Related references
Note: Only part of the references are listed.Differential analysis of gene regulation at transcript resolution with RNA-seq
Cole Trapnell et al.
NATURE BIOTECHNOLOGY (2013)
The UCSC Genome Browser database: extensions and updates 2013
Laurence R. Meyer et al.
NUCLEIC ACIDS RESEARCH (2013)
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Andrea Franceschini et al.
NUCLEIC ACIDS RESEARCH (2013)
The BioGRID interaction database: 2013 update
Andrew Chatr-aryamontri et al.
NUCLEIC ACIDS RESEARCH (2013)
NCBI GEO: archive for functional genomics data sets-update
Tanya Barrett et al.
NUCLEIC ACIDS RESEARCH (2013)
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
Sam Ng et al.
BIOINFORMATICS (2012)
SCALCE: boosting sequence compression algorithms using locally consistent encoding
Faraz Hach et al.
BIOINFORMATICS (2012)
Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins
Eric T. Wang et al.
CELL (2012)
Comparative Analysis of Protein Networks: Hard Problems, Practical Solutions
Nir Atias et al.
COMMUNICATIONS OF THE ACM (2012)
De novo discovery of mutated driver pathways in cancer
Fabio Vandin et al.
GENOME RESEARCH (2012)
Efficient de novo assembly of large genomes using compressed data structures
Jared T. Simpson et al.
GENOME RESEARCH (2012)
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg et al.
GENOME RESEARCH (2012)
Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study
Renaud Gaujoux et al.
INFECTION GENETICS AND EVOLUTION (2012)
Comprehensive molecular characterization of human colon and rectal cancer
Donna M. Muzny et al.
NATURE (2012)
Comprehensive molecular portraits of human breast tumours
Daniel C. Koboldt et al.
NATURE (2012)
Architecture of the human regulatory network derived from ENCODE data
Mark B. Gerstein et al.
NATURE (2012)
Compressive genomics
Po-Ru Loh et al.
NATURE BIOTECHNOLOGY (2012)
The ENCODE project
Natalie de Souza
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
Oliver Stegle et al.
NATURE PROTOCOLS (2012)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell et al.
NATURE PROTOCOLS (2012)
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
Terrence S. Furey
NATURE REVIEWS GENETICS (2012)
Genome-wide identification of miRNA targets by PAR-CLIP
Markus Hafner et al.
METHODS (2012)
GReEn: a tool for efficient compression of genome resequencing data
Armando J. Pinho et al.
NUCLEIC ACIDS RESEARCH (2012)
The core regulation module of stress-responsive regulatory networks in yeast
Dongsan Kim et al.
NUCLEIC ACIDS RESEARCH (2012)
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways
Nurcan Tuncbag et al.
NUCLEIC ACIDS RESEARCH (2012)
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
Aaron K. Wong et al.
NUCLEIC ACIDS RESEARCH (2012)
Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
Francesco Vezzi et al.
PLOS ONE (2012)
Subtype and pathway specific responses to anticancer compounds in breast cancer
Laura M. Heiser et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Making sense out of massive data by going beyond differential expression
Patrick R. Schmid et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Identification of RNA-protein interaction networks using PAR-CLIP
Manuel Ascano et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2012)
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers
Nathan P. Palmer et al.
GENOME BIOLOGY (2012)
Compression of DNA sequence reads in FASTQ format
Sebastian Deorowicz et al.
BIOINFORMATICS (2011)
Recovering key biological constituents through sparse representation of gene expression
Yosef Prat et al.
BIOINFORMATICS (2011)
MINE: Module Identification in Networks
Kahn Rhrissorrakrai et al.
BMC BIOINFORMATICS (2011)
Biological interaction networks are conserved at the module level
Guy E. Zinman et al.
BMC SYSTEMS BIOLOGY (2011)
Riding the wave of biological data
Michael Gross
CURRENT BIOLOGY (2011)
Cactus: Algorithms for genome multiple sequence alignment
Benedict Paten et al.
GENOME RESEARCH (2011)
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Dent Earl et al.
GENOME RESEARCH (2011)
Efficient storage of high throughput DNA sequencing data using reference-based compression
Markus Hsi-Yang Fritz et al.
GENOME RESEARCH (2011)
A probabilistic disease-gene finder for personal genomes
Mark Yandell et al.
GENOME RESEARCH (2011)
Algorithms for Detecting Significantly Mutated Pathways in Cancer
Fabio Vandin et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2011)
In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites
Anna-Carina Jungkamp et al.
MOLECULAR CELL (2011)
How to apply de Bruijn graphs to genome assembly
Phillip E. C. Compeau et al.
NATURE BIOTECHNOLOGY (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
Computational methods for transcriptome annotation and quantification using RNA-seq
Manuel Garber et al.
NATURE METHODS (2011)
IsoBase: a database of functionally related proteins across PPI networks
Daniel Park et al.
NUCLEIC ACIDS RESEARCH (2011)
Reactome: a database of reactions, pathways and biological processes
David Croft et al.
NUCLEIC ACIDS RESEARCH (2011)
A novel compression tool for efficient storage of genome resequencing data
Congmao Wang et al.
NUCLEIC ACIDS RESEARCH (2011)
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
Alex Lan et al.
NUCLEIC ACIDS RESEARCH (2011)
On the Future of Genomic Data
Scott D. Kahn
SCIENCE (2011)
Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
Marina Sirota et al.
SCIENCE TRANSLATIONAL MEDICINE (2011)
Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
Wenyuan Li et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
Yoo-Ah Kim et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes
Leopold Parts et al.
PLOS GENETICS (2011)
Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology
Elizabeth J. Rossin et al.
PLOS GENETICS (2011)
DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization
Sinan Erten et al.
BIODATA MINING (2011)
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Daehwan Kim et al.
GENOME BIOLOGY (2011)
High-throughput DNA sequencing - concepts and limitations
Martin Kircher et al.
BIOESSAYS (2010)
Statistical expression deconvolution from mixed tissue samples
Jennifer Clarke et al.
BIOINFORMATICS (2010)
The power of protein interaction networks for associating genes with diseases
Saket Navlakha et al.
BIOINFORMATICS (2010)
SPICi: a fast clustering algorithm for large biological networks
Peng Jiang et al.
BIOINFORMATICS (2010)
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Charles J. Vaske et al.
BIOINFORMATICS (2010)
G-SQZ: compact encoding of genomic sequence and quality data
Waibhav Tembe et al.
BIOINFORMATICS (2010)
Fast and accurate long-read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2010)
Assembly complexity of prokaryotic genomes using short reads
Carl Kingsford et al.
BMC BIOINFORMATICS (2010)
In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data
Yipeng Wang et al.
CANCER RESEARCH (2010)
An Integrated Approach to Uncover Drivers of Cancer
Uri David Akavia et al.
CELL (2010)
De novo assembly of human genomes with massively parallel short read sequencing
Ruiqiang Li et al.
GENOME RESEARCH (2010)
Assembly of large genomes using second-generation sequencing
Michael C. Schatz et al.
GENOME RESEARCH (2010)
Cloud computing and the DNA data race
Michael C. Schatz et al.
NATURE BIOTECHNOLOGY (2010)
Predicting causal effects in large-scale systems from observational data
Marloes H. Maathuis et al.
NATURE METHODS (2010)
Cell type-specific gene expression differences in complex tissues
Shai S. Shen-Orr et al.
NATURE METHODS (2010)
mrsFAST: a cache-oblivious algorithm for short-read mapping
Faraz Hach et al.
NATURE METHODS (2010)
A method and server for predicting damaging missense mutations
Ivan A. Adzhubei et al.
NATURE METHODS (2010)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation
Michael L. Metzker
NATURE REVIEWS GENETICS (2010)
Tackling the widespread and critical impact of batch effects in high-throughput data
Jeffrey T. Leek et al.
NATURE REVIEWS GENETICS (2010)
Automated Network Analysis Identifies Core Pathways in Glioblastoma
Ethan Cerami et al.
PLOS ONE (2010)
Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks
Recep Colak et al.
PLOS ONE (2010)
DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases
Igor Ulitsky et al.
PLOS ONE (2010)
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Mark B. Gerstein et al.
SCIENCE (2010)
A Quick Guide to Large-Scale Genomic Data Mining
Curtis Huttenhower et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets
Manikandan Narayanan et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Associating Genes and Protein Complexes with Disease via Network Propagation
Oron Vanunu et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
The case for cloud computing in genome informatics
Lincoln D. Stein
GENOME BIOLOGY (2010)
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Jeremy Goecks et al.
GENOME BIOLOGY (2010)
Differential expression analysis for sequence count data
Simon Anders et al.
GENOME BIOLOGY (2010)
Human genomes as email attachments
Scott Christley et al.
BIOINFORMATICS (2009)
Functionally guided alignment of protein interaction networks for module detection
Waqar Ali et al.
BIOINFORMATICS (2009)
Module networks revisited: computational assessment and prioritization of model predictions
Anagha Joshi et al.
BIOINFORMATICS (2009)
Data structures and compression algorithms for genomic sequence data
Marty C. Brandon et al.
BIOINFORMATICS (2009)
IsoRankN: spectral methods for global alignment of multiple protein networks
Chung-Shou Liao et al.
BIOINFORMATICS (2009)
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell et al.
BIOINFORMATICS (2009)
SOAP2: an improved ultrafast tool for short read alignment
Ruiqiang Li et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Reverse engineering module networks by PSO-RNN hybrid modeling
Yuji Zhang et al.
BMC GENOMICS (2009)
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
Tom Michoel et al.
BMC SYSTEMS BIOLOGY (2009)
ABySS: A parallel assembler for short read sequence data
Jared T. Simpson et al.
GENOME RESEARCH (2009)
Disease signatures are robust across tissues and experiments
Joel T. Dudley et al.
MOLECULAR SYSTEMS BIOLOGY (2009)
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
Esti Yeger-Lotem et al.
NATURE GENETICS (2009)
Sense from sequence reads: methods for alignment and assembly
Paul Flicek et al.
NATURE METHODS (2009)
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
Prateek Kumar et al.
NATURE PROTOCOLS (2009)
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
Matthias Gstaiger et al.
NATURE REVIEWS GENETICS (2009)
RNA-Seq: a revolutionary tool for transcriptomics
Zhong Wang et al.
NATURE REVIEWS GENETICS (2009)
Modularity and interactions in the genetics of gene expression
Oren Litvin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Nicholas T. Ingolia et al.
SCIENCE (2009)
Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks
Shao-shan Carol Huang et al.
SCIENCE SIGNALING (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Walking the interactome for prioritization of candidate disease genes
Sebastian Koehler et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2008)
Next-Generation DNA Sequencing Methods
Elaine R. Mardis
Annual Review of Genomics and Human Genetics (2008)
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
Osamu Hirose et al.
BIOINFORMATICS (2008)
SOAP: short oligonucleotide alignment program
Ruiqiang Li et al.
BIOINFORMATICS (2008)
TiGER: A database for tissue-specific gene expression and regulation
Xiong Liu et al.
BMC BIOINFORMATICS (2008)
Gene module level analysis: identification to networks and dynamics
Xuewei Wang et al.
CURRENT OPINION IN BIOTECHNOLOGY (2008)
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
John C. Marioni et al.
GENOME RESEARCH (2008)
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Jonathan Butler et al.
GENOME RESEARCH (2008)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
eQED: an efficient method for interpreting eQTL associations using protein networks
Silpa Suthram et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi et al.
NATURE METHODS (2008)
Global alignment of multiple protein interaction networks with application to functional orthology detection
Rohit Singh et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Organization of Physical Interactomes as Uncovered by Network Schemas
Eric Banks et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
NetGrep: fast network schema searches in interactomes
Eric Banks et al.
GENOME BIOLOGY (2008)
The diploid genome sequence of an individual human
Samuel Levy et al.
PLOS BIOLOGY (2007)
Functional annotation of regulatory pathways
Jayesh Pandey et al.
BIOINFORMATICS (2007)
Nested effects models for high-dimensional phenotyping screens
Florian Markowetz et al.
BIOINFORMATICS (2007)
The human disease network
Kwang-Il Goh et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Identification of functional modules using network topology and high-throughput data
Igor Ulitsky et al.
BMC SYSTEMS BIOLOGY (2007)
Innovation - The Connectivity Map: a new tool for biomedical research
Justin Lamb
NATURE REVIEWS CANCER (2007)
Graemlin: General and robust alignment of multiple large interaction networks
Jason Flannick et al.
GENOME RESEARCH (2006)
An integrative approach for causal gene identification and gene regulatory pathway inference
Zhidong Tu et al.
BIOINFORMATICS (2006)
Pairwise alignment of protein interaction networks
M Koyutürk et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2006)
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression
Osamu Ogasawara et al.
NUCLEIC ACIDS RESEARCH (2006)
Microarray data analysis: from disarray to consolidation and consensus
DB Allison et al.
NATURE REVIEWS GENETICS (2006)
Metagenomics: DNA sequencing of environmental samples
SG Tringe et al.
NATURE REVIEWS GENETICS (2005)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
A Subramanian et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Indexing compressed text
P Ferragina et al.
JOURNAL OF THE ACM (2005)
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
E Nabieva et al.
BIOINFORMATICS (2005)
A gene expression map of Arabidopsis thaliana development
M Schmid et al.
NATURE GENETICS (2005)
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
A Tanay et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Physical network models
CH Yeang et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2004)
Bioconductor: open software development for computational biology and bioinformatics
RC Gentleman et al.
GENOME BIOLOGY (2004)
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
BP Kelley et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations
P Lu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
E Segal et al.
NATURE GENETICS (2003)
Individuality and variation in gene expression patterns in human blood
AR Whitney et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Whole-genome sequence assembly for mammalian genomes: Arachne 2
DB Jaffe et al.
GENOME RESEARCH (2003)
Cytoscape: A software environment for integrated models of biomolecular interaction networks
P Shannon et al.
GENOME RESEARCH (2003)
The use and analysis of microarray data
A Butte
NATURE REVIEWS DRUG DISCOVERY (2002)
Transitive functional annotation by shortest-path analysis of gene expression data
XH Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
High-throughput gene mapping in Caenorhabditis elegans
KA Swan et al.
GENOME RESEARCH (2002)
ARACHNE: A whole-genome shotgun assembler
S Batzoglou et al.
GENOME RESEARCH (2002)
Principal component analysis for clustering gene expression data
KY Yeung et al.
BIOINFORMATICS (2001)
An Eulerian path approach to DNA fragment assembly
PA Pevzner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Initial sequencing and analysis of the human genome
ES Lander et al.
NATURE (2001)
Share Paper
