Published in BMC Bioinformatics on December 21, 2010
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics (2010) 2.37
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome. Nat Genet (2012) 1.61
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One (2013) 1.61
Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet (2015) 1.47
Hadoop-BAM: directly manipulating next generation sequencing data in the cloud. Bioinformatics (2012) 1.24
Targeted massively parallel sequencing provides comprehensive genetic diagnosis for patients with disorders of sex development. Clin Genet (2012) 1.18
JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol (2016) 1.09
Gigwa-Genotype investigator for genome-wide analyses. Gigascience (2016) 1.07
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. Genomics (2012) 1.02
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. Bioinformatics (2013) 1.01
Enabling large-scale biomedical analysis in the cloud. Biomed Res Int (2013) 1.01
Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. Biomed Res Int (2013) 0.93
Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1. Nat Genet (2012) 0.89
Data management practices for collaborative research. Front Psychiatry (2011) 0.89
Big Data Application in Biomedical Research and Health Care: A Literature Review. Biomed Inform Insights (2016) 0.86
Bio and health informatics meets cloud : BioVLab as an example. Health Inf Sci Syst (2013) 0.82
SeqHBase: a big data toolset for family based sequencing data analysis. J Med Genet (2015) 0.81
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. Biomed Res Int (2015) 0.80
Single-cell Transcriptome Study as Big Data. Genomics Proteomics Bioinformatics (2016) 0.79
Cloud based metalearning system for predictive modeling of biomedical data. ScientificWorldJournal (2014) 0.79
BigQ: a NoSQL based framework to handle genomic variants in i2b2. BMC Bioinformatics (2015) 0.77
Comparative Genomics Reveal the Diversity of Restriction Methylation Systems in Listeria monocytogenes. Appl Environ Microbiol (2016) 0.76
Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival. IEEE EMBS Int Conf Biomed Health Inform (2016) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
The human genome browser at UCSC. Genome Res (2002) 168.23
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med (2009) 33.09
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
A comprehensive catalogue of somatic mutations from a human cancer genome. Nature (2009) 24.27
Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24
Ensembl 2007. Nucleic Acids Res (2006) 20.10
A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics (2007) 8.47
Single-molecule sequencing of an individual human genome. Nat Biotechnol (2009) 8.35
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet (2010) 2.99
Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (2008) 20.68
Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet (2008) 20.38
Effect of early versus deferred antiretroviral therapy for HIV on survival. N Engl J Med (2009) 19.90
Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation. Nature (2010) 18.69
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
Gene expression profiling of gliomas strongly predicts survival. Cancer Res (2004) 7.79
BFAST: an alignment tool for large scale genome resequencing. PLoS One (2009) 7.48
Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet (2008) 7.13
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45
DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med (2011) 4.98
Melanoma whole-exome sequencing identifies (V600E)B-RAF amplification-mediated acquired B-RAF inhibitor resistance. Nat Commun (2012) 4.94
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med (2006) 4.63
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene (2003) 3.83
A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet (2010) 3.42
Distinct transcription profiles of primary and secondary glioblastoma subgroups. Cancer Res (2006) 3.41
DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med (2012) 3.18
Gene expression profiling identifies molecular subtypes of gliomas. Oncogene (2003) 3.13
Gene expression profile correlates with T-cell infiltration and relative survival in glioblastoma patients vaccinated with dendritic cell immunotherapy. Clin Cancer Res (2010) 3.05
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A (2006) 3.03
Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science (2004) 3.01
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet (2010) 2.99
Individual common variants exert weak effects on the risk for autism spectrum disorderspi. Hum Mol Genet (2012) 2.46
Molecular analysis of glioblastoma: pathway profiling and its implications for patient therapy. Cancer Biol Ther (2003) 2.38
Celsius: a community resource for Affymetrix microarray data. Genome Biol (2007) 2.38
C-terminal truncations in human 3'-5' DNA exonuclease TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy. Nat Genet (2007) 2.35
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics (2008) 2.29
Evidence for sex-specific risk alleles in autism spectrum disorder. Am J Hum Genet (2004) 2.24
Gain-of-function mutations in TRPV4 cause autosomal dominant brachyolmia. Nat Genet (2008) 2.24
Home environmental intervention in inner-city asthma: a randomized controlled clinical trial. Ann Allergy Asthma Immunol (2005) 2.20
Primary glioblastomas express mesenchymal stem-like properties. Mol Cancer Res (2006) 2.18
Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res (2004) 2.17
Cold urticaria, immunodeficiency, and autoimmunity related to PLCG2 deletions. N Engl J Med (2012) 2.08
Mortality in patients hospitalized for asthma exacerbations in the United States. Am J Respir Crit Care Med (2006) 2.07
Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science (2013) 2.00
Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res (2008) 1.96
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
Local alignment of two-base encoded DNA sequence. BMC Bioinformatics (2009) 1.94
ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome. Nat Genet (2012) 1.93
Mutations in PYCR1 cause cutis laxa with progeroid features. Nat Genet (2009) 1.89
Oxysterols are novel activators of the hedgehog signaling pathway in pluripotent mesenchymal cells. J Biol Chem (2007) 1.83
Lethal skeletal dysplasia in mice and humans lacking the golgin GMAP-210. N Engl J Med (2010) 1.81
Fyn and SRC are effectors of oncogenic epidermal growth factor receptor signaling in glioblastoma patients. Cancer Res (2009) 1.79
Family-based genome-wide association scan of attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry (2010) 1.79
Maternal embryonic leucine zipper kinase (MELK) regulates multipotent neural progenitor proliferation. J Cell Biol (2005) 1.74
Identification of EpCAM as the gene for congenital tufting enteropathy. Gastroenterology (2008) 1.65
Replication of autism linkage: fine-mapping peak at 17q21. Am J Hum Genet (2005) 1.65
A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics (2004) 1.65
DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci (2004) 1.64
Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet (2011) 1.63
A genomewide scan for loci involved in attention-deficit/hyperactivity disorder. Am J Hum Genet (2002) 1.63
Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome. Nat Genet (2012) 1.61
Pontocerebellar hypoplasia type 1: clinical spectrum and relevance of EXOSC3 mutations. Neurology (2013) 1.61
Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome. Am J Hum Genet (2009) 1.59
Relationship between gene expression and enhancement in glioblastoma multiforme: exploratory DNA microarray analysis. Radiology (2008) 1.58
SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science (2013) 1.57
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol (2010) 1.56
Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics (2009) 1.55
CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium. Nat Genet (2012) 1.54
Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nat Genet (2012) 1.52
Accuracy of phenotyping of autistic children based on Internet implemented parent report. Am J Med Genet B Neuropsychiatr Genet (2010) 1.51
Indoor exposures to air pollutants and allergens in the homes of asthmatic children in inner-city Baltimore. Environ Res (2005) 1.51
Do high-resolution CT findings of usual interstitial pneumonitis obviate lung biopsy? Views of pulmonologists. Respiration (2005) 1.51
Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet (2008) 1.48
FXR regulates organic solute transporters alpha and beta in the adrenal gland, kidney, and intestine. J Lipid Res (2005) 1.44
Pretest risk assessment in suspected acute pulmonary embolism. Acad Radiol (2008) 1.44
A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet (2011) 1.43
Collaborative analysis of DRD4 and DAT genotypes in population-defined ADHD subtypes. J Child Psychol Psychiatry (2005) 1.40
Detection of a microRNA signal in an in vivo expression set of mRNAs. PLoS One (2007) 1.40
Genetic linkage of attention-deficit/hyperactivity disorder on chromosome 16p13, in a region implicated in autism. Am J Hum Genet (2002) 1.39
Multiple self-healing squamous epithelioma is caused by a disease-specific spectrum of mutations in TGFBR1. Nat Genet (2011) 1.39
Availability, requesting practices, and barriers to referral for high-resolution CT of the lungs: results of a survey of U.S. pulmonologists. Acad Radiol (2002) 1.39
A genomewide scan for attention-deficit/hyperactivity disorder in an extended sample: suggestive linkage on 17p11. Am J Hum Genet (2003) 1.36
Relationship between survival and edema in malignant gliomas: role of vascular endothelial growth factor and neuronal pentraxin 2. Clin Cancer Res (2007) 1.35
Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. Brief Bioinform (2014) 1.32
Molecular properties of CD133+ glioblastoma stem cells derived from treatment-refractory recurrent brain tumors. J Neurooncol (2009) 1.32
Hospitalizations for tuberculosis in the United States in 2000: predictors of in-hospital mortality. Chest (2004) 1.29
Stem cell associated gene expression in glioblastoma multiforme: relationship to survival and the subventricular zone. J Neurooncol (2009) 1.26
Predicting the severity of Duchenne muscular dystrophy: implications for treatment. Neurology (2010) 1.25
The prevalence of rat allergen in inner-city homes and its relationship to sensitization and asthma morbidity. J Allergy Clin Immunol (2003) 1.25
CT pulmonary angiography is the first-line imaging test for acute pulmonary embolism: a survey of US clinicians. Acad Radiol (2006) 1.24
Loss of CHSY1, a secreted FRINGE enzyme, causes syndromic brachydactyly in humans via increased NOTCH signaling. Am J Hum Genet (2010) 1.24
EGFR mutation-induced alternative splicing of Max contributes to growth of glycolytic tumors in brain cancer. Cell Metab (2013) 1.23
Prevalence and psychiatric comorbidity of attention-deficit/hyperactivity disorder in an adolescent Finnish population. J Am Acad Child Adolesc Psychiatry (2007) 1.22