Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

Induction of a Unique Isoform of theNCOA7Oxidation Resistance Gene by Interferon β-1b

(2015) Lijian Yu et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct

(2014) U. M. Gundra et al.   BLOOD

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

(2014) I. Gupta et al.   Molecular Systems Biology

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

(2014) Foad Rouhani et al.   PLoS Genetics

Brain-expressed 3′UTR extensions strengthen miRNA cross-talk between ion channel/transporter encoding mRNAs

(2014) Claudia C. Wehrspaun et al.   Frontiers in Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Flexible analysis of RNA-seq data using mixed effects models

(2013) Ernest Turro et al.   BIOINFORMATICS

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Minimal Differentiation of Classical Monocytes as They Survey Steady-State Tissues and Transport Antigen to Lymph Nodes

(2013) Claudia Jakubzick et al.   IMMUNITY

Monocytes, Peripheral Blood Mononuclear Cells, and THP-1 Cells Exhibit Different Cytokine Expression Patterns following Stimulation with Lipopolysaccharide

(2013) Anita Schildberger et al.   MEDIATORS OF INFLAMMATION

Macrophage biology in development, homeostasis and disease

(2013) Thomas A. Wynn et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions

(2013) Bonnie van Wilgenburg et al.   PLoS One

MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation

(2013) Julian P. Venables et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

The Chemokine Superfamily Revisited

(2012) Albert Zlotnik et al.   IMMUNITY

Macrophage plasticity and polarization in tissue repair and remodelling

(2012) Alberto Mantovani et al.   JOURNAL OF PATHOLOGY

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

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

Differentiation and gene expression profile of tumor-associated macrophages

(2012) Astrid Schmieder et al.   SEMINARS IN CANCER BIOLOGY

Derivation and Functional Analysis of Patient-Specific Induced Pluripotent Stem Cells as an In Vitro Model of Chronic Granulomatous Disease

(2012) Yan Jiang et al.   STEM CELLS

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Monocytic cells derived from human embryonic stem cells and fetal liver share common differentiation pathways and homeostatic functions

(2010) O. Klimchenko et al.   BLOOD

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages

(2010) F. Ginhoux et al.   SCIENCE

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Oxysterol Binding Protein–related Protein 9 (ORP9) Is a Cholesterol Transfer Protein That Regulates Golgi Structure and Function

(2009) Mike Ngo et al.   MOLECULAR BIOLOGY OF THE CELL

Signaling Pathways Controlling Pluripotency and Early Cell Fate Decisions of Human Induced Pluripotent Stem Cells

(2009) Ludovic Vallier et al.   STEM CELLS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Homogeneous monocytes and macrophages from human embryonic stem cells following coculture-free differentiation in M-CSF and IL-3

(2008) Karl R. Karlsson et al.   EXPERIMENTAL HEMATOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

The inflammasome recognizes cytosolic microbial and host DNA and triggers an innate immune response

(2008) Daniel A. Muruve et al.   NATURE

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE