Published in PLoS One on September 03, 2013
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39
Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology. BMC Genomics (2016) 1.38
Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun (2015) 1.02
Metagenomic profiling of known and unknown microbes with microbeGPS. PLoS One (2015) 0.84
Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Sci Rep (2014) 0.82
ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinformatics (2015) 0.82
Association between changes in reproductive activity and D-glucose metabolism in the tephritid fruit fly, Bactrocera dorsalis (Hendel). Sci Rep (2014) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol (1999) 40.46
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008) 29.20
The NIH Human Microbiome Project. Genome Res (2009) 24.61
Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04
Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer (2002) 15.46
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80
Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods (2009) 8.15
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (2011) 6.20
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res (2011) 5.58
The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci (2006) 4.47
PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol (2011) 3.57
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics (2011) 2.55
Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One (2010) 2.40
Dual RNA-seq of pathogen and host. Nat Rev Microbiol (2012) 2.32
Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics (2008) 2.31
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics (2009) 2.13
MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics (2010) 2.12
Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS One (2011) 1.62
The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS One (2011) 1.53
Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS One (2012) 1.24
Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros (2012) 1.23
Nucleotide sequences of cDNAs for human papillomavirus type 18 transcripts in HeLa cells. J Virol (1988) 1.22
Brd4-independent transcriptional repression function of the papillomavirus e2 proteins. J Virol (2007) 1.19
Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res (2012) 1.11
Primary human cervical carcinoma cells require human papillomavirus E6 and E7 expression for ongoing proliferation. Virology (2011) 1.01
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One (2012) 0.99
Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog (2012) 0.98
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res (2011) 0.94
ClaMS: A Classifier for Metagenomic Sequences. Stand Genomic Sci (2011) 0.93
A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics (2012) 0.88
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences. Bioinformatics (2009) 0.87
Metatranscriptomics and pyrosequencing facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens. PLoS One (2012) 0.84
ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics (2005) 6.12
RelEx--relation extraction using dependency parse trees. Bioinformatics (2006) 4.81
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA (2008) 3.13
A simple approach for protein name identification: prospects and limits. BMC Bioinformatics (2005) 3.12
Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput (2003) 3.03
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. Nat Cell Biol (2013) 2.52
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26
Large-scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis. Arthritis Rheum (2006) 2.13
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Quantitative proteomics of the integrin adhesome show a myosin II-dependent recruitment of LIM domain proteins. EMBO Rep (2011) 1.96
Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe (2010) 1.91
Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res (2010) 1.80
Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput (2003) 1.76
Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog (2009) 1.67
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics (2010) 1.57
Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics (2006) 1.54
Gene and protein nomenclature in public databases. BMC Bioinformatics (2006) 1.52
Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J Comput Biol (2009) 1.51
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One (2007) 1.42
Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog (2012) 1.40
Inferring gene regulatory networks by ANOVA. Bioinformatics (2012) 1.39
Alternative splicing and protein structure evolution. Nucleic Acids Res (2007) 1.35
BioWeka--extending the Weka framework for bioinformatics. Bioinformatics (2007) 1.26
Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol Biosyst (2007) 1.25
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res (2012) 1.24
Microarrays: how many do you need? J Comput Biol (2003) 1.19
A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS One (2012) 1.17
New methods for joint analysis of biological networks and expression data. Bioinformatics (2004) 1.17
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics (2004) 1.16
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. BMC Struct Biol (2009) 1.16
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics (2011) 1.15
Genome-wide assessment of AU-rich elements by the AREScore algorithm. PLoS Genet (2012) 1.15
The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathog (2011) 1.14
Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics (2007) 1.14
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics (2005) 1.11
Protein structure alignment considering phenotypic plasticity. Bioinformatics (2008) 1.09
Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics (2011) 1.07
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One (2009) 1.07
Microarray analyses of transdifferentiated mesenchymal stem cells. J Cell Biochem (2008) 1.06
ProCope--protein complex prediction and evaluation. Bioinformatics (2008) 1.05
Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics (2005) 1.05
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics (2007) 0.99
MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One (2011) 0.99
Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog (2012) 0.98
Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrization. PLoS One (2010) 0.98
Gene expression profiling of serum- and interleukin-1 beta-stimulated primary human adult articular chondrocytes--a molecular analysis based on chondrocytes isolated from one donor. Cytokine (2005) 0.98
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PLoS Pathog (2013) 0.98
Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics (2006) 0.97
Identifying active transcription factors and kinases from expression data using pathway queries. Bioinformatics (2005) 0.96
ToPNet--an application for interactive analysis of expression data and biological networks. Bioinformatics (2004) 0.95
ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res (2007) 0.95
Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set. BMC Biotechnol (2013) 0.93
Gene expression in chondrocytes assessed with use of microarrays. J Bone Joint Surg Am (2003) 0.92
Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol (Camb) (2012) 0.92
Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum. PLoS Comput Biol (2009) 0.91
Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng (2005) 0.91
Rigorous assessment of gene set enrichment tests. Bioinformatics (2012) 0.91
Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathog (2013) 0.90
Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture. J Vis Exp (2013) 0.89
Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics (2010) 0.89
Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses. Clin Orthop Relat Res (2004) 0.88
PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol (2013) 0.88
A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics (2012) 0.88
Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics (2007) 0.87
Toward the complete interactome. Nat Biotechnol (2006) 0.87
Identifying the topology of protein complexes from affinity purification assays. Bioinformatics (2009) 0.87
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics (2008) 0.86
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. PLoS Comput Biol (2010) 0.85
ProML--the protein markup language for specification of protein sequences, structures and families. In Silico Biol (2002) 0.85
Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection. J Virol (2013) 0.85
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics (2008) 0.82
Clonal expansion analysis of transposon insertions by high-throughput sequencing identifies candidate cancer genes in a PiggyBac mutagenesis screen. PLoS One (2013) 0.82
Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis. Methods Mol Med (2004) 0.82
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res (2013) 0.82
Improving fold recognition of protein threading by experimental distance constraints. In Silico Biol (2002) 0.81
HALO--a Java framework for precise transcript half-life determination. Bioinformatics (2010) 0.81
Detecting outlier peptides in quantitative high-throughput mass spectrometry data. J Proteomics (2012) 0.81
Complementing the Eukaryotic Protein Interactome. PLoS One (2013) 0.81
Normalization and gene p-value estimation: issues in microarray data processing. Bioinform Biol Insights (2008) 0.80
Knowledge representation model for systems-level analysis of signal transduction networks. Genome Inform (2004) 0.80
Web servicing the biological office. Bioinformatics (2005) 0.80