Hot Links, Media and Outreach
Hot Links
Pubmed https://pubmed.ncbi.nlm.nih.gov/
Alternativ, falls Pubmed nicht verfügbar: Europe PMC https://europepmc.org/
Alignment/Stammbäume
CLUSTALW/Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/
MUSCLE https://www.ebi.ac.uk/Tools/msa/muscle/
PHYLIP https://evolution.genetics.washington.edu/phylip.html
Datensätze zu biologische Größen/Biotechnologie/synthetische Biologie
BioNumbers https://bionumbers.hms.harvard.edu
BioBricks https://biobricks.org/
GoSynthetic https://gosyn.bioapps.biozentrum.uni-wuerzburg.de/index.php
Dotplot
Dotter https://sonnhammer.sbc.su.se/Dotter.html
GEPARD https://mips.gsf.de/services/analysis/gepard
JDotter https://athena.bioc.uvic.ca/virology-ca-tools/jdotter/
Funktionsdatenbanken
Functional Glycomics https://www.functionalglycomics.org/; https://ncfg.hms.harvard.edu/
Gene Ontology https://www.geneontology.org
Gehirn-Baupläne
Blue Brain Projekt (EU) https://bluebrain.epfl.ch/
Brain Activity Atlas https://www.brainactivityatlas.org/
Brain Activity Projekt (USA) https://www.braininitiative.nih.gov/
Connectome-Projekt https://www.openconnectomeproject.org
Mouse Brain Connectivity Atlas https://mouse.brain-map.org/static/atlas
Neuroaktivitätsdetektion https://www.ncbi.nlm.nih.gov/pubmed/23537512
Temporal lobe https://www.temporal-lobe.com/background/connectome
Virtual Insect Brain Lab https://www.neurofly.de/
WormWiring https://wormwiring.org/
Wurmatlas https://www.wormatlas.org/
Genomannotation/Genannotation/Sequenzanalyse/Online-Bibliotheken/Experimetelle
Datensätze
BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi
GenScan https://genes.mit.edu/GENSCAN.html
RepeatMasker https://www.repeatmasker.org/
ENCODE https://www.encodeproject.org
Ensembl https://www.ensembl.org/Homo_sapiens/Info/Index
GATK Workshop https://software.broadinstitute.org/gatk/guide/
article?id=7869#1.3
Genomic Science Program https://genomics.energy.gov
Human Genome Project https://web.ornl.gov/sci/techresources/Human_Genome/
index.shtml
UCSC https://genome.ucsc.edu/
DDBJ (DNA Data Bank of Japan) https://www.ddbj.nig.ac.jp/
EBI https://www.ebi.ac.uk/services
European Bioinformatics Institute (Portal), besonders gut für Bioinformatik: Bioperl, Biojava, Programm-Module
iGEM Parts https://igem.org/Main_Page
MEDLINE/NCBI/PubMed https://www.ncbi.nlm.nih.gov/pubmed/
National Center of Biotechnology Information: Allgemeiner Einstieg, viele Datenbanken und Software (Portal)
NIH https://www.genome.gov
OMIM https://www.omim.org/
Swiss Bioinformatics Institute (Portal mit dem Expert Protein Analysis System): https://www.sib.swiss/
WebDirectory https://www.biologydir.com/over-population/p1.html
Computational Population Biology https://compbio.cs.uic.edu/
GENEVESTIGATOR https://genevestigator.com/gv/
GEO https://www.ncbi.nlm.nih.gov/geo/
Grafikprogramme, Modellierung und Netzwerkanalyse
CellDesigner https://www.celldesigner.org/
CellNetAnalyzer https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html
Cytoscape https://www.cytoscape.org/
COBRA https://opencobra.github.io/
COPASI https://copasi.org/
Flux balance analysis https://systemsbiology.ucsd.edu/Downloads/FluxBalanceAnalysis
Jimena https://www.bioinfo.biozentrum.uni-wuerzburg.de/computing/jimena_c/
MATLAB https://de.mathworks.com/products/matlab.html
Metatool https://pinguin.biologie.uni-jena.de/bioinformatik/networks/metatool/
Odefy https://www.helmholtz-muenchen.de/icb/software/odefy/index.html
PLAS https://enzymology.fc.ul.pt/software/plas/
PottersWheel https://www.potterswheel.de/Pages/
SQUAD https://www.vital-it.ch/software/SQUAD
YANA/YANAsquare https://www.bioinfo.biozentrum.uni-wuerzburg.de/computing/yanasquare/
Interaktionsdatenbank, Medikamenten-Interaktionsdatenbank
catRAPID https://s.tartaglialab.com/page/catrapid_group
HPRD https://hprd.org/
iHOP https://www.ihop-net.org/UniPub/iHOP/
KEGG https://www.genome.jp/kegg/
NPInter https://www.bioinfo.org/NPInter/
PlateletWeb https://plateletweb.bioapps.biozentrum.uni-wuerzburg.de/plateletweb.php
Roche Pathways https://biochemical-pathways.com/#/map/1
STRING https://string-db.org
DrumPID https://drumpid.bioapps.biozentrum.uni-wuerzburg.de/compounds/index.php
STITCH https://stitch.embl.de/
EcoCyc https://ecocyc.org/
Lokalisations-/Motiv-Vorhersage
LocP https://ekhidna2.biocenter.helsinki.fi/LOCP/
LocSigDB https://genome.unmc.edu/LocSigDB/
nucloc https://www.nucloc.org/
NucPred https://www.sbc.su.se/~maccallr/nucpred/
SignalP https://www.cbs.dtu.dk/services/SignalP/
TMHMM https://www.cbs.dtu.dk/services/TMHMM/
Functional Glycomics https://www.functionalglycomics.org/
ELM https://elm.eu.org/
Programmiersprachen
Biojava https://biojava.org/
BioPerl https://bioperl.org/
C++ https://www.cplusplus.com/
Java https://www.oracle.com/technetwork/java/index.html
Perl https://www.perl.org/
Python https://www.python.org/
R https://cran.r-project.org/
Bioconductor https://www.bioconductor.org/
Promotoranalyse
AIModules https://aimodules.heinzelab.de/#/
ALGGEN PROMO
https://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.
