Published in Mol Oncol on December 09, 2008
Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology. J Transl Med (2009) 1.31
Copy number abnormalities in sporadic canine colorectal cancers. Genome Res (2010) 0.95
Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels. J Clin Bioinforma (2011) 0.82
MicroRNA signatures as biomarkers and therapeutic target for CNS embryonal tumors: the pros and the cons. Int J Mol Sci (2014) 0.81
Principles of modular tumor therapy. Cancer Microenviron (2009) 0.78
Pediatric oncology and the future of oncological imaging. Pediatr Radiol (2011) 0.77
An Interactive Tool for Animating Biology, and Its Use in Spatial and Temporal Modeling of a Cancerous Tumor and Its Microenvironment. PLoS One (2015) 0.76
The tumor as an organ: comprehensive spatial and temporal modeling of the tumor and its microenvironment. BMC Bioinformatics (2016) 0.75
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
International network of cancer genome projects. Nature (2010) 20.35
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
The human disease network. Proc Natl Acad Sci U S A (2007) 19.58
Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97
Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol (2002) 16.75
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature (2010) 14.62
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 13.51
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
Identification of virus-encoded microRNAs. Science (2004) 12.56
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Drug-target network. Nat Biotechnol (2007) 11.15
Towards a knowledge-based Human Protein Atlas. Nat Biotechnol (2010) 11.05
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med (2013) 9.65
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
Regulation of cell death: the calcium-apoptosis link. Nat Rev Mol Cell Biol (2003) 9.07
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell (2006) 8.61
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics (2004) 8.29
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Mass spectrometry and protein analysis. Science (2006) 8.05
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat Immunol (2009) 7.93
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res (2005) 7.63
Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell (2007) 7.60
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature (2009) 7.37
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol (2004) 7.23
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
The DNA sequence of the human X chromosome. Nature (2005) 6.97
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Functional atlas of the integrin adhesome. Nat Cell Biol (2007) 6.89
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A (2006) 6.80