19992019
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Research Output 1999 2019

2019

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., Levin, A. M., Eng, C., Yazdanbakhsh, M., Wilson, J. G., Marrugo, J., Lange, L. A., Williams, L. K., Watson, H., Ware, L. B., Olopade, C. O. & 26 others, Olopade, O., Oliveira, R. R., Ober, C., Nicolae, D. L., Meyers, D. A., Mayorga, A., Knight-Madden, J., Hartert, T., Hansel, N., Foreman, M. G., Ford, J. G., Faruque, M. U., Dunston, G. M., Caraballo, L., Burchard, E. G., Bleecker, E. R., Araujo, M. I., Herrera-Paz, E. F., Campbell, M., Foster, C., Taub, M. A., Beaty, T. L., Ruczinski, I., Mathias, R., Barnes, K. C. & Salzberg, S. L., Jan 1 2019, In : Nature Genetics. 51, 1, p. 30-35 6 p.

Research output: Contribution to journalLetter

High-Throughput Nucleotide Sequencing
Genome
Human Genome
DNA
Population
Open Access
asthma
loci
Asthma
Genes
Chromosomes

Comprehensive Profiling of HIV Antibody Evolution

Eshleman, S., Laeyendecker, O. B., Kammers, K., Chen, A., Sivay, M. V., Kottapalli, S., Sie, B. M., Yuan, T., Monaco, D. R., Mohan, D., Wansley, D., Kula, T., Morrison, C., Elledge, S. J., Brookmeyer, R., Ruczinski, I. & Larman, H., Apr 30 2019, In : Cell Reports. 27, 5, p. 1422-1433.e4

Research output: Contribution to journalArticle

Open Access
HIV Antibodies
Peptides
Antibodies
HIV Infections
Bacteriophages

Correction to: Assembly of a pan-genome from deep sequencing of 910 humans of African descent (Nature Genetics, (2019), 51, 1, (30-35), 10.1038/s41588-018-0273-y)

Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., Levin, A. M., Eng, C., Yazdanbakhsh, M., Wilson, J. G., Marrugo, J., Lange, L. A., Williams, L. K., Watson, H., Ware, L. B., Olopade, C. O. & 26 others, Olopade, O., Oliveira, R. R., Ober, C., Nicolae, D. L., Meyers, D. A., Mayorga, A., Knight-Madden, J., Hartert, T., Hansel, N., Foreman, M. G., Ford, J. G., Faruque, M. U., Dunston, G. M., Caraballo, L., Burchard, E. G., Bleecker, E. R., Araujo, M. I., Herrera-Paz, E. F., Campbell, M., Foster, C., Taub, M. A., Beaty, T. L., Ruczinski, I., Mathias, R., Barnes, K. C. & Salzberg, S. L., Jan 1 2019, In : Nature Genetics. 51, 2, 1 p.

Research output: Contribution to journalComment/debate

High-Throughput Nucleotide Sequencing
Genome

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

Fu, J. M., Leslie, E. J., Scott, A. F., Murray, J. C., Marazita, M. L., Beaty, T. L., Scharpf, R. B. & Ruczinski, I., Feb 15 2019, In : Bioinformatics. 35, 4, p. 571-578 8 p.

Research output: Contribution to journalArticle

Open Access
Formal methods
Deletion
Sequencing
Scalability
Minimum Distance

Detection of rare disease variants in extended pedigrees using RVS

Sherman, T., Fu, J., Scharpf, R. B., Bureau, A. & Ruczinski, I., Jul 15 2019, In : Bioinformatics. 35, 14, p. 2509-2511 3 p., bty976.

Research output: Contribution to journalArticle

Open Access
Pedigree
Rare Diseases
Software
Linkage
Bioinformatics

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

Harris, D. N., Ruczinski, I., Yanek, L., Becker, L., Becker, D. M., Guio, H., Cui, T., Chilton, F. H., Mathias, R. & O'Connor, T. D., May 1 2019, In : Genome biology and evolution. 11, 5, p. 1417-1430 14 p.

Research output: Contribution to journalArticle

Open Access
Fatty Acid Desaturases
stearoyl-CoA desaturase
fatty acid metabolism
Hominidae
Unsaturated Fatty Acids

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

Wang, A. W., Avramopoulos, D., Lori, A., Mulle, J., Conneely, K., Powers, A., Duncan, E., Almli, L., Massa, N., McGrath, J., Schwartz, A. C., Goes, F. S., Weng, L., Wang, R., Yolken, R. H., Ruczinski, I., Gillespie, C. F., Jovanovic, T., Ressler, K., Pulver, A. E. & 1 others, Pearce, B. D., Jun 8 2019, In : Progress in Neuro-Psychopharmacology and Biological Psychiatry. 92, p. 133-147 15 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Toxoplasmosis
Schizophrenia
Toxoplasma
Chitinases

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

Tietz, T., Selinski, S., Golka, K., Hengstler, J. G., Gripp, S., Ickstadt, K., Ruczinski, I. & Schwender, H., Jan 1 2019, In : Archives of Toxicology.

Research output: Contribution to journalArticle

Data structures
Testing
Recurrence
Survival Analysis
Urinary Bladder Neoplasms

Replicated methylation changes associated with eczema herpeticum and allergic response

Boorgula, M. P., Taub, M. A., Rafaels, N., Daya, M., Campbell, M., Chavan, S., Shetty, A., Cheadle, C., Barkataki, S., Fan, J., David, G., Beaty, T. H., Ruczinski, I., Hanifin, J., Schneider, L. C., Gallo, R. L., Paller, A. S., Beck, L. A., Leung, D. Y., Mathias, R. & 1 others, Barnes, K. C., Aug 23 2019, In : Clinical Epigenetics. 11, 1, 122.

Research output: Contribution to journalArticle

Open Access
Kaposi Varicelliform Eruption
Atopic Dermatitis
Methylation
Eosinophils
Genome

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

Immune Tolerance Network LEAP Study Team, Jan 1 2019, In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticle

Open Access
Peanut Hypersensitivity
Arachis
2018

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

NHLBI TOPMed Lipids Working Group, Dec 1 2018, In : Nature Communications. 9, 1, 3391.

Research output: Contribution to journalArticle

sequencing
genome
cholesterol
lipoproteins
blood

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

Zekavat, S. M., Ruotsalainen, S., Handsaker, R. E., Alver, M., Bloom, J., Poterba, T., Seed, C., Ernst, J., Chaffin, M., Engreitz, J., Peloso, G. M., Manichaikul, A., Yang, C., Ryan, K. A., Fu, M., Johnson, W. C., Tsai, M., Budoff, M., Ramachandran, V. S., Cupples, L. A. & 323 others, Rotter, J. I., Rich, S. S., Post, W. S., Mitchell, B. D., Correa, A., Metspalu, A., Wilson, J. G., Salomaa, V., Kellis, M., Daly, M. J., Neale, B. M., McCarroll, S., Surakka, I., Esko, T., Ganna, A., Ripatti, S., Kathiresan, S., Natarajan, P., Abe, N., Abecasis, G., Albert, C., Allred, N. P., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Beaty, T. L., Becker, D. M., Becker, L., Beer, R., Begum, F., Beitelshees, A., Benjamin, E., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Boerwinkle, E., Borecki, I., Bowler, R., Brody, J., Broeckel, U., Broome, J., Bunting, K., Burchard, E., Cardwell, J., Carty, C., Casaburi, R., Casella, J. F., Chang, C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Chen, Y. D. I., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Cornell, E., Crandall, C., Crapo, J., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., Das, S., David, S., Davis, C., Daya, M., Andrade, M. D., Debaun, M., Deka, R., Demeo, D., Devine, S., Do, R., Duan, Q., Duggirala, R., Durda, P., Dutcher, S., Eaton, C., Ekunwe, L., Ellinor, P., Emery, L., Farber, C., Farnam, L., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, Y., Gass, M., Gelb, B., Geng, X., Germer, S., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Gu, C. C., Guan, Y., Guo, X., Haessler, J., Hall, M., Harris, D., Hawley, N., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jain, D., Jaquish, C., Jhun, M. A., Johnsen, J., Johnson, A., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kaufman, L., Kelly, S., Kenny, E., Kessler, M., Khan, A., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Krauter, S., Lange, C., Lange, E., Lange, L., Laurie, C., Laurie, C., Leboff, M., Lee, S. S., Lee, W. J., Lefaive, J., Levine, D., Levy, D., Lewis, J., Li, Y., Lin, H., Lin, K. H., Liu, S., Liu, Y., Loos, R., Lubitz, S., Lunetta, K., Luo, J., Mahaney, M., Make, B., Manson, J. A., Margolin, L., Martin, L., Mathai, S., Mathias, R., McArdle, P., McDonald, M. L., McFarland, S., McGarvey, S., Mei, H., Meyers, D. A., Mikulla, J., Min, N., Minear, M., Minster, R. L., Montasser, M. E., Musani, S., Mwasongwe, S., Mychaleckyj, J. C., Nadkarni, G., Naik, R. P., Nekhai, S., Nickerson, D., North, K., O'connell, J., O'connor, T., Ochs-Balcom, H., Pankow, J., Papanicolaou, G., Parker, M., Parsa, A., Penchev, S., Peralta, J. M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L., Phillips, S., Pollin, T., Becker, J. P., Boorgula, M. P., Preuss, M., Prokopenko, D., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Regan, E., Reiner, A., Rice, K., Roden, D., Roselli, C., Ruczinski, I., Russell, P., Ruuska, S., Sakornsakolpat, P., Salimi, S., Salzberg, S. L., Sandow, K., Sankaran, V., Scheller, C., Schmidt, E., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Sheehan, V., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Smith, J., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Sofer, T., Sotoodehnia, N., Stilp, A., Streeten, E., Sung, Y. J., Sylvia, J., Szpiro, A., Sztalryd, C., Taliun, D., Tang, H., Taub, M. A., Taylor, K., Taylor, S., Telen, M., Thornton, T. A., Tinker, L., Tirschwell, D., Tiwari, H., Tracy, R., Vaidya, D., Vandehaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wan, E., Wang, F. F., Watson, K., Weeks, D. E., Weir, B., Weiss, S., Weng, L. C., Willer, C., Williams, K., Williams, L. K., Wilson, C., Wong, Q., Xu, H., Yanek, L., Yang, I., Yang, R., Zaghloul, N., Zhang, Y., Zhao, S. X., Zhao, W., Zheng, X., Zhi, D., Zhou, X., Zody, M. & Zoellner, S., Dec 1 2018, In : Nature Communications. 9, 1, 2606.

Research output: Contribution to journalArticle

lipoproteins
Lipoprotein(a)
genome
Cardiovascular Diseases
Genes
document markup languages
lipoproteins
Lipoprotein(a)
HTML
genome

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

Parks, S., Avramopoulos, D., Mulle, J., McGrath, J., Wang, R., Goes, F. S., Conneely, K., Ruczinski, I., Yolken, R. H., Pulver, A. E. & Pearce, B. D., Jan 1 2018, (Accepted/In press) In : Brain, Behavior, and Immunity.

Research output: Contribution to journalArticle

Histocompatibility Testing
Psychiatry
Genome
Schizophrenia
Infection

Inferring disease risk genes from sequencing data in multiplex pedigrees through sharing of rare variants

Bureau, A., Begum, F., Taub, M. A., Hetmanski, J. B., Parker, M. M., Albacha-Hejazi, H., Scott, A. F., Murray, J. C., Marazita, M. L., Bailey-Wilson, J. E., Beaty, T. L. & Ruczinski, I., Jan 1 2018, (Accepted/In press) In : Genetic Epidemiology.

Research output: Contribution to journalArticle

Pedigree
Genes
Exome
Haplotypes
Software

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

CAAPA consortium, Jun 1 2018, In : GigaScience. 7, 6, giy052.

Research output: Contribution to journalComment/debate

Computer Communication Networks
Merging
Computing Methodologies
Exome
Workflow

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

NHLBI GO Exome Sequencing Project, Pulmonary Arterial Hypertension (PAH), Severe Asthma Research Program (SARP), Women’s Health Initiative (WHI), Anthropometry Project Team, Blood Count/Hematology Project Team, Blood Pressure Project Team, Data Flow Working Group, Early MI Project Team, ELSI Working Group, Executive Committee, Family Study Project Team, Lipids Project Team, Lung Project Team, Personal Genomics Project Team, Phenotype and Harmonization Working Group, Population Genetics and Statistical Analysis Working Group, Publications and Presentations Working Group, Quantitative Analysis Ad Hoc Task Group, Sequencing and Genotyping Working Group & 15 others, Steering Committee, Stroke Project Team, Structural Variation Working Group, Subclinical/Quantitative Project Team, Acute Lung Injury (ALI), Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS), Chronic Obstructive Pulmonary Disease (COPDGene), Coronary Artery Risk Development in Young Adults (CARDIA), Cystic Fibrosis (CF), Early Pseudomonas Infection Control (EPIC), Framingham Heart Study (FHS), Jackson Heart Study (JHS), Lung Health Study (LHS) & Multi-Ethnic Study of Atherosclerosis (MESA), Oct 1 2018, In : Human Genetics. 137, 10, p. 795-806 12 p.

Research output: Contribution to journalArticle

Polyps
Colorectal Neoplasms
Genes
Penetrance
Genetic Testing

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

Keramati, A. R., Yanek, L., Iyer, K., Taub, M. A., Ruczinski, I., Becker, D. M., Becker, L., Faraday, N. & Mathias, R., Mar 18 2018, (Accepted/In press) In : Platelets. p. 1-7 7 p.

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
Platelet Aggregation
African Americans
Aspirin
Genome-Wide Association Study

The genetics of smoking in individuals with chronic obstructive pulmonary disease

Obeidat, M., Zhou, G., Li, X., Hansel, N., Rafaels, N., Mathias, R., Ruczinski, I., Beaty, T. L., Barnes, K. C., Paré, P. D. & Sin, D. D., Apr 10 2018, In : Respiratory Research. 19, 1, 59.

Research output: Contribution to journalArticle

Chronic Obstructive Pulmonary Disease
Smoking Cessation
Cotinine
Smoking
Genome-Wide Association Study

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

Reynolds, L. M., Howard, T. D., Ruczinski, I., Kanchan, K., Seeds, M. C., Mathias, R. & Chilton, F. H., Mar 1 2018, In : PLoS One. 13, 3, e0194610.

Research output: Contribution to journalArticle

Fatty Acid Desaturases
stearoyl-CoA desaturase
Gene expression
Tissue
Gene Expression

Whole exome sequencing analysis in severe chronic obstructive pulmonary disease

Qiao, D., Ameli, A., Prokopenko, D., Chen, H., Kho, A. T., Parker, M. M., Morrow, J., Hobbs, B. D., Liu, Y., Beaty, T. L., Crapo, J. D., Barnes, K. C., Nickerson, D. A., Bamshad, M., Hersh, C. P., Lomas, D. A., Agusti, A., Make, B. J., Calverley, P. M. A., Donner, C. F. & 12 others, Wouters, E. F., Vestbo, J., Paré, P. D., Levy, R. D., Rennard, S. I., Tal-Singer, R., Spitz, M. R., Sharma, A., Ruczinski, I., Lange, C., Silverman, E. K. & Cho, M. H., Nov 1 2018, In : Human Molecular Genetics. 27, 21, p. 3801-3812 12 p.

Research output: Contribution to journalArticle

Exome
Chronic Obstructive Pulmonary Disease
Genes
Case-Control Studies
Cutis Laxa
2017

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

Xiao, Y., Taub, M. A., Ruczinski, I., Begum, F., Hetmanski, J. B., Schwender, H., Leslie, E. J., Koboldt, D. C., Murray, J. C., Marazita, M. L. & Beaty, T. L., Apr 1 2017, In : Genetic Epidemiology. 41, 3, p. 244-250 7 p.

Research output: Contribution to journalArticle

Nucleotides
Genes
Cleft Lip
Live Birth
Cleft Palate

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

Qiao, D., Lange, C., Laird, N. M., Won, S., Hersh, C. P., Morrow, J., Hobbs, B. D., Lutz, S. M., Ruczinski, I., Beaty, T. L., Silverman, E. K. & Cho, M. H., May 1 2017, In : Genetic Epidemiology. 41, 4, p. 309-319 11 p.

Research output: Contribution to journalArticle

Genes
Exome
Phenotype
Penetrance
Pedigree

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

Yu, Y., Zuo, X., He, M., Gao, J., Fu, Y., Qin, C., Meng, L., Wang, W., Song, Y., Cheng, Y., Zhou, F., Chen, G., Zheng, X., Wang, X., Liang, B., Zhu, Z., Fu, X., Sheng, Y., Hao, J., Liu, Z. & 10 others, Yan, H., Mangold, E., Ruczinski, I., Liu, J., Marazita, M. L., Ludwig, K. U., Beaty, T. L., Zhang, X., Sun, L. & Bian, Z., Feb 24 2017, In : Nature Communications. 8, 14364.

Research output: Contribution to journalArticle

Genetic Heterogeneity
Palate
genome
Cleft Lip
loci

Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets

Wain, L. V., Shrine, N., Artigas, M. S., Erzurumluoglu, A. M., Noyvert, B., Bossini-Castillo, L., Obeidat, ME., Henry, A. P., Portelli, M. A., Hall, R. J., Billington, C. K., Rimington, T. L., Fenech, A. G., John, C., Blake, T., Jackson, V. E., Allen, R. J., Prins, B. P., Campbell, A., Porteous, D. J. & 86 others, Jarvelin, M. R., Wielscher, M., James, A. L., Hui, J., Wareham, N. J., Zhao, J. H., Wilson, J. F., Joshi, P. K., Stubbe, B., Rawal, R., Schulz, H., Imboden, M., Probst-Hensch, N. M., Karrasch, S., Gieger, C., Deary, I. J., Harris, S. E., Marten, J., Rudan, I., Enroth, S., Gyllensten, U., Kerr, S. M., Polasek, O., Kähönen, M., Surakka, I., Vitart, V., Hayward, C., Lehtimäki, T., Raitakari, O. T., Evans, D. M., Henderson, A. J., Pennell, C. E., Wang, C. A., Sly, P. D., Wan, E. S., Busch, R., Hobbs, B. D., Litonjua, A. A., Sparrow, D. W., Gulsvik, A., Bakke, P. S., Crapo, J. D., Beaty, T. L., Hansel, N., Mathias, R., Ruczinski, I., Barnes, K. C., Bossé, Y., Joubert, P., Van Den Berge, M., Brandsma, C. A., Paré, P. D., Sin, D. D., Nickle, D. C., Hao, K., Gottesman, O., Dewey, F. E., Bruse, S. E., Carey, D. J., Kirchner, H. L., Jonsson, S., Thorleifsson, G., Jonsdottir, I., Gislason, T., Stefansson, K., Schurmann, C., Nadkarni, G., Bottinger, E. P., Loos, R. J. F., Walters, R. G., Chen, Z., Millwood, I. Y., Vaucher, J., Kurmi, O. P., Li, L., Hansell, A. L., Brightling, C., Zeggini, E., Cho, M. H., Silverman, E. K., Sayers, I., Trynka, G., Morris, A. P., Strachan, D. P., Hall, I. P. & Tobin, M. D., Mar 1 2017, In : Nature Genetics. 49, 3, p. 416-425 10 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Chronic Obstructive Pulmonary Disease
Lung
Drug Repositioning
Inositol Phosphates

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

Consortia CAAPA Consortium, Jan 1 2017, In : Scientific Reports. 7, 46398.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Genome
Population
Asthma
Genome-Wide Association Study
megakaryocytes
Induced Pluripotent Stem Cells
Megakaryocytes
Stem cells
transcriptomics

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

International COPD Genetics Consortium, Lung eQTL Consortium, Lung Health Study, Nov 1 2017, In : The European respiratory journal. 50, 5

Research output: Contribution to journalArticle

Pulmonary Surfactant-Associated Protein D
Random Allocation
Chronic Obstructive Pulmonary Disease
Blood Proteins
Lung

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

Rahbar, E., Ainsworth, H. C., Howard, T. D., Hawkins, G. A., Ruczinski, I., Mathias, R., Seeds, M. C., Sergeant, S., Hixson, J. E., Herrington, D. M., Langefeld, C. D. & Chilton, F. H., Sep 1 2017, In : PLoS One. 12, 9, e0180903.

Research output: Contribution to journalArticle

Fatty Acid Desaturases
stearoyl-CoA desaturase
Methylation
Nucleic Acid Regulatory Sequences
DNA methylation

Whole exome association of rare deletions in multiplex oral cleft families

Fu, J., Beaty, T. L., Scott, A. F., Hetmanski, J., Parker, M. M., Wilson, J. E. B., Marazita, M. L., Mangold, E., Albacha-Hejazi, H., Murray, J. C., Bureau, A., Carey, J., Cristiano, S., Ruczinski, I. & Scharpf, R. B., Jan 1 2017, In : Genetic Epidemiology. 41, 1, p. 61-69 9 p.

Research output: Contribution to journalArticle

Exome
Nucleotides
Genome
DNA
2016

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

Mathias, R., Taub, M. A., Gignoux, C. R., Fu, W., Musharoff, S., O'Connor, T. D., Vergara, C., Torgerson, D. G., Pino-Yanes, M., Shringarpure, S. S., Huang, L., Rafaels, N., Boorgula, M. P., Johnston, H. R., Ortega, V. E., Levin, A. M., Song, W., Torres, R., Padhukasahasram, B., Eng, C. & 42 others, Mejia-Mejia, D. A., Ferguson, T., Qin, Z. S., Scott, A. F., Yazdanbakhsh, M., Wilson, J. G., Marrugo, J., Lange, L. A., Kumar, R., Avila, P. C., Williams, L. K., Watson, H., Ware, L. B., Olopade, C., Olopade, O., Oliveira, R., Ober, C., Nicolae, D. L., Meyers, D., Mayorga, A., Knight-Madden, J., Hartert, T., Hansel, N., Foreman, M. G., Ford, J. G., Faruque, M. U., Dunston, G. M., Caraballo, L., Burchard, E. G., Bleecker, E., Araujo, M. I., Herrera-Paz, E. F., Gietzen, K., Grus, W. E., Bamshad, M., Bustamante, C. D., Kenny, E. E., Hernandez, R. D., Beaty, T. L., Ruczinski, I., Akey, J. & Barnes, K. C., Oct 11 2016, In : Nature Communications. 7, 12522.

Research output: Contribution to journalArticle

Western hemisphere
genome
admixtures
Genes
Genome

Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

Kessler, M. D., Yerges-Armstrong, L., Taub, M. A., Shetty, A. C., Maloney, K., Jeng, L. J. B., Ruczinski, I., Levin, A. M., Williams, L. K., Beaty, T. L., Mathias, R., Barnes, K. C. & O'Connor, T. D., Oct 11 2016, In : Nature Communications. 7, 12521.

Research output: Contribution to journalArticle

Precision Medicine
medicine
Medicine
Databases
Genes

Hemizygous deletion on chromosome 3p26.1 is associated with heavy smoking among African American subjects in the COPDGene study

Begum, F., Ruczinski, I., Hokanson, J. E., Lutz, S. M., Parker, M. M., Cho, M. H., Hetmanski, J. B., Scharpf, R. B., Crapo, J. D., Silverman, E. K. & Beaty, T. L., Oct 1 2016, In : PLoS One. 11, 10, e0164134.

Research output: Contribution to journalArticle

Chromosome Deletion
African Americans
Chromosomes
atherosclerosis
Atherosclerosis

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

Gao, L., Emond, M. J., Louie, T., Cheadle, C., Berger, A. E., Rafaels, N., Vergara, C., Kim, Y., Taub, M. A., Ruczinski, I., Mathai, S., Rich, S. S., Nickerson, D. A., Hummers, L., Bamshad, M. J., Hassoun, P. M., Mathias, R. & Barnes, K. C., Jan 1 2016, In : Arthritis and Rheumatology. 68, 1, p. 191-200 10 p.

Research output: Contribution to journalArticle

Exome
Systemic Scleroderma
Pulmonary Hypertension
Odds Ratio
Ubiquitin-Protein Ligase Complexes

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

Begum, F., Ruczinski, I., Li, S., Silverman, E. K., Cho, M. H., Lynch, D. A., Curran-Everett, D., Crapo, J., Scharpf, R. B., Parker, M. M., Hetmanski, J. B. & Beaty, T. L., Jan 1 2016, In : Genetic Epidemiology. 40, 1, p. 81-88 8 p.

Research output: Contribution to journalArticle

Total Lung Capacity
Chronic Obstructive Pulmonary Disease
Cohort Studies
Genome-Wide Association Study
Phenotype

The role of ST2 and ST2 genetic variants in schistosomiasis

Long, X., Daya, M., Zhao, J., Rafaels, N., Liang, H., Potee, J., Campbell, M., Zhang, B., Araujo, M. I., Oliveira, R. R., Mathias, R., Gao, L., Ruczinski, I., Georas, S. N., Vercelli, D., Beaty, T. L., Barnes, K. C., Chen, X. & Chen, Q., Jun 29 2016, (Accepted/In press) In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticle

Schistosomiasis
Liver
Liver Cirrhosis
Single Nucleotide Polymorphism
Schistosoma japonicum
2015

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

Younkin, S. G., Scharpf, R. B., Schwender, H., Parker, M. M., Scott, A. F., Marazita, M. L., Beaty, T. L. & Ruczinski, I., 2015, In : Birth Defects Research Part A - Clinical and Molecular Teratology. 103, 4, p. 276-283 8 p.

Research output: Contribution to journalArticle

DNA Copy Number Variations
Overlapping Genes
Genome
Multiple Birth Offspring
Chromosome Deletion

An IL-13 promoter polymorphism associated with liver fibrosis in patients with Schistosoma japonicum

Long, X., Chen, Q., Zhao, J., Rafaels, N., Mathias, P., Liang, H., Potee, J., Campbell, M., Zhang, B., Gao, L., Georas, S. N., Vercelli, D., Beaty, T. L., Ruczinski, I., Mathias, R., Barnes, K. C. & Chen, X., Aug 10 2015, In : PLoS One. 10, 8, e0135360.

Research output: Contribution to journalArticle

Schistosoma japonicum
schistosomiasis
liver cirrhosis
Interleukin-13
Schistosomiasis

Detecting significant changes in protein abundance

Kammers, K., Cole, R. N., Tiengwe, C. & Ruczinski, I., Jun 1 2015, In : EuPA Open Proteomics. 7, p. 11-19 9 p.

Research output: Contribution to journalArticle

Proteomics
Mass spectrometry
Mass Spectrometry
Proteins
Software

Genome-wide association study identification of novel loci associated with airway responsiveness in chronic obstructive pulmonary disease

Hansel, N., Pare, P. D., Rafaels, N., Sin, D. D., Sandford, A., Daley, D., Vergara, C., Huang, L., Mark Elliott, W., Pascoe, C. D., Arsenault, B. A., Postma, D. S., Marike Boezen, H., Bosse, Y., Van Den Berge, M., Hiemstra, P. S., Cho, M. H., Litonjua, A. A., Sparrow, D., Ober, C. & 7 others, Wise, R. A., Connett, J., Neptune, E., Beaty, T. L., Ruczinski, I., Mathias, R. & Barnes, K. C., Aug 1 2015, In : American Journal of Respiratory Cell and Molecular Biology. 53, 2, p. 226-234 9 p.

Research output: Contribution to journalArticle

Pulmonary diseases
Genome-Wide Association Study
Chronic Obstructive Pulmonary Disease
Genes
Association reactions

Genome-wide association study of schizophrenia in Ashkenazi Jews

Goes, F. S., Mcgrath, J., Avramopoulos, D., Wolyniec, P., Pirooznia, M., Ruczinski, I., Nestadt, G., Kenny, E. E., Vacic, V., Peters, I., Lencz, T., Darvasi, A., Mulle, J. G., Warren, S. T. & Pulver, A. E., Dec 1 2015, In : American Journal of Medical Genetics - Neuropsychiatric Genetics. 168, 8, p. 649-659 11 p.

Research output: Contribution to journalArticle

Jews
Genome-Wide Association Study
Schizophrenia
Meta-Analysis
Genome

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

Leslie, E. J., Taub, M. A., Liu, H., Steinberg, K. M., Koboldt, D. C., Zhang, Q., Carlson, J. C., Hetmanski, J. B., Wang, H., Larson, D. E., Fulton, R. S., Kousa, Y. A., Fakhouri, W. D., Naji, A., Ruczinski, I., Begum, F., Parker, M. M., Busch, T., Standley, J., Rigdon, J. & 14 others, Hecht, J. T., Scott, A. F., Wehby, G. L., Christensen, K., Czeizel, A. E., Deleyiannis, F. W. B., Schutte, B. C., Wilson, R. K., Cornell, R. A., Lidral, A. C., Weinstock, G. M., Beaty, T. L., Marazita, M. L. & Murray, J. C., Mar 5 2015, In : American Journal of Human Genetics. 96, 3, p. 397-411 15 p.

Research output: Contribution to journalArticle

Cleft Lip
Genome-Wide Association Study
Cleft Palate
Mutation
Neural Crest

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

Sergeant, S., Ruczinski, I., Ivester, P., Lee, T. C., Morgan, T. M., Nicklas, B. J., Mathias, R. & Chilton, F. H., Nov 6 2015, In : British Journal of Nutrition. 115, 2, p. 251-261 11 p.

Research output: Contribution to journalArticle

Fatty Acids
Lipids
Direction compound
Biomarkers
Cholesterol

Infection and inflammation in schizophrenia and bipolar disorder: A genome wide study for interactions with genetic variation

Avramopoulos, D., Pearce, B. D., McGrath, J., Wolyniec, P., Wang, R., Eckart, N., Hatzimanolis, A., Goes, F. S., Nestadt, G., Mulle, J., Coneely, K., Hopkins, M., Ruczinski, I., Yolken, R. H. & Pulver, A. E., Mar 17 2015, In : PLoS One. 10, 3, e0116696.

Research output: Contribution to journalArticle

Bipolar Disorder
Schizophrenia
Genes
inflammation
Genome
Nepal
Biomarkers
Proteome
proteome
biomarkers
Genome-Wide Association Study
Prostate-Specific Antigen
Single Nucleotide Polymorphism
Prostatic Neoplasms
Alleles

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

Gao, L., Bin, L., Rafaels, N. M., Huang, L., Potee, J., Ruczinski, I., Beaty, T. L., Paller, A. S., Schneider, L. C., Gallo, R., Hanifin, J. M., Beck, L. A., Geha, R. S., Mathias, R., Barnes, K. C. & Leung, D. Y. M., Dec 1 2015, In : The Journal of Allergy and Clinical Immunology. 136, 6, p. 1591-1600 10 p.

Research output: Contribution to journalArticle

Kaposi Varicelliform Eruption
High-Throughput Nucleotide Sequencing
Interferons
Genes
Eczema
2014

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

Younkin, S. G., Scharpf, R. B., Schwender, H., Parker, M. M., Scott, A. F., Marazita, M. L., Beaty, T. L. & Ruczinski, I., Feb 14 2014, In : BMC Genetics. 15, 24.

Research output: Contribution to journalArticle

Cleft Lip
Cleft Palate
Genome
Multiple Birth Offspring
DNA

Analytic power and sample size calculation for the genotypic transmission/disequilibrium test in case-parent trio studies

Neumann, C., Taub, M. A., Younkin, S. G., Beaty, T. L., Ruczinski, I. & Schwender, H., Nov 1 2014, In : Biometrical Journal. 56, 6, p. 1076-1092 17 p.

Research output: Contribution to journalArticle

Sample Size Calculation
Sample Size
Single Nucleotide Polymorphism
Genotype
Single nucleotide Polymorphism