Published in Bioinformatics on July 09, 2013
Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics (2014) 2.37
Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med (2013) 1.68
Comparison of somatic mutation calling methods in amplicon and whole exome sequence data. BMC Genomics (2014) 1.53
OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data. PLoS One (2014) 1.44
Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature (2015) 1.34
Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform (2014) 1.13
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Res (2014) 1.05
Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol (2014) 1.05
Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing. Hum Mutat (2015) 1.00
BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity. BMC Bioinformatics (2014) 0.99
Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. BMC Genomics (2013) 0.92
High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer. Genome Biol (2015) 0.89
Detailed comparison of two popular variant calling packages for exome and targeted exon studies. PeerJ (2014) 0.88
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. Bioinformatics (2014) 0.86
An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biol (2015) 0.85
Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2). Front Genet (2015) 0.83
Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples. PLoS One (2015) 0.82
TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol. Nat Commun (2016) 0.81
Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data. PLoS One (2016) 0.81
SCNVSim: somatic copy number variation and structure variation simulator. BMC Bioinformatics (2015) 0.81
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PLoS One (2014) 0.81
In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data. Sci Rep (2016) 0.79
The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations. Blood (2014) 0.78
ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification. PLoS One (2015) 0.77
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics (2017) 0.75
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. Oncotarget (2016) 0.75
MixClone: a mixture model for inferring tumor subclonal populations. BMC Genomics (2015) 0.75
Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data. BMC Bioinformatics (2016) 0.75
Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Med (2017) 0.75
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
A comprehensive catalogue of somatic mutations from a human cancer genome. Nature (2009) 24.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (2009) 16.04
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90
Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet (2010) 10.15
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics (2011) 5.62
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics (2012) 5.04
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics (2012) 3.21
Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics (2011) 2.98
Human cancers express mutator phenotypes: origin, consequences and targeting. Nat Rev Cancer (2011) 2.77
Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics (2003) 2.46
Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet (2010) 2.39
Mutational heterogeneity in human cancers: origin and consequences. Annu Rev Pathol (2010) 2.02
Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res (2011) 1.75
The difference in p53 mutations between cancers of the upper and lower gastrointestinal tract. Digestion (2009) 1.02
Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis. Proc Natl Acad Sci U S A (2002) 0.99
Tumour heterogeneity and drug resistance: personalising cancer medicine through functional genomics. Biochem Pharmacol (2011) 0.97
Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics (2005) 10.64
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Frequency of major molecular responses to imatinib or interferon alfa plus cytarabine in newly diagnosed chronic myeloid leukemia. N Engl J Med (2003) 6.68
Dynamics of chronic myeloid leukaemia. Nature (2005) 6.63
Sequential ABL kinase inhibitor therapy selects for compound drug-resistant BCR-ABL mutations with altered oncogenic potency. J Clin Invest (2007) 4.07
Rare and novel epidermal growth factor receptor mutations in non-small-cell lung cancer and lack of clinical response to gefitinib in two cases. J Thorac Oncol (2012) 3.45
Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia. Nat Genet (2011) 3.41
Safety and efficacy of imatinib cessation for CML patients with stable undetectable minimal residual disease: results from the TWISTER study. Blood (2013) 3.23
Dasatinib induces complete hematologic and cytogenetic responses in patients with imatinib-resistant or -intolerant chronic myeloid leukemia in blast crisis. Blood (2006) 2.94
RANK signals from CD4(+)3(-) inducer cells regulate development of Aire-expressing epithelial cells in the thymic medulla. J Exp Med (2007) 2.91
Dasatinib treatment of chronic-phase chronic myeloid leukemia: analysis of responses according to preexisting BCR-ABL mutations. Blood (2009) 2.87
Medullary thymic epithelial cells expressing Aire represent a unique lineage derived from cells expressing claudin. Nat Immunol (2007) 2.61
Impact of baseline BCR-ABL mutations on response to nilotinib in patients with chronic myeloid leukemia in chronic phase. J Clin Oncol (2009) 2.56
Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci U S A (2005) 2.56
Gene dosage--limiting role of Aire in thymic expression, clonal deletion, and organ-specific autoimmunity. J Exp Med (2004) 2.43
Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance. Blood (2011) 2.25
Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics (2004) 2.25
Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics (2008) 2.14
Autoantigen-specific interactions with CD4+ thymocytes control mature medullary thymic epithelial cell cellularity. Immunity (2008) 2.07
Autoimmune polyendocrine syndrome type 1 and NALP5, a parathyroid autoantigen. N Engl J Med (2008) 2.01
Redefining epithelial progenitor potential in the developing thymus. Eur J Immunol (2007) 1.81
Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nat Genet (2007) 1.79
Impact of early dose intensity on cytogenetic and molecular responses in chronic- phase CML patients receiving 600 mg/day of imatinib as initial therapy. Blood (2008) 1.64
Knobloch syndrome: novel mutations in COL18A1, evidence for genetic heterogeneity, and a functionally impaired polymorphism in endostatin. Hum Mutat (2004) 1.61
The transmembrane serine protease (TMPRSS3) mutated in deafness DFNB8/10 activates the epithelial sodium channel (ENaC) in vitro. Hum Mol Genet (2002) 1.58
Establishment and validation of analytical reference panels for the standardization of quantitative BCR-ABL1 measurements on the international scale. Clin Chem (2013) 1.58
Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS One (2013) 1.57
BCR-ABL transcript dynamics support the hypothesis that leukemic stem cells are reduced during imatinib treatment. Clin Cancer Res (2011) 1.56
A physical map of the bovine genome. Genome Biol (2007) 1.56
A specific anti-Aire antibody reveals aire expression is restricted to medullary thymic epithelial cells and not expressed in periphery. J Immunol (2008) 1.46
Molecular monitoring of BCR-ABL as a guide to clinical management in chronic myeloid leukaemia. Blood Rev (2005) 1.45
Sensitive detection of BCR-ABL1 mutations in patients with chronic myeloid leukemia after imatinib resistance is predictive of outcome during subsequent therapy. J Clin Oncol (2011) 1.38
Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype. J Immunol (2009) 1.32
Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis. Plant Cell (2011) 1.32
Molecular cloning and characterization of a novel gene family of four ancient conserved domain proteins (ACDP). Gene (2003) 1.31
Establishment of the first World Health Organization International Genetic Reference Panel for quantitation of BCR-ABL mRNA. Blood (2010) 1.26
Spliceosome mutations in hematopoietic malignancies. Nat Genet (2011) 1.23
In vitro sensitivity to imatinib-induced inhibition of ABL kinase activity is predictive of molecular response in patients with de novo CML. Blood (2005) 1.21
Deep sequencing analysis of the developing mouse brain reveals a novel microRNA. BMC Genomics (2011) 1.19
Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients. J Mol Med (Berl) (2001) 1.19
Practical advice for determining the role of BCR-ABL mutations in guiding tyrosine kinase inhibitor therapy in patients with chronic myeloid leukemia. Cancer (2010) 1.14
Identification and sequence analysis of chicken Toll-like receptors. Immunogenetics (2004) 1.14
Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Res (2010) 1.14
Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biol (2009) 1.14
Poor response to second-line kinase inhibitors in chronic myeloid leukemia patients with multiple low-level mutations, irrespective of their resistance profile. Blood (2011) 1.13
The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci. BMC Bioinformatics (2006) 1.13
Autoimmune regulator deficiency results in decreased expression of CCR4 and CCR7 ligands and in delayed migration of CD4+ thymocytes. J Immunol (2009) 1.13
Interferon autoantibodies associated with AIRE deficiency decrease the expression of IFN-stimulated genes. Blood (2008) 1.12
Nedd4-WW domain-binding protein 5 (Ndfip1) is associated with neuronal survival after acute cortical brain injury. J Neurosci (2006) 1.10
Mice deficient for the type II transmembrane serine protease, TMPRSS1/hepsin, exhibit profound hearing loss. Am J Pathol (2007) 1.08
MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol (2003) 1.07
Modulation of Aire regulates the expression of tissue-restricted antigens. Mol Immunol (2007) 1.07
Hematopoietic defects in the Ts1Cje mouse model of Down syndrome. Blood (2008) 1.07
Expression of Aire and the early wave of apoptosis in spermatogenesis. J Immunol (2008) 1.06
The lymphotoxin pathway regulates Aire-independent expression of ectopic genes and chemokines in thymic stromal cells. J Immunol (2008) 1.05
Post-Aire maturation of thymic medullary epithelial cells involves selective expression of keratinocyte-specific autoantigens. Front Immunol (2012) 1.03
A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse model. Neurotox Res (2009) 1.03
Molecular monitoring of chronic myeloid leukemia. Semin Hematol (2003) 1.03
AIRE's CARD revealed, a new structure for central tolerance provokes transcriptional plasticity. J Biol Chem (2007) 1.03
Ablation and regeneration of tolerance-inducing medullary thymic epithelial cells after cyclosporine, cyclophosphamide, and dexamethasone treatment. J Immunol (2009) 1.02
Sequential phases in the development of Aire-expressing medullary thymic epithelial cells involve distinct cellular input. Eur J Immunol (2008) 1.02
Sheep endogenous betaretroviruses (enJSRVs) and the hyaluronidase 2 (HYAL2) receptor in the ovine uterus and conceptus. Biol Reprod (2005) 1.02
An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss. Hum Mutat (2008) 1.02
Widespread horizontal transfer of retrotransposons. Proc Natl Acad Sci U S A (2012) 1.02
Discovery and characterization of an epithelial-specific galectin in the endometrium that forms crystals in the trophectoderm. Proc Natl Acad Sci U S A (2004) 1.00
Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes. PLoS One (2012) 0.98
Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood (2011) 0.98
ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J Clin Endocrinol Metab (2014) 0.97
Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS One (2013) 0.95
SHP-1 expression accounts for resistance to imatinib treatment in Philadelphia chromosome-positive cells derived from patients with chronic myeloid leukemia. Blood (2011) 0.94
Tmprss3, a transmembrane serine protease deficient in human DFNB8/10 deafness, is critical for cochlear hair cell survival at the onset of hearing. J Biol Chem (2011) 0.94
Identification of endometrial genes regulated by early pregnancy, progesterone, and interferon tau in the ovine uterus. Biol Reprod (2005) 0.94
GATA2 is required for lymphatic vessel valve development and maintenance. J Clin Invest (2015) 0.93
Tyrosine kinase inhibitor resistance in chronic myeloid leukemia cell lines: investigating resistance pathways. Leuk Lymphoma (2011) 0.93
Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks. BMC Genomics (2014) 0.93
AML1 interconnected pathways of leukemogenesis. Cancer Invest (2003) 0.93
Spatiotemporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis. Cereb Cortex (2010) 0.93
DNA methylation signatures of the AIRE promoter in thymic epithelial cells, thymomas and normal tissues. Mol Immunol (2011) 0.92
Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome. PLoS One (2010) 0.92
Genetic regulators of myelopoiesis and leukemic signaling identified by gene profiling and linear modeling. J Leukoc Biol (2006) 0.92
QTL global meta-analysis: are trait determining genes clustered? BMC Genomics (2009) 0.92
Monitoring disease response to tyrosine kinase inhibitor therapy in CML. Hematology Am Soc Hematol Educ Program (2009) 0.91
Expression of three spalt (sal) gene homologues in zebrafish embryos. Dev Genes Evol (2002) 0.91
Bovine Genome Database: integrated tools for genome annotation and discovery. Nucleic Acids Res (2010) 0.90
Discovery of candidate genes and pathways in the endometrium regulating ovine blastocyst growth and conceptus elongation. Physiol Genomics (2009) 0.90
Decreased phosphatidylethanolamine binding protein expression correlates with Abeta accumulation in the Tg2576 mouse model of Alzheimer's disease. Neurobiol Aging (2005) 0.89