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.

Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease.

Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning.

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.

C₆₀ fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy.

A combined tissue-engineered/in silico signature tool patient stratification in lung cancer.

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data.

Genetic profiling and surface proteome analysis of human atrial stromal cells and rat ventricular epicardium-derived cells reveals novel insights into their cardiogenic potential.

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

IZKF