Computational Biology & Bioinformatics Team: Currently 2 senior research scientists (Joohyun Kim and Nayong Kim) focused on assisting bioinformatics and broader computational biology efforts, especially in connection with LBRN = Louisiana Biomedical Research Network
CCT search underway to hire a “Senior Bioinformatics Computational Scientist”
Software tools
- R/Bioconductor/Biopython
- Protein Gene Prediction : Glimmer, GenMark.Hmm-p
- ncRNA Gene Finding : Infernal, CMFinder, RNAz, Evofold
- Homology Sequence Match : exonerate, BLAST
- DNA motif Finding : MEME
- Comparative genomics : CGView, DAVID
- Functional genomics : GSEA, pathway analyses
- Microarray analysis : R/Bioconductor modules
- SNP : diBayes (Bioscope), BFAST, SAMTools, SOAPsnp
- CNV : (Bioscope) and others
- Small InDel : (Bioscope), SAMTools and others
- Mapping : SSAHA2, BFAST, BWA, SHRiMP2, Novoalign, Bowtie, MAQ, Stampy, SOAP2
- De Novo Assembly : EDENA, NGS Cell, ABySS, Velvet
- Misc (NGS Seq. Analysis): samtools, ARTEMIS, BamView
- Misc (others) : blast2GO, DAVID
- RNA-Seq : TopHat/TopHat-fusion, Cufflinks, Scripture, OASES, Trinity, and othes
- ChIP-Seq : MACS, and many
- Phylogeny : MrBayes and others
- Molecular Dynamics : NAMD, CHARMM, Gromacs, LAMMPS, TINKER
- Visualization tools : VMD, IGV, BamView, Gbrowse
- Genome Analysis Framework : Bioscope, GATK, and GALALXY, CloudBurst, CloudBlast, Crossbow, …
- DARE-NGS - DARE (Dynamic Application Runtime Environment)-based Science Gateway
November 2012 Joel Tohline presentation: PDF | PPT
