High-throughput sequencing for biology and medicine.

Big Data: Astronomical or Genomical? PLoS Biol (2015) 2.59

BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Min (2015) 1.40

Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics (2014) 1.33

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome Med (2014) 1.31

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. BMC Genomics (2014) 1.02

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Database (Oxford) (2015) 0.97

Timely approaches to identify probiotic species of the genus Lactobacillus. Gut Pathog (2013) 0.95

dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biol (2014) 0.95

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array. Proc Natl Acad Sci U S A (2016) 0.93

Autoimmune and autoinflammatory mechanisms in uveitis. Semin Immunopathol (2014) 0.91

Genetics of proteasome diseases. Scientifica (Cairo) (2013) 0.90

PATHOME: an algorithm for accurately detecting differentially expressed subpathways. Oncogene (2014) 0.89

Single-cell transcriptome sequencing: recent advances and remaining challenges. F1000Res (2016) 0.88

Highly sensitive and ultrafast read mapping for RNA-seq analysis. DNA Res (2016) 0.87

Single Cell Analysis: From Technology to Biology and Medicine. Single Cell Biol (2014) 0.86

Ancient Venom Systems: A Review on Cnidaria Toxins. Toxins (Basel) (2015) 0.86

metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res (2014) 0.86

Foetal radiography for suspected skeletal dysplasia: technique, normal appearances, diagnostic approach. Pediatr Radiol (2014) 0.84

Biological data sciences in genome research. Genome Res (2015) 0.83

Investigating intratumour heterogeneity by single-cell sequencing. Asian J Androl (2013) 0.81

RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PLoS One (2013) 0.80

Sequence analysis by iterated maps, a review. Brief Bioinform (2013) 0.80

Variability in the immune system: of vaccine responses and immune states. Curr Opin Immunol (2013) 0.80

OrthoClust: an orthology-based network framework for clustering data across multiple species. Genome Biol (2014) 0.80

Emerging tools for synthetic genome design. Mol Cells (2013) 0.79

Inferring epigenetic dynamics from kin correlations. Proc Natl Acad Sci U S A (2015) 0.79

Analytical tools for the study of cellular glycosylation in the immune system. Front Immunol (2013) 0.79

TDP-43 affects splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways. Nucleic Acids Res (2015) 0.79

Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med (2014) 0.79

Molecular and genetic inflammation networks in major human diseases. Mol Biosyst (2016) 0.79

From integrative genomics to systems genetics in the rat to link genotypes to phenotypes. Dis Model Mech (2016) 0.79

Complex Homology and the Evolution of Nervous Systems. Trends Ecol Evol (2015) 0.79

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. BMC Genomics (2014) 0.79

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol (2015) 0.78

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array. Proc Natl Acad Sci U S A (2016) 0.78

Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. J Am Stat Assoc (2015) 0.78

Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks. ACS Synth Biol (2014) 0.78

Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis. Cell Res (2014) 0.78

Fibroblasts: the missing link between fibrotic lung diseases of different etiologies? Respir Res (2013) 0.78

Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Brief Bioinform (2015) 0.77

Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B. Mol Med Rep (2016) 0.77

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput Biol (2017) 0.77

Systems approaches to human autoimmune diseases. Curr Opin Immunol (2013) 0.76

Computational strategies for a system-level understanding of metabolism. Metabolites (2014) 0.76

From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PLoS One (2015) 0.76

Current challenges in bacterial transcriptomics. Genomics Inform (2013) 0.76

Combination of Sonodynamic and Photodynamic Therapy against Cancer Would Be Effective through Using a Regulated Size of Nanoparticles. Nanosci Nanoeng (2016) 0.76

Databases and tools for constructing signal transduction networks in cancer. BMB Rep (2017) 0.75

Computational characterisation of cancer molecular profiles derived using next generation sequencing. Contemp Oncol (Pozn) (2015) 0.75

Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales. Genome Biol Evol (2015) 0.75

Reading and writing omes. Mol Syst Biol (2013) 0.75

Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq. RNA Biol (2015) 0.75

Clinicians' expectations for gene-driven cancer therapy. Clin Med Insights Oncol (2014) 0.75

PVT: an efficient computational procedure to speed up next-generation sequence analysis. BMC Bioinformatics (2014) 0.75

Large-scale machine learning for metagenomics sequence classification. Bioinformatics (2015) 0.75

Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Res (2016) 0.75

Rapidly discriminate commercial medicinal Pulsatilla chinensis (Bge.) Regel from its adulterants using ITS2 barcoding and specific PCR-RFLP assay. Sci Rep (2017) 0.75

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data. PLoS One (2016) 0.75

Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. Sci Rep (2017) 0.75

DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A (1977) 790.54

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

A map of human genome variation from population-scale sequencing. Nature (2010) 121.13

High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

The International HapMap Project. Nature (2003) 73.65

Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

Global variation in copy number in the human genome. Nature (2006) 57.50

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04

Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57

Stochastic gene expression in a single cell. Science (2002) 34.54

Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28

Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27

Exome sequencing identifies the cause of a mendelian disorder. Nat Genet (2009) 32.06

Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04

Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

The clonal evolution of tumor cell populations. Science (1976) 24.39

Capturing chromosome conformation. Science (2002) 23.93

The cancer genome. Nature (2009) 23.13

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75

Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13

Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28

Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23

The NCBI dbGaP database of genotypes and phenotypes. Nat Genet (2007) 17.93

The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science (2005) 17.00

A high-resolution survey of deletion polymorphism in the human genome. Nat Genet (2005) 16.99

Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell (2011) 16.72

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48

Stability and flexibility of epigenetic gene regulation in mammalian development. Nature (2007) 14.57

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32

Role for DNA methylation in genomic imprinting. Nature (1993) 12.65

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32

An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16

Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13

Next-generation sequencing transforms today's biology. Nat Methods (2007) 11.93

mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71

Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47

Molecular mechanisms of long noncoding RNAs. Mol Cell (2011) 11.44

Mutational processes molding the genomes of 21 breast cancers. Cell (2012) 11.22

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet (2006) 11.02

The life history of 21 breast cancers. Cell (2012) 10.59

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17

Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol (2002) 9.83

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet (2008) 9.52

Variation in transcription factor binding among humans. Science (2010) 9.33

Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature (2006) 9.30

Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med (2011) 9.03

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet (2006) 8.99

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69

Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell (2009) 8.69

Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A (2008) 8.38

Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet (2000) 8.33

Nuclear organization of the genome and the potential for gene regulation. Nature (2007) 8.22

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87

Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res (2006) 7.72

Mapping human genetic diversity in Asia. Science (2009) 7.40

The gene encoding phosphodiesterase 4D confers risk of ischemic stroke. Nat Genet (2003) 7.37

Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet (2011) 7.31

Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11

Global histone modification patterns predict risk of prostate cancer recurrence. Nature (2005) 7.03

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell (2011) 6.83

CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25

Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell (2010) 6.24

Tumor heterogeneity. Cancer Res (1984) 6.17

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell (2012) 6.07

Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature (2011) 5.95

Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet (2009) 5.93

Tumor heterogeneity: causes and consequences. Biochim Biophys Acta (2009) 5.90

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2011) 5.79

Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79

The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods (2006) 5.72

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet (2011) 5.67

Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62

Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol (2006) 5.17

Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16

G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat Cell Biol (2006) 5.16

CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04

DNA methylation and gene silencing in cancer. Nat Clin Pract Oncol (2005) 5.02

Chromosome territories. Cold Spring Harb Perspect Biol (2010) 5.00

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet (2012) 4.84

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet (2012) 4.82

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62

Whole-genome sequencing for optimized patient management. Sci Transl Med (2011) 4.51

Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32

Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47

Variation in transcription factor binding among humans. Science (2010) 9.33

An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15

Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med (2012) 3.53

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet (2011) 3.14

Landscape of next-generation sequencing technologies. Anal Chem (2011) 2.58

Host-virus interaction: a new role for microRNAs. Retrovirology (2006) 1.88

Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology (2008) 1.87

Microtubule capture by the cleavage apparatus is required for proper spindle positioning in yeast. Genes Dev (2002) 1.76

Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a. Proc Natl Acad Sci U S A (2009) 1.64

Extensive genetic variation in somatic human tissues. Proc Natl Acad Sci U S A (2012) 1.56

Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A (2012) 1.56

Upregulation of miR-23a-27a-24-2 cluster induces caspase-dependent and -independent apoptosis in human embryonic kidney cells. PLoS One (2009) 1.54

Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif. RNA (2008) 1.34

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res (2012) 1.30

Host-virus genome interactions: macro roles for microRNAs. Cell Microbiol (2007) 1.28

Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA (2009) 1.27

Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. Nucleic Acids Res (2006) 1.26

Impacts of variation in the human genome on gene regulation. J Mol Biol (2013) 1.17

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. PLoS Genet (2012) 1.14

A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proc Natl Acad Sci U S A (2012) 1.12

Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. BMC Bioinformatics (2012) 1.09

Defective sphingosine 1-phosphate receptor 1 (S1P1) phosphorylation exacerbates TH17-mediated autoimmune neuroinflammation. Nat Immunol (2013) 1.05

Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res (2013) 1.01

Incomplete penetrance and variable expressivity: is there a microRNA connection? Bioessays (2009) 0.88

Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers. Biol Direct (2013) 0.88

Inhibition of neuronal cholesterol biosynthesis with lovastatin leads to impaired synaptic vesicle release even in the presence of lipoproteins or geranylgeraniol. J Neurochem (2011) 0.87

Shared functions of plant and mammalian StAR-related lipid transfer (START) domains in modulating transcription factor activity. BMC Biol (2014) 0.83

Extended lifespan and reduced adiposity in mice lacking the FAT10 gene. Proc Natl Acad Sci U S A (2014) 0.82

Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Pharmacogenomics (2014) 0.79

microRNA: an emerging therapeutic. ChemMedChem (2007) 0.78

Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype. G3 (Bethesda) (2012) 0.78

Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature (2015) 0.77

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration. Proc Natl Acad Sci U S A (2013) 0.77

The variable somatic genome. Cell Cycle (2012) 0.76

Divergence in a master variator generates distinct phenotypes and transcriptional responses. Genes Dev (2014) 0.76

EPHB4 kinase-inactivating mutations cause autosomal dominant lymphatic-related hydrops fetalis. J Clin Invest (2016) 0.76

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A (2014) 0.76

Specific plasma autoantibody reactivity in myelodysplastic syndromes. Sci Rep (2013) 0.75

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell (2015) 0.75

A simple method for incorporating dynamic effects of intronic miRNA mediated regulation. Mol Biosyst (2012) 0.75