Today’s tip of the week is a quick introduction to ChromoHub. ChromoHub is an annotated phylogeny of chromatin-mediated signaling genes. As the ChromoHub site says these are “genes involved in writing, reading and erasing the histone code.” These are epigenetic modifications that emerging as target classes for future drug therapies. ChromoHub maps annotated information about these [...]
Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December. Oh, that’s not what this tip [...]
Over 2 years ago I did a tip of the week on Phosida (links to Phosida). Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools [...]
In our ongoing pursuit of up-to-date tutorials, I’ve been tracking changes that are occurring at resources and planning our updates accordingly. Protein resources are especially going to keep me out of trouble this summer, because their developers and curators have been busy! I’ve compiled a short synopsis below, and would appreciate [...]
BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. [...]
Royal Society and Académie des sciences Microsoft Award was won by Peer Bork this year. The award is funded by Microsoft (250,000 euro) and is given to recognise and reward scientists working in Europe who have made a major contribution to the advancement of science through the use of computational methods. It was awarded to [...]
I recently read an article in Science entitled “Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions” written by Choudhary et al. The research uses “high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 proteins” and “demonstrate[s] that the regulatory scope of lysine acetylation is broad and comparable with that of other [...]
This week I’m going to introduce a tool that searches a whole bunch of resources for you with one single click. Harvester, from the Karlsruhe Institute of Technology, offers a really simple interface for searching. If your species is one of the ones collected in their search, you will find that Harvester will enable you [...]
Bioinformatics.org is a great organization and web site (disclosure: I’ve taught an online course with them ) and they regularly have online course in the field of bioinformatics that are more in the theory and analysis area of bioinformatics (where ours is more in the use and access of resources). If you need bringing up [...]
In the previous post I briefly mentioned a paper coming out of the Bork lab at EMBL. The lab just made public a new tool: STITCH, “a resource to explore known and predicted interactions of chemicals and proteins.” This is a sister project to STRING, a great tool for exploring the interactions of proteins
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