Robert B Scharpf

Associate Professor

19972019
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Research Output 1997 2019

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Article
2019

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

Dynamics of tumor and immune responses during immune checkpoint blockade in non–small cell lung cancer

Anagnostou, V., Forde, P., White, J. R., Niknafs, N., Hruban, C., Naidoo, J., Marrone, K., Ashok Sivakumar, I. K., Bruhm, D. C., Rosner, S., Phallen, J., Leal, A., Adleff, V., Smith, K., Cottrell, T. R., Rhymee, L., Palsgrove, D. N., Hann, C., Levy, B., Feliciano, J. & 16 others, Georgiades, C. S., Verde, F., Illei, P. B., Li, Q. K., Gabrielson, E., Brock, M. V., Isbell, J. M., Sauter, J. L., Taube, J. M., Scharpf, R. B., Karchin, R., Pardoll, A. M., Chaft, J. E., Hellmann, M. D., Brahmer, J. & Velculescu, V. E., Jan 1 2019, In : Cancer Research. 79, 6, p. 1214-1225 12 p.

Research output: Contribution to journalArticle

Open Access
Non-Small Cell Lung Carcinoma
DNA
Neoplasms
Therapeutics
Confidence Intervals

Early noninvasive detection of response to targeted therapy in non–small cell lung cancer

Phallen, J., Leal, A., Woodward, B. D., Forde, P., Naidoo, J., Marrone, K., Brahmer, J., Fiksel, J., Medina, J. E., Cristiano, S., Palsgrove, D. N., Gocke, C., Bruhm, D. C., Keshavarzian, P., Adleff, V., Weihe, E., Anagnostou, V., Scharpf, R. B., Velculescu, V. E. & Husain, H., Jan 1 2019, In : Cancer Research. 79, 6, p. 1204-1213 10 p.

Research output: Contribution to journalArticle

Open Access
Non-Small Cell Lung Carcinoma
DNA
Neoplasms
Circulating Neoplastic Cells
Therapeutics

Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations

Fischer, C. G., Beleva Guthrie, V., Braxton, A. M., Zheng, L., Wang, P., Song, Q., Griffin, J. F., Chianchiano, P. E., Hosoda, W., Niknafs, N., Springer, S., Dal Molin, M., Masica, D., Scharpf, R. B., Thompson, E., He, J., Wolfgang, C., Hruban, R. H., Roberts, N., O'Broin-Lennon, A. M. & 3 others, Jiao, Y., Karchin, R. & Wood, L. D., Oct 1 2019, In : Gastroenterology. 157, 4, p. 1123-1137.e22

Research output: Contribution to journalArticle

Clone Cells
Mutation
Neoplasms
Carcinogenesis
Pancreatic Neoplasms
2018

Genome-Wide Association Study of Serum Fructosamine and Glycated Albumin in Adults Without Diagnosed Diabetes: Results From the Atherosclerosis Risk in Communities Study

Loomis, S. J., Li, M., Maruthur, N., Baldridge, A. S., North, K. E., Mei, H., Morrison, A., Carson, A. P., Pankow, J. S., Boerwinkle, E., Scharpf, R. B., Rasmussen-Torvik, L. J., Coresh, J., Duggal, P., Köttgen, A. & Selvin, E., Aug 1 2018, In : Diabetes. 67, 8, p. 1684-1696 13 p.

Research output: Contribution to journalArticle

Fructosamine
Genome-Wide Association Study
Serum Albumin
Atherosclerosis
Single Nucleotide Polymorphism

Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines

Papp, E., Hallberg, D., Konecny, G. E., Bruhm, D. C., Adleff, V., Noë, M., Kagiampakis, I., Palsgrove, D., Conklin, D., Kinose, Y., White, J. R., Press, M. F., Drapkin, R., Easwaran, H., Baylin, S. B., Slamon, D., Velculescu, V. E. & Scharpf, R. B., Nov 27 2018, In : Cell Reports. 25, 9, p. 2617-2633 17 p.

Research output: Contribution to journalArticle

Epigenomics
Ovarian Neoplasms
Tumors
Mitogen-Activated Protein Kinase Kinases
Cells

Neoadjuvant PD-1 blockade in resectable lung cancer

Forde, P., Chaft, J. E., Smith, K., Anagnostou, V., Cottrell, T. R., Hellmann, M. D., Zahurak, M., Broderick, S., Yang, S. C., Jones, D. R., Battafarano, R. J., Velez, M. J., Rekhtman, N., Olah, Z., Verde, F., Naidoo, J., Marrone, K., Guo, H., Sidhom, J. W., Zhang, J. & 15 others, Caushi, J. X., Chan, H. Y., Scharpf, R. B., White, J., Gabrielson, E., Wang, H., Rosner, G., Rusch, V., Wolchok, J. D., Merghoub, T., Taube, J. M., Velculescu, V. E., Topalian, S., Brahmer, J. & Pardoll, A. M., May 24 2018, In : New England Journal of Medicine. 378, 21, p. 1976-1986 11 p.

Research output: Contribution to journalArticle

Lung Neoplasms
Clone Cells
Neoplasms
Non-Small Cell Lung Carcinoma
T-Lymphocytes
2017

Direct detection of early-stage cancers using circulating tumor DNA

Phallen, J., Sausen, M., Adleff, V., Leal, A., Hruban, C., White, J., Anagnostou, V., Fiksel, J., Cristiano, S., Papp, E., Speir, S., Reinert, T., Orntoft, M. B. W., Woodward, B. D., Murphy, D., Parpart-Li, S., Riley, D., Nesselbush, M., Sengamalay, N., Georgiadis, A. & 17 others, Li, Q. K., Madsen, M. R., Mortensen, F. V., Huiskens, J., Punt, C., Van Grieken, N., Fijneman, R., Meijer, G., Husain, H., Scharpf, R. B., Diaz, L. A., Jones, S., Angiuoli, S., Ørntoft, T., Nielsen, H. J., Andersen, C. L. & Velculescu, V. E., Aug 16 2017, In : Science Translational Medicine. 9, 403, eaan2415.

Research output: Contribution to journalArticle

Early Detection of Cancer
DNA
Neoplasms
High-Throughput Nucleotide Sequencing
Mutation

Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

Anagnostou, V., Smith, K., Forde, P., Niknafs, N., Bhattacharya, R., White, J., Zhang, T., Adleff, V., Phallen, J., Wali, N., Hruban, C., Guthrie, V. B., Rodgers, K., Naidoo, J., Kang, H., Sharfman, W., Georgiades, C. S., Verde, F., Illei, P. B., Li, Q. K. & 9 others, Gabrielson, E., Brock, M. V., Zahnow, C., Baylin, S. B., Scharpf, R. B., Brahmer, J., Karchin, R., Pardoll, A. M. & Velculescu, V. E., Mar 1 2017, In : Cancer Discovery. 7, 3, p. 264-276 13 p.

Research output: Contribution to journalArticle

Non-Small Cell Lung Carcinoma
Neoplasms
T-Lymphocytes
Mutation
T-Cell Antigen Receptor

GATA3 frameshift mutation promotes tumor growth in human luminal breast cancer cells and induces transcriptional changes seen in primary GATA3 mutant breast cancers

Gustin, J. P., Miller, J., Farag, M., Marc Rosen, D., Thomas, M., Scharpf, R. B. & Lauring, J., Jan 1 2017, In : Oncotarget. 8, 61, p. 103415-103427 13 p.

Research output: Contribution to journalArticle

Frameshift Mutation
Breast Neoplasms
Mutation
Growth
Neoplasms

Genome-wide association of copy number polymorphisms and kidney function

Li, M., Carey, J., Cristiano, S., Susztak, K., Coresh, J., Boerwinkle, E., Kao, W. H. L., Beaty, T. L., Köttgen, A. & Scharpf, R. B., Jan 1 2017, In : PLoS One. 12, 1, e0170815.

Research output: Contribution to journalArticle

DNA Copy Number Variations
glomerular filtration rate
renal function
Polymorphism
Glomerular Filtration Rate

High grade serous ovarian carcinomas originate in the fallopian tube

Labidi-Galy, S. I., Papp, E., Hallberg, D., Niknafs, N., Adleff, V., Noe, M., Bhattacharya, R., Novak, M., Jones, S., Phallen, J., Hruban, C. A., Hirsch, M. S., Lin, D. I., Schwartz, L., Maire, C. L., Tille, J. C., Bowden, M., Ayhan, A., Wood, L. D., Scharpf, R. B. & 6 others, Kurman, R. J., Wang, T-L., Shih, I. M., Karchin, R., Drapkin, R. & Velculescu, V. E., Dec 1 2017, In : Nature Communications. 8, 1, 1093.

Research output: Contribution to journalArticle

Fallopian Tubes
Carcinoma in Situ
Tumors
grade
cancer

The loss of GSTM1 associates with kidney failure and heart failure

Tin, A., Scharpf, R. B., Estrella, M. M., Yu, B., Grove, M. L., Chang, P. P., Matsushita, K., Köttgen, A., Arking, D., Boerwinkle, E., Le, T. H., Coresh, J. & Grams, M., Nov 1 2017, In : Journal of the American Society of Nephrology. 28, 11, p. 3345-3352 8 p.

Research output: Contribution to journalArticle

Glutathione Transferase
Renal Insufficiency
Heart Failure
Exome

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

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

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
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

Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients

Sausen, M., Phallen, J., Adleff, V., Jones, S., Leary, R. J., Barrett, M. T., Anagnostou, V., Parpart-Li, S., Murphy, D., Li, Q. K., Hruban, C. A., Scharpf, R. B., White, J. R., O'Dwyer, P. J., Allen, P. J., Eshleman, J., Thompson, C. B., Klimstra, D. S., Linehan, D. C., Maitra, A. & 6 others, Hruban, R. H., Diaz, L. A., Von Hoff, D. D., Johansen, J. S., Drebin, J. A. & Velculescu, V. E., Jul 7 2015, In : Nature Communications. 6, 7686.

Research output: Contribution to journalArticle

Pancreatic Neoplasms
Tumors
tumors
cancer
Neoplasms

NDRG1 links p53 with proliferation-mediated centrosome homeostasis and genome stability

Croessmann, S., Wong, H. Y., Zabransky, D. J., Chu, D., Mendonca, J., Sharmaa, A., Mohseni, M., Rosen, D. M., Scharpf, R. B., Cidado, J., Cochran, R. L., Parsons, H. A., Dalton, W., Erlanger, B., Button, B., Cravero, K., Kyker-Snowman, K., Beaver, J., Kachhap, S., Hurley, P. & 2 others, Lauring, J. & Park, B. H., Sep 15 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 37, p. 11583-11588 6 p.

Research output: Contribution to journalArticle

Centrosome
Genomic Instability
Homeostasis
Genes
Neoplasms

The genomic landscape of response to EGFR blockade in colorectal cancer

Bertotti, A., Papp, E., Jones, S., Adleff, V., Anagnostou, V., Lupo, B., Sausen, M., Phallen, J., Hruban, C. A., Tokheim, C., Niknafs, N., Nesselbush, M., Lytle, K., Sassi, F., Cottino, F., Migliardi, G., Zanella, E. R., Ribero, D., Russolillo, N., Mellano, A. & 15 others, Muratore, A., Paraluppi, G., Salizzoni, M., Marsoni, S., Kragh, M., Lantto, J., Cassingena, A., Li, Q. K., Karchin, R., Scharpf, R. B., Sartore-Bianchi, A., Siena, S., Diaz, L. A., Trusolino, L. & Velculescu, V. E., Oct 8 2015, In : Nature. 526, 7572, p. 263-267 5 p.

Research output: Contribution to journalArticle

Epidermal Growth Factor Receptor
Colorectal Neoplasms
Neoplasms
Therapeutics
Transplants
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

Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma

Scott, A. F., Mohr, D. W., Ling, H., Scharpf, R. B., Zhang, P. & Liptak, G. S., 2014, In : Genes. 5, 2, p. 366-384 19 p.

Research output: Contribution to journalArticle

Small Cell Carcinoma
Prostate
Neoplasms
Exome
Loss of Heterozygosity

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

Scharpf, R. B., Mireles, L., Yang, Q., Köttgen, A., Ruczinski, I., Susztak, K., Halper-Stromberg, E., Tin, A., Cristiano, S., Chakravarti, A., Boerwinkle, E., Fox, C. S., Coresh, J. & Linda Kao, W. H., Jul 9 2014, In : BMC Genetics. 15, 81.

Research output: Contribution to journalArticle

DNA Copy Number Variations
Uric Acid
Single Nucleotide Polymorphism
Serum
Atherosclerosis

Detecting disease variants in case-parent trio studies using the bioconductor software package trio.

Schwender, H., Li, Q., Neumann, C., Taub, M. A., Younkin, S. G., Berger, P., Scharpf, R. B., Beaty, T. L. & Ruczinski, I., 2014, In : Genetic Epidemiology. 38, 6, p. 516-522 7 p.

Research output: Contribution to journalArticle

Software
Gene-Environment Interaction
Workflow
Sample Size
Genes

MACROD2 overexpression mediates estrogen independent growth and tamoxifen resistance in breast cancers

Mohseni, M., Cidado, J., Croessmann, S., Cravero, K., Cimino-Mathews, A. M., Wong, H. Y., Scharpf, R. B., Zabransky, D. J., Abukhdeir, A. M., Garay, J. P., Wang, G. M., Beaver, J., Cochran, R. L., Blair, B. G., Rosen, D. M., Erlanger, B., Argani, P., Hurley, P., Lauring, J. & Park, B. H., Dec 9 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 49, p. 17606-17611 6 p.

Research output: Contribution to journalArticle

Tamoxifen
Estrogens
Breast Neoplasms
Growth
Estrogen Receptor alpha
2012

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

Laurie, C. C., Laurie, C. A., Rice, K., Doheny, K., Zelnick, L. R., McHugh, C. P., Ling, H., Hetrick, K. N., Pugh, E., Amos, C., Wei, Q., Wang, L. E., Lee, J. E., Barnes, K. C., Hansel, N., Mathias, R., Daley, D., Beaty, T. L., Scott, A. F., Ruczinski, I. & 53 others, Scharpf, R. B., Bierut, L. J., Hartz, S. M., Landi, M. T., Freedman, N. D., Goldin, L. R., Ginsburg, D., Li, J., Desch, K. C., Strom, S. S., Blot, W. J., Signorello, L. B., Ingles, S. A., Chanock, S. J., Berndt, S. I., Le Marchand, L., Henderson, B. E., Monroe, K. R., Heit, J. A., De Andrade, M., Armasu, S. M., Regnier, C., Lowe, W. L., Hayes, M. G., Marazita, M. L., Feingold, E., Murray, J. C., Melbye, M., Feenstra, B., Kang, J. H., Wiggs, J. L., Jarvik, G. P., McDavid, A. N., Seshan, V. E., Mirel, D. B., Crenshaw, A., Sharopova, N., Wise, A., Shen, J., Crosslin, D. R., Levine, D. M., Zheng, X., Udren, J. I., Bennett, S., Nelson, S. C., Gogarten, S. M., Conomos, M. P., Heagerty, P., Manolio, T., Pasquale, L. R., Haiman, C. A., Caporaso, N. & Weir, B. S., Jun 2012, In : Nature Genetics. 44, 6, p. 642-650 9 p.

Research output: Contribution to journalArticle

Mosaicism
Parturition
Chromosome Duplication
Uniparental Disomy
Abnormal Karyotype

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

Scharpf, R. B., Beaty, T. L., Schwender, H., Younkin, S. G., Scott, A. F. & Ruczinski, I., Dec 12 2012, In : BMC Bioinformatics. 13, 1, 330.

Research output: Contribution to journalArticle

Hidden Markov models
Single Nucleotide Polymorphism
Joints
Markov Model
Genomics
2011

A multilevel model to address batch effects in copy number estimation using SNP arrays

Scharpf, R. B., Ruczinski, I., Carvalho, B., Doan, B., Chakravarti, A. & Irizarry, R. A., Jan 2011, In : Biostatistics. 12, 1, p. 33-50 18 p.

Research output: Contribution to journalArticle

Multilevel Models
Single nucleotide Polymorphism
Batch
Single Nucleotide Polymorphism
DNA Copy Number Variations

Influence of Diabetes Mellitus Type 2 and Prolonged Estrogen Exposure on Risk of Breast Cancer Among Women in Armenia

Khachatryan, L., Scharpf, R. B. & Kagan, S., 2011, In : Health Care for Women International. 32, 11, p. 953-971 19 p.

Research output: Contribution to journalArticle

Armenia
Type 2 Diabetes Mellitus
Estrogens
Breast Neoplasms
Induced Abortion

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

Halper-Stromberg, E., Frelin, L., Ruczinski, I., Scharpf, R. B., Jie, C., Carvalho, B., Hao, H., Hetrick, K., Jedlicka, A. E., Dziedzic, A., Doheny, K., Scott, A. F., Baylin, S. B., Pevsner, J. A., Spencer, F. & Irizarry, R. A., Apr 2011, In : Bioinformatics. 27, 8, p. 1052-1060 9 p., btr106.

Research output: Contribution to journalArticle

DNA Copy Number Variations
Benchmarking
Performance Assessment
Microarrays
Nucleotides

Using the r package crlmm for genotyping and copy number estimation

Scharpf, R. B., Irizarry, R. A., Ritchie, M. E., Carvalho, B. & Ruczinski, I., 2011, In : Journal of Statistical Software. 40, 12, p. 1-32 32 p.

Research output: Contribution to journalArticle

Phenotype
Batch
Estimate
Measures of Association
Multilevel Models
2010

Cross-platform comparison of two pancreatic cancer phenotypes

Scharpf, R. B., Iacobuzio-Donahue, C. A., Cope, L., Ruczinski, I., Garrett-Mayer, E., Lakkur, S., Campagna, D. & Parmigiani, G., 2010, In : Cancer Informatics. 9, p. 257-264 8 p.

Research output: Contribution to journalArticle

Pancreatic Neoplasms
Phenotype
Cell Line
Artifacts
Gene Expression

R classes and methods for SNP array data.

Scharpf, R. B. & Ruczinski, I., 2010, In : Methods in molecular biology (Clifton, N.J.). 593, p. 67-79 13 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Software
Programming Languages

Tackling the widespread and critical impact of batch effects in high-throughput data

Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K. & Irizarry, R. A., Oct 14 2010, In : Nature Reviews Genetics. 11, 10, p. 733-739 7 p.

Research output: Contribution to journalArticle

Epigenomics
Artifacts
Technology
Gene Expression
Proteins
2009

A Bayesian model for cross-study differential gene expression

Scharpf, R. B., Tjelmeland, H., Parmigiani, G. & Nobel, A. B., Dec 2009, In : Journal of the American Statistical Association. 104, 488, p. 1295-1310 16 p.

Research output: Contribution to journalArticle

Differential Expression
Bayesian Model
Gene Expression
Estrogen Receptor
Shrinkage

Genome-wide association study of blood pressure and hypertension

Levy, D., Ehret, G. B., Rice, K., Verwoert, G. C., Launer, L. J., Dehghan, A., Glazer, N. L., Morrison, A. C., Johnson, A. D., Aspelund, T., Aulchenko, Y., Lumley, T., Köttgen, A., Vasan, R. S., Rivadeneira, F., Eiriksdottir, G., Guo, X., Arking, D., Mitchell, G. F., Mattace-Raso, F. U. S. & 24 others, Smith, A. V., Taylor, K., Scharpf, R. B., Hwang, S. J., Sijbrands, E. J. G., Bis, J., Harris, T. B., Ganesh, S. K., O'Donnell, C. J., Hofman, A., Rotter, J. I., Coresh, J., Benjamin, E. J., Uitterlinden, A. G., Heiss, G., Fox, C. S., Witteman, J. C. M., Boerwinkle, E., Wang, T. J., Gudnason, V., Larson, M. G., Chakravarti, A., Psaty, B. M. & Van Duijn, C. M., Jun 2009, In : Nature Genetics. 41, 6, p. 677-687 11 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Blood Pressure
Hypertension
Single Nucleotide Polymorphism
Meta-Analysis
Conjugacy
Genomics
High Throughput
Linear Models
Linear Model

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

Köttgen, A., Glazer, N. L., Dehghan, A., Hwang, S. J., Katz, R., Li, M., Yang, Q., Gudnason, V., Launer, L. J., Harris, T. B., Smith, A. V., Arking, D., Astor, B. C., Boerwinkle, E., Ehret, G. B., Ruczinski, I., Scharpf, R. B., Ida Chen, Y. D., De Boer, I. H., Haritunians, T. & 19 others, Lumley, T., Sarnak, M., Siscovick, D., Benjamin, E. J., Levy, D., Upadhyay, A., Aulchenko, Y. S., Hofman, A., Rivadeneira, F., Uitterlinden, A. G., Van Duijn, C. M., Chasman, D. I., Paré, G., Ridker, P. M., Kao, W. H. L., Witteman, J. C., Coresh, J., Shlipak, M. G. & Fox, C. S., Jun 2009, In : Nature Genetics. 41, 6, p. 712-717 6 p.

Research output: Contribution to journalArticle

Chronic Renal Insufficiency
Kidney
Cystatin C
Genome-Wide Association Study
Kidney Diseases

Processing and analyzing Affymetrix SNP chips with Bioconductor

Carvalho, B., Irizarry, R. A., Scharpf, R. B. & Carey, V. J., 2009, In : Statistics in Biosciences. 1, 2, p. 160-180 21 p.

Research output: Contribution to journalArticle

Genotype
Single Nucleotide Polymorphism
Chip
Probe
Processing

Rejoinder

Scharpf, R. B., Tjelmeland., H., Parmigiani., G. & Nobel, A. B., Dec 2009, In : Journal of the American Statistical Association. 104, 488, p. 1318-1323 6 p.

Research output: Contribution to journalArticle

2008

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

Scharpf, R. B., Parmigiani, G., Pevsner, J. A. & Ruczinski, I., Jun 2008, In : Annals of Applied Statistics. 2, 2, p. 687-713 27 p.

Research output: Contribution to journalArticle

Single nucleotide Polymorphism
Hidden Markov models
Nucleotides
Polymorphism
Markov Model
2007

Pre-processing Agilent microarray data

Zahurak, M., Parmigiani, G., Yu, W., Scharpf, R. B., Berman, D., Schaeffer, E., Shabbeer, S. & Cope, L., May 1 2007, In : BMC Bioinformatics. 8, 142.

Research output: Contribution to journalArticle

Microarrays
Background Subtraction
Microarray Data
Normalization
Preprocessing

SNPchip: R classes and methods for SNP array data

Scharpf, R. B., Ting, J. C., Pevsner, J. A. & Ruczinski, I., Mar 2007, In : Bioinformatics. 23, 5, p. 627-628 2 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Chip
Genes
Genome
Microarrays

When should one subtract background fluorescence in 2-color microarrays?

Scharpf, R. B., Iacobuzio-Donahue, C. A., Sneddon, J. B. & Parmigiani, G., Oct 2007, In : Biostatistics. 8, 4, p. 695-707 13 p.

Research output: Contribution to journalArticle

Microarray
Fluorescence
Background Subtraction
Color
Noise
2005

Regulation of platelet granule exocytosis by S-nitrosylation

Morrell, C. N., Matsushita, K., Chiles, K., Scharpf, R. B., Yamakuchi, M., Mason, R. J. A., Bergmeier, W., Mankowski, J. L., Baldwin, W. M., Faraday, N. & Lowenstein, C. J., Mar 8 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 10, p. 3782-3787 6 p.

Research output: Contribution to journalArticle

Exocytosis
N-Ethylmaleimide-Sensitive Proteins
Blood Platelets
Nitric Oxide
Platelet Activation
2004

Platelet gene polymorphisms and cardiac risk assessment in vascular surgical patients

Faraday, N., Martinez, E. A., Scharpf, R. B., Kasch-Semenza, L., Dorman, T., Pronovost, P. J., Perler, B. A., Gerstenblith, G., Bray, P. F. & Fleisher, L. A., Dec 2004, In : Anesthesiology. 101, 6, p. 1291-1297 7 p.

Research output: Contribution to journalArticle

Blood Vessels
Blood Platelets
Odds Ratio
Integrin beta3
Myocardial Ischemia
2003

Statistical modeling and visualization of molecular profiles in cancer

Scharpf, R. B., Garrett, E. S., Hu, J. & Parmigiani, G., Mar 1 2003, In : BioTechniques. 34, 3 SUPPL.

Research output: Contribution to journalArticle

Visualization
Microarrays
Neoplasms
Gene expression
Noise
2002

Utility of whole blood hemostatometry using The Clot Signature Analyzer® for assessment of hemostasis in cardiac surgery

Faraday, N., Guallar, E., Sera, V. A., Bolton, E. D., Scharpf, R. B., Cartarius, A. M., Emery, K., Concord, J. & Kickler, T. S., 2002, In : Anesthesiology. 96, 5, p. 1115-1122 8 p.

Research output: Contribution to journalArticle

Hemostasis
Thoracic Surgery
Hemostatics
Cardiopulmonary Bypass
Thrombosis
2001
P-Selectin
Thromboxanes
Platelet Aggregation
Leukocytes
Blood Platelets