Collected Websites

Deep Sequencing

• Sequence Read Archive
• A review of ChIP-seq and RNA-seq studies
• RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays, GSE11045, SRA000299
• Mapping and quantifying mammalian transcriptomes by RNA-Seq, SRA001030
• SEQanswers: software list.
• Antisense RNA
• RNA-Seq: a revolutionary tool for transcriptomics
• DNA-Seq Tech: 08 Next-generation DNA sequencing; 09 Next-generation DNA sequencing techniques
• Genomic Variants: review

Genomic Annotation

• Genome Browser: Human genome,Annotation database,Table Schema,FTP server, MySQL access(not working ?).
• NIH: Gene database, FTP
• Map View from NCBI: Human
• From Bioconductor
  • Affy Human 133a
  • Affy Human 133a 2.0
  • Illumina Human

Alignment

• NGS Alignment Algorithm Index
  • MAQ
  • rSeq
  • Bowtie
  • Tophat
  • Novoalign
• Visualization
• Exonerate
• Spaln
• Intro Sense from sequence reads: methods for alignment and assembly

Gene Network

• Bioinformatics enrichment tool List
,Classification, Paper.
• Biological Pathways
  • KEGG regulatory pathways - H.sapiens , KEGG API
  • BioCarta
• DAVID Gene Sets analysis
• Pathway Guide : contains information of 200+ biological pathway resources
• Visualization
  • Cytoscape with GUI
  • Graphviz from ATT, fast!
  • Osprey
• A Co-expression network (3416 nodes-22,163 edges) built from 3182 arrays cross (humans, flies, worms, and yeast)
• Network analysis at Yale (Topnet)
• Albert-László Barabási and his student Reka Albert

Gene Expression

• NetAffx Analysis Center
• GEO@NCBI
• Stanford MicroArray Database
• Some datasets I used: GSE2034, GSE2990, GSE3284(MTC)

Proteins

• Human Protein Reference Database (HPRD), a review about human PPI data
• Protein classifications: CATH, SCOP

Computational Genetics

• dbSNP
• Hapmap
• Martview (SNP Mapping)
• Haploview
• Statistical Genetics@Umich
• Chi Square Caculator
• SNP map
• Common Stat Genet Concepts, PDF
• Genetic Association Study 101
• Genetic Power Calculator
• LocusZoom
• SNAP
• GenGen
• SeattleSeq
• top candidates for natural selection

Motif finding

• ABS: Database of Annotated regulatory Binding Sites
• Database of Transcriptional Start Sites
• MEME
• BioProspector
• TRANSFAC

Good tools

• Batch ID Converter, covers a lot

Genome Website

• Ensembl
• SGD
• Wormbase
• Flybase
• MGI

Machine learning

• Weka
• Gist (SVM)
• LIBSVM
• Penalized linear model by Jelle Goeman

CS Conference ranking1, 2, Journal ranking. Not official, for reference only

STAT

• statsci

  STAT in JAVA

  • Jakarta
  • JSIM, this site has a lot.
  • Sundar's STAT JAVA
  • Mhstatman, I once got ANOVA from it.
  • Math Tool

  STAT in C/C++

  • GSL
  • Gateway
  • from mathtool

Video Sources

• ICML07
• KDD07
• Newton Seminars

Cluster

• qsub

Good Software

• cutpdf; Jabref; PDF-Xchange Viewer

Latex

• Latex Wiki
• Latex Cookbook
• Some bibliography styles
• Math Sci
• Zentral Math
• DBLP
• Reference sheet for natbib usage
• Squeezing Space in LaTeX
• LaTeX Styles
• File format conversion: jpg, ps, eps, png, bmp, etc.