Published in J Comput Biol on March 01, 2006
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations. Nucleic Acids Res (2010) 0.86
UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics (2012) 0.84
A unifying model of genome evolution under parsimony. BMC Bioinformatics (2014) 0.78
Sorting permutations by cut-circularize-linearize-and-paste operations. BMC Genomics (2011) 0.77
Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res (2008) 5.12
Efficient q-gram filters for finding all epsilon-matches over a given length. J Comput Biol (2006) 4.24
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
Updating benchtop sequencing performance comparison. Nat Biotechnol (2013) 2.66
Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (2006) 2.55
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. BMC Microbiol (2007) 2.52
The solution space of sorting by DCJ. J Comput Biol (2010) 1.98
r2cat: synteny plots and comparative assembly. Bioinformatics (2009) 1.95
MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics (2008) 1.83
Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res (2011) 1.81
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics (2009) 1.81
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics (2004) 1.73
Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PLoS One (2012) 1.68
Double cut and join with insertions and deletions. J Comput Biol (2011) 1.61
A novel approach to remote homology detection: jumping alignments. J Comput Biol (2002) 1.45
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J Biotechnol (2008) 1.41
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics (2011) 1.37
Large scale hierarchical clustering of protein sequences. BMC Bioinformatics (2005) 1.28
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol (2009) 1.26
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics (2010) 1.24
Partitioning biological data with transitivity clustering. Nat Methods (2010) 1.23
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics (2012) 1.21
Restricted DCJ model: rearrangement problems with chromosome reincorporation. J Comput Biol (2011) 1.20
Phylogenetic comparative assembly. Algorithms Mol Biol (2010) 1.16
Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. J Biotechnol (2011) 1.15
GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Res (2006) 1.14
On the weight of indels in genomic distances. BMC Bioinformatics (2011) 1.05
Computation of median gene clusters. J Comput Biol (2009) 1.04
Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.02
Genomic distance under gene substitutions. BMC Bioinformatics (2011) 0.99
Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics (2003) 0.96
Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res (2008) 0.96
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics (2009) 0.93
Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a β chain CDR3 sequence associated with hepatitis-induced pathogenesis. Haematologica (2013) 0.90
On the inversion-indel distance. BMC Bioinformatics (2013) 0.88
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. J Biotechnol (2012) 0.88
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics (2012) 0.86
Gene family assignment-free comparative genomics. BMC Bioinformatics (2012) 0.85
UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics (2012) 0.84
Consistency of sequence-based gene clusters. J Comput Biol (2011) 0.83
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics (2013) 0.81
Gecko and GhostFam: rigorous and efficient gene cluster detection in prokaryotic genomes. Methods Mol Biol (2007) 0.81
On the similarity of sets of permutations and its applications to genome comparison. J Comput Biol (2006) 0.80
BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics (2013) 0.79
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. J Biotechnol (2012) 0.78
Statistics for approximate gene clusters. BMC Bioinformatics (2013) 0.78
Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics (2006) 0.78
Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics (2012) 0.77
Identifying gene clusters by discovering common intervals in indeterminate strings. BMC Genomics (2014) 0.76
Sorting Linear Genomes with Rearrangements and Indels. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.76
Swiftly computing center strings. BMC Bioinformatics (2011) 0.75
The European conference on computational biology. Drug Discov Today (2003) 0.75
Finding nested common intervals efficiently. J Comput Biol (2010) 0.75
Rearrangement models and single-cut operations. J Comput Biol (2010) 0.75
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics (2009) 0.75