Automated assembly of molecular mechanisms at scale from text mining and curated databases

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

(2022) Laura M Doherty et al.   eLife

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data

(2021) Kenichi Shimada et al.   eLife

Data-Driven Math Model of FLT3-ITD Acute Myeloid Leukemia Reveals Potential Therapeutic Targets

(2021) David J. Wooten et al.   Journal of Personalized Medicine

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

(2021) Marek Ostaszewski et al.   Molecular Systems Biology

Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation

(2021) Mila Glavaški et al.   BioData Mining

Author-sourced capture of pathway knowledge in computable form using Biofactoid

(2021) Jeffrey V Wong et al.   eLife

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

Centralized scientific communities are less likely to generate replicable results

(2019) Valentin Danchev et al.   eLife

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

(2019) Joshua M. Dempster et al.   Nature Communications

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining

(2018) John A. Bachman et al.   BMC BIOINFORMATICS

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

(2018) David Westergaard et al.   PLoS Computational Biology

IL-4 and IL-13 Receptor Signaling From 4PS to Insulin Receptor Substrate 2: There and Back Again, a Historical View

(2018) Achsah D. Keegan et al.   Frontiers in Immunology

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

(2018) Joshua Pan et al.   Cell Systems

Large-scale automated machine reading discovers new cancer-driving mechanisms

(2018) Marco A Valenzuela-Escárcega et al.   Database-The Journal of Biological Databases and Curation

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

(2018) Rezarta Islamaj Doğan et al.   Database-The Journal of Biological Databases and Curation

From word models to executable models of signaling networks using automated assembly

(2017) Benjamin M Gyori et al.   Molecular Systems Biology

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

(2017) Daniel Scott Himmelstein et al.   eLife

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

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

(2016) Dénes Türei et al.   NATURE METHODS

The focal adhesion-associated proteins DOCK5 and GIT2 comprise a rheostat in control of epithelial invasion

(2016) S R Frank et al.   ONCOGENE

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

(2016) Nurcan Tuncbag et al.   PLoS Computational Biology

Pathway-Based Genomics Prediction using Generalized Elastic Net

(2016) Artem Sokolov et al.   PLoS Computational Biology

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

(2015) Manabu Torii et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Perspective: Sustaining the big-data ecosystem

(2015) Philip E. Bourne et al.   NATURE

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

SIGNOR: a database of causal relationships between biological entities

(2015) Livia Perfetto et al.   NUCLEIC ACIDS RESEARCH

The Rab6-regulated KIF1C kinesin motor domain contributes to Golgi organization

(2015) Peter L Lee et al.   eLife

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

(2015) Özgün Babur et al.   GENOME BIOLOGY

Event-based text mining for biology and functional genomics

(2014) S. Ananiadou et al.   Briefings in Functional Genomics

powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions

(2014) Jeff Alstott et al.   PLoS One

Heterogeneous Intracellular Trafficking Dynamics of Brain-Derived Neurotrophic Factor Complexes in the Neuronal Soma Revealed by Single Quantum Dot Tracking

(2014) Anke Vermehren-Schmaedick et al.   PLoS One

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

Human skin neural crest progenitor cells are susceptible to BRAF V600E -induced transformation

(2013) S M Kumar et al.   ONCOGENE

ErbB2-Dependent Chemotaxis Requires Microtubule Capture and Stabilization Coordinated by Distinct Signaling Pathways

(2013) Khedidja Benseddik et al.   PLoS One

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

(2013) Sofie Van Landeghem et al.   PLoS One

emcee: The MCMC Hammer

(2013) Daniel Foreman-Mackey et al.   PUBLICATIONS OF THE ASTRONOMICAL SOCIETY OF THE PACIFIC

PYK-2 is Tyrosine Phosphorylated after Activation of Pituitary Adenylate Cyclase Activating Polypeptide Receptors in Lung Cancer Cells

(2012) Terry W. Moody et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Pirh2, a Ubiquitin E3 Ligase, Inhibits p73 Transcriptional Activity by Promoting Its Ubiquitination

(2011) H. Wu et al.   MOLECULAR CANCER RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

PathText: a text mining integrator for biological pathway visualizations

(2010) B. Kemper et al.   BIOINFORMATICS

RhoA/Rho-kinase and vascular diseases: what is the link?

(2010) Kenia Pedrosa Nunes et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Differential control of TAp73 and  Np73 protein stability by the ring finger ubiquitin ligase PIR2

(2010) B. S. Sayan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChiBE: interactive visualization and manipulation of BioPAX pathway models

(2009) Ozgun Babur et al.   BIOINFORMATICS

ROCK Isoform Regulation of Myosin Phosphatase and Contractility in Vascular Smooth Muscle Cells

(2009) Yuepeng Wang et al.   CIRCULATION RESEARCH

TrkB Signaling Is Required for Both the Induction and Maintenance of Tissue and Nerve Injury-Induced Persistent Pain

(2009) X. Wang et al.   JOURNAL OF NEUROSCIENCE

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Power-Law Distributions in Empirical Data

(2009) Aaron Clauset et al.   SIAM REVIEW

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Oncogenic BRAF Regulates Melanoma Proliferation through the Lineage Specific Factor MITF

(2008) Claudia Wellbrock et al.   PLoS One