Published in Bioinformatics on January 28, 2010
RNA-guided human genome engineering via Cas9. Science (2013) 48.29
HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (2014) 23.22
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res (2011) 11.03
Software for computing and annotating genomic ranges. PLoS Comput Biol (2013) 8.20
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature (2014) 5.45
Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med (2014) 4.98
Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol (2013) 4.72
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol (2013) 4.67
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet (2013) 4.40
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res (2013) 4.33
Predicting effective microRNA target sites in mammalian mRNAs. Elife (2015) 4.30
Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science (2014) 4.28
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell (2013) 4.28
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res (2010) 4.22
Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol (2011) 4.18
Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics (2014) 4.16
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell (2012) 4.10
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature (2013) 3.77
Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet (2011) 3.70
BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics (2011) 3.59
The landscape of long noncoding RNAs in the human transcriptome. Nat Genet (2015) 3.58
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (2011) 3.55
Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science (2014) 3.16
Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature (2012) 3.08
The genetic landscape of mutations in Burkitt lymphoma. Nat Genet (2012) 3.03
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet (2012) 2.92
Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol (2013) 2.91
Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet (2014) 2.86
Enhancer transcripts mark active estrogen receptor binding sites. Genome Res (2013) 2.82
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics (2014) 2.81
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science (2012) 2.81
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res (2013) 2.77
RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell (2012) 2.77
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature (2011) 2.70
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol (2014) 2.65
CONTRA: copy number analysis for targeted resequencing. Bioinformatics (2012) 2.64
BEDOPS: high-performance genomic feature operations. Bioinformatics (2012) 2.62
Population genomics of Bronze Age Eurasia. Nature (2015) 2.58
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 2.53
A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods (2015) 2.52
Plasmodium Infection Promotes Genomic Instability and AID-Dependent B Cell Lymphoma. Cell (2015) 2.51
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol (2011) 2.47
Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet (2012) 2.45
DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature (2012) 2.44
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol (2013) 2.44
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res (2013) 2.43
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet (2013) 2.42
Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res (2014) 2.36
Genomic variation in natural populations of Drosophila melanogaster. Genetics (2012) 2.33
Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature (2014) 2.33
Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol (2010) 2.32
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Biogeography and individuality shape function in the human skin metagenome. Nature (2014) 2.27
Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. Nat Biotechnol (2011) 2.23
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One (2013) 2.22
Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell (2014) 2.20
Rapid evolutionary response to a transmissible cancer in Tasmanian devils. Nat Commun (2016) 2.19
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol (2015) 2.19
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol (2011) 2.18
LUMPY: a probabilistic framework for structural variant discovery. Genome Biol (2014) 2.17
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
lobSTR: A short tandem repeat profiler for personal genomes. Genome Res (2012) 2.08
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Complex multi-enhancer contacts captured by genome architecture mapping. Nature (2017) 2.04
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature (2014) 2.04
DNMT1-interacting RNAs block gene-specific DNA methylation. Nature (2013) 2.04
Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell (2012) 2.02
Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice. Nat Med (2017) 2.02
KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (2012) 1.99
Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol (2012) 1.97
The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol (2012) 1.96
A long noncoding RNA protects the heart from pathological hypertrophy. Nature (2014) 1.96
Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain (2013) 1.95
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (2014) 1.94
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell (2015) 1.94
Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol (2012) 1.94
An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics (2011) 1.92
Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet (2013) 1.92
Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell (2015) 1.92
Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc (2013) 1.91
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet (2011) 1.91
Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. Mol Cell (2014) 1.90
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res (2015) 1.89
The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet (2011) 1.88
The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature (2016) 1.88
Polyploidy can drive rapid adaptation in yeast. Nature (2015) 1.87
RNA-seq differential expression studies: more sequence or more replication? Bioinformatics (2013) 1.87
Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature (2014) 1.86
The genome sequence of the colonial chordate, Botryllus schlosseri. Elife (2013) 1.86
Medical implications of technical accuracy in genome sequencing. Genome Med (2016) 1.86
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
The human genome browser at UCSC. Genome Res (2002) 168.23
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science (2002) 17.04
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res (2010) 4.22
Mosaic copy number variation in human neurons. Science (2013) 3.57
Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet (2012) 2.45
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res (2013) 2.43
Recurrent DNA copy number variation in the laboratory mouse. Nat Genet (2007) 2.40
LUMPY: a probabilistic framework for structural variant discovery. Genome Biol (2014) 2.17
YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics (2012) 1.67
Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell (2011) 1.54
Transformation of natural genetic variation into Haemophilus influenzae genomes. PLoS Pathog (2011) 1.32
Characterizing complex structural variation in germline and somatic genomes. Trends Genet (2011) 1.25
Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A (2006) 1.01
Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics (2012) 0.96
DNA structural variants as genetic risk factors for the long QT syndrome. J Am Coll Cardiol (2011) 0.81
Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells. Nucleic Acids Res (2012) 0.79
GEM: crystal-clear DNA alignment. Nat Methods (2012) 0.75