Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

Large-scale learning of combinatorial transcriptional dynamics from gene expression

(2011) H. M. Shahzad Asif et al.   BIOINFORMATICS

Physical Module Networks: an integrative approach for reconstructing transcription regulation

(2011) N. Novershtern et al.   BIOINFORMATICS

Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

(2011) Kuo-Jang Kao et al.   BMC CANCER

Discovering Biological Progression Underlying Microarray Samples

(2011) Peng Qiu et al.   PLoS Computational Biology

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Drug-Induced Regulation of Target Expression

(2010) Murat Iskar et al.   PLoS Computational Biology

GATE: software for the analysis and visualization of high-dimensional time series expression data

(2009) Ben D. MacArthur et al.   BIOINFORMATICS

KEA: kinase enrichment analysis

(2009) A. Lachmann et al.   BIOINFORMATICS

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks

(2009) Avi Ma'ayan et al.   BMC Systems Biology

The Gene Ontology in 2010: extensions and refinements

(2009)   NUCLEIC ACIDS RESEARCH

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

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Defining Developmental Potency and Cell Lineage Trajectories by Expression Profiling of Differentiating Mouse Embryonic Stem Cells

(2008) K. Aiba et al.   DNA RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Wnt antagonism inhibits hepatic stellate cell activation and liver fibrosis

(2007) Jason H. Cheng et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY