Shannon McWeeney

Professor, PhD, Division Head

  • Mail Code: BICC, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239-3098

  • 5832 Citations
  • 40 h-Index
19952020
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Research Output 1997 2019

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Article
2015
18 Citations (Scopus)

Limited clinical utility of a genetic risk score for the prediction of fracture risk in elderly subjects

Eriksson, J., Evans, D. S., Nielson, C., Shen, J., Srikanth, P., Hochberg, M., McWeeney, S., Cawthon, P. M., Wilmot, B., Zmuda, J., Tranah, G., Mirel, D. B., Challa, S., Mooney, M., Crenshaw, A., Karlsson, M., Mellström, D., Vandenput, L., Orwoll, E. & Ohlsson, C., Jan 1 2015, In : Journal of Bone and Mineral Research. 30, 1, p. 184-194 11 p.

Research output: Contribution to journalArticle

Bone Density
Osteoporotic Fractures
Sweden
Area Under Curve
Meta-Analysis
21 Citations (Scopus)

Maternal high-fat diet and obesity compromise fetal hematopoiesis

Kamimae-Lanning, A. N., Krasnow, S., Goloviznina, N. A., Zhu, X., Roth-Carter, Q. R., Levasseur, P. R., Jeng, S., McWeeney, S., Kurre, P. & Marks, D., Jan 1 2015, In : Molecular Metabolism. 4, 1, p. 25-38 14 p.

Research output: Contribution to journalArticle

Hematopoiesis
High Fat Diet
Hematopoietic Stem Cells
Obesity
Mothers

plethy: Management of whole body plethysmography data in R

Bottomly, D., Wilmot, B. & McWeeney, S., Apr 29 2015, In : BMC Bioinformatics. 16, 1, 134.

Research output: Contribution to journalArticle

Whole Body Plethysmography
Plethysmography
Exploratory Data Analysis
Mouse
Severe Acute Respiratory Syndrome
4 Citations (Scopus)

Splicing landscape of the eight collaborative cross founder strains

Zheng, C., Wilmot, B., Walter, N. A. R., Oberbeck, D., Kawane, S., Searles, R., McWeeney, S. & Hitzemann, R., Feb 5 2015, In : BMC Genomics. 16, 1, 52.

Research output: Contribution to journalArticle

Transcriptome
Exons
Population
High-Throughput Nucleotide Sequencing
Inbred Strains Mice
8 Citations (Scopus)

Therapeutically targetable ALK mutations in leukemia

Maxson, J., Davare, M., Luty, S. B., Eide, C. A., Chang, B., Loriaux, M., Tognon, C. E., Bottomly, D., Wilmot, B., McWeeney, S., Druker, B. & Tyner, J., Jun 1 2015, In : Cancer Research. 75, 11, p. 2146-2150 5 p.

Research output: Contribution to journalArticle

Leukemia
Mutation
Phosphotransferases
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Point Mutation
7 Citations (Scopus)

Use of semantic workflows to enhance transparency and reproducibility in clinical omics

Zheng, C., Ratnakar, V., Gil, Y. & McWeeney, S., Jul 25 2015, In : Genome Medicine. 7, 1, 73.

Research output: Contribution to journalArticle

Workflow
Semantics
Patient Safety
Galaxies
2014
15 Citations (Scopus)

A comprehensive collection of systems biology data characterizing the host response to viral infection

Aevermann, B. D., Pickett, B. E., Kumar, S., Klem, E. B., Agnihothram, S., Askovich, P. S., Bankhead, A., Bolles, M., Carter, V., Chang, J., Clauss, T. R. W., Dash, P., Diercks, A. H., Eisfeld, A. J., Ellis, A., Fan, S., Ferris, M. T., Gralinski, L. E., Green, R. R., Gritsenko, M. A. & 48 others, Hatta, M., Heegel, R. A., Jacobs, J. M., Jeng, S., Josset, L., Kaiser, S. M., Kelly, S., Law, G. L., Li, C., Li, J., Long, C., Luna, M. L., Matzke, M., McDermott, J., Menachery, V., Metz, T. O., Mitchell, H., Monroe, M. E., Navarro, G., Neumann, G., Podyminogin, R. L., Purvine, S. O., Rosenberger, C. M., Sanders, C. J., Schepmoes, A. A., Shukla, A. K., Sims, A., Sova, P., Tam, V. C., Tchitchek, N., Thomas, P. G., Tilton, S. C., Totura, A., Wang, J., Webb-Robertson, B. J., Wen, J., Weiss, J. M., Yang, F., Yount, B., Zhang, Q., McWeeney, S., Smith, R. D., Waters, K. M., Kawaoka, Y., Baric, R., Aderem, A., Katze, M. G. & Scheuermann, R. H., Oct 14 2014, In : Scientific data. 1, 140033.

Research output: Contribution to journalArticle

Systems Biology
Pathogens
Virus Diseases
Viruses
Virus
15 Citations (Scopus)

BCR-ABL1 promotes leukemia by converting p27 into a cytoplasmic oncoprotein

Agarwal, A., Mackenzie, R. J., Besson, A., Jeng, S., Carey, A., LaTocha, D. H., Fleischman, A. G., Duquesnes, N., Eide, C. A., Vasudevan, K. B., Loriaux, M., Firpo, E., Cortes, J. E., McWeeney, S., O'Hare, T., Roberts, J. M., Druker, B. & Deininger, M. W., Nov 20 2014, In : Blood. 124, 22, p. 3260-3273 14 p.

Research output: Contribution to journalArticle

Oncogene Proteins
Leukemia, Myelogenous, Chronic, BCR-ABL Positive
Tumors
Leukemia
Cyclin-Dependent Kinases
3 Citations (Scopus)

Challenges in secondary analysis of high throughput screening data.

Blucher, A. S. & McWeeney, S., 2014, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 114-124 11 p.

Research output: Contribution to journalArticle

Drug Repositioning
Practice Guidelines
Biological Assay
Databases
Costs and Cost Analysis
15 Citations (Scopus)

Corepressor Rcor1 is essential for murine erythropoiesis

Yao, H., Goldman, D., Nechiporuk, T., Kawane, S., McWeeney, S., Tyner, J., Fan, G., Kerenyi, M. A., Orkin, S. H., Fleming, W. & Mandel, G., May 15 2014, In : Blood. 123, 20, p. 3175-3184 10 p.

Research output: Contribution to journalArticle

Co-Repressor Proteins
Erythropoiesis
Genes
Erythroblasts
Colony-Stimulating Factor Receptors
60 Citations (Scopus)

Cytomegalovirus miRNAs target secretory pathway genes to facilitate formation of the virion assembly compartment and reduce cytokine secretion

Hook, L. M., Grey, F., Grabski, R., Tirabassi, R., Doyle, T., Hancock, M., Landais, I., Jeng, S., McWeeney, S., Britt, W. & Nelson, J., Mar 12 2014, In : Cell Host and Microbe. 15, 3, p. 363-373 11 p.

Research output: Contribution to journalArticle

Secretory Pathway
Cytomegalovirus
MicroRNAs
Virion
Cytokines
1 Citation (Scopus)

Data integration and reproducibility for high-throughput transcriptomics

Mooney, M. & McWeeney, S., 2014, In : International Review of Neurobiology. 116, p. 55-71 17 p.

Research output: Contribution to journalArticle

Transcriptome
Practice Guidelines
Computer Simulation
Research Personnel
Guidelines
17 Citations (Scopus)

Dual-Trait Selection for Ethanol Consumption and Withdrawal: Genetic and Transcriptional Network Effects

Metten, P., Iancu, O., Spence, S. E., Walter, N. A. R., Oberbeck, D., Harrington, C. C., Colville, A., McWeeney, S., Phillips, T., Buck, K., Crabbe, J. J., Belknap, J. & Hitzemann, R., Dec 1 2014, In : Alcoholism: Clinical and Experimental Research. 38, 12, p. 2915-2924 10 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Quantitative Trait Loci
Chromosomes
Ethanol
Genes
56 Citations (Scopus)

Functional and genomic context in pathway analysis of GWAS data

Mooney, M., Nigg, J., McWeeney, S. & Wilmot, B., 2014, In : Trends in Genetics. 30, 9, p. 390-400 11 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Genes
Single Nucleotide Polymorphism
Information Storage and Retrieval
Disease Susceptibility
10 Citations (Scopus)

Introduction to sequencing the brain transcriptome

Hitzemann, R., Darakjian, P., Walter, N., Iancu, O., Searles, R. & McWeeney, S., 2014, In : International Review of Neurobiology. 116, p. 1-19 19 p.

Research output: Contribution to journalArticle

Transcriptome
RNA
Brain
Untranslated RNA
Gene Regulatory Networks
2 Citations (Scopus)

Oligomask: A framework for assessing and removing the effect of genetic variants on microarray probes

Bottomly, D., Wilmot, B. & McWeeney, S., 2014, In : R Journal. 6, 1, p. 159-163 5 p.

Research output: Contribution to journalArticle

Microarrays
Microarray
Probe
Messenger RNA
Experiment

'Pitfalls in the application of gene set analysis to genetics studies': A response

Mooney, M., Nigg, J., McWeeney, S. & Wilmot, B., Dec 1 2014, In : Trends in Genetics. 30, 12, p. 514-515 2 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Human Genome
Genetic Predisposition to Disease
Genomics
Single Nucleotide Polymorphism
7 Citations (Scopus)
Gene Expression
2013
66 Citations (Scopus)

Androgen Receptor Promotes Ligand-Independent Prostate Cancer Progression through c-Myc Upregulation

Gao, L., Schwartzman, J., Gibbs, A., Lisac, R., Kleinschmidt, R., Wilmot, B., Bottomly, D., Coleman, I., Nelson, P., McWeeney, S. & Alumkal, J., May 21 2013, In : PLoS One. 8, 5, e63563.

Research output: Contribution to journalArticle

Androgen Receptors
prostatic neoplasms
Prostatic Neoplasms
Up-Regulation
Ligands
8 Citations (Scopus)

A simulation framework to investigate in vitro viral infection dynamics

Bankhead, A., Mancini, E., Sims, A. C., Baric, R. S., McWeeney, S. & Sloot, P. M. A., 2013, In : Journal of Computational Science. 4, 3, p. 127-134 8 p.

Research output: Contribution to journalArticle

Simulation Framework
Viruses
Infection
Virus
Severe Acute Respiratory Syndrome
15 Citations (Scopus)

A systems framework for vaccine design.

Mooney, M., McWeeney, S., Canderan, G. & Sékaly, R. P., Oct 2013, In : Current Opinion in Immunology. 25, 5, p. 551-555 5 p.

Research output: Contribution to journalArticle

Vaccines
Host-Pathogen Interactions
Precision Medicine
Systems Biology
Immunity
4 Citations (Scopus)
Precision Medicine
Genes
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Small Interfering RNA
Genome
17 Citations (Scopus)

Copy number variation analysis in 98 individuals with PHACE syndrome

Siegel, D. H., Shieh, J. T. C., Kwon, E. K., Baselga, E., Blei, F., Cordisco, M., Dobyns, W. B., Duffy, K. J., Garzon, M. C., Gibbs, D. L., Grimmer, J. F., Hayflick, S., Krol, A., Kwok, P. Y., Lorier, R., Matter, A., McWeeney, S., Metry, D., Mitchell, S., Pope, E. & 8 others, Santoro, J. L., Stevenson, D. A., Bayrak-Toydemir, P., Wilmot, B., Worthey, E. A., Frieden, I. J., Drolet, B. A. & Broeckel, U., Mar 2013, In : Journal of Investigative Dermatology. 133, 3, p. 677-684 8 p.

Research output: Contribution to journalArticle

Genes
Defects
Aortic Coarctation
Centromere
Hemangioma
15 Citations (Scopus)

Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules

Iancu, O., Oberbeck, D., Darakjian, P., Kawane, S., Erk, J., McWeeney, S. & Hitzemann, R., Mar 21 2013, In : PLoS One. 8, 3, e58951.

Research output: Contribution to journalArticle

Catalepsy
Haloperidol
Electric network analysis
haloperidol
genetic techniques and protocols
46 Citations (Scopus)

Genes, behavior and next-generation RNA sequencing

Hitzemann, R., Bottomly, D., Darakjian, P., Walter, N., Iancu, O., Searles, R., Wilmot, B. & McWeeney, S., Feb 2013, In : Genes, Brain and Behavior. 12, 1, p. 1-12 12 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
RNA
Genes
Brain
Untranslated RNA
14 Citations (Scopus)

Genetic factors involved in risk for methamphetamine intake and sensitization

Belknap, J., McWeeney, S., Reed, C., Burkhart-Kasch, S., McKinnon, C. S., Li, N., Baba, H., Scibelli, A. C., Hitzemann, R. & Phillips, T., Dec 2013, In : Mammalian Genome. 24, 11-12, p. 446-458 13 p.

Research output: Contribution to journalArticle

Methamphetamine
Drinking
Quantitative Trait Loci
Chromosomes, Human, Pair 10
Opioid Analgesics
6 Citations (Scopus)

HitWalker: Variant prioritization for personalized functional cancer genomics

Bottomly, D., Wilmot, B., Tyner, J., Eide, C. A., Loriaux, M., Druker, B. & McWeeney, S., Feb 15 2013, In : Bioinformatics. 29, 4, p. 509-510 2 p.

Research output: Contribution to journalArticle

Prioritization
Genomics
Cancer
Program documentation
Proteins
26 Citations (Scopus)

Human Mycobacterium tuberculosis CD8 T Cell Antigens/Epitopes Identified by a Proteomic Peptide Library

Lewinsohn, D., Swarbrick, G. M., Cansler, M. E., Null, M. D., Rajaraman, V., Frieder, M. M., Sherman, D. R., McWeeney, S. & Lewinsohn, D., Jun 21 2013, In : PLoS One. 8, 6, e67016.

Research output: Contribution to journalArticle

peptide libraries
CD8 Antigens
Peptide Library
T-Lymphocyte Epitopes
T-cells
38 Citations (Scopus)

Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury

Gralinski, L. E., Bankhead, A., Jeng, S., Menachery, V. D., Proll, S., Belisle, S. E., Matzke, M., Webb-Robertson, B. J. M., Luna, M. L., Shukla, A. K., Ferris, M. T., Bolles, M., Chang, J., Aicher, L., Waters, K. M., Smith, R. D., Metz, T. O., Law, G. L., Katze, M. G., McWeeney, S. & 1 others, Baric, R. S., Aug 6 2013, In : mBio. 4, 4

Research output: Contribution to journalArticle

Severe Acute Respiratory Syndrome
Coronavirus
Acute Lung Injury
Coronavirus Infections
Urokinase-Type Plasminogen Activator
107 Citations (Scopus)

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

Ferris, M. T., Aylor, D. L., Bottomly, D., Whitmore, A. C., Aicher, L. D., Bell, T. A., Bradel-Tretheway, B., Bryan, J. T., Buus, R. J., Gralinski, L. E., Haagmans, B. L., McMillan, L., Miller, D. R., Rosenzweig, E., Valdar, W., Wang, J., Churchill, G. A., Threadgill, D. W., McWeeney, S., Katze, M. G. & 3 others, Pardo-Manuel de Villena, F., Baric, R. S. & Heise, M. T., Feb 2013, In : PLoS Pathogens. 9, 2, e1003196.

Research output: Contribution to journalArticle

Human Influenza
Quantitative Trait Loci
Weight Loss
Virus Replication
Viruses
15 Citations (Scopus)

Multi-omic network signatures of disease

Gibbs, D. L., Gralinski, L., Baric, R. S. & McWeeney, S., 2013, In : Frontiers in Genetics. 4, JAN, Article 309.

Research output: Contribution to journalArticle

National Institute of Allergy and Infectious Diseases (U.S.)
SARS Virus
Phenotype
Virology
Proteome
278 Citations (Scopus)

Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML

Maxson, J., Gotlib, J., Pollyea, D. A., Fleischman, A. G., Agarwal, A., Eide, C. A., Bottomly, D., Wilmot, B., McWeeney, S., Tognon, C. E., Pond, J. B., Collins, R. H., Goueli, B., Stephen, T. O., Michael, W. D., Chang, B., Loriaux, M., Druker, B. & Tyner, J., 2013, In : New England Journal of Medicine. 368, 19, p. 1781-1790 10 p.

Research output: Contribution to journalArticle

Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative
Leukemia, Neutrophilic, Chronic
Mutation
Phosphotransferases
Neoplasms
18 Citations (Scopus)

Protein co-expression network analysis (ProCoNA)

Gibbs, D. L., Baratt, A., Baric, R. S., Kawaoka, Y., Smith, R. D., Orwoll, E., Katze, M. G. & McWeeney, S., Jun 1 2013, In : Journal of Clinical Bioinformatics. 3, 1, 11.

Research output: Contribution to journalArticle

Proteins
Proteomics
Peptides
Gene Ontology
Peptide Mapping
33 Citations (Scopus)

Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells

Sims, A. C., Tilton, S. C., Menachery, V. D., Gralinski, L. E., Schäfer, A., Matzke, M. M., Webb-Robertson, B. J. M., Chang, J., Luna, M. L., Long, C. E., Shukla, A. K., Bankhead, A. R., Burkett, S. E., Zornetzer, G., Tseng, C. T. K., Metz, T. O., Pickles, R., McWeeney, S., Smith, R. D., Katze, M. G. & 2 others, Waters, K. M. & Barica, R. S., Apr 2013, In : Journal of Virology. 87, 7, p. 3885-3902 18 p.

Research output: Contribution to journalArticle

Severe Acute Respiratory Syndrome
Coronavirus
Cell Nucleus Active Transport
imports
transcription (genetics)
46 Citations (Scopus)

Selection for drinking in the dark alters brain gene coexpression networks

Iancu, O., Oberbeck, D., Darakjian, P., Metten, P., McWeeney, S., Crabbe, J. J. & Hitzemann, R., Aug 2013, In : Alcoholism: Clinical and Experimental Research. 37, 8, p. 1295-1303 9 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Drinking
Brain
Genes
Phenotype
13 Citations (Scopus)

Systems immunogenetics of vaccines

Mooney, M., McWeeney, S. & Sékaly, R. P., Apr 2013, In : Seminars in Immunology. 25, 2, p. 124-129 6 p.

Research output: Contribution to journalArticle

Immunogenetics
Vaccines
Precision Medicine
Virus Diseases
Population
2012
5 Citations (Scopus)
Quantitative Trait Loci
Chromosomes
Population
Genome
Gene Expression
65 Citations (Scopus)

Expression quantitative trait loci for extreme host response to influenza A in pre-collaborative cross mice

Bottomly, D., Ferris, M. T., Aicher, L. D., Rosenzweig, E., Whitmore, A., Aylor, D. L., Haagmans, B. L., Gralinski, L. E., Bradel-Tretheway, B. G., Bryan, J. T., Threadgill, D. W., De Villena, F. P. M., Baric, R. S., Katze, M. G., Heise, M. & McWeeney, S., Feb 2012, In : G3: Genes, Genomes, Genetics. 2, 2, p. 213-221 9 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Human Influenza
Virus Diseases
Infection
Population
19 Citations (Scopus)

Gene networks and haloperidol-induced catalepsy

Iancu, O., Darakjian, P., Malmanger, B., Walter, N. A. R., McWeeney, S. & Hitzemann, R., Feb 2012, In : Genes, Brain and Behavior. 11, 1, p. 29-37 9 p.

Research output: Contribution to journalArticle

Catalepsy
Gene Regulatory Networks
Haloperidol
Corpus Striatum
Metabolic Networks and Pathways
12 Citations (Scopus)

Heritability of serum sodium concentration: Evidence for sex- and ethnic-specific effects

Wilmot, B., Saroja Voruganti, V., Chang, Y. P. C., Fu, Y., Chen, Z., Taylor, H. A., Wilson, J. G., Gipson, T., Shah, V. O., Umans, J. G., Flessner, M. F., Hitzemann, R., Shuldiner, A. R., Comuzzie, A. G., McWeeney, S., Zager, P. G., Maccluer, J. W., Cole, S. A. & Cohen, D., Feb 2012, In : Physiological Genomics. 44, 3, p. 220-228 9 p.

Research output: Contribution to journalArticle

North American Indians
Sodium
Serum
Glomerular Filtration Rate
Glucose
12 Citations (Scopus)

Immune response gene profiles in the term placenta depend upon maternal muscle mass

O'Tierney, P. F., Lewis, R. M., McWeeney, S., Hanson, M. A., Inskip, H. M., Morgan, T., Barker, D. J., Bagby, G., Cooper, C., Godfrey, K. M. & Thornburg, K., Oct 2012, In : Reproductive Sciences. 19, 10, p. 1041-1056 16 p.

Research output: Contribution to journalArticle

Placenta
Mothers
Muscles
Genes
Immune System Phenomena
14 Citations (Scopus)
Genome-Wide Association Study
Single Nucleotide Polymorphism
Genes
Genetic algorithms
Genetic Algorithm
247 Citations (Scopus)

The genome architecture of the collaborative cross mouse genetic reference population

Iraqi, F. A., Mahajne, M., Salaymah, Y., Sandovski, H., Tayem, H., Vered, K., Balmer, L., Hall, M., Manship, G., Morahan, G., Pettit, K., Scholten, J., Tweedie, K., Wallace, A., Weerasekera, L., Cleak, J., Durrant, C., Goodstadt, L., Mott, R., Yalcin, B. & 110 others, Aylor, D. L., Baric, R. S., Bell, T. A., Bendt, K. M., Brennan, J., Brooks, J. D., Buus, R. J., Crowley, J. J., Calaway, J. D., Calaway, M. E., Cholka, A., Darr, D. B., Didion, J. P., Dorman, A., Everett, E. T., Ferris, M. T., Mathes, W. F., Fu, C. P., Gooch, T. J., Goodson, S. G., Gralinski, L. E., Hansen, S. D., Heise, M. T., Hoel, J., Hua, K., Kapita, M. C., Lee, S., Lenarcic, A. B., Liu, E. Y., Liu, H., McMillan, L., Magnuson, T. R., Manly, K. F., Miller, D. R., O'Brien, D. A., Odet, F., Pakatci, I. K., Pan, W., de Villena, F. P. M., Perou, C. M., Pomp, D., Quackenbush, C. R., Robinson, N. N., Sharpless, N. E., Shaw, G. D., Spence, J. S., Sullivan, P. F., Sun, W., Tarantino, L. M., Valdar, W., Wang, J., Wang, W., Welsh, C. E., Whitmore, A., Wiltshire, T., Wright, F. A., Xie, Y., Yun, Z., Zhabotynsky, V., Zhang, Z., Zou, F., Powell, C., Steigerwalt, J., Threadgill, D. W., Chesler, E. J., Churchill, G. A., Gatti, D. M., Korstanje, R., Svenson, K. L., Collins, F. S., Crawford, N., Hunter, K., Samir, N., Kelada, P., Peck, B. C. E., Reilly, K., Tavarez, U., Bottomly, D., Hitzemann, R., McWeeney, S., Frelinger, J., Krovi, H., Phillippi, J., Spritz, R. A., Aicher, L., Katze, M., Rosenzweig, E., Shusterman, A., Nashef, A., Weiss, E. I., Houri-Haddad, Y., Soller, M., Williams, R. W., Schughart, K., Yang, H., French, J. E., Benson, A. K., Kim, J., Legge, R., Low, S. J., Ma, F., Martinez, I., Walter, J., Broman, K. W., Hallgrimsson, B., Klein, O., Weinstock, G., Warren, W. C., Yang, Y. V. & Schwartz, D., Feb 2012, In : Genetics. 190, 2, p. 389-401 13 p.

Research output: Contribution to journalArticle

Genetic Crosses
Population Genetics
Genome
Breeding
Population
79 Citations (Scopus)

Utilizing RNA-Seq data for de novo coexpression network inference

Iancu, O., Kawane, S., Bottomly, D., Searles, R., Hitzemann, R. & McWeeney, S., Jun 2012, In : Bioinformatics. 28, 12, p. 1592-1597 6 p., bts245.

Research output: Contribution to journalArticle

RNA
Microarrays
Corpus Striatum
Network Structure
Microarray
2011
13 Citations (Scopus)

A DNA methylation microarray-based study identifies ERG as a gene commonly methylated in prostate cancer

Schwartzman, J., Mongoue-Tchokote, S., Gibbs, A., Gao, L., Corless, C., Jin, J., Zarour, L., Higano, C., True, L. D., Vessella, R. L., Wilmot, B., Bottomly, D., McWeeney, S., Bova, S. G., Partin, A. W., Mori, M. T. & Alumkal, J., Oct 2011, In : Epigenetics. 6, 10, p. 1248-1256 9 p.

Research output: Contribution to journalArticle

DNA Methylation
Oligonucleotide Array Sequence Analysis
Prostatic Neoplasms
Genes
Prostate
8 Citations (Scopus)

Computational detection of alternative exon usage

Laderas, T. G., Walter, N. A. R., Mooney, M., Vartanian, K., Darakjian, P., Buck, K., Harrington, C. C., Belknap, J., Hitzemann, R. & McWeeney, S., 2011, In : Frontiers in Neuroscience. MAY, Article 69.

Research output: Contribution to journalArticle

Exons
Statistical Models
Molecular Sequence Annotation
Workflow
Genetic Models
27 Citations (Scopus)

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

McDermott, J. E., Shankaran, H., Eisfeld, A. J., Belisle, S. E., Neuman, G., Li, C., McWeeney, S., Sabourin, C., Kawaoka, Y., Katze, M. G. & Waters, K. M., Nov 11 2011, In : BMC Systems Biology. 5, 190.

Research output: Contribution to journalArticle

Cell Culture
Influenza in Birds
Influenza
Macaca
Virus Diseases
126 Citations (Scopus)

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

Bottomly, D., Walter, N. A. R., Hunter, J. E., Darakjian, P., Kawane, S., Buck, K., Searles, R., Mooney, M., McWeeney, S. & Hitzemann, R., 2011, In : PLoS One. 6, 3, e17820.

Research output: Contribution to journalArticle

Inbred DBA Mouse
Microarrays
Gene expression
RNA
Gene Expression
54 Citations (Scopus)

Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus

Li, C., Bankhead, A., Eisfeld, A. J., Hatta, Y., Jeng, S., Chang, J. H., Aicher, L. D., Proll, S., Ellis, A. L., Law, G. L., Waters, K. M., Neumann, G., Katze, M. G., McWeeney, S. & Kawaoka, Y., Nov 2011, In : Journal of Virology. 85, 21, p. 10955-10967 13 p.

Research output: Contribution to journalArticle

Influenza in Birds
avian influenza
Orthomyxoviridae
Influenza A virus
H5N1 Subtype Influenza A Virus
4 Citations (Scopus)

Microcephaly genes and risk of late-onset Alzheimer disease

Erten-Lyons, D., Wilmot, B., Anur, P., McWeeney, S., Westaway, S., Silbert, L., Kramer, P. & Kaye, J., Jul 2011, In : Alzheimer Disease and Associated Disorders. 25, 3, p. 276-282 7 p.

Research output: Contribution to journalArticle

Microcephaly
Alzheimer Disease
Genes
Brain
Genetic Models