HELPFUL RESOURCES

Some useful resources and tools we use in our research and want to share with you.

cBioPortal – Visualization, analysis and download of large scale cancer genomics datasets

Cancer Cell line Encyclopedia (Broad)

Cancer Therapy response Portal (Broad) – Links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity

DepMap – Database showing the dependency of a gene of interest in different cancer types, based on published loss-of-function/RNAi screens; integrates Project Achilles and the Avana/Ceres datasets

Interactome Insider – Tool to assess protein-protein interactions, explore disease mutations and study mutation profiles

ICGC Cancer Genome Projects – Cancer genome database

Tumor Portal – Genes, Cancers, DNA Mutations & Annotations (Eric Lander and Gad Getz labs)

Mutation aligner – Enables exploration of somatic mutation hotspots in protein domains in cancer (Sander lab)

Cancer Rx – Database correlating drug sensitivity with genomic data in cancer

ENCODE – Interactive webface providing information on DNA elements in the human genome

STRING – Database of known and predicted protein-protein interaction networks

COSMIC – Catalogue of somatic mutations in cancer (Sanger Institute)

ENRICHR – Gene set enrichment analysis tool to analyse gene lists/data sets for enriched pathways or GO terms (Ma’ayan lab)

WebGestalt – Gene set enrichment analysis tool (Zhang lab)

DAVID – Functional annotation tool for gene lists

NEB restriction enzyme list and sequence recognition motifs

Addgene plasmid database and helpful information and guides cloning elements, viruses and other cool cloning technologies


Different sgRNA design and evaluation tools:
VBCScore – sgRNA score developed at the VBC incorporating guide activity, protein features and indel formation (Link to publication)
Compounds

MIT CommKit – Communications guide from the Broad institute

iBiology – Instructive videos on different areas in biology.

Keep Science Going – A resource for online tutorials and webinars for home office.

Nature Online Resources

The PhD collection – Articles for future and current PhD students.

Scientific data collection – Articles on scientific data, collaboration and publishing.

Mentoring collection – Articles with advice for (future) mentors and mentees.

Science careers and mental health collection – Articles with a focus on mental health for PhD students and scientists in general.

Nature Masterclasses – Next to paid content also free resources, e.g. on Peer Review.

Comic relief: xkcd If things stop working altogether.

In addition to mailing lists, RSS feeds are useful to stay informed about your field of research:

Feedly

Inoreader

The Obenauf lab is on GitHub

Hannes Zuber and Anna recently gave a lecture about “Current Trends in Cancer Research: Cancer Genomes, Genetic Tools and Immunotherapy”