cgi?dirDB=TF_8.3
Genomatix https://www.genomatix.de/
JASPAR https://jaspar.genereg.net/cgi-bin/jaspar_db.pl
MotifMap https://motifmap.igb.uci.edu/
TESS https://www.cbil.upenn.edu/tess/
TRANSFAC https://www.gene-regulation.com/pub/databases.html
Proteinanalyse
AnDom
https://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.
html
CATH https://www.cathdb.info/
Conserved Domains https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
ExPASy https://www.expasy.org
InterPro https://www.ebi.ac.uk/interpro/
MODELLER https://salilab.org/modeller/tutorial/
PDB https://www.rcsb.org/pdb/home/home.do
Pfam https://pfam.xfam.org/
ProDom https://prodom.prabi.fr/prodom/current/html/home.php
PRODORIC https://prodoric.tu-bs.de/
PROSITE https://prosite.expasy.org
PyMOL https://www.pymol.org/
QUARK https://zhanglab.ccmb.med.umich.edu/QUARK/
Ramachandran-Plot https://mordred.bioc.cam.ac.uk/~rapper/rampage.php
RasMol https://www.openrasmol.org/
SCOP (old) https://scop.mrc-lmb.cam.ac.uk/scop/
SCOPe updated https://scop.berkeley.edu/
SMART https://smart.embl-heidelberg.de/
SWISS-MODEL https://swissmodel.expasy.org
UniProt/Swiss-Prot https://www.uniprot.org/
RNA-Analyse
ITS2 https://its2.bioapps.biozentrum.uni-wuerzburg.de/
LNCipedia https://www.lncipedia.org/
mfold Webserver https://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form
microRNA.org/miRanda https://www.microrna.org/microrna/home.do
miRBase https://www.mirbase.org/
regRNA https://regrna2.mbc.nctu.edu.tw/ (not working, use instead RFAM):
Rfam https://rfam.xfam.org/
Riboswitch-Finder https://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/
RNAAnalyzer https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/
RNAfold Webserver https://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
TargetScan https://www.targetscan.org
tRNAscan https://lowelab.ucsc.edu/tRNAscan-SE/
Vienna Package https://www.tbi.univie.ac.at/RNA/
Media and Outreach
The majority of our papers is full available as free PMC articles, i.e. :
Thomas Dandekar
Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro.
HPLC-ESI-MS method for C60 fullerene mitochondrial content quantification.
In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection.
Identification of Antifungal Targets Based on Computer Modeling.
A combined tissue-engineered/in silico signature tool patient stratification in lung cancer.
Jörg Schultz
Elena Bencúrová
Marcus Dittrich
Alexander Keller
Tobias Müller
Matthias Wolf
"Bioinformatik" (Dandekar and Kunz, second edition WS 2021, english edition SS 2023)
"Regulatory RNA" (Dandekar and Sharma, 1998)
"RNA Motifs and Regulatory Elements" (Dandekar, ed.; Dandekar, Bengert, Ostareck and Ostareck-Lederer, 2002)
"Auxins and Cytokinins in Plant Biology" (Dandekar and Naseem, 2017)
Sendung "Retten Super-Pflanzen unser Klima?" am 17.06.2020 bei "nano" in 3Sat
(Link zur Mediathek: https://www.3sat.de/wissen/nano/200617-co2-absorber-genpflanzen-mit-klimaturbo-100.html)
Sendung "Bioinformatik" am 13.02.2014 bei "Scobel" in 3sat