Recon3D enables a three-dimensional view of gene variation in human metabolism

Envisioning the future of ‘big data’ biomedicine

(2017) Alex A.T. Bui et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

(2017) German A. Preciat Gonzalez et al.   Journal of Cheminformatics

Reaction Decoder Tool (RDT): extracting features from chemical reactions

(2016) Syed Asad Rahman et al.   BIOINFORMATICS

Systems biology of the structural proteome

(2016) Elizabeth Brunk et al.   BMC Systems Biology

An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers

(2016) Genaro R. Villa et al.   CANCER CELL

A Next Generation Multiscale View of Inborn Errors of Metabolism

(2016) Carmen A. Argmann et al.   Cell Metabolism

Inhibition of SOAT1 Suppresses Glioblastoma Growth via Blocking SREBP-1-Mediated Lipogenesis

(2016) F. Geng et al.   CLINICAL CANCER RESEARCH

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain

(2016) Roman A. Laskowski et al.   HUMAN MOLECULAR GENETICS

Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach

(2016) Zheng Zhao et al.   JOURNAL OF MEDICINAL CHEMISTRY

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Protein-structure-guided discovery of functional mutations across 19 cancer types

(2016) Beifang Niu et al.   NATURE GENETICS

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism

(2016) Nathan Mih et al.   PLoS Computational Biology

Mutation Drivers of Immunological Responses to Cancer

(2016) E. Porta-Pardo et al.   Cancer Immunology Research

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

(2015) Elizabeth Brunk et al.   CHEMICAL REVIEWS

Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

(2015) Matthew T Chang et al.   NATURE BIOTECHNOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

NGL Viewer: a web application for molecular visualization

(2015) Alexander S. Rose et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

(2015) Daniel C. Zielinski et al.   Nature Communications

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

(2015) Francesco Gatto et al.   Scientific Reports

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

(2015) Aarash Bordbar et al.   Cell Systems

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

Modeling the effects of commonly used drugs on human metabolism

(2014) Swagatika Sahoo et al.   FEBS Journal

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation

(2014) Maria Livia Famiglietti et al.   HUMAN MUTATION

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

(2014) Lake-Ee Quek et al.   JOURNAL OF BIOTECHNOLOGY

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database

(2014) Akhil Kumar et al.   Journal of Chemical Information and Modeling

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

(2014) Swagatika Sahoo et al.   Frontiers in Physiology

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

(2013) Dong Xu et al.   Scientific Reports

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization

(2011) Eric L. First et al.   Journal of Chemical Information and Modeling

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Targeting the correct HDAC(s) to treat cognitive disorders

(2010) André Fischer et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Bile acid transporters

(2009) Paul A. Dawson et al.   JOURNAL OF LIPID RESEARCH