Gene expression variability across cells and species shapes innate immunity

Rapid Evolution of Primate Type 2 Immune Response Factors Linked to Asthma Susceptibility

(2017) Matthew F. Barber et al.   Genome Biology and Evolution

Innate Immune Receptors as Competitive Determinants of Cell Fate

(2017) Kate M. Franz et al.   MOLECULAR CELL

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Adaptive Evolution of Gene Expression in Drosophila

(2017) Armita Nourmohammad et al.   Cell Reports

Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells

(2017) Andre J. Faure et al.   Cell Systems

Evolution of Gene Regulation in Humans

(2016) Steven K. Reilly et al.   Annual Review of Genomics and Human Genetics

Pangolin genomes and the evolution of mammalian scales and immunity

(2016) Siew Woh Choo et al.   GENOME RESEARCH

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew

(2016) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter architectures and developmental gene regulation

(2016) Vanja Haberle et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Viruses are a dominant driver of protein adaptation in mammals

(2016) David Enard et al.   eLife

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

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

Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales

(2015) Benjamin A. Braun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic control of type I IFN signalling by an integrated network of negative regulators

(2015) Rebecca A. Porritt et al.   TRENDS IN IMMUNOLOGY

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

Molecular principles of human virus protein–protein interactions

(2014) Rachita Ramachandra Halehalli et al.   BIOINFORMATICS

Human genome variability, natural selection and infectious diseases

(2014) Matteo Fumagalli et al.   CURRENT OPINION IN IMMUNOLOGY

The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease

(2014) Jessica F Brinkworth et al.   CURRENT OPINION IN IMMUNOLOGY

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

VirusMentha: a new resource for virus-host protein interactions

(2014) Alberto Calderone et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Heterogeneity in immune responses: from populations to single cells

(2014) Rahul Satija et al.   TRENDS IN IMMUNOLOGY

Biphasic RLR-IFN-  Response Controls the Balance between Antiviral Immunity and Cell Damage

(2013) S.-Y. Hwang et al.   JOURNAL OF IMMUNOLOGY

Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes

(2013) R. Malfavon-Borja et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Virological View of Innate Immune Recognition

(2012) Akiko Iwasaki   Annual Review of Microbiology

Extensive evolutionary and functional diversity among mammalian AIM2-like receptors

(2012) Rebecca L. Brunette et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Into the Eye of the Cytokine Storm

(2012) J. R. Tisoncik et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response

(2012) Ulfert Rand et al.   Molecular Systems Biology

Viral immune modulators perturb the human molecular network by common and unique strategies

(2012) Andreas Pichlmair et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

(2012) K. Schroder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic Expression of the Interferon-β Gene

(2012) Mingwei Zhao et al.   PLOS BIOLOGY

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

(2012) John A. Capra et al.   PLoS Computational Biology

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Pathogen Recognition by the Innate Immune System

(2011) Himanshu Kumar et al.   INTERNATIONAL REVIEWS OF IMMUNOLOGY

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

Type I interferons: crucial participants in disease amplification in autoimmunity

(2010) John C. Hall et al.   Nature Reviews Rheumatology

Contrasts between adaptive coding and noncoding changes during human evolution

(2010) Ralph Haygood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Comparison of Innate Immune Signaling Pathways in Primates

(2010) Luis B. Barreiro et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Molecular evolution of the antiretroviral TRIM5 gene

(2009) Welkin E. Johnson et al.   IMMUNOGENETICS

From evolutionary genetics to human immunology: how selection shapes host defence genes

(2009) Luis B. Barreiro et al.   NATURE REVIEWS GENETICS

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens