Published in Technol Cancer Res Treat on April 01, 2010
Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis. PLoS One (2013) 1.00
Learning dysregulated pathways in cancers from differential variability analysis. Cancer Inform (2014) 0.94
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics (2011) 0.90
Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs. Cell Stress Chaperones (2015) 0.88
The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. BMC Bioinformatics (2012) 0.88
Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data. Expert Opin Med Diagn (2013) 0.86
What mRNA Abundances Can Tell us about Metabolism. Metabolites (2012) 0.86
Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence. BMC Genomics (2013) 0.85
Multiclass cancer classification based on gene expression comparison. Stat Appl Genet Mol Biol (2014) 0.81
Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis. BMC Bioinformatics (2012) 0.81
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. BMC Bioinformatics (2013) 0.80
Big data and computational biology strategy for personalized prognosis. Oncotarget (2016) 0.79
switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinformatics (2014) 0.78
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. Oncogenesis (2016) 0.76
An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. Oncotarget (2016) 0.76
Tamoxifen therapy benefit predictive signature coupled with prognostic signature of post-operative recurrent risk for early stage ER+ breast cancer. Oncotarget (2015) 0.76
An individualised signature for predicting response with concordant survival benefit for lung adenocarcinoma patients receiving platinum-based chemotherapy. Br J Cancer (2016) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27
Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet (2005) 17.75
Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med (2001) 16.65
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics (2007) 6.63
Is cross-validation valid for small-sample microarray classification? Bioinformatics (2004) 5.19
Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. Cancer Res (2002) 3.90
Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48
Classifying gene expression profiles from pairwise mRNA comparisons. Stat Appl Genet Mol Biol (2004) 3.45
Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics (2005) 3.24
Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin Chem (2002) 3.05
Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling. Oncogene (2003) 2.82
An interferon-related gene signature for DNA damage resistance is a predictive marker for chemotherapy and radiation for breast cancer. Proc Natl Acad Sci U S A (2008) 2.64
Boosting for tumor classification with gene expression data. Bioinformatics (2003) 2.64
Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A (2007) 2.38
Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol (2004) 2.14
Molecular classification of multiple tumor types. Bioinformatics (2001) 2.02
Cell and tumor classification using gene expression data: construction of forests. Proc Natl Acad Sci U S A (2003) 1.95
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics (2005) 1.91
Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines. FEBS Lett (2003) 1.90
Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics (2007) 1.74
Antitumor effects and biomarkers of activity of AZD0530, a Src inhibitor, in pancreatic cancer. Clin Cancer Res (2009) 1.53
Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics (2008) 1.48
A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acute myeloid leukemia. Blood (2007) 1.48
The tspair package for finding top scoring pair classifiers in R. Bioinformatics (2009) 1.18
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics (2009) 1.15
Pattern identification and classification in gene expression data using an autoassociative neural network model. Biotechnol Bioeng (2003) 1.08
Protein subnetwork markers improve prediction of cancer outcome. Mol Syst Biol (2007) 1.05
The biology of antihormone failure in breast cancer. Breast Cancer Res Treat (2003) 0.96
A CART-based approach to discover emerging patterns in microarray data. Bioinformatics (2003) 0.95
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. BMC Genomics (2009) 0.91
WITHDRAWN: Tamoxifen for early breast cancer. Cochrane Database Syst Rev (2008) 0.89
Historical perspective on hormonal therapy of advanced breast cancer. Clin Ther (2002) 0.85
Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics (2005) 3.24
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol (2005) 2.82
Comparison of network-based pathway analysis methods. Trends Biotechnol (2004) 2.78
Metabolic pathways in the post-genome era. Trends Biochem Sci (2003) 2.57
A systems approach to prion disease. Mol Syst Biol (2009) 2.49
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2010) 2.39
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem (2004) 2.26
Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci U S A (2008) 1.95
Extreme pathways and Kirchhoff's second law. Biophys J (2002) 1.95
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics (2005) 1.91
Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics (2007) 1.74
A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med (2013) 1.69
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J Theor Biol (2002) 1.69
Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res (2002) 1.64
Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol (2006) 1.48
Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics (2008) 1.48
Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proc Natl Acad Sci U S A (2011) 1.43
Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol (2010) 1.38
Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Appl Microbiol Biotechnol (2009) 1.30
A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A (2011) 1.30
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS Comput Biol (2006) 1.25
Computational medicine: translating models to clinical care. Sci Transl Med (2012) 1.25
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol (2012) 1.24
Metabolite coupling in genome-scale metabolic networks. BMC Bioinformatics (2006) 1.22
Molecular signatures from omics data: from chaos to consensus. Biotechnol J (2012) 1.17
Integrating big data and actionable health coaching to optimize wellness. BMC Med (2015) 1.16
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics (2009) 1.15
Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data. Proteomics (2007) 1.15
Demystifying disease, democratizing health care. Sci Transl Med (2014) 1.14
Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett (2008) 1.12
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS (2004) 1.10
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford) (2013) 1.09
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol (2011) 1.09
Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol (2003) 1.07
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J (2009) 1.06
Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proc Natl Acad Sci U S A (2013) 1.06
Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. Proc Natl Acad Sci U S A (2013) 1.06
A simple and reproducible breast cancer prognostic test. BMC Genomics (2013) 1.03
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol (2014) 0.99
Network biology methods integrating biological data for translational science. Brief Bioinform (2012) 0.99
Genome-scale modeling for metabolic engineering. J Ind Microbiol Biotechnol (2015) 0.99
Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug. Mol Cell Proteomics (2010) 0.98
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. J Bacteriol (2011) 0.97
Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. Environ Microbiol (2013) 0.93
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC Bioinformatics (2006) 0.92
Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One (2011) 0.91
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. BMC Genomics (2009) 0.91
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics (2011) 0.90
The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. BMC Bioinformatics (2012) 0.88
Research resource: whole transcriptome RNA sequencing detects multiple 1α,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. Mol Endocrinol (2012) 0.86
Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages. J Proteome Res (2011) 0.83
Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions. Phys Rev Lett (2010) 0.83
A coarse-to-fine strategy for multiclass shape detection. IEEE Trans Pattern Anal Mach Intell (2004) 0.83
Genetic co-occurrence network across sequenced microbes. PLoS Comput Biol (2011) 0.83
Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J (2013) 0.82
Systems pharmacology modeling: an approach to improving drug safety. Biopharm Drug Dispos (2013) 0.82
Relative expression analysis for identifying perturbed pathways. Conf Proc IEEE Eng Med Biol Soc (2009) 0.82
A comprehensive statistical model for cell signaling. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.82
Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas. PLoS One (2013) 0.81
Identification of family-determining residues in PHD fingers. Nucleic Acids Res (2010) 0.81
Systems approach to neurodegenerative disease biomarker discovery. Annu Rev Pharmacol Toxicol (2013) 0.81
Mechanistic modeling of aberrant energy metabolism in human disease. Front Physiol (2012) 0.80
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. BMC Bioinformatics (2013) 0.80
Systems biology of embryogenesis. Reprod Fertil Dev (2010) 0.79
Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol (2013) 0.79
The limits of de novo DNA motif discovery. PLoS One (2012) 0.79
Comparing machines and humans on a visual categorization test. Proc Natl Acad Sci U S A (2011) 0.79
A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism). Methods Mol Biol (2013) 0.79
Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. Appl Environ Microbiol (2013) 0.78
Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. Zebrafish (2014) 0.78
An argument for mechanism-based statistical inference in cancer. Hum Genet (2014) 0.77
Learning multivariate distributions by competitive assembly of marginals. IEEE Trans Pattern Anal Mach Intell (2013) 0.77
Systems approaches to molecular cancer diagnostics. Discov Med (2010) 0.76
Identification of direction in gene networks from expression and methylation. BMC Syst Biol (2013) 0.75
Corrigendum: Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.Htt(Q111/+) model of Huntington's disease. Sci Rep (2017) 0.75
Editorial: Systems biology for biotech applications. Biotechnol J (2010) 0.75
A statistical framework for image category search from a mental picture. IEEE Trans Pattern Anal Mach Intell (2009) 0.75
Real-world image annotation and retrieval: an introduction to the special section. IEEE Trans Pattern Anal Mach Intell (2008) 0.75