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THALLINGER LAB
[Journals] [Meetings] [Institutions][Tools] [microRNA][NGS][Bioinformatics] [Microarrays] [Databases] [Glossary]


RELATED LINKS


JOURNALS


Am Journal of Physiology
Annual Reviews
Biochemical Journal
Bioinformatics
Biostatistics
Biotechniques
BMC Bioinformatics
BMC Genomics
BMC Medical Genomics
BMC Systems Biology
Briefings in Bioinformatics
Cell
Cell Metabolism
Comparative and Functional Genomics
Current Biology
Developmental Cell
Diabetes
EMBO Journal
Endocrine Reviews
FEBS Letters
Functional & Integrative Genomics
Gene
Genes & Development
Genome Biology
Genome Medicine
Genome Research
Genomics
Human Molecular Genetics
International Journal of Obesity
Journal of Biological Chemistry
Journal of Biology
Journal of Cell Science
Journal of Lipid Research
Journal of Molecular Biology
Mammalian Genome
Molecular and Cellular Biology
Molecular Cell
Molecular Systems Biology
Molecular&Cellular Proteomics
Nature
Nature Biotechnology
Nature Cell Biology
Nature Genetics
Nature Medicine
Nature Methods
Nature Review Genetics
New England Journal of Medicine
Nucleic Acid Research
Physiological Genomics
PLoS Biology
PLoS Computational Biology
PLoS Genetics
PLoS Medicine
PLoS ONE
PNAS
RNA
Science
Stem Cells
The Am. Journal of Human Genetics
The Journal of Cell Biology (JCB)
The Journal of Clinical Endocrinology & Metabolism
The Journal of Clinical Investigation
The Journal of Computational Biology


MEETINGS


Adipose Tissue Biology (Keystone Symposia J3)
Keystone, CO, USA, Jan 24-29, 2010

CHI Next Generation Sequencing
San Diego, CA, USA, Mar 15-19, 2010

Dynamics of Eukaryotic Transcription during Development (C4)
Big Sky, MO, USA, Apr 07-12, 2010

Diabetes (Keystone Symposia Z6)
Whistler, BC, Canada, Apr 12-17, 2010

4th ESF Conference on Functional Genomics and Disease
Dresden, Germany, Apr 14-17, 2010

International Conference on Research in Computational Molecular Biology (RECOMB2010)
Lisbon, Portugal, Apr 25-28, 2010

International Conference on Intelligent Systems for Molecular Biology (ISMB2010)
Boston, MA, Canada, Jul 11-13, 2010

Systems Biology: Networks (CSHL/WT)
Hinxton, UK, Aug 11-15, 2010

Genome Informatics (CSHL/WT)
Hinxton, UK, Sep 15-19, 2010

International Conference on Systems Biology (ICSB2010)
Edinburgh, Scotland, UK, Oct 11-14, 2010



UNIVERSITIES AND INSTITUTIONS


Graz University of Technology (TUG)
Karl-Franzens-University Graz (KFUG)
National Institutes of Health (NIH)
The Institute for Genomic Research (TIGR)
Washington University in St Louis (WU) - Computational Biology
European Molecular Biology Laboratory (EMBL)
Whitehead Institute (MIT)
University of California, Santa Cruz (UCSC) - Computational Biology
European Bioinformatics Institute (EBI)
Yale University
Cold Spring Harbour Laboratory (CSHL)
Harvard University
The Jackson Laboratory (TJL)
Princeton University
National Center for Biotechnology Information (NCBI)
Stanford University
The Institute of Physical and Chemical Research (RIKEN)
San Diego Supercomputer Center (SDSC)
Research Institute of Molecular Pathology (IMP)
Instite for Molecular Biotechnology (IMBA)
Karolinska Institutet
Weizmann Institute of Science - Genome and Bioinformatics
Institut Pasteur
University of Cambridge
The Wadsworth Center
Berkeley Lab
German Cancer Research Center (DKFZ)
Los Alamos National Laboratory (LANL)
The Salk Institute for Biological Sciences
South African National Bioinformatics Institute (SANBI)
International Society for Computational Biology (ISCB)
Howard Hughes Medical Institute (HHMI)
Medical Research Council (MRC)
The Wellcome Trust
National Science Foundation
Austrian Science Fund (FWF)
Austrian Academy of Science
The Max Planck Society


TOOLS



Promoter and regulatory sequence tools


Ahab
Align ACE
ANN-Spec
Asap
BEST
BioProspector
BoCaTFBS
CEAS
Clover
ClusterBuster
CisRed
Cister
CisModule
CisView
CoMoDis
CompareProspector
Consensus
ConSite
CORE_TF
CORG
CREAD
CREME
CRSD
DiRE
DBTSS
Expander
GeneACT
Genomatix Tools
Gibbs Motif Sampler
GLAM
GRESA
The Improbizer
INCLUsive (MotifSampler, MotifScanner, MotifLocator)
MAPPER
MAST
Match
MatInspector
MatrixREDUCE
MDScan
MEME
MITRA
MoD Tools
Monkey
MotifExplorer
Motif Regressor
MotifSampler
MPromDb
MSCAN
MultiModule
NestedMICA
NHR Scan
NUBIScan
Oligo/dyad-analysis
OMG_Prom
oPOSSUM
ORegAnno
OTFBS
PASTAA
Phylofoot
PhyME
PReMod
Promoter Analysis Pipeline (PAP)
PromoterInspector
PromoSer
Pscan
QuickScore
REDUCE
Regulatory Sequence Analysis Tools
SeSiMCMC
Stubb
TAMO
TESS
TFM-Explorer
TFSEARCH
THEME
TOUCAN2
TRES
VISTA
VOMBAT
WebMOTIFS
Weeder
W-ChIPMotifs
YMF

MicroRNA target prediction


Argonaute microRNA database · [1]
DIANA MicroT · [1]
ElMMo MiRNA Prediction Server · [1]
MAMI Meta Mir:target Interference
microInspector · [1]
miRacle
miRBase Targets · [1]
MiRanda · [1]
MiRecords · [1]
MiRex Infobase of microRNA gene expression
MiRGator · [1]
MiRGen · [1]
miRNAMap · [1]
miRNA - Target Gene Prediction at EMBL · [1, 2, 3]
MiRTar · [1]
miRU · [1]
miTarget · [1]
mirWIP · [1]
NBmiRTAR · [1]
PicTar · [1]
PITA · [1]
RNA22 · [2]
RNAhybrid · [1, 2]
STarMir · [1]
Tarbase · [1]
TargetBoost · [1]
TargetCombo · [1, 2, 3]
TargetScan/TargetScanS · [1, 2]

Other sequence tools


Annotator
BIOCCELERATOR
BLAST
ClustalW
CpG Islands
ExPASy Proteomic Tools
FASTA
Genie
GENSCAN
GlimmerM
Pratt
PSI-BLAST
Protein Explorer - RasMol
Repeatmasker
Reverse Complement Nucleotid Sequence
SAM
SIM4
Swiss PdbViewer
Tandem Repeats Finder
The USC Sequence Alignment Server
UTR- extender
WebCutter
Wise2

NEXT GENERATION SEQUENCING


Integrated solutions

CLCbio Genomics Workbench
Galaxy
Genomatix
JMP Genomics
NextGENe
SeqMan Genome Analyser
SHORE
SlimSearch

Align/Assemble to a reference

BFAST
Bowtie
BWA
ELAND
Exonerate
GenomeMapper
GMAP
gnumap
MAQ
MOSAIK
MrFAST and MrsFAST
MUMmer
Novocraft
PASS
RMAP
SeqMap
SHRiMP
Slider
SOAP
SSAHA
SOCS
SWIFT
SXOligoSearch
Vmatch
Zoom

De novo Align/Assemble

ABySS
ALLPATHS
Edena
EULER-SR
MIRA2
SEQAN
SHARCGS
SSAKE
SOAPdenovo
VCAKE
Velvet

SNP/Indel Discovery

ssahaSNP
PolyBayesShort
PyroBayes

Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database

EagleView
LookSeq
MapView
SAM
STADEN
XMatchView

Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq

BS-Seq
CHiPSeq
CNV-Seq
FindPeaks
MACS
PeakSeq
QuEST
SISSRs

Alternate Base Calling

Rolexa
Alta-cyclic

Transcriptomics

ERANGE
G-Mo.R-Se
MapNext
QPalma
RSAT
TopHat


DATABASES



Gene expression databases


ArrayExpress
Gene Expression Omnibus (GEO)
ChipperDB
Diabetes Genome Anatomy Project (DGAP)
Cancer Genome Anatomy Project
caARRAY (NCI)
EXALT
CELSIUS
Gene Expression Data Portal (NCI)
NIH Neuroscience Microarray Consortium
MUSC DNA Microarray Database
Public Expression Profiling Resource (PEPR)
Gene Expression Open Source System (GEOSS)
CleanEx
Genevestigator
Mouse Atlas of Gene Expression
GOLD.db
Macrophage Expression Atlas (GPXdb)
TIGR PGA Rat Data
ChipDB
The Gene Expression Database (GXD)
List of Lists Annotated (LOLA)
Stanford MicroArray Database (SMD)
yeast Microarray Global Viewer (yMGV)
Gene Expression Atlas
M-CHIPS
ONCOMINE
Human Gene Expression Index (HuGE Index)
READ: Riken Expression Array Database
BASE
EPConDB
GeneNote
RefExA
Cancer Gene Expression Database

Lipidomics databases


Cyberlipid Center
LIPID MAPS
Lipid Bank
LIPIDAG
LIPIDAT
Lipid Molecular Structure Database (LMSD)
Lipoxygenases Database (LOX-DB)
GOLD.db
The Lipid Library
Lipomics
LipidProfiles
European Lipidomics Initiative
Oxylipin Profiling Database
Sphingomap

Sequence and other databases


GenBank (NCBI)
EMBL - EBI
DDBJ
Feature Definition
Human Genome Resources (NCBI)
Human Genome - Golden Path (USCS)
Human and Drosophila Genome (Celera)
ENSEMBL (EBI, Sanger)
GOLD - Genome Projects
GDB - The Genome Database
Mouse Genome Informatics
FlyBase
The C. elegans Genome Project
The Zebrafish Information Network
The Arabidopsis Information Resource (tair)
Saccharomyces Genome Database (SGD)
TIGR - Comprehensive Microbal Resource (CMR)
SWISS-PROT and TrEMBL
Protein Information Resource (PIR)
MIPS
InterPro
Pfam
PROSITE
SMART
ProDom
PRINTS
BLOCKS
TIGRFAMs
Protein Domain Profile Analysis (BMERC)
PDB
SWISS-MODEL
BIND
DIP
KEGG
Unigene
TIGR - Gene Indices
Unigene
Stack
TRANSFAC
Eukaryotic Promoter Database (EPD)
Saccharomyces cerevisiae Promoter Database (SCPD)
GeneCards
NAR Database Listing
Health Sciences Library System
Databases on Medicine and Molecular Biology


BIOINFORMATICS


Bioinformatics and Genomics Resources
BCM - Search Launcher
Sequence Analysis Tools (NIH)
Biology WorkBench (SDSC)
EBI
NCBI
Pacific Symposium on Biocomputing - Proceedings
The International Society for Computational Biology
bioinformatik.de
ExPASy
The USC Sequence Alignment Server
BioNetbook
BMERC
Atelier BioInformartique (aBi)
Amos' links
Genamics SoftwareSeek
CMS Molecular Biology Resource
Bioplanet


MICROARRAY LINKS


Microarrays MediaBook
The Brown Lab - Stanford University
TIGR Microarray Resources
NHGRI - Microarray project
Microarray Centre Ontario Cancer Institute
The Genomics Group at the Children's Hospital of Philadelphia
UCLA Human Genetics DNA Microarray Core
Terry Speed's Microarray Data Analysis Group Page
The Rockefeller University Gene Array Facility
Weinstein Lab - NCI
Albert Einstein College of Medicine (AECOM)
Microarray Expression Data Analysis References
Microarrays.org
Stanford MicroArray Forum
Yahoo's e-group on Microarrays
Microarray Data Analysis Page - Rockefeller University
The Microarray Site - Nature Genetics
Gary Churchill's Statistcal Genetics Group
Stanford Microarray Database (SMD)
MicroArray Informatics at the EBI
Microarray Links (YF Leung)
Gene-Chips (Leming Shi)


GLOSSARY


Amino Acid Information
Biochemistry
BioMolecular Research Tools
Biotechnology Terms
Cell Biology Topics
Dictionary Cell and Mol Biology
DNA from the beginning
Genetics Science Learning Center
Genome Glossary
Genome Glossary (HGP)
Glossary of Genetic Terms
Image Library IMB Jena
Info Center ETHZ
IUPAC Nomenclature
MedBioWorld
MIT Biology Hypertextbook
Molecular Biology Protocols
NHGRI - Glossary of Genetic Terms
Online Textbooks Life Sciences
Primer on Molecular Genetics
Roche 4 Medizin Lexikon
A New View Of Statistics
Algorithms, Data Structures
BLAST Glossery
Numerical Recipes in C
StatSoft - Glossary
The Data Analysis BriefBook
The Bioinformatics Resource Page