Published in Nat Biotechnol on January 01, 2011
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc (2013) 13.33
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME. Bioinformatics (2011) 8.23
Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature (2012) 7.76
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet (2014) 5.74
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
Integrative clinical genomics of advanced prostate cancer. Cell (2015) 5.29
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature (2012) 5.23
Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med (2012) 5.16
Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res (2012) 5.12
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science (2015) 4.88
The genetic landscape of high-risk neuroblastoma. Nat Genet (2013) 4.71
De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes. Nat Genet (2012) 4.51
Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun (2013) 4.35
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities. Nature (2012) 4.26
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nat Genet (2013) 4.03
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Using exome sequencing to reveal mutations in TREM2 presenting as a frontotemporal dementia-like syndrome without bone involvement. JAMA Neurol (2013) 3.70
Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol (2015) 3.64
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. Nat Genet (2012) 3.43
The UCSC genome browser and associated tools. Brief Bioinform (2012) 3.29
Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A (2013) 3.25
Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet (2012) 3.14
Whole-genome characterization of chemoresistant ovarian cancer. Nature (2015) 3.06
Quantifying prion disease penetrance using large population control cohorts. Sci Transl Med (2016) 3.04
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
The genetic landscape of mutations in Burkitt lymphoma. Nat Genet (2012) 3.03
Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood (2012) 2.98
Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics (2011) 2.98
Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics (2012) 2.92
Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol (2013) 2.91
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Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat Genet (2012) 2.80
The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature (2012) 2.80
Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol (2011) 2.78
A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67
Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet (2013) 2.66
deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res (2014) 2.66
The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio (2013) 2.64
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood (2012) 2.51
ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol (2012) 2.51
Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res (2013) 2.50
A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov (2013) 2.49
The landscape of kinase fusions in cancer. Nat Commun (2014) 2.48
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res (2013) 2.43
A largely random AAV integration profile after LPLD gene therapy. Nat Med (2013) 2.42
Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia. Nat Genet (2013) 2.38
Mutations in the TGF-β repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm. Nat Genet (2012) 2.34
A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol (2013) 2.33
Mutation altering the miR-184 seed region causes familial keratoconus with cataract. Am J Hum Genet (2011) 2.33
Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev (2011) 2.31
Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. PLoS Biol (2012) 2.29
Efficiency and power as a function of sequence coverage, SNP array density, and imputation. PLoS Comput Biol (2012) 2.29
Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn (2013) 2.20
Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet (2011) 2.20
Mutations in the gene PRRT2 cause paroxysmal kinesigenic dyskinesia with infantile convulsions. Cell Rep (2011) 2.17
Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res (2012) 2.15
A transcription factor-based mechanism for mouse heterochromatin formation. Nat Struct Mol Biol (2012) 2.15
BRAF inhibitor vemurafenib improves the antitumor activity of adoptive cell immunotherapy. Cancer Res (2012) 2.14
Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res (2013) 2.12
Somatic SETBP1 mutations in myeloid malignancies. Nat Genet (2013) 2.12
SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics (2011) 2.11
Melanoma adapts to RAF/MEK inhibitors through FOXD3-mediated upregulation of ERBB3. J Clin Invest (2013) 2.11
Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov (2014) 2.09
Correction of a pathogenic gene mutation in human embryos. Nature (2017) 2.09
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell (2016) 2.04
Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem (2012) 2.03
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics (2011) 2.02
PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics (2011) 2.02
Ovarian cancer cell line panel (OCCP): clinical importance of in vitro morphological subtypes. PLoS One (2014) 1.99
Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets. Nat Commun (2015) 1.94
A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res (2012) 1.92
Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell (2015) 1.92
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet (2011) 1.91
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat Genet (2015) 1.89
Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells. Cell (2016) 1.88
Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog (2012) 1.85
Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell (2014) 1.85
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood (2013) 1.84
Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet Med (2015) 1.84
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife (2013) 1.84
The mutational landscape of adenoid cystic carcinoma. Nat Genet (2013) 1.83
Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol (2013) 1.81
Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med (2014) 1.80
Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases. Nat Methods (2012) 1.79
A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Mol Biol Evol (2015) 1.79
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Tablet--next generation sequence assembly visualization. Bioinformatics (2009) 11.75
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (2009) 10.30
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res (2008) 7.50
MapView: visualization of short reads alignment on a desktop computer. Bioinformatics (2009) 6.77
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
Savant: genome browser for high-throughput sequencing data. Bioinformatics (2010) 6.51
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
MicroRNA expression profiles classify human cancers. Nature (2005) 69.12
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
GenePattern 2.0. Nat Genet (2006) 29.07
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature (2013) 20.16
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
BRAF mutation predicts sensitivity to MEK inhibition. Nature (2005) 17.14
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature (2005) 15.28
Genetic mapping in human disease. Science (2008) 15.12
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
High-throughput oncogene mutation profiling in human cancer. Nat Genet (2007) 12.68
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46