Liu Chunyu's References

Genome DB	Polymorphisms	Expression & Regulation	Protein
Neuroscience	Behavior	Psychiatric Diseases	Model Genomes
Evolution	Bioinformatics	Protocols	Statistics
Fundings	News & Progress	Journals	Living

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Major Gateways

• Liu's Lab
• Department of Psychiatry, University of Chicago
• Biological Science Division, University of Chicago
• University of Chicago
• U of C Library
• U of C Electronic Journal Titles
• ISI Knowledge (ISI, JCR)
• POPS - Main Menu (purchase in U of C)
• Quick Reference Cards (local version)

Genome DB

• G2D: Gene to Disease, selection of candidate genes www.bork.embl-heidelberg.de
  
• Mendelian Inheritance in Man Online Mendelian Inheritance in Man

• Gene Mutation Data Human Gene Mutation Database (as the name)
• Genatlas (Gene Map, Disease Map & others)  GENATLAS

•  Working Draft Sequence from UCSC
•   Genomes Guide: External Links from NCBI
• Human chromosome  Human Chromosome Launchpad
• best integrated map (U can search any ID) UDB Integrated Map for Chromosome
• Marshfield linkage map  Center for Medical Genetics - Marshfield, WI USA
•  RHdb query (you may get nothing return)
•   HGSI: Human Genome Sequencing Index, View Targets
• Genome Database (all kinds of Map) The Genome Database
• STS Map An STS-Based Map of the Human Genome
•  SHGC RH Mapping Index
• Genethon Welcome to Genethon
• search for SHGC number on TNG4 panel:  TNG RHdb Data Release
• Search sanger center only marker name: (stSG)  acedb13: classes
• RH Mapping:  Radiation Hybrid Mapping Information Page
• RH map online software  RHO server: starting...
• Stanford TNG & G3 map server  RH Server

• The National Center for Biotechnology Information
• Unigene UniGene-Human
• Gene Nomenclature Nomenclature Home Page
• Trace Name Entry Form (for IMAGE EST trace files)
•  www.PubGene.org (literature-based gene data mining)

• PIR The Protein Information Resource (PIR)
• EMBL SRS
• ExPAsy ExPASy
• Protein Society Protein Society Homepage
• OWL non-redundant protein sequence database OWL-Web
• Swissprot ExPASy Molecular Biology Server
• PDB WWW Home Page

Polymorphisms

Expression & Regulation

Protein

Neuroscience

Behavior

Psychiatric Diseases

Model Genomes

Evolution

Bioinformatics

Computational Molecular biology at NIH
   Sequence Alignment Tools and Others:

• 123 Genomics - Sequence analysis, data mining, gene hunting, genomic mining, protein analysis, structure prediction
• ABIM Online analysis tools                        
• Tools for Multiple Alignments
• Toucan - Regulatory Sequence Analysis - Gene Regulation Bioinformatics
• Workshop X - Comparative Sequence Analysis
• Oligonucleotide Properties Calculator
• PupaSNP
• Comparative Genomics Center at Lawrence Livermore National Laboratory (ECR, rVista, Eshadow, etc)
• Useful Module:  EMBOSS
• JEMBOSS
• Sanger CVS cvsweb.sanger.ac.uk
• Sanger software   http://www.sanger.ac.uk/Software/
• TIGR www.tigr.org/software/
• NCBI www.ncbi.nlm.nih.gov/Tools/index.html
• NCBI ftp: ftp://ftp.ncbi.nih.gov/toolbox/
• Computational Biology Software
• NCBI BLAST FTP:  ftp://ftp.ncbi.nih.gov/blast/
• USC package: (incld: Procrustes ) www-hto.usc.edu/software/index.html
• Embl service: www.bork.emblheidelberg.de:8080/ 
• Jim Kent's Web Page
• PCR Primer design and PCR setup

One of the best Tm calculator http://www.basic.nwu.edu/biotools/oligocalc.html

Linker collection:  DNA & RNA Tools at Univ. of Washington
           SIM4 - a program to align cDNA and genomic DNA

               Batch Entrez, to get a batch of sequence in FASTA/GB format  Batch Entrez
               RepeatMasker  http://ftp.genome.washington.edu/RM/RepeatMasker.html

               Bioinformatics tools series:  3rd Millenium Services (*****)
           Official REBASE Homepage
           RepBase
           Webcutter 2.0
           MSPcrunch: A BLAST post-processing filter (Sonnhammer, Durbin)
           Biowire.com
           PCR primer design
                good software for RE site analysis WWWtacg Ver 2.38 Form (at HGMP)

Integrated system:
           UK MRC HGMP-RC (NIX, GLUE etc)
           Biology WorkBench 3.2  (One of the best)
           www.doubletwist.com
           eBioinformatics - Bioinformatics service provider including BioNavigator
           ORNL Genome Analysis Pipeline - Eukaryotic  (BAC ends db search, pipeline)

        BCM search launcher: BCM Search Launcher Home Page

Individual program:
                gDNA aligment: PipMaker  PipMaker (excellent ware for gDNA aligment and comparison)
                gDNA WebGene Home Page (gene prediction, a group of individual tools for gDNA analysis)
               gDNA analysis:  EbEST (repeatmasker, BLAST dbEST and TIGR-HT)
                GeneExpress Prediction and database:   GeneExpress system
           SNP analysis (NCI SNP analysis engine:  44597, chloe)

     Web Hubs and Services
           ZDNet Software Library - Search Results
           TUCOWS United States Affiliates!
           Linkage software list
           Genetic Linkage Analysis Software (NIH software list)
           LINKAGE: User's Guide
    UC  GCG Users Group Website

    Solaris software house:  Solaris Package Archive

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Protocols 

• The Wellcome Trust Centre for Human Genetics  & its genotyping page http://www.well.ox.ac.uk/core-genotyping/
• Vector sequence database
• Protocols on the World Wide Web --Hugh Griffin's Jump Station to Protocols, Books, Manuals, etc.
• A Selection of Molecular Biology Protocols -- A list of sites with protocols, by Hugh Griffin and published in Analytical Biochemistry 239, 120-122 (1996)
• Elsevier Trends Technical Tips Online -- Technical tips, reviewed protocols, very useful
• Recombinant DNA Isolation, Cloning, and Sequencing Protocols . Bruce Roe, Department of Chemistry and Biochemistry, University of Oklahoma (fantastic, comprehensive manual of DNA manipulation techniques)
• PCR and multiplex PCR: guide and troubleshooting -- a great site for PCR techniques and troubleshooting from Octavian Henegariu at Indiana University
• Protocols from the Douglas Crawford Laboratory (Molecular Biology and Biochemistry Division of the School of Biological Sciences at The University of Missouri Kansas City)
• Molecular Biology Techniques Manual . Ed Rybicki, Department of Microbiology, University of Cape Town, SA
• The Nest Group Molecular Protocols and Application Guides
• Ambros Lab, Developmental Genetics Protocols (Dartmouth College)
• The E. coli Index . Good comprehensive list of Molecular Biology Web resources.
• BIOSCI/bionet Electronic Newsgroup Network for Biology
• bionet.molbio.methds-reagnts : Usenet Newsgroup
• Bionet Methods-Reagents Frequently Asked Questions
• Bionet Molecular Biology Methods and Reagents FAQ
• Cell and Molecular Biology Online . Well researched and up-to-date listings of links of interest to cell and molecular biologists (methods, journals, professional societies, positions, etc.)
• Worthington Biochemical Search Engine . Search an index of biochemistry and molecular biology sites
• Standard Genetic Code
• Bioinformatics (my list)
• Molecular Expressions: Microscope Introduction
• Normal Lab's_Protocol
• A wonderful NA teaching website
• Chromosome-specific BLAST at Sanger Center
•  PCR Guide.html
• NWFSC Molecular Biology Protocols
• http://bioinformatics.weizmann.ac.il/databases/codon/hum.cod

• RPC BAC LIBRARY  BAC/PAC RESOURCES - Pieter De Jong, Roswell Park Cancer Institute
• Censor Server Data Entry Form - to remove vector sequence online
•  About SHGC : Mapping and Sequencing FAQ (RH mapping)
•  Genome Analysis linker  Genomic analysis
•  

Statistics

News & Progress

Journals

• Autosearch for literature BioMail Submission  (user: cliu; pass: all773)
• PubMed (Medline Reference) )  Advanced PubMed
• ISI / JCR & Current Contents
• BA:   BA Gateway through ovid
• Nature Nature - International weekly journal of science (abstract)
• Science Science Online (title)
• PNAS The Proceedings of the National Academy of Sciences
• (Human Genome Digest, full-text) Human Genome Project Publications
• Human Molecular Genetics (Online) (abstract)
• Gene  
• Journals  (linkers Patent Bibliographic and AIDS Databases )
• Patent 1:  IBM Intellectual Property Network (Patent searching)
• Patent 2:  PatentMiner - Secure Patent Searching - Full Patent Text - Images
• Patent 3: Intellectual Property Digital Library (PCT patent searching)

 


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Fundings

Funding: HFSP Home Page & GrantsNet

Living

Directory

WebXchange: Directory Search (UC hospital pager by words)

Shopping 

• Complete Shopping Guide to Local Sales in the Chicago area - ShoppingList.com
• Yahoo! Shopping
• DealTime.com: Comparison Shop for Almost Anything
• mySimon inc. - Comparison Shopping
• dash
• buy.com  onsale.com netmarket.com mercata.com
• techbargains.com - Find the best bargains, coupons, and deals on Computer Hardware, Software, and Electronics
• StreetPrices.com: Your Low Price Search Engine
• Online company rating:  Search Results (type the company name in superfind)    mySimon:
• SlickDeals.net
• Offers from FatWallet.com!

Mail/Package checking

• Chinese EMS
• USPS
• Welcome to fedex.com
• UPS Home Page

Flight tickets:

• CHICAGO AIR FARES lowest flight tickets
• Airfare search results (by Departure City)
• http://www.expedia.com/
• http://www.southwest.com/
• http://www.cheaptickets.com/

Disease & Mutation & Literature
    

Protocol

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Company
    

Electronic Journal
  
Others:
 

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Model Genome:
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Software:

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     Chromosome 13

Bipolar
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Reference
           Important nuclear acid properties, unit conversion, enzyme properties
 

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SNP Project