Proteomic discovery of chemical probes that perturb protein complexes in human cells

The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive‐strand RNA viruses

(2022) Boris Bonaventure et al.   EMBO REPORTS

Targeted Protein Degradation by Electrophilic PROTACs that Stereoselectively and Site-Specifically Engage DCAF1

(2022) Yongfeng Tao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective inhibitors of JAK1 targeting an isoform-restricted allosteric cysteine

(2022) Madeline E. Kavanagh et al.   Nature Chemical Biology

Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain

(2022) Hannah C. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rise of Molecular Glues

(2021) Stuart L. Schreiber   CELL

Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries

(2021) Miljan Kuljanin et al.   NATURE BIOTECHNOLOGY

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Reimagining Druggability Using Chemoproteomic Platforms

(2021) Jessica N. Spradlin et al.   ACCOUNTS OF CHEMICAL RESEARCH

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

(2021) Edward L. Huttlin et al.   CELL

ABHD17 regulation of plasma membrane palmitoylation and N-Ras-dependent cancer growth

(2021) Jarrett R. Remsberg et al.   Nature Chemical Biology

Discovery of M-1121 as an Orally Active Covalent Inhibitor of Menin-MLL Interaction Capable of Achieving Complete and Long-Lasting Tumor Regression

(2021) Meng Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

A proteome-wide atlas of lysine-reactive chemistry

(2021) Mikail E. Abbasov et al.   Nature Chemistry

Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments

(2021) Michael A. Skinnider et al.   NATURE METHODS

Protein interaction landscapes revealed by advanced in vivo cross-linking–mass spectrometry

(2021) Andrew Wheat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors

(2021) Constantin Cretu et al.   Nature Communications

Liganding Functional Tyrosine Sites on Proteins Using Sulfur–Triazole Exchange Chemistry

(2020) Jeffrey W. Brulet et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective Mediator dependence of cell-type-specifying transcription

(2020) Martin G. Jaeger et al.   NATURE GENETICS

An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells

(2020) Ekaterina V. Vinogradova et al.   CELL

Molecular architecture of the human 17S U2 snRNP

(2020) Zhenwei Zhang et al.   NATURE

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

A mass spectrometry-based proteome map of drug action in lung cancer cell lines

(2020) Benjamin Ruprecht et al.   Nature Chemical Biology

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

(2020) Behnam Nabet et al.   Nature Communications

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

Lysine-Targeted Inhibitors and Chemoproteomic Probes

(2019) Adolfo Cuesta et al.   Annual Review of Biochemistry

Reactive-cysteine profiling for drug discovery

(2019) Aaron J Maurais et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Expanding chemogenomic space using chemoproteomics

(2019) Lyn H. Jones   BIOORGANIC & MEDICINAL CHEMISTRY

Somatic SF3B1 mutations in myelodysplastic syndrome with ring sideroblasts and chronic lymphocytic leukaemia

(2019) Allister Foy et al.   JOURNAL OF CLINICAL PATHOLOGY

High throughput discovery of functional protein modifications by Hotspot Thermal Profiling

(2019) Jun X. Huang et al.   NATURE METHODS

Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

(2019) Yujia Wang et al.   Nature Chemistry

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes

(2019) Anna L. Mallam et al.   Cell Reports

Therapeutic approaches to treat human spliceosomal diseases

(2019) Anthony B DeNicola et al.   CURRENT OPINION IN BIOTECHNOLOGY

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

(2019) Daniel Liu   PeerJ

Targeting Aberrant Splicing in Myelodysplastic Syndromes

(2019) Andrew M. Brunner et al.   HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA

OUP accepted manuscript

(2018)   BIOINFORMATICS

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

(2018) José Navarrete-Perea et al.   JOURNAL OF PROTEOME RESEARCH

Advancing translational research and precision medicine with targeted proteomics

(2018) Anuli Christiana Uzozie et al.   Journal of Proteomics

Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds

(2018) Constantin Cretu et al.   MOLECULAR CELL

H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

(2018) Michael Seiler et al.   NATURE MEDICINE

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

(2018) Chris Soon Heng Tan et al.   SCIENCE

GOnet: a tool for interactive Gene Ontology analysis

(2018) Mikhail Pomaznoy et al.   BMC BIOINFORMATICS

A Chemical Biology View of Bioactive Small Molecules and a Binder-Based Approach to Connect Biology to Precision Medicines

(2018) Stuart L. Schreiber   ISRAEL JOURNAL OF CHEMISTRY

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Acalabrutinib (ACP-196): A Covalent Bruton Tyrosine Kinase Inhibitor with a Differentiated Selectivity and In Vivo Potency Profile

(2017) Tjeerd Barf et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Transcription control by the ENL YEATS domain in acute leukaemia

(2017) Michael A. Erb et al.   NATURE

Global profiling of lysine reactivity and ligandability in the human proteome

(2017) Stephan M. Hacker et al.   Nature Chemistry

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

From basic apoptosis discoveries to advanced selective BCL-2 family inhibitors

(2017) Avi Ashkenazi et al.   NATURE REVIEWS DRUG DISCOVERY

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

The Mammalian Proteasome Activator PA28 Forms an Asymmetric α 4 β 3 Complex

(2017) Eva M. Huber et al.   STRUCTURE

Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A–SF3b complex

(2017) Teng Teng et al.   Nature Communications

Global Membrane Protein Interactome Analysis usingIn vivoCrosslinking and Mass Spectrometry-based Protein Correlation Profiling

(2016) Mark Larance et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-wide covalent ligand discovery in native biological systems

(2016) Keriann M. Backus et al.   NATURE

Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases

(2016) Ying-Nan P. Chen et al.   NATURE

Inhibition of Mcl-1 through covalent modification of a noncatalytic lysine side chain

(2016) Gizem Akçay et al.   Nature Chemical Biology

Therapeutic targeting of splicing in cancer

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Comparative proteomic profiling of refractory/relapsed multiple myeloma reveals biomarkers involved in resistance to bortezomib-based therapy

(2016) Dominik Dytfeld et al.   Oncotarget

The Design of Covalent Allosteric Drugs

(2015) Ruth Nussinov et al.   Annual Review of Pharmacology and Toxicology

The proteasome immunosubunits, PA28 and ER-aminopeptidase 1 protect melanoma cells from efficient MART-126-35-specific T-cell recognition

(2015) Martin Keller et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality

(2014) Michelle R. Arkin et al.   CHEMISTRY & BIOLOGY

PA28αβ Reduces Size and Increases Hydrophilicity of 20S Immunoproteasome Peptide Products

(2014) Mary Raule et al.   CHEMISTRY & BIOLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Targeting Protein-Protein Interaction by Small Molecules

(2013) Lingyan Jin et al.   Annual Review of Pharmacology and Toxicology

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

(2013) Y. Liao et al.   BIOINFORMATICS

Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics

(2013) Kathryn J. Kirkwood et al.   MOLECULAR & CELLULAR PROTEOMICS

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

(2013) Jonathan M. Ostrem et al.   NATURE

Fragment-Based Approaches in Drug Discovery and Chemical Biology

(2012) Duncan E. Scott et al.   BIOCHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Features of protein–protein interactions that translate into potent inhibitors: topology, surface area and affinity

(2012) Matthew C. Smith et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Fluorescence-Based Phenotypic Selection Allows Forward Genetic Screens in Haploid Human Cells

(2012) Lidia M. Duncan et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY