StanDep: Capturing transcriptomic variability improves context-specific metabolic models

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

(2019) Anne Richelle et al.   PLoS Computational Biology

Assessing key decisions for transcriptomic data integration in biochemical networks

(2019) Anne Richelle et al.   PLoS Computational Biology

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

GeneGini: Assessment via the Gini Coefficient of Reference “Housekeeping” Genes and Diverse Human Transporter Expression Profiles

(2018) Steve O'Hagan et al.   Cell Systems

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

(2017) Robin M Meyers et al.   NATURE GENETICS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms

(2016) Maria P. Pacheco et al.   Frontiers in Physiology

A Caenorhabditis elegans Genome-Scale Metabolic Network Model

(2016) L. Safak Yilmaz et al.   Cell Systems

Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method

(2016) Luis Tobalina et al.   PLoS One

Quantitative bacterial transcriptomics with RNA-seq

(2015) James P Creecy et al.   CURRENT OPINION IN MICROBIOLOGY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

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

(2014) Adil Mardinoglu et al.   Nature Communications

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Methods for integration of transcriptomic data in genome-scale metabolic models

(2014) Min Kyung Kim et al.   Computational and Structural Biotechnology Journal

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Transcriptome and proteome quantification of a tumor model provides novel insights into post‐transcriptional gene regulation

(2013) Christoph Jüschke et al.   GENOME BIOLOGY

The evolution of genome-scale models of cancer metabolism

(2013) Nathan E. Lewis et al.   Frontiers in Physiology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Biotinidase deficiency: “if you have to have an inherited metabolic disease, this is the one to have”

(2012) Barry Wolf   GENETICS IN MEDICINE

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Biotinidase is a Novel Marker for Papillary Thyroid Cancer Aggressiveness

(2012) Anthony K.-C. So et al.   PLoS One

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

(2012) M. Jain et al.   SCIENCE

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

(2010) Un-Beom Kang et al.   BMC CANCER

Reactive oxygen species, oxidative stress, and cell death correlate with level of CoQ10 deficiency

(2010) Catarina M. Quinzii et al.   FASEB JOURNAL

N-linked glycosylation is required for optimal proteolytic activation of membrane-bound transcription factor CREB-H

(2010) C.-P. Chan et al.   JOURNAL OF CELL SCIENCE

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3

(2009) Donatella Cimini et al.   BMC Systems Biology

GTP Cyclohydrolase I Expression, Protein, and Activity Determine Intracellular Tetrahydrobiopterin Levels, Independent of GTP Cyclohydrolase Feedback Regulatory Protein Expression

(2009) Amy L. Tatham et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Glycan Structures in Animal Tissues

(2008) Alison V. Nairn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Profiling the expression pattern of GPI transamidase complex subunits in human cancer

(2008) Jatin K Nagpal et al.   MODERN PATHOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Modeling Hybridoma Cell Metabolism Using a Generic Genome-Scale Metabolic Model of Mus musculus

(2005) Kashif Sheikh et al.   BIOTECHNOLOGY PROGRESS