Published in Nucleic Acids Res on July 01, 2006
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Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res (2005) 18.85
Multiple sequence alignment using partial order graphs. Bioinformatics (2002) 13.70
Expression of a large family of POU-domain regulatory genes in mammalian brain development. Nature (1989) 5.68
De novo repeat classification and fragment assembly. Genome Res (2004) 4.58
A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res (2004) 2.73
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
Brn-3.0: a POU-domain protein expressed in the sensory, immune, and endocrine systems that functions on elements distinct from known octamer motifs. Proc Natl Acad Sci U S A (1993) 1.79
Identifying repeat domains in large genomes. Genome Biol (2006) 1.58
International network of cancer genome projects. Nature (2010) 20.35
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
The mutational landscape of lethal castration-resistant prostate cancer. Nature (2012) 11.82
Algorithms for detecting significantly mutated pathways in cancer. J Comput Biol (2011) 3.53
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
A geometric approach for classification and comparison of structural variants. Bioinformatics (2009) 2.79
A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res (2004) 2.73
De novo discovery of mutated driver pathways in cancer. Genome Res (2011) 2.72
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol (2008) 2.40
Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res (2006) 2.09
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol (2013) 1.98
The mutational landscape of adenoid cystic carcinoma. Nat Genet (2013) 1.83
Bayesian analysis of rare variants in genetic association studies. Genet Epidemiol (2011) 1.73
Simultaneous identification of multiple driver pathways in cancer. PLoS Comput Biol (2013) 1.71
Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci U S A (2011) 1.64
Discovery of mutated subnetworks associated with clinical data in cancer. Pac Symp Biocomput (2012) 1.61
Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects. PLoS Genet (2011) 1.61
Identifying repeat domains in large genomes. Genome Biol (2006) 1.58
An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol (2012) 1.56
Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia. Leuk Res (2008) 1.42
Epigenome-wide association study of fasting measures of glucose, insulin, and HOMA-IR in the Genetics of Lipid Lowering Drugs and Diet Network study. Diabetes (2013) 1.38
A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Mol Cell Proteomics (2009) 1.25
Quantitative time-resolved phosphoproteomic analysis of mast cell signaling. J Immunol (2007) 1.16
Length bias correction for RNA-seq data in gene set analyses. Bioinformatics (2011) 1.15
Advances for studying clonal evolution in cancer. Cancer Lett (2013) 1.14
Expression signature of IFN/STAT1 signaling genes predicts poor survival outcome in glioblastoma multiforme in a subtype-specific manner. PLoS One (2012) 1.11
Structural variation analysis with strobe reads. Bioinformatics (2010) 1.05
Haplotype-based methods for detecting uncommon causal variants with common SNPs. Genet Epidemiol (2012) 1.04
Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants. Genet Epidemiol (2013) 1.04
Network analysis of GWAS data. Curr Opin Genet Dev (2013) 1.02
Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice, and Untyped Rate. Stat Interface (2011) 1.01
Analysis of segmental duplications via duplication distance. Bioinformatics (2008) 1.00
Identification of polymorphic inversions from genotypes. BMC Bioinformatics (2012) 0.99
Identification and frequency estimation of inversion polymorphisms from haplotype data. J Comput Biol (2010) 0.97
Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (2007) 0.96
Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics (2008) 0.95
Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinformatics (2011) 0.94
Reconstructing cancer genomes from paired-end sequencing data. BMC Bioinformatics (2012) 0.93
A parsimony approach to analysis of human segmental duplications. Pac Symp Biocomput (2009) 0.91
Pathway-based approaches for sequencing-based genome-wide association studies. Genet Epidemiol (2013) 0.90
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol Biol (2010) 0.89
Epigenetic Signatures of Cigarette Smoking. Circ Cardiovasc Genet (2016) 0.88
Gremlin: an interactive visualization model for analyzing genomic rearrangements. IEEE Trans Vis Comput Graph (2010) 0.88
Vitronectin inhibits neutrophil apoptosis through activation of integrin-associated signaling pathways. Am J Respir Cell Mol Biol (2012) 0.88
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads. Bioinformatics (2013) 0.87
A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence. Hum Genet (2013) 0.86
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. BMC Genomics (2012) 0.86
Parsimony and likelihood reconstruction of human segmental duplications. Bioinformatics (2010) 0.86
Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters. Gene (2005) 0.85
Statistical quantification of methylation levels by next-generation sequencing. PLoS One (2011) 0.84
Integrated genomics of ovarian xenograft tumor progression and chemotherapy response. BMC Cancer (2011) 0.84
Finding driver pathways in cancer: models and algorithms. Algorithms Mol Biol (2012) 0.81
Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells. PLoS One (2012) 0.80
Admixture Mapping of Subclinical Atherosclerosis and Subsequent Clinical Events Among African Americans in 2 Large Cohort Studies. Circ Cardiovasc Genet (2017) 0.80
Optimizing PCR assays for DNA-based cancer diagnostics. J Comput Biol (2010) 0.80
Reconstructing genome mixtures from partial adjacencies. BMC Bioinformatics (2012) 0.79
A genome-wide study of lipid response to fenofibrate in Caucasians: a combined analysis of the GOLDN and ACCORD studies. Pharmacogenet Genomics (2016) 0.79
Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion. Mol Biol Evol (2010) 0.79
Cyclosporine-mediated allograft fibrosis is associated with micro-RNA-21 through AKT signaling. Transpl Int (2014) 0.79
Use of ECMO in the Management of Severe Acute Respiratory Distress Syndrome: A Survey of Academic Medical Centers in the United States. ASAIO J (2015) 0.76
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell (2016) 0.76
Modeling cell heterogeneity: from single-cell variations to mixed cells. Pac Symp Biocomput (2013) 0.75
Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes. BMC Genomics (2014) 0.75
Statistics for next generation sequencing - meeting report. Front Genet (2012) 0.75
Systematic investigation of predicted effect of nonsynonymous SNPs in human prion protein gene: a molecular modeling and molecular dynamics study. J Biomol Struct Dyn (2013) 0.75
PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population. Chronobiol Int (2014) 0.75