In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target

Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade

(2021) Shengqing Stan Gu et al.   Cancer Discovery

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

TIMER2.0 for analysis of tumor-infiltrating immune cells

(2020) Taiwen Li et al.   NUCLEIC ACIDS RESEARCH

Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPβ in Microglia

(2020) Ada Ndoja et al.   CELL

Functional genomic landscape of cancer-intrinsic evasion of killing by T cells

(2020) Keith A. Lawson et al.   NATURE

Genome-wide Screens Identify Lineage- and Tumor-Specific Genes Modulating MHC-I- and MHC-II-Restricted Immunosurveillance of Human Lymphomas

(2020) Devin Dersh et al.   IMMUNITY

Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo

(2019) Adan Codina et al.   Cell Systems

Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute

(2019) Binbin Wang et al.   Nature Protocols

Breast Cancer Treatment

(2019) Adrienne G. Waks et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

(2019) Luca Cassetta et al.   CANCER CELL

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

(2019) Shaojuan Li et al.   NUCLEIC ACIDS RESEARCH

Genetic diversity of tumors with mismatch repair deficiency influences anti–PD-1 immunotherapy response

(2019) Rajarsi Mandal et al.   SCIENCE

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

CCL5 promotes breast cancer recurrence through macrophage recruitment in residual tumors

(2019) Andrea Walens et al.   eLife

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16

(2019) Xiaoyu Zhang et al.   Nature Chemical Biology

Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

(2019) Joseph L. Benci et al.   CELL

Sustained Type I interferon signaling as a mechanism of resistance to PD-1 blockade

(2019) Nicolas Jacquelot et al.   CELL RESEARCH

More Than Just Attractive: How CCL2 Influences Myeloid Cell Behavior Beyond Chemotaxis

(2019) Martha Gschwandtner et al.   Frontiers in Immunology

Improved design and analysis of CRISPR knockout screens

(2018) Chen-Hao Chen et al.   BIOINFORMATICS

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations

(2018) Rinath Jeselsohn et al.   CANCER CELL

CD10 + GPR77 + Cancer-Associated Fibroblasts Promote Cancer Formation and Chemoresistance by Sustaining Cancer Stemness

(2018) Shicheng Su et al.   CELL

JAK2 and PD-L1 Amplification Enhance the Dynamic Expression of PD-L1 in Triple-negative Breast Cancer

(2018) Meixuan Chen et al.   Clinical Breast Cancer

Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands

(2018) Lara N. Gechijian et al.   Nature Chemical Biology

DNA repair processes are critical mediators of p53-dependent tumor suppression

(2018) Ana Janic et al.   NATURE MEDICINE

Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy

(2018) Tengfei Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti–PD-1 treatment

(2018) Elisa Peranzoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

(2018) Deng Pan et al.   SCIENCE

High levels of CCL2 or CCL4 in the tumor microenvironment predict unfavorable survival in lung adenocarcinoma

(2018) Lei Li et al.   Thoracic Cancer

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Substrate binding allosterically relieves autoinhibition of the pseudokinase TRIB1

(2018) Sam A. Jamieson et al.   Science Signaling

Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

(2018) Jeffrey J. Ishizuka et al.   NATURE

Targeting macrophages: therapeutic approaches in cancer

(2018) Luca Cassetta et al.   NATURE REVIEWS DRUG DISCOVERY

Atezolizumab and Nab-Paclitaxel in Advanced Triple-Negative Breast Cancer

(2018) Peter Schmid et al.   NEW ENGLAND JOURNAL OF MEDICINE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

Janus Kinase 1 Plays a Critical Role in Mammary Cancer Progression

(2018) Barbara L. Wehde et al.   Cell Reports

MDM2/X inhibitors under clinical evaluation: perspectives for the management of hematological malignancies and pediatric cancer

(2017) Veronica Tisato et al.   Journal of Hematology & Oncology

Macrophages as Key Drivers of Cancer Progression and Metastasis

(2017) Sebastian R. Nielsen et al.   MEDIATORS OF INFLAMMATION

Tumor-derived CXCL5 promotes human colorectal cancer metastasis through activation of the ERK/Elk-1/Snail and AKT/GSK3β/β-catenin pathways

(2017) Jingkun Zhao et al.   Molecular Cancer

Identification of CMTM6 and CMTM4 as PD-L1 protein regulators

(2017) Riccardo Mezzadra et al.   NATURE

CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity

(2017) Marian L. Burr et al.   NATURE

In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target

(2017) Robert T. Manguso et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

The eukaryotic linear motif resource – 2018 update

(2017) Marc Gouw et al.   NUCLEIC ACIDS RESEARCH

Degrons in cancer

(2017) Bálint Mészáros et al.   Science Signaling

Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease

(2017) Patrick A. Eyers et al.   TRENDS IN CELL BIOLOGY

Mechanisms and Dynamics of T Cell-Mediated Cytotoxicity In Vivo

(2017) Stephan Halle et al.   TRENDS IN IMMUNOLOGY

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Degrons in cancer

(2017) Bálint Mészáros et al.   Science Signaling

Prevalence and Spectrum of Germline Cancer Susceptibility Gene Mutations Among Patients With Early-Onset Colorectal Cancer

(2017) Rachel Pearlman et al.   JAMA Oncology

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

(2016) Qian Qin et al.   BMC BIOINFORMATICS

TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer

(2016) Anna C. Groner et al.   CANCER CELL

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

(2016) Joseph L. Benci et al.   CELL

Pembrolizumab in Patients With Advanced Triple-Negative Breast Cancer: Phase Ib KEYNOTE-012 Study

(2016) Rita Nanda et al.   JOURNAL OF CLINICAL ONCOLOGY

High Infiltration of Tumor-Associated Macrophages Influences Poor Prognosis in Human Gastric Cancer Patients, Associates With the Phenomenon of EMT

(2016) Jia Zhang et al.   MEDICINE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease

(2016) Giampaolo Bianchini et al.   Nature Reviews Clinical Oncology

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

Mechanistic validation of a clinical lead stapled peptide that reactivates p53 by dual HDM2 and HDMX targeting

(2016) F Wachter et al.   ONCOGENE

Targeting the CCL2-CCR2 signaling axis in cancer metastasis

(2016) Su Yin Lim et al.   Oncotarget

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Therapeutic antitumor immunity by checkpoint blockade is enhanced by ibrutinib, an inhibitor of both BTK and ITK

(2015) Idit Sagiv-Barfi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Mechanism of CCAAT-Enhancer Binding Protein Recruitment by the TRIB1 Pseudokinase

(2015) James M. Murphy et al.   STRUCTURE

Interferons and the Immunogenic Effects of Cancer Therapy

(2015) Andy J. Minn   TRENDS IN IMMUNOLOGY

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Potent and Selective Small-Molecule Inhibitors of cIAP1/2 Proteins Reveal That the Binding of Smac Mimetics to XIAP BIR3 Is Not Required for Their Effective Induction of Cell Death in Tumor Cells

(2014) Haiying Sun et al.   ACS Chemical Biology

Tumor-Associated Macrophages: From Mechanisms to Therapy

(2014) Roy Noy et al.   IMMUNITY

Eradication of metastatic mouse cancers resistant to immune checkpoint blockade by suppression of myeloid-derived cells

(2014) K. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering and Reversing Tumor Immune Suppression

(2013) Greg T. Motz et al.   IMMUNITY

Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages

(2013) Takashi Satoh et al.   NATURE

Neutralizing Tumor-Promoting Chronic Inflammation: A Magic Bullet?

(2013) L. M. Coussens et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

IFN-γ, IL-17 and TGF-β involvement in shaping the tumor microenvironment: The significance of modulating such cytokines in treating malignant solid tumors

(2011) Heba A Alshaker et al.   Cancer Cell International

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Good COP1 or bad COP1? In vivo veritas

(2011) Wenyi Wei et al.   JOURNAL OF CLINICAL INVESTIGATION

Cop1 constitutively regulates c-Jun protein stability and functions as a tumor suppressor in mice

(2011) Domenico Migliorini et al.   JOURNAL OF CLINICAL INVESTIGATION

COP1 is a tumour suppressor that causes degradation of ETS transcription factors

(2011) Alberto C. Vitari et al.   NATURE

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

(2011) Bin-Zhi Qian et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Immunity, Inflammation, and Cancer

(2010) Sergei I. Grivennikov et al.   CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY