Protein Expression Control Analysis
- SourceForge repository with software
- Tutorial (small example dataset with code, input and output data and explanations):
Proteomics Tools and Databases
- APEX Protocol – Perl scripts for APEX calculations
- APEX Quantitative Proteomics Tool – developed by John Braisted and colleagues at the J. Craig Venter Insitute, Rockville, MD.
- Mass Spectrometry Data Repository – Proteomics RAW data
- MSpresso – Supplementary information
- PeptideProphet, ProteinProphet – as part of the Transproteomic Pipeline software for mass spectrometry data analysis
- Proteogest – in silico protein digest and description of biophysical peptide properties
- Peptide Detectability Predictor – for LC/MS Ion Traps
- Publication by Mallick et al. on sequence features determining peptide MS detectability
- AAindex – database of amino acid properties
Collaborators (former and current)
- Dr. Dan Finley (Harvard, USA)
- Dr. Hyungwon Choi (Singapore National University, Singapore)
- Dr. Joel McManus (Carnegie Mellon University, Pittsburgh, USA)
- Dr. Markus Landthaler (Max-Delbrueck-Center Berlin, Germany)
- Dr. Edward M. Marcotte (University of Texas at Austin, USA)
- Dr. Luiz O. Penalva (University of Texas at San Antonio, USA)
- Dr. George Georgiou (University of Texas at Austin, USA)
- Dr. William Press (University of Texas at Austin, USA)
- Dr. Dan Miranker (University of Texas at Austin, USA)
- Dr. Alexander Brodzky (Brown University, USA)
- Dr. John Braisted, Dr. Srilatha Kuntumalla (JC Venter Institute, USA)
PhD and Postdoc scholarship opportunities
- Boehringer Ingelheim Foundation (not only for Germans)
- DAAD (for Germans to go abroad, for others to go to Germany)
- DFG (for Germans to go abroad, for others to go to Germany)
- in the US – Life Science Research Foundation
- in Europe – EMBO
- worldwide – Human Frontier Science Program
- Surviving grad school (useful not just for PhD students)
Faculty job search for postdocs (random advice)
When starting the job search / while applying/interviewing:
- Read the respective sections in the HHMI book on “Making the right moves”
- Read “At the Helm” by Kathy Barker
- Organize (with your fellow postdocs) a lunchmeeting with some professors and ask them all your questions
- Ask if you can sit in in Chalk Talks
- Organize mock Chalk Talks with your fellow postdocs
- Lots of advice here: https://tomprof.stanford.edu/
Once you have a lab/job offer/etc
- Go to the CSHL course on Leadership in Bioscience, it’s great!
- Sign up to this email list: https://tomprof.stanford.edu/
- Go to one of the EMBO workshops
- Read the respective book by Carl Cohen on “Lab Dynamics”
- Go to Carl Cohen’s website
- Read “At the Helm” by Kathy Barker
- Read the respective sections in the HHMI Book on “Making the right moves”
- Read Mohammed Noor’s book “You are hired! Now what?”
- Read “Every other Thursday” and see if you want to start a ‘self-help’ group like that
- Talk talk talk to your colleagues
- If you don’t have much teaching experience or are not from the US, take a course prior to be thrown into it. I highly recommend Barbara Houtz’s Scientists Teaching Science online course, e.g. via the New York Academy of Sciences!
- You have just landed a fantastic job. Enjoy! 🙂
Miscellaneous
- OpenWetWare.org – for sharing protocols etc
- Quartzy – for lab organization
- Christine’s thoughts on How to Write a Paper
- Ten Simple Rules on How to Write a Paper
- Ten Simple Rules on How to Review a Paper
- Ten Simple Rules for Getting a Grant