4.6 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Protein function prediction using domain families

Robert Rentzsch et al.

BMC BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

APPRIS: annotation of principal and alternative splice isoforms

Jose Manuel Rodriguez et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biotechnology & Applied Microbiology

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

Mar Gonzalez-Porta et al.

GENOME BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Tailoring of Membrane Proteins by Alternative Splicing of Pre-mRNA

Kathleen F. Mittendorf et al.

BIOCHEMISTRY (2012)

Article Biotechnology & Applied Microbiology

Functional genomics in Drosophila models of human disease

Ko-Fan Chen et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2012)

Review Medicine, Research & Experimental

The Tumor Suppressor Gene ARF as a Sensor of Oxidative Stress

M. Liontos et al.

CURRENT MOLECULAR MEDICINE (2012)

Article Biochemistry & Molecular Biology

GENCODE: The reference human genome annotation for The ENCODE Project

Jennifer Harrow et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Julia Fruehwald et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Multidisciplinary Sciences

Landscape of transcription in human cells

Sarah Djebali et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

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

Cole Trapnell et al.

NATURE PROTOCOLS (2012)

Article Multidisciplinary Sciences

Text Mining Improves Prediction of Protein Functional Sites

Karin M. Verspoor et al.

PLOS ONE (2012)

Article Biochemical Research Methods

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

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

Inference of Isoforms from Short Sequence Reads

Jianxing Feng et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Dynamic usage of alternative splicing exons during mouse retina development

Jun Wan et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

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

Richard M. Myers et al.

PLOS BIOLOGY (2011)

Review Biochemical Research Methods

Graphlet Kernels for Prediction of Functional Residues in Protein Structures

Vladimir Vacic et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2010)

Article Multidisciplinary Sciences

Deciphering the splicing code

Yoseph Barash et al.

NATURE (2010)

Article Biochemical Research Methods

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

Ambrish Roy et al.

NATURE PROTOCOLS (2010)

Article Biochemistry & Molecular Biology

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

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

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

Regina Bohnert et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

Yuanfang Guan et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Review Biochemistry & Molecular Biology

Alternative splicing and disease

Jamal Tazi et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2009)

Article Biochemical Research Methods

Statistical inferences for isoform expression in RNA-Seq

Hui Jiang et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Review Clinical Neurology

Ataxias with Autosomal, X-Chromosomal or Maternal Inheritance

Josef Finsterer

CANADIAN JOURNAL OF NEUROLOGICAL SCIENCES (2009)

Article Biochemistry & Molecular Biology

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

Albert J. Vilella et al.

GENOME RESEARCH (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemical Research Methods

Prediction of protein functional residues from sequence by probability density estimation

J. D. Fischer et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Biotechnology & Applied Microbiology

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

Yuanfang Guan et al.

GENOME BIOLOGY (2008)

Article Biotechnology & Applied Microbiology

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

Lourdes Pena-Castillo et al.

GENOME BIOLOGY (2008)

Article Biochemical Research Methods

Determination and validation of principal gene products

Michael L. Tress et al.

BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Protein kinase C-dependent control of Bcl-x alternative splicing

Timothee Revil et al.

MOLECULAR AND CELLULAR BIOLOGY (2007)

Article Biochemical Research Methods

Exploring the functional landscape of gene expression: directed search of large microarray compendia

Matthew A. Hibbs et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse mode of breast cancer

Jeffrey R. Whiteaker et al.

JOURNAL OF PROTEOME RESEARCH (2007)

Review Oncology

Computational prediction of cancer-gene function

Pingzhao Hu et al.

NATURE REVIEWS CANCER (2007)

Review Biochemistry & Molecular Biology

Alternative splicing in cancer: Noise, functional, or systematic?

Rolf I. Skotheim et al.

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Finding function: evaluation methods for functional genomic data

Chad L. Myers et al.

BMC GENOMICS (2006)

Article Biochemistry & Molecular Biology

Alternative splicing switches the divalent cation selectivity of TRPM3 channels

J Oberwinkler et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Review Cell Biology

Understanding alternative splicing: Towards a cellular code

AJ Matlin et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2005)

Article Biochemical Research Methods

Estimating misclassification error with small samples via bootstrap cross-validation

WJJ Fu et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

TM-align: a protein structure alignment algorithm based on the TM-score

Y Zhang et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Prediction of functional modules based on comparative genome analysis and Gene Ontology application

HW Wu et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Global identification of human transcribed sequences with genome tiling arrays

P Bertone et al.

SCIENCE (2004)

Article Biochemical Research Methods

TANDEM: matching proteins with tandem mass spectra

R Craig et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

The Gene Ontology (GO) database and informatics resource

MA Harris et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

Predicting protein function from protein/protein interaction data: a probabilistic approach

Stanley Letovsky et al.

BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Prediction of protein functional domains from sequences using artificial neural networks

J Murvai et al.

GENOME RESEARCH (2001)