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- Visualization of the protein-coding regions with a self adaptive spectral rotation approach
- Automated construction and testing of multi-locus gene-gene associations
- Statistical confidence measures for genome maps: application to the validation of genome assemblies
- Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data
- Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips
- High-quality annotation of promoter regions for 913 bacterial genomes
- PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes
- Pre-calculated protein structure alignments at the RCSB PDB website
- The SMARTCyp cytochrome P450 metabolism prediction server
- R/qtl: high-throughput multiple QTL mapping
Nucleic Acids Research
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- Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment
- Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage
- SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
- An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting
Bioinformatics
- Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
- FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases
- RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
- Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
- Higher-order Markov models for metagenomic sequence classification
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bogdan's blog
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
Submitted by bogdan on Mon, 2008-04-14 22:42AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes - Motivation: Genomes contain biologically significant information that extends beyond that encoded in genes.
The effect of sequence quality on sequence alignment
Submitted by bogdan on Fri, 2008-04-11 00:28The effect of sequence quality on sequence alignment - Motivation: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values.