special issue of Nature Methods was to create a practical resource giving biologists an overview of current computational methods and tools used for visualizing biological data. The issue consists of five commissioned reviews - covering visualization of genomes, alignments & phylogenies, macromolecular structures, image data, and systems biology data - plus a commentary article summarizing key challenges and perspectives in visualizing biological data.
VIZBI, an international conference series on 'Visualizing Biological Data', bringing together researchers using visualization to study genomes, transcripts, proteins, cells, organisms, and populations. VIZBI reviews the state of the art and highlights future challenges - it is held annually in March, alternating between Europe and the USA, and is funded by EMBO and NIH to run until at least 2016.
2010 and 2011 are freely available on video, as are many of the slides used by the speakers. In addition, the posters from 2010 and 2011 are also available.
ISMB 2010, a group of us initiated the first ‘Killer App Award’ to recognize excellence in creating new tools or systems that are of direct, practical benefit to experimental life scientists. The second ‘Killer App Award’ at ISMB 2011 was very popular, and the Award is set to become a regular ISMB tradition.
ISMB is a serious, world-class scientific meeting of around 2,000 bioinformaticians - we certainly don't need to have wild, fun parties: but then again, why not?! Since 2008 I have been leading a series of ISMB parties - for many participants, this large, annual social event is the highlight of the conference, and it has now become an ISMB tradition.
Aquaria is a new, free web resource for biologists that simplifies the process of gaining insight from protein structures. For any protein sequence, Aquaria shows all related structures; with one click the sequence can be mapped onto the structure; one more click and the structure is colored by features, e.g., domains, SNPs, or posttranslational modification sites. See our article in Nature Methods.
Reflect is a free service that tags gene, protein, and small molecule names in any web page within a few seconds; clicking on a tag opens a popup with detailed information. It can be used with any browser, or via an API. See our webinar and our articles in Nature Biotechnology & J. Web Semantics. Reflect was developed at EMBL and the University of Copenhagen.
Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect has now been adopted by Cell Press and ScienceDirect, and has used by many life scientists to analyze seven million documents in the past year.
Martini is a free, easy-to-use tool for characterizing differences between two sets of genes. Martini differs from comparible tools in that it is based on keywords extracted from Medline abstracts and it supports a much wider range of species; testing it against several similar tools using several benchmarks, it was generally more detailed, precise, and accurate. See our article in Nucleic Acid Research; Martini was developed at EMBL.
article in PLoS ONE, we analyzed global gene expression changes in people with Progeria and found that the protein Rb is a key factor in Progeria, and that targetting this protein may help premature aging. This was a collaboration with the Djabali lab at Columbia University, NY.
4 July 2016
Seminar on Data visualization in bioinformatics: Exploring the 'dark' proteome at 2016 Winter School in Mathematical & Computational Biology, Brisbane, Australia.
7 July 2016
Highlight talk on Unexpected features of the dark proteome at ISMB 2016, 24th Annual International Conference on Intelligent Systems for Molecular Biology, Orlando, USA.
21–23 November 2016
Keynote talk on Data visualization in bioinformatics: Exploring the 'dark' proteome at ISCB-LA A2B2C Bioinformatics Conference 2016, the 4th fourth International Society for Computational Biology Latin America Bioinformatics Conference, Buenos Aires, Argentina.
9–11 April 2016
Talk on Data visualization and the 'dark' proteome, at the 2016 Hunter Meetig, Hunter Valley, Australia.