The human liver-specific proteome defined by transcriptomics and antibody-based profiling

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

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

(2014) Adil Mardinoglu et al.   Nature Communications

Molecular Prognostic Profile of Egyptian HCC Cases Infected with Hepatitis C Virus

(2013) Abdel-Rahman N. Zekri et al.   Asian Pacific Journal of Cancer Prevention

Genome-scale modeling of human metabolism - a systems biology approach

(2013) Adil Mardinoglu et al.   Biotechnology Journal

Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data

(2013) Shaolei Teng et al.   BMC Medical Genomics

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Plasma Fibroblast Growth Factor 23 Concentration Is Increased and Predicts Mortality in Patients on the Liver-Transplant Waiting List

(2013) Dominique Prié et al.   PLoS One

Hepatocellular carcinoma in non-alcoholic fatty liver disease: An emerging menace

(2012) György Baffy et al.   JOURNAL OF HEPATOLOGY

Contribution of Antibody-based Protein Profiling to the Human Chromosome-centric Proteome Project (C-HPP)

(2012) Linn Fagerberg et al.   JOURNAL OF PROTEOME RESEARCH

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

Expression of SLCO1B3 is associated with intratumoral cholestasis and CTNNB1 mutations in hepatocellular carcinoma

(2011) Shigeki Sekine et al.   CANCER SCIENCE

Analysis of Global and Absorption, Distribution, Metabolism, and Elimination Gene Expression in the Progressive Stages of Human Nonalcoholic Fatty Liver Disease

(2011) A. D. Lake et al.   DRUG METABOLISM AND DISPOSITION

Systems medicine and metabolic modelling

(2011) A. Mardinoglu et al.   JOURNAL OF INTERNAL MEDICINE

Clinicopathological and prognostic significance of serum and tissue Dickkopf-1 levels in human hepatocellular carcinoma

(2011) Edmund Kwok-Kwan Tung et al.   LIVER INTERNATIONAL

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

VeryGene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery

(2011) Xiaoqin Yang et al.   PHYSIOLOGICAL GENOMICS

RNA-Seq Analyses Generate Comprehensive Transcriptomic Landscape and Reveal Complex Transcript Patterns in Hepatocellular Carcinoma

(2011) Qichao Huang et al.   PLoS One

TiSGeD: a database for tissue-specific genes

(2010) S. J. Xiao et al.   BIOINFORMATICS

Plasma metabolomic profile in nonalcoholic fatty liver disease

(2010) Satish C. Kalhan et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Digital Genome-Wide ncRNA Expression, Including SnoRNAs, across 11 Human Tissues Using PolyA-Neutral Amplification

(2010) John C. Castle et al.   PLoS One

Creation of an antibody-based subcellular protein atlas

(2010) Emma Lundberg et al.   PROTEOMICS

Evidence of aberrant lipid metabolism in hepatitis C and hepatocellular carcinoma

(2010) Jian-Min Wu et al.   HPB

Serum fetuin A/ 2HS-glycoprotein levels in patients with non-alcoholic fatty liver disease: relation with liver fibrosis

(2010) Y. Yilmaz et al.   ANNALS OF CLINICAL BIOCHEMISTRY

Serum proteomics and biomarker discovery across the spectrum of nonalcoholic fatty liver disease

(2009) Lauren N. Bell et al.   HEPATOLOGY

Latest findings in phosphate homeostasis

(2009) Dominique Prié et al.   KIDNEY INTERNATIONAL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS