Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks

Understudied proteins: opportunities and challenges for functional proteomics

(2022) Georg Kustatscher et al.   NATURE METHODS

PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data

(2021) Enio Gjerga et al.   JOURNAL OF PROTEOME RESEARCH

Genome-scale mechanistic modeling of signaling pathways made easy: a Bioconductor / cytoscape / web server framework for the analysis of omic data

(2021) Kinza Rian et al.   Computational and Structural Biotechnology Journal

Single-cell proteomics takes centre stage

(2021) Jeffrey M. Perkel   NATURE

Impact of phosphorylation on thermal stability of proteins

(2021) Clément M. Potel et al.   NATURE METHODS

Transcription factors: Bridge between cell signaling and gene regulation

(2021) Paula Weidemüller et al.   PROTEOMICS

The reactome pathway knowledgebase 2022

(2021) Marc Gillespie et al.   NUCLEIC ACIDS RESEARCH

Every gene can (and possibly will) be associated with cancer

(2021) João Pedro de Magalhães   TRENDS IN GENETICS

Toward modeling metabolic state from single-cell transcriptomics

(2021) Karin Hrovatin et al.   Molecular Metabolism

Personalized signaling models for personalized treatments

(2020) Julio Saez‐Rodriguez et al.   Molecular Systems Biology

Microscaled proteogenomic methods for precision oncology

(2020) Shankha Satpathy et al.   Nature Communications

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

(2020) Dorte B. Bekker-Jensen et al.   Nature Communications

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

(2020) Vasundra Touré et al.   BIOINFORMATICS

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

(2020) Fernando Cruz et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions

(2020) Rose Oughtred et al.   PROTEIN SCIENCE

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

(2020) Valentina Cappelletti et al.   CELL

Why do pathway methods work better than they should?

(2020) Bence Szalai et al.   FEBS LETTERS

WikiPathways: connecting communities

(2020) Marvin Martens et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Benchmark Problems for Dynamic Modeling of Intracellular Processes

(2019) Helge Hass et al.   BIOINFORMATICS

Illuminating the dark phosphoproteome

(2019) Elise J. Needham et al.   Science Signaling

PubTator central: automated concept annotation for biomedical full text articles

(2019) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Targeted and Untargeted Proteomics Approaches in Biomarker Development

(2019) Constance A. Sobsey et al.   PROTEOMICS

The functional landscape of the human phosphoproteome

(2019) David Ochoa et al.   NATURE BIOTECHNOLOGY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

A critical comparison of topology-based pathway analysis methods

(2018) Ivana Ihnatova et al.   PLoS One

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Gene annotation bias impedes biomedical research

(2018) Winston A. Haynes et al.   Scientific Reports

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

(2018) Ali Sinan Köksal et al.   Cell Reports

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

(2017) Amar Koleti et al.   NUCLEIC ACIDS RESEARCH

Transcriptomics technologies

(2017) Rohan Lowe et al.   PLoS Computational Biology

Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer

(2016) Justin M. Drake et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

(2016) Marta R. Hidalgo et al.   Oncotarget

Logical Modeling and Dynamical Analysis of Cellular Networks

(2016) Wassim Abou-Jaoudé et al.   Frontiers in Genetics

Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip

(2015) Matthias Blazek et al.   LAB ON A CHIP

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

(2015) Camille D. A. Terfve et al.   Nature Communications

Subpathway Analysis based on Signaling-Pathway Impact Analysis of Signaling Pathway

(2015) Xianbin Li et al.   PLoS One

Global analysis of protein structural changes in complex proteomes

(2014) Yuehan Feng et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Dynamic architecture of a protein kinase

(2014) C. L. McClendon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

Translation of SBGN maps: Process Description to Activity Flow

(2013) Torsten Vogt et al.   BMC Systems Biology

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

(2013) M. J. Ellis et al.   Cancer Discovery

Differential Expression Analysis for Pathways

(2013) Winston A. Haynes et al.   PLoS Computational Biology

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

Assessing statistical significance in causal graphs

(2012) Leonid Chindelevitch et al.   BMC BIOINFORMATICS

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

TEAK: Topology Enrichment Analysis frameworK for detecting activated biological subpathways

(2012) Thair Judeh et al.   NUCLEIC ACIDS RESEARCH

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

Post-translational modifications in signal integration

(2010) Yonathan Lissanu Deribe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Feedback Loops Shape Cellular Signals in Space and Time

(2008) O. Brandman et al.   SCIENCE