An interactive reference framework for modeling a dynamic immune system

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

(2015) Eli R Zunder et al.   Nature Protocols

Systems-Level Analysis of Innate Immunity

(2014) Daniel E. Zak et al.   Annual Review of Immunology

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining

(2014) Gregory K. Behbehani et al.   CYTOMETRY PART A

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Predicting Drug Responsiveness in Human Cancers Using Genetically Engineered Mice

(2013) J. Usary et al.   CLINICAL CANCER RESEARCH

Genotype to phenotype via network analysis

(2013) Hannah Carter et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Thymus-homing dendritic cells in central tolerance

(2013) Husein Hadeiba et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Tissue-Resident Macrophages Self-Maintain Locally throughout Adult Life with Minimal Contribution from Circulating Monocytes

(2013) Daigo Hashimoto et al.   IMMUNITY

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

NeXO Web: the NeXO ontology database and visualization platform

(2013) Janusz Dutkowski et al.   NUCLEIC ACIDS RESEARCH

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

Circadian Gene Bmal1 Regulates Diurnal Oscillations of Ly6Chi Inflammatory Monocytes

(2013) K. D. Nguyen et al.   SCIENCE

A platinum-based covalent viability reagent for single-cell mass cytometry

(2012) Harris G. Fienberg et al.   CYTOMETRY PART A

Kupffer cells express a unique combination of phenotypic and functional characteristics compared with splenic and peritoneal macrophages

(2012) Dowty Movita et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

(2012) Orit Rozenblatt-Rosen et al.   NATURE

A FOXO3–IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses

(2012) Vladimir Litvak et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Deciphering the transcriptional network of the dendritic cell lineage

(2012) Jennifer C Miller et al.   NATURE IMMUNOLOGY

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

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

The role of bioinformatics in studying rheumatic and autoimmune disorders

(2011) Marina Sirota et al.   Nature Reviews Rheumatology

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Mucosal-associated invariant T cells: unconventional development and function

(2011) Lionel Le Bourhis et al.   TRENDS IN IMMUNOLOGY

Publication of optimized multicolor immunofluorescence panels

(2010) Yolanda Mahnke et al.   CYTOMETRY PART A

Highly multiparametric analysis by mass cytometry

(2010) Olga Ornatsky et al.   JOURNAL OF IMMUNOLOGICAL METHODS

How host defense is encoded in the mammalian genome

(2010) Bruce Beutler et al.   MAMMALIAN GENOME

Maturation of mouse NK cells is a 4-stage developmental program

(2009) L. Chiossone et al.   BLOOD

Alveolar Macrophages Transport Pathogens to Lung Draining Lymph Nodes

(2009) A. C. Kirby et al.   JOURNAL OF IMMUNOLOGY

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

A unique B2 B cell subset in the intestine

(2008) Yasuyo Shimomura et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY