List of works - Shannon K. McWeeney

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two: National Harbor, MD, USA. 9-13 November 2016

scientific article published oln 16 November 2016

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

scientific article

A Mouse Model of Chronic West Nile Virus Disease

scientific article (publication date: November 2016)

A Simulation Framework to Investigate in vitro Viral Infection Dynamics

article

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

scientific article

A systems framework for vaccine design

scientific article published on October 2013

A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs

scientific article

Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID).

scientific article published on 12 April 2017

An antisense transcript induced by Wnt/beta-catenin signaling decreases E2F4.

scientific article published on 22 November 2006

Androgen receptor promotes ligand-independent prostate cancer progression through c-Myc upregulation

scientific article

Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection

scientific article published on 21 September 2020

Brain size genes and risk of dementia

article

CSF1R inhibitors exhibit antitumor activity in acute myeloid leukemia by blocking paracrine signals from support cells

scientific article published on 13 November 2018

Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms

scientific article published in Nature Communications

Comparison of methods to identify aberrant expression patterns in individual patients: augmenting our toolkit for precision medicine

scientific article

Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross

scientific article published on 01 April 2020

Complex genetics of interactions of alcohol and CNS function and behavior

scientific article

Computational detection of alternative exon usage

scientific article

Consensus framework for exploring microarray data using multiple clustering methods

scientific article

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

scientific article

Convergence of Divergent Tumors: A Systems Biology Approach of Tumor-specific Signaling

Copy number variation analysis in 98 individuals with PHACE syndrome

scientific article published on 25 October 2012

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations

scientific article

Cross-species molecular dissection across alcohol behavioral domains

scientific article published on 06 December 2017

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

scientific article

DNA microarray and proteomic strategies for understanding alcohol action

scientific article published on April 2006

Data integration and reproducibility for high-throughput transcriptomics

scientific article

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.

scientific article

Deoxyribonucleic acid microarray analysis of gene expression pattern in the arcuate nucleus/ventromedial nucleus of hypothalamus during lactation

scientific article published on 7 July 2005

Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure

scientific article

Differential network analysis reveals genetic effects on catalepsy modules

scientific article

Distribution of menin-occupied regions in chromatin specifies a broad role of menin in transcriptional regulation

scientific article

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

scientific article published on 30 September 2016

Dual-trait selection for ethanol consumption and withdrawal: genetic and transcriptional network effects

scientific article published in December 2014

ERBB2/HER2 mutations are transforming and therapeutically targetable in leukemia

scientific article published on 04 May 2020

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

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

scientific article

Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice

scientific article published on February 2012

Functional and genomic context in pathway analysis of GWAS data

scientific article

Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma

scientific article published on 25 August 2020

Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs

scientific article published on 22 June 2018

Gene networks and haloperidol-induced catalepsy.

scientific article

Genes, behavior and next-generation RNA sequencing.

scientific article published on 28 December 2012

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse

scientific article

Genetic factors involved in risk for methamphetamine intake and sensitization.

scientific article published on 13 November 2013

Genetics, Behavior, and Brain Dopamine Systems

article

Genomic landscape of neutrophilic leukemias of ambiguous diagnosis

scientific article published on 31 July 2019

High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs.

scientific article

HitWalker: variant prioritization for personalized functional cancer genomics

scientific article

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

scientific article

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

scientific article

Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq

scientific article

Immune Predictors of Mortality After Ribonucleic Acid Virus Infection

scientific article published on 01 March 2020

Influenza vaccination of pregnant women: attitudes and behaviors of Oregon physician prenatal care providers

scientific article published on April 2015

LSD1 activates a lethal prostate cancer gene network independently of its demethylase function.

scientific article published on 26 March 2018

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

scientific article

Localization of TFIIB binding regions using serial analysis of chromatin occupancy

scientific article

Locus and population specific evolution in HLA class II genes.

scientific article published on January 1999

MIFlowCyt: the minimum information about a Flow Cytometry Experiment

scientific article

Mapping cellular transcriptosomes in autopsied Alzheimer's disease subjects and relevant animal models

scientific article

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

scientific article published on 06 August 2013

Microcephaly genes and risk of late-onset Alzheimer disease

scientific article

Modeling host genetic regulation of influenza pathogenesis in the collaborative cross

scientific article (publication date: February 2013)

Multi-omic network signatures of disease.

scientific article published on 07 January 2014

Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia

scientific article published on 29 November 2019

Occupancy classification of position weight matrix-inferred transcription factor binding sites.

scientific article

On the integration of alcohol-related quantitative trait loci and gene expression analyses

scientific article published in October 2004

Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML

scientific article

Protein co-expression network analysis (ProCoNA).

scientific article published on June 2013

Protein database and quantitative analysis considerations when integrating genetics and proteomics to compare mouse strains.

scientific article

REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation-differentiation balance in the developing brain

scientific article published on 03 January 2017

Recurrent cyclin D2 mutations in myeloid neoplasms.

scientific article published on 20 June 2017

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

scientific article published on 30 January 2013

Renal gene and protein expression signatures for prediction of kidney disease progression

scientific article

Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia

scientific article published on 08 June 2020

SNPs matter: impact on detection of differential expression.

scientific article

Selection for drinking in the dark alters brain gene coexpression networks.

scientific article published on 29 March 2013

Similar gene expression profiles do not imply similar tissue functions

scientific article

Splicing landscape of the eight collaborative cross founder strains.

scientific article

Synthetic lethality of TNK2 inhibition in PTPN11-mutant leukemia

scientific article published on 17 July 2018

Systems immunogenetics of vaccines

scientific article (publication date: April 2013)

TandTRAQ: an open-source tool for integrated protein identification and quantitation

scientific article published on 25 September 2007

Teaching data science fundamentals through realistic synthetic clinical cardiovascular data

scholarly article published 12 December 2017

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Plasmodium genome database

scientific article published in Nature

The TP53 Apoptotic Network Is a Primary Mediator of Resistance to BCL2 Inhibition in AML Cells

scientific article published on 02 May 2019

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

scientific article

The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits

scientific article published on 31 December 2013

Translational gene mapping of cognitive decline

scientific article published on 14 December 2006

Utilizing RNA-Seq data for de novo coexpression network inference

scientific article

List of works by Shannon K. McWeeney

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two: National Harbor, MD, USA. 9-13 November 2016

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

A Mouse Model of Chronic West Nile Virus Disease

A Simulation Framework to Investigate in vitro Viral Infection Dynamics

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

A systems framework for vaccine design

A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs

Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID).

An antisense transcript induced by Wnt/beta-catenin signaling decreases E2F4.

Androgen receptor promotes ligand-independent prostate cancer progression through c-Myc upregulation

Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection

Brain size genes and risk of dementia

CSF1R inhibitors exhibit antitumor activity in acute myeloid leukemia by blocking paracrine signals from support cells

Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms

Comparison of methods to identify aberrant expression patterns in individual patients: augmenting our toolkit for precision medicine

Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross

Complex genetics of interactions of alcohol and CNS function and behavior

Computational detection of alternative exon usage

Consensus framework for exploring microarray data using multiple clustering methods

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

Convergence of Divergent Tumors: A Systems Biology Approach of Tumor-specific Signaling

Copy number variation analysis in 98 individuals with PHACE syndrome

Corrigendum: The BioPAX community standard for pathway data sharing

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations

Cross-species molecular dissection across alcohol behavioral domains

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

DNA microarray and proteomic strategies for understanding alcohol action

Data integration and reproducibility for high-throughput transcriptomics

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.

Deoxyribonucleic acid microarray analysis of gene expression pattern in the arcuate nucleus/ventromedial nucleus of hypothalamus during lactation

Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure

Differential network analysis reveals genetic effects on catalepsy modules

Distribution of menin-occupied regions in chromatin specifies a broad role of menin in transcriptional regulation

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

Dual-trait selection for ethanol consumption and withdrawal: genetic and transcriptional network effects

ERBB2/HER2 mutations are transforming and therapeutically targetable in leukemia

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

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

Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice

Functional and genomic context in pathway analysis of GWAS data

Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma

Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs

Gene networks and haloperidol-induced catalepsy.

Genes, behavior and next-generation RNA sequencing.

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse

Genetic factors involved in risk for methamphetamine intake and sensitization.

Genetics, Behavior, and Brain Dopamine Systems

Genomic landscape of neutrophilic leukemias of ambiguous diagnosis

High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs.

HitWalker: variant prioritization for personalized functional cancer genomics

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

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

Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq

Immune Predictors of Mortality After Ribonucleic Acid Virus Infection

Influenza vaccination of pregnant women: attitudes and behaviors of Oregon physician prenatal care providers

LSD1 activates a lethal prostate cancer gene network independently of its demethylase function.

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

Localization of TFIIB binding regions using serial analysis of chromatin occupancy

Locus and population specific evolution in HLA class II genes.

MIFlowCyt: the minimum information about a Flow Cytometry Experiment

Mapping cellular transcriptosomes in autopsied Alzheimer's disease subjects and relevant animal models

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

Microcephaly genes and risk of late-onset Alzheimer disease

Modeling host genetic regulation of influenza pathogenesis in the collaborative cross

Multi-omic network signatures of disease.

Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia

Occupancy classification of position weight matrix-inferred transcription factor binding sites.

On the integration of alcohol-related quantitative trait loci and gene expression analyses

Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML

Protein co-expression network analysis (ProCoNA).

Protein database and quantitative analysis considerations when integrating genetics and proteomics to compare mouse strains.

REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation-differentiation balance in the developing brain

Recurrent cyclin D2 mutations in myeloid neoplasms.

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

Renal gene and protein expression signatures for prediction of kidney disease progression

Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia

SNPs matter: impact on detection of differential expression.

Selection for drinking in the dark alters brain gene coexpression networks.

Similar gene expression profiles do not imply similar tissue functions