System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Statistical modeling using early markers of innate immunity to explain variation in humoral responses to influenza vaccine in older adults

(2015) Richard B. Kennedy et al.   VACCINE

Profiles of influenza A/H1N1 vaccine response using hemagglutination-inhibition titers

(2015) Robert M Jacobson et al.   Human Vaccines & Immunotherapeutics

The Impact of Immunosenescence on Humoral Immune Response Variation after Influenza A/H1N1 Vaccination in Older Subjects

(2015) Iana H. Haralambieva et al.   PLoS One

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination

(2015) Kristen L. Hoek et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data

(2014) Youtao Lu et al.   BMC Medical Genomics

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses

(2014) John S. Tsang et al.   CELL

A systems biology approach to the effect of aging, immunosenescence and vaccine response

(2014) Gregory A Poland et al.   CURRENT OPINION IN IMMUNOLOGY

MACE: model based analysis of ChIP-exo

(2014) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

(2014) S. Saeed et al.   SCIENCE

Turkey Versus Guinea Pig Red Blood Cells: Hemagglutination Differences Alter Hemagglutination Inhibition Responses Against Influenza A/H1N1

(2014) Inna G. Ovsyannikova et al.   VIRAL IMMUNOLOGY

Detection of Influenza A/H1N1-Specific Human IgG-Secreting B Cells in Older Adults by ELISPOT Assay

(2014) Scott D. Painter et al.   VIRAL IMMUNOLOGY

Age-related variations in the methylome associated with gene expression in human monocytes and T cells

(2014) Lindsay M. Reynolds et al.   Nature Communications

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

(2014) James R Wagner et al.   GENOME BIOLOGY

A comprehensive overview of Infinium HumanMethylation450 data processing

(2013) S. Dedeurwaerder et al.   BRIEFINGS IN BIOINFORMATICS

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Transcriptomic profiles of high and low antibody responders to smallpox vaccine

(2013) R B Kennedy et al.   GENES AND IMMUNITY

DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation

(2013) A. Y. Lai et al.   GENOME RESEARCH

Granzyme B ELISPOT assay to measure influenza-specific cellular immunity

(2013) Hannah M. Salk et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function

(2013) C. D. Scharer et al.   JOURNAL OF IMMUNOLOGY

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness

(2013) D. Furman et al.   Molecular Systems Biology

A new world of Polycombs: unexpected partnerships and emerging functions

(2013) Yuri B. Schwartz et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination

(2013) Iana H. Haralambieva et al.   PLoS One

Vaccinomics, adversomics, and the immune response network theory: Individualized vaccinology in the 21st century

(2013) Gregory A. Poland et al.   SEMINARS IN IMMUNOLOGY

Leptin and leptin-related gene polymorphisms, obesity, and influenza A/H1N1 vaccine-induced immune responses in older individuals

(2013) Inna G. Ovsyannikova et al.   VACCINE

Using epigenetics to define vaccine-induced memory T cells

(2013) Ben Youngblood et al.   Current Opinion in Virology

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

(2013) Yi-An Ko et al.   GENOME BIOLOGY

Transcriptional and Epigenetic Control of T Helper Cell Specification: Molecular Mechanisms Underlying Commitment and Plasticity

(2012) Yuka Kanno et al.   Annual Review of Immunology

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters

(2012) David D O’Keefe et al.   BMC GENOMICS

Insights into the epigenetic mechanisms controlling pancreatic carcinogenesis

(2012) Angela L. McCleary-Wheeler et al.   CANCER LETTERS

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Interindividual variability and co-regulation of DNA methylation differ among blood cell populations

(2012) Monique Jacoby et al.   Epigenetics

Understanding the immune response to seasonal influenza vaccination in older adults: a systems biology approach

(2012) Nathaniel D Lambert et al.   Expert Review of Vaccines

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Germinal center selection and the development of memory B and plasma cells

(2012) Mark J. Shlomchik et al.   IMMUNOLOGICAL REVIEWS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

The Transcription Factor Encyclopedia

(2012) Dimas Yusuf et al.   GENOME BIOLOGY

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42

(2011) B. Misselwitz et al.   Molecular Systems Biology

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

Evaluation of the Infinium Methylation 450K technology

(2011) Sarah Dedeurwaerder et al.   Epigenomics

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

(2010) Pan Du et al.   BMC BIOINFORMATICS

A longitudinal study of epigenetic variation in twins

(2010) Chloe Chung Yi Wong et al.   Epigenetics

The Neurosecretory Vesicle Protein Phogrin Functions as a Phosphatidylinositol Phosphatase to Regulate Insulin Secretion

(2010) Leslie A. Caromile et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Estimating Influenza-Associated Deaths in the United States

(2009) William W. Thompson et al.   AMERICAN JOURNAL OF PUBLIC HEALTH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Biology of Immune Responses to Vaccines in Elderly Persons

(2008) Birgit Weinberger et al.   CLINICAL INFECTIOUS DISEASES

Language: Disputed definitions

(2008)   NATURE

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

(2008) Jens Wrammert et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Maternal infection leads to abnormal gene regulation and brain atrophy in mouse offspring: Implications for genesis of neurodevelopmental disorders

(2008) S. Hossein Fatemi et al.   SCHIZOPHRENIA RESEARCH