Application guide for omics approaches to cell signaling

Annotation of human cancers with EGFR signaling–associated protein complexes using proximity ligation assays

(2015) Matthew A. Smith et al.   Science Signaling

Annotation of human cancers with EGFR signaling–associated protein complexes using proximity ligation assays

(2015) Matthew A. Smith et al.   Science Signaling

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Haploid animal cells

(2014) A. Wutz   DEVELOPMENT

Kinase Substrate Sensor (KISS), a MammalianIn SituProtein Interaction Sensor

(2014) Sam Lievens et al.   MOLECULAR & CELLULAR PROTEOMICS

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy

(2014) Kilian V. M. Huber et al.   NATURE

DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells

(2014) Yegor Smurnyy et al.   Nature Chemical Biology

DrugTargetSeqR: a genomics- and CRISPR-Cas9–based method to analyze drug targets

(2014) Corynn Kasap et al.   Nature Chemical Biology

The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells

(2014) Julia Petschnigg et al.   NATURE METHODS

An infrared reporter to detect spatiotemporal dynamics of protein-protein interactions

(2014) Emmanuelle Tchekanda et al.   NATURE METHODS

RNAi screening comes of age: improved techniques and complementary approaches

(2014) Stephanie E. Mohr et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The growing landscape of lysine acetylation links metabolism and cell signalling

(2014) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens

(2014) A. Franceschini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications

(2014) Christian Tiede et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel Visualization of Multiple Protein Complexes in Individual Cells in Tumor Tissue

(2013) Karl-Johan Leuchowius et al.   MOLECULAR & CELLULAR PROTEOMICS

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy

(2013) Samuel A. Hasson et al.   NATURE

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains

(2013) F. Sha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Protein Interaction Network of the Mammalian Hippo Pathway Reveals Mechanisms of Kinase-Phosphatase Interactions

(2013) A. L. Couzens et al.   Science Signaling

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

A CRISPR CASe for high-throughput silencing

(2013) Jacob Heintze et al.   Frontiers in Genetics

Dynamic Reprogramming of the Kinome in Response to Targeted MEK Inhibition in Triple-Negative Breast Cancer

(2012) James S. Duncan et al.   CELL

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

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

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

M-Track: detecting short-lived protein-protein interactions in vivo

(2012) Aurora Zuzuarregui et al.   NATURE METHODS

Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation

(2012) Gucci Jijuan Gu et al.   New Biotechnology

Signaling in Innate Immunity and Inflammation

(2012) K. Newton et al.   Cold Spring Harbor Perspectives in Biology

RNAi Screening Reveals Proteasome- and Cullin3-Dependent Stages in Vaccinia Virus Infection

(2012) Jason Mercer et al.   Cell Reports

On programmed ribosomal frameshifting: the alternative proteomes

(2012) Robin Ketteler   Frontiers in Genetics

Targeting the SH2-Kinase Interface in Bcr-Abl Inhibits Leukemogenesis

(2011) Florian Grebien et al.   CELL

Teaching an Old Scaffold New Tricks: Monobodies Constructed Using Alternative Surfaces of the FN3 Scaffold

(2011) Akiko Koide et al.   JOURNAL OF MOLECULAR BIOLOGY

Chemical Genetic Screen for AMPKα2 Substrates Uncovers a Network of Proteins Involved in Mitosis

(2011) Max R. Banko et al.   MOLECULAR CELL

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

(2011) Marcus Bantscheff et al.   NATURE BIOTECHNOLOGY

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer

(2011) Markus K Muellner et al.   Nature Chemical Biology

An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of the Wnt/wingless signaling pathway

(2011) F. C. Gonsalves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) S. C. Bendall et al.   SCIENCE

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Interactive proteomics research technologies: recent applications and advances

(2010) Julia Petschnigg et al.   CURRENT OPINION IN BIOTECHNOLOGY

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

(2010) Heinz Neumann et al.   NATURE

Rapid behavior-based identification of neuroactive small molecules in the zebrafish

(2010) David Kokel et al.   Nature Chemical Biology

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain

(2010) John Wojcik et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

A Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras Oncogene

(2009) Ji Luo et al.   CELL

Visualization of molecular interactions using bimolecular fluorescence complementation analysis: Characteristics of protein fragment complementation

(2009) Tom K. Kerppola   CHEMICAL SOCIETY REVIEWS

Choosing the best treatment strategy for chronic myeloid leukemia patients resistant to imatinib: weighing the efficacy and safety of individual drugs with BCR-ABL mutations and patient history

(2009) E Jabbour et al.   LEUKEMIA

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology

Chemical genetic screening in the zebrafish embryo

(2009) Charles K Kaufman et al.   Nature Protocols

Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6

(2009) Y. Lissanu Deribe et al.   Science Signaling

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

(2009) Frederic D. Bushman et al.   PLoS Pathogens

Fluorescence-based methods in the study of protein–protein interactions in living cells

(2008) Francisco Ciruela   CURRENT OPINION IN BIOTECHNOLOGY

Kinase-Selective Enrichment Enables Quantitative Phosphoproteomics of the Kinome across the Cell Cycle

(2008) Henrik Daub et al.   MOLECULAR CELL

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS