestry individuals with asthma.

T. Beaty, E. Bleecker, D. Nicolae, 2020, The Journal of allergy and clinical immunology.

Variants of DENND1B associated with asthma in children.

Ingo Ruczinski, James Flory, Terri H Beaty, 2010, The New England journal of medicine.

Imputation Methods to Improve Inference in Snp Association Studies

Ingo Ruczinski, Michael LeBlanc, James Y Dai, 2022 .

African and non‐African admixture components in African Americans and an African Caribbean population

T. Beaty, I. Ruczinski, K. Barnes, 2010, Genetic epidemiology.

Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum

I. Ruczinski, K. Barnes, R. Mathias, 2021, Allergy.

Targeted deep sequencing identifies rare loss-of-function variants in IFNGR1 for risk of atopic dermatitis complicated by eczema herpeticum.

T. Beaty, I. Ruczinski, K. Barnes, 2015, The Journal of allergy and clinical immunology.

Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation.

Kevin W Plaxco, David Baker, Ingo Ruczinski, 2002, Journal of molecular biology.

HIV Antibody Profiles in HIV Controllers and Persons With Treatment-Induced Viral Suppression

Richard D Moore, I. Ruczinski, C. Morrison, 2021, Frontiers in Immunology.

Comprehensive Profiling of HIV Antibody Evolution

S. Elledge, R. Brookmeyer, I. Ruczinski, 2019, Cell reports.

Replicated methylation changes associated with eczema herpeticum and allergic response

T. Beaty, I. Ruczinski, Jinshui Fan, 2019, Clinical Epigenetics.

Genome-wide study identifies two loci associated with lung function decline in mild to moderate COPD

Toshiko Tanaka, L. Ferrucci, D. Postma, 2012, Human Genetics.

Identification of a specific intronic PEAR1 gene variant associated with greater platelet aggregability and protein expression.

Andrew D. Johnson, A. Gylfason, U. Thorsteinsdóttir, 2011, Blood.

Rare loss of function variants in candidate genes and risk of colorectal cancer

Taylor J. Maxwell, Jennifer G. Robinson, Andrew J. Sanford, 2018, Human Genetics.

A community-based study of nucleotide excision repair polymorphisms in relation to risk of non-melanoma skin cancer

I. Ruczinski, Y. Shugart, A. Alberg, 2012, The Journal of investigative dermatology.

Infection and Inflammation in Schizophrenia and Bipolar Disorder: A Genome Wide Study for Interactions with Genetic Variation

R. Yolken, I. Ruczinski, D. Avramopoulos, 2015, PloS one.

Oesophageal squamous cell carcinoma in high-risk Chinese populations: Possible role for vascular epithelial growth factor A.

T. Beaty, N. Hu, I. Ruczinski, 2014, European journal of cancer.

Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios

T. Beaty, I. Ruczinski, M. Taub, 2021, PLoS genetics.

The impact of FADS genetic variants on ω6 polyunsaturated fatty acid metabolism in African Americans

I. Ruczinski, L. Becker, K. Barnes, 2011, BMC Genetics.

Logic Regression — Methods and Software

Ingo Ruczinski, Charles Kooperberg, Michael LeBlanc, 2003 .

Increased genetic vulnerability to smoking at CHRNA5 in early-onset smokers.

Sarah H. Stephens, Sarah M. Hartz, M. Jarvelin, 2012, Archives of general psychiatry.

Polymorphisms Influencing Prostate-Specific Antigen Concentration May Bias Genome-Wide Association Studies on Prostate Cancer

I. Ruczinski, Jianfeng Xu, W. Isaacs, 2014, Cancer Epidemiology, Biomarkers & Prevention.

HLA alleles and sustained peanut consumption promote IgG4 responses in subjects protected from peanut allergy

I. Ruczinski, K. Barnes, R. Mathias, 2022, The Journal of clinical investigation.

Protein folding: Defining a “standard” set of experimental conditions and a preliminary kinetic data set of two‐state proteins

Kevin W Plaxco, Ingo Ruczinski, Fabrizio Chiti, 2005, Protein science : a publication of the Protein Society.

Title Testing of Snps and Snp Interactions in Case-parent Trio Studies

I. Ruczinski, M. Taub, H. Schwender, 2013 .

Uncovering the DNA methylation landscape in key regulatory regions within the FADS cluster

I. Ruczinski, C. Langefeld, G. Hawkins, 2017, PloS one.

Detection of rare disease variants in extended pedigrees using RVS

Ingo Ruczinski, Alexandre Bureau, Jack M. Fu, 2018, Bioinform..

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality.

S. Elledge, A. Casadevall, J. Weiner, 2021, The Journal of clinical investigation.

Breast Cancer Risk is not Associated with Polymorphic Forms of Xeroderma Pigmentosum Genes in a Cohort of Women from Washington County, Maryland

I. Ruczinski, K. Helzlsouer, T. Jorgensen, 2006, Breast Cancer Research and Treatment.

A population-based study of hedgehog pathway gene variants in relation to the dual risk of basal cell carcinoma plus another cancer.

I. Ruczinski, A. Alberg, B. Kessing, 2012, Cancer epidemiology.

Hemizygous Deletion on Chromosome 3p26.1 Is Associated with Heavy Smoking among African American Subjects in the COPDGene Study

J. Hokanson, T. Beaty, E. Silverman, 2016, PloS one.

A flexible and nearly optimal sequential testing approach to randomized testing: QUICK‐STOP

Ingo Ruczinski, Christoph Lange, Edwin K Silverman, 2019, Genetic epidemiology.

Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations

I. Ruczinski, L. Mandarino, S. Rich, 2021, Communications Biology.

Prospective clinical trial examining the impact of genetic variation in FADS1 on the metabolism of linoleic acid- and ɣ-linolenic acid-containing botanical oils.

I. Ruczinski, R. Mathias, P. Ivester, 2020, The American journal of clinical nutrition.

Tissue-specific impact of FADS cluster variants on FADS1 and FADS2 gene expression

I. Ruczinski, R. Mathias, F. Chilton, 2018, PloS one.

Impact of methods used to express levels of circulating fatty acids on the degree and direction of associations with blood lipids in humans

I. Ruczinski, B. Nicklas, R. Mathias, 2015, British Journal of Nutrition.

Adaptive Evolution of the FADS Gene Cluster within Africa

I. Ruczinski, J. Akey, K. Barnes, 2012, PloS one.

Evidence of Gene−Environment Interaction for Two Genes on Chromosome 4 and Environmental Tobacco Smoke in Controlling the Risk of Nonsyndromic Cleft Palate

T. Beaty, I. Ruczinski, M. Taub, 2014, PloS one.

A Risk Prediction Model for Mortality Among Smokers in the COPDGene® Study.

E. Regan, D. Lynch, R. Casaburi, 2020, Chronic obstructive pulmonary diseases.

Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole‐Exome Sequencing

D. Nickerson, I. Ruczinski, M. Taub, 2016, Arthritis & rheumatology.

The Plasma Proteome Identifies Expected and Novel Proteins Correlated with Micronutrient Status in Undernourished Nepalese Children 1 – 3

R. Cole, I. Ruczinski, T. Boronina, 2013 .

Cruciferous Vegetable Intake and Lung Cancer Risk: A Nested Case-Control Study Matched on Cigarette Smoking

T. Lam, I. Ruczinski, Y. Shugart, 2010, Cancer Epidemiology, Biomarkers & Prevention.

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality

S. Elledge, A. Casadevall, J. Weiner, 2020, medRxiv.

Statistical inference from multiple iTRAQ experiments without using common reference standards.

Ingo Ruczinski, Damon H May, James D Yager, 2013, Journal of proteome research.

Secondary analyses for genome‐wide association studies using expression quantitative trait loci

R. Scharpf, I. Ruczinski, M. Taub, 2021, medRxiv.

Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis

Alyssa C. Frazee, J. Leek, I. Ruczinski, 2017, PloS one.

Copy number variants of GSTM1 and GSTT1 in relation to lung cancer risk in a prospective cohort study.

T. Lam, I. Ruczinski, Kelly Li, 2009, Annals of epidemiology.

Surfactant protein D is a causal risk factor for COPD: results of Mendelian randomisation

M. Obeidat, Y. Bossé, K. Hao, 2017, European Respiratory Journal.

Using the R Package crlmm for Genotyping and Copy Number Estimation.

Matthew E Ritchie, Ingo Ruczinski, Rafael A Irizarry, 2011, Journal of statistical software.

Identifying interacting SNPs using Monte Carlo logic regression

Ingo Ruczinski, Charles Kooperberg, C. Kooperberg, 2005, Genetic epidemiology.

Clonal haematopoiesis and risk of chronic liver disease

Andrew D. Johnson, Benjamin D. Heavner, May E. Montasser, 2023, Nature.

Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio

Ingo Ruczinski, Jonathan Pevsner, Elisha D O Roberson, 2007, Human mutation.

Dimensional Scaling of the Large Majority of Chemically Unfolded Proteins Is Indistinguishable from Random Coil Behavior

I. Ruczinski, K. Plaxco, T. Dillon, 2004 .

Epidermal Differentiation Complex Genetic Variation in Atopic Dermatitis and Peanut Allergy.

I. Ruczinski, R. Mathias, G. Lack, 2022, Journal of Allergy and Clinical Immunology.

The MALT1 locus and peanut avoidance in the risk for peanut allergy.

I. Ruczinski, K. Barnes, R. Mathias, 2019, The Journal of allergy and clinical immunology.

Sequence Analysis Using Logic Regression

C Kooperberg, M. LeBlanc, C. Kooperberg, 2001, Genetic epidemiology.

Replicated methylation changes associated with eczema herpeticum and allergic response

T. Beaty, I. Ruczinski, Jinshui Fan, 2019, Clinical Epigenetics.

The role of ST2 and ST2 genetic variants in schistosomiasis

T. Beaty, I. Ruczinski, K. Barnes, 2017, The Journal of allergy and clinical immunology.

Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data

R. Scharpf, I. Ruczinski, H. B. Larman, 2022, bioRxiv.

Genome-wide association study in two populations to determine genetic variants associated with Toxoplasma gondii infection and relationship to schizophrenia risk

K. Ressler, I. Ruczinski, K. Conneely, 2019, Progress in Neuro-Psychopharmacology and Biological Psychiatry.

The genetics of smoking in individuals with chronic obstructive pulmonary disease

M. Obeidat, T. Beaty, I. Ruczinski, 2018, Respiratory Research.

A combined genome-wide linkage and association approach to find susceptibility loci for platelet function phenotypes in European American and African American families with coronary artery disease

Alexander F. Wilson, A. F. Wilson, I. Ruczinski, 2010, BMC Medical Genomics.

Inferring Disease Risk Genes from Sequencing Data in Multiplex Pedigrees Through Sharing of Rare Variants

Ingo Ruczinski, Alexandre Bureau, Ferdouse Begum, 2018, bioRxiv.

Gene‐based segregation method for identifying rare variants in family‐based sequencing studies

Ingo Ruczinski, Christoph Lange, Sungho Won, 2017, Genetic epidemiology.

An APOO Pseudogene on Chromosome 5q Is Associated With Low-Density Lipoprotein Cholesterol Levels

Ivana V. Yang, Andrew D. Johnson, Ryan D. Hernandez, 2018, Circulation.

Maternal serum proteome changes between the first and third trimester of pregnancy in rural southern Nepal.

R. Cole, I. Ruczinski, J. Yager, 2012, Placenta.

A Bayesian Hierarchical Model for Signal Extraction from Protein Microarrays

T. Louis, I. Ruczinski, A. Wesolowski, 2022, bioRxiv.

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations

E. Boerwinkle, R. Scharpf, A. Chakravarti, 2014, BMC Genetics.

Genome-wide study identifies two loci associated with lung function decline in mild to moderate COPD

Toshiko Tanaka, L. Ferrucci, D. Postma, 2012, Human Genetics.

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files

Ingo Ruczinski, Fusheng Wang, Jingjing Gao, 2018, GigaScience.

Nature Genetics Advance Online Publication Recombination Rates in Admixed Individuals Identified by Ancestry-based Inference

K. Veeramah, N. Freimer, T. Beaty, 2022 .

Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma

Andrew D. Johnson, Benjamin D. Heavner, May E. Montasser, 2023, EBioMedicine.

Whole genome sequence analysis of pulmonary function and COPD in 19,996 multiethnic participants.

Sina A. Gharib, L. Wain, N. Shrine, 2020 .

PUBLISHED VERSION

Martin T. Wells, Sina A. Gharib, M. Fornage, 2014 .

Novel bioinformatic methods and machine learning approaches reveal candidate biomarkers of the intensity and timing of past exposure to Plasmodium falciparum

T. Louis, I. Ruczinski, A. Wesolowski, 2023, PLOS Global Public Health.

A Pre-Processing Pipeline to Quantify, Visualize and Reduce Technical Variation in Protein Microarray Studies

T. Louis, I. Ruczinski, A. Wesolowski, 2021, bioRxiv.

Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

Andrew D. Johnson, May E. Montasser, Nicholette D. Palmer, 2020, Nature Genetics.

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

Andrew D. Johnson, Benjamin D. Heavner, May E. Montasser, 2020, medRxiv.

Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes

Benjamin J. Strober, Nicholette D. Palmer, M. Gladwin, 2023, bioRxiv.

Identification of interactions of binary variables associated with survival time using survivalFS

K. Ickstadt, I. Ruczinski, J. Hengstler, 2019, Archives of Toxicology.

Nature Genetics Advance Online Publication Recombination Rates in Admixed Individuals Identified by Ancestry-based Inference

K. Veeramah, N. Freimer, T. Beaty, 2022 .

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

Jason C. Ting, Ying Ye, George H. Thomas, 2006, BMC Bioinformatics.

Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci

S. Cichon, T. Beaty, T. Wienker, 2012, Nature Genetics.

Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.

Tom R. Gaunt, Tom S. Price, Deepak L. Bhatt, 2012, American journal of human genetics.

Detecting Disease Variants in Case‐Parent Trio Studies Using the Bioconductor Software Package trio

T. Beaty, R. Scharpf, I. Ruczinski, 2014, Genetic epidemiology.

Imputation methods to improve inference in SNP association studies

I. Ruczinski, C. Kooperberg, James Y. Dai, 2006, Genetic Epidemiology.

Hypothesis-driven candidate gene association studies: practical design and analytical considerations.

I. Ruczinski, Y. Shugart, A. Alberg, 2009, American journal of epidemiology.

Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

Andrew D. Johnson, Benjamin D. Heavner, May E. Montasser, 2021, Nature Communications.

Polymorphisms Influencing Prostate-Specific Antigen Concentration May Bias Genome-Wide Association Studies on Prostate Cancer

I. Ruczinski, Jianfeng Xu, W. Isaacs, 2014, Cancer Epidemiology, Biomarkers & Prevention.

1 Title : Evolution of Hominin Polyunsaturated Fatty Acid Metabolism : From Africa to the New World

I. Ruczinski, L. Becker, D. Becker, 2017 .

PUBLISHED VERSION

Trina, Charles J. Marsh, Oliver R. Wearn, 2014 .

HLA typing using genome wide data reveals susceptibility types for infections in a psychiatric disease enriched sample

I. Ruczinski, K. Conneely, D. Avramopoulos, 2018, Brain, behavior, and immunity.

R classes and methods for SNP array data.

R. Scharpf, I. Ruczinski, 2010, Methods in molecular biology.

A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

Benjamin D. Heavner, May E. Montasser, Nicholette D. Palmer, 2022, Nature Methods.

Comprehensive profiling of pre-infection antibodies identifies HIV targets associated with viremic control and viral load

I. Ruczinski, O. Laeyendecker, J. Blankson, 2023, Frontiers in immunology.

Erratum: Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci (American Journal of Human Genetics (2012) 90 (410-425))

Tom R. Gaunt, Tom S. Price, Deepak L. Bhatt, 2012 .

On the precision of experimentally determined protein folding rates and ϕ‐values

Kevin W Plaxco, Ingo Ruczinski, Tobin R Sosnick, 2006, Protein science : a publication of the Protein Society.

Large-Scale Genome-Wide Association Studies and Meta-Analyses of Longitudinal Change in Adult Lung Function

Martin T. Wells, Bonnie R. Joubert, M. Fornage, 2014, PloS one.

Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations

C. Rotimi, I. Ruczinski, M. Taub, 2024, Nature Communications.