Biotechnology Links
Literature Search
Pub-Med PubCrawler E-Journals(by UT)
Journals/Magazines of interest
Nature(W) Science(W) PNAS(W) Cell(BW) Nature review Genetics(M) Nature review Drug discovery(M)
Nature review Molecular cell biology(M) Nature_genetics(M) Nature_biotech(M) PLOS(M)
Genome_biology(M) Genome_Research(M) Trends in Genetics(M) Briefings in Bioinformatics(3M)
Bioinformatics(M) Molecular Systems Biology(M) BMC bioinformatics(M)
The New Atlantis (A Journal of Technology Society)
Research Groups
Marcotte Lab(UT Austin) Church Lab(Harvard) Bork Lab(EMBL) Barabasi Lab(Notre Dame) Brutlag Lab(Stanford)
Gerstein Lab(Yale) Ideker Lab(UCSD) Palsson Lab(UCSD) Jim Kent(UCSC) Stein Lab(CSH) Brown Lab(Stanford)
Eisen Lab(Berkley) Vidal Lab(Harvard) Alter Lab (UT) Levchenko Lab (Johns Hopkins) Roth Lab (Harvard)
Alber Lab (PSU) Bader Lab (Johns Hopkins) Endy Lab (MIT, Synthetic Biology) Troyaskaya Lab (Princeton)
Arkin Lab (Berkley) Bulyk Lab (Harvard) Emili Lab (U of Tronto) Finley Lab (Fly interactome mapping)
McBeath Lab (Harvard) Boone Lab (U of Toronto) Tyers Lab (U of Toronto) Parag Mallick (UCLA) James Tour (Rice)
Ben Lehner (CRG spain) Amasino Lab (FT control) Sheen Lab (Plant signaling)
Academic societies
ISCB: International society of computational biology
American scientific affiliation: a fellowship of christians in science
UT Center for Systems and Synthetic Biology (CSSB)
UT BioDM
Major Institutes
HHMI TIGR NCBI The Sanger Center EBI CASB(center for algorithmic and systems biology)
Blogs and News
BRIC: Korean Biology Network The Personal Genome: blog about genome and society slashdotcom: News for Nerds and stuff that matters
Very useful Tutorial & Link sites
1. Bioinformatics cources
Stanford BMI214 by Altman
UT Bioinformatics course (CH391L)
2. LIFE SCIENCE
DNA from the beginning: great source for those who want to learn biology.
Cell biology Animation
NOVA online, Cracking the code of life
SIS/Draw: chemical drawing program, free for academic and personal user
3. Computer Science & Bioinformatics
Algorithm Repository by SUNY Stony Brook
HMM tutorial by University of Leeds
Pattern Recognition tutorial by Dr. Richard O. Duda (Very Good)
Feature selection or clustering tutorial also by Dr. Duda
Clustering Alorithm
4. Probability & Statistics
The R Project for Statistics R intro by Faraway(UM)
Virtual Lab in Probability & Stat: Definitly the BEST of the best
HyperStat Online: online material for studying statistics & probability
Curvefit.com: Introduction of data analysis in biological science
Bayesian Statistics: by Bell Lab
Probability Theory- the logic of science: Probability book with Bayesian view, first 3 chapters are free
Graphical Model & Bayesian Network: very nice tutorial site by MIT AI lab
Bayesian Belief Net: another good tutorial on Bayesian Net
Bayesian Net and application
SISA(Simple Iterative Statistical Analysis): provide many expaination and on line calculation
5. Linear algebra & Data Mining & AI & Machine Learning
WEKA documentation: Open Environment for Knowledge Analysis
YELE: Yet Another Learning Environment
DAta Mining tutorials: by CMU, Andrew Moore (very good)
DAta Mining tutorials: by UT, Joydeep Ghosh
kernel-machines.org: the entry to the SVM universe
Variational-Bayes.org: the entry to the VB methods
Boosting.org: to the Boosting methods
MDL.org: Minimum Dscription Length
FAQs on Artificial Neural Network : very good
MIT Linear Algebra video lecture
CS391L: Machine Learning offered by UT
KDnuggets: DATA Mining Portal site (very useful)
6. High throughput data generation and analysis
7 keys to successful microarray data analysis
DNA sequencing by emulsion-based method
MPSS(Massive Parallel Signature Sequencing)
7. Other Educational Resources
MIT OpenCourseWare
Bio-DATABASE
1. Gateways
Entrez - a retrieval system for searching many linked databases (by NCBI)
SRS (The Sequence Retrieval System) - Another gateway for many different databases (by EBI)
PIR (Protein Information Resource) - For protein only (by Georgetown University)
ExPASy (Expert Protein Analysis System): proteomics server of the Swiss Institute of Bioinformatics
MIPS (Munich Information center for Protein Sequences)
2. Genome Sequence DB
NCBI: All genome sequence data are available - synchronized with EMBL Data Library and DNA Data Bank of Japan
Ensembl: Genome browser (for many Eukaryotic genomes)
euGenes (Eukaryote Genome information) by Indiana Univ.
Human Genome Project Working Draft by UCSC: human and mouse genome
Human Genome Project Information: by DOE
SGD: yeast Saccharomyces cerevisiae database
FlyBase: Drosophila melanogaster genome database
WormBase: C. elegans genome database
FANTOM (functional annotation of mouse) : by RIKEN
GeneQuiz: A system for automated large-scale sequence analysis
Genome statistics: Link page for monitoring genome research progress (by weizmann institute)
DOGS (Database Of Genome Size) by Center for Biological Sequence Analysis
GOLD (Genome OnLine Database)
CMR (comprehensive microbial resource) by TIGR
3. Protein Sequence and Structure DB
SWISS-PROT: Annotated amino acid sequence database by Swiss Institute of Bioinformatics; a part of ExPASy
PDB (protein data bank): repository for the processing and distribution of 3-D biological macromolecular (not only protein) structure data
4. Protein Family and Motif DB
BLOCKS by Fred Hutchinson Cancer center: server only
Modules: DB for mobile protein domains (by P. Bork Lab)
Pfam:Protein family database by Sanger Center
ProtoMap: Automatic protein hierarchical classification for all SWISS-PROT and trEMBL proteins by Cornell
PROSITE: motif library, server and program
PRINTS: server only
ProDom: automatically generated from swiss-pro and trEMBL
SMART: Simple Modular Architecture Research Tool
5. Ortholog DB
COGs (Clusters of Orthologous Groups of proteins): Phylogenetic classification of proteins encoded in complete genomes by NCBI
InParanoid: DB of pairwise orthologs
6. Protein structure classification DB
CATH (Class, Architecture, Topology, Homologous superfamily)
SCOP (Structural Classification of Proteins): according to evolutionary origin and sequence/structural similarity
7. Transcriptome and Proteom DB
dbEST: Expression Sequence Tag DataBase by NCBI
InterPro: Integrated tool for the Proteom analysis (by EMBL-EBI)- cross-referencing system
SAGEmap: Serial Analysis of Gene Expression Tag to gene mapping by NCBI
SMD: Stanford Microarray DB
8. Network & Pathway DB
KEGG (Kyoto Encyclopedia of Genes and Genomes)
WIT (What is there?)
EMP (Enzyme Metabolic Pathway)
PFBP (Protein Function and Biochemical Pathways)
BioCyc (included EcoCyc/MetaCyc): genome and metabolic pathway database for a single organism
BIND (Biomolecule Interaction Network Database)
DIP: Database of Interacting Proteins by UCLA
9. Genetic disorder DB
OMIM: Online catalog of human genes and genetic disorders
HGVbase (Human Genome Variation database) by EBI
The Human Gene Mutation DB by UWCM
The SNP consortium
dbSNP:Single Nucleotide Polymorphism database by NCBI
10. Other
Human DNA repair enzyme DB
Enzyme DB: The Comprehensive Enzyme Information System
Bioinformatics Tools
1. Gene finding
GrailEXP by Ork Ridge National Laboratory(use neuralnetwork)
GENSCAN by MIT(use HMM)
GeneMark by GIT(use HMM)
ORF Finder by NCBI
PROCRUSTES
Wise2 by Sanger Center
2. Pairwise alignment
Dotter: A dot matrix program for sequence analysis
BLAST by NCBI
FASTA by U of Virginia
SSAHA by sanger
e-PCR for short sequence like PCR primer
3. Multiple alignment
ClustalW
ClustalX
WebLogos by TIGR
4. Phylogenetic Analysis
PHYLIP: program package only
5. Discovery of New Motif from multiple alignment
HMMER (by HMM)
MEME
6. Comparative Genomics
GenomeAtlasby CBS
ACT(Artemis Comparison Tool): A DNA seq comparison viewerby Sanger
MUMmerby TIGR
PipMaker
7. Tree Drawing Programs
PhyloDraw
8. Protein Structure Visualization
Browser plugins
Rasmol (Tutorial) Cn3D Swiss-PDB viewer
Standalone
MolMol Tutorial)
9. Protein Topology Analysis
TOPS
10. Superimposing two protein structures
ProFit
11. Structural alignment
DaliLite (standalone version of DALI)
12. Protein 2D strcture Prediction
Predict
PredictProtein
PSIpred
PROF: used neural network
EVA (EValuation of automatic protein structure prediction): to asses the best prediction server
13.Protein 3D structuer prediction - by Homology modeling
CPHmodels
ModBase: a DB of comparative models of proteins from complete genomes
MODELLER: build the homology model
Swiss-MODEL
TRITON (Mutant modeling based on wild type by MODELLER)
14. Protein TM (trans membrane region) prediction
TMHMM
TopPred2
15. Sequence Feature detection
CBS Prediction Server
Promoter Scan
16. micro RNA target prediction
TargetScan

Information tech Links
1. IT terminology & literature & Free-wares
Webopedia: CS dictionary SourceForge.net: Open Sources download Whatis.com: Hi-tech dictionary
2. LINUX (The most powerful OS)
Linux Software Encyclopedia: Excellent resource of linux applications RH LINUX
Vim Unix text editor
User manual (pdf) by Bram Moolenaar Ref Card (pdf) & complete reference
Emacs
Ref Card (pdf), tutorial
3. Computer Language, module references
C/C++
Data_Structure_and_Algorithm_in_C++_Source_Codes
Progamming in C++ by Steven: very good
Programming challenge:sample codes
JAVA
java.sun.com: The only complete resource for JAVA language
PERL
Perldoc: Perl documentation
CPAN (Comprehensive Perl Archive Network)
Bio-Perl
Python
python.org
Bio-Python
4. Networking Tools
SSH Communications Security
Putty
WS_FTP LE: windows ftp tool, free for academic user
VNC (Virtual Network computing): free remote display system
5. Others
TextPad: powerful editor for Windows
CNET: hi-tech portal site

My Ph.D. work: Interspersed repeats in Human Genome
What is repetitive DNA and Interspersed repeats (IR)?
What is transposable element which is majority of IR?
Tools to study Repeat sequences
RepeatMasker and others
RepBase: DB of repetitive DNA maintained by Genetic Information Research Institute (zzn26z)
IS DB: Everything about IS elements
Papers: about IR (by Smit A F) about Repbase