Tissue-based map of the human proteome

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

(2014) Caroline Kampf et al.   FASEB JOURNAL

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

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

(2014) D. Djureinovic et al.   MOLECULAR HUMAN REPRODUCTION

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

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

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

RNA Deep Sequencing as a Tool for Selection of Cell Lines for Systematic Subcellular Localization of All Human Proteins

(2012) Frida Danielsson et al.   JOURNAL OF PROTEOME RESEARCH

neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects

(2012) Pascale Gaudet et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

(2012) Young-Ki Paik et al.   NATURE BIOTECHNOLOGY

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

ELIXIR: a distributed infrastructure for European biological data

(2012) Lindsey C. Crosswell et al.   TRENDS IN BIOTECHNOLOGY

Systems medicine and metabolic modelling

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

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Pathways of unconventional protein secretion

(2010) Walter Nickel   CURRENT OPINION IN BIOTECHNOLOGY

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

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2010) H. Kawaji et al.   NUCLEIC ACIDS RESEARCH

Prediction of the human membrane proteome

(2010) Linn Fagerberg et al.   PROTEOMICS

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transmembrane protein topology prediction using support vector machines

(2009) Timothy Nugent et al.   BMC BIOINFORMATICS

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

(2008) Håkan Viklund et al.   BIOINFORMATICS

Prediction of membrane-protein topology from first principles

(2008) A. Bernsel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA