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Biology

PhD position in Statistical Protein Structure Prediction, Copenhagen, Denmark

One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact […]

The 2014 International Biocuration Conference

Hi all, I’m happy to say that the 2014 International Biocuration Conference is off to a good start. I have attended this excellent meeting twice before, and this year I am honored to be on the organizing committee. There was a lot of work behind the scenes, and we have agreed on five session topics.  […]

Quit smoking, more bacteria will like you

As an ex-smoker I can attest to this: quitting is  hard.  It can also make you fat. I gained quite a few kilos when I quit, and those took a long time to lose. Happily, these days I am spending money on running marathons rather than on cigarettes. Weight gain after smoking cessation is fairly […]

Postdoctoral Position in Computational Bioengineering (Rice University)

The Kavraki group at Rice University is looking to hire an enthusiastic postdoctoral researcher to enhance their research efforts in computational structural biology, drug design, and computational bioengineering. The group has significant expertise in the development of methods for motion planning for complex systems in robotics. Their Open Motion Planning Library (OMPL, http://ompl.kavrakilab.org) is now […]

Announcement: WikiProject Computational Biology Competition

WikiProject Computational Biology/ISCB competition announcement 2013 The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology. A key component of the ISCB’s mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at […]

The Bio* projects: a history in graphs

Yesterday I received an email from Kristjan Liiva, a student at  RWTH Aachen University Germany. Kristjan has developed a really cool dashboard to analyze and visualize the development of collaborative OSS projects by mining their mailing lists and software repositories.  (If the link doesn’t work, try again later; the project is heavily under development). The […]

OK, you saw it here first

  (For those who don’t get it.)

The Second Critical Assessment of protein Function Annotations

Announcing CAFA 2: The Second Critical Assessment of protein Function Annotations Friends and Colleagues, We are pleased to announce the Second Critical Assessment of protein Function Annotation (CAFA) challenge. In CAFA 2, we would like to evaluate the performance of protein function prediction tools/methods (in old and new scenarios) and also expand the challenge to […]

Aphid attacks should be reported through the fungusphone

We like to think of ourselves as the better results of evolution. We humans are particularly proud of our ability to communicate, having invented cell phones, the Internet, and extended forelimb digits as sophisticated means of communication not found anywhere else in nature. Not true. Where there is life, there is communication. Vocal, visual, chemical. […]

Squeezing DNA

The state of biology today:   Our main problem is turning these DNA data into useful information. Finding genes and other functional genomic element, characterizing them, understