Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

Ataxias with Autosomal, X-Chromosomal or Maternal Inheritance

(2014) Josef Finsterer   CANADIAN JOURNAL OF NEUROLOGICAL SCIENCES

Protein function prediction using domain families

(2013) Robert Rentzsch et al.   BMC BIOINFORMATICS

Alternative Splice Variants, a New Class of Protein Cancer Biomarker Candidates: Findings in Pancreatic Cancer and Breast Cancer with Systems Biology Implications

(2013) Gilbert S. Omenn et al.   DISEASE MARKERS

Innovations in proteomic profiling of cancers: Alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology

(2013) Gilbert S. Omenn et al.   Journal of Proteomics

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

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

Tailoring of Membrane Proteins by Alternative Splicing of Pre-mRNA

(2012) Kathleen F. Mittendorf et al.   BIOCHEMISTRY

Functional genomics in Drosophila models of human disease

(2012) K.-F. Chen et al.   Briefings in Functional Genomics

The Tumor Suppressor Gene ARF as a Sensor of Oxidative Stress

(2012) M. Liontos et al.   CURRENT MOLECULAR MEDICINE

Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer

(2012) H. Liang et al.   GENOME RESEARCH

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Alternative Splicing of a Protein Domain Indispensable for Function of Transient Receptor Potential Melastatin 3 (TRPM3) Ion Channels

(2012) Julia Frühwald et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T ) in chordoma

(2012) Andrew C Nelson et al.   JOURNAL OF PATHOLOGY

Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics

(2012) Roland Schmitz et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Text Mining Improves Prediction of Protein Functional Sites

(2012) Karin M. Verspoor et al.   PLoS One

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

(2011) Hyunsoo Kim et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

(2011) Edouard I Severing et al.   BMC PLANT BIOLOGY

Inference of Isoforms from Short Sequence Reads

(2011) Jianxing Feng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Functional Implications of Structural Predictions for Alternative Splice Proteins Expressed in Her2/neu–Induced Breast Cancers

(2011) Rajasree Menon et al.   JOURNAL OF PROTEOME RESEARCH

Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders

(2011) Jorge E. S. de Souza et al.   NUCLEIC ACIDS RESEARCH

Dynamic usage of alternative splicing exons during mouse retina development

(2011) Jun Wan et al.   NUCLEIC ACIDS RESEARCH

Prediction of functionally important residues in globular proteins from unusual central distances of amino acids

(2011) Marek Kochańczyk   BMC STRUCTURAL BIOLOGY

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Graphlet Kernels for Prediction of Functional Residues in Protein Structures

(2010) Vladimir Vacic et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder

(2010) Hedi Hegyi et al.   NUCLEIC ACIDS RESEARCH

rQuant.web: a tool for RNA-Seq-based transcript quantitation

(2010) R. Bohnert et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

(2010) Yuanfang Guan et al.   PLoS Computational Biology

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing and disease

(2008) Jamal Tazi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Predicting gene function in a hierarchical context with an ensemble of classifiers

(2008) Yuanfang Guan et al.   GENOME BIOLOGY

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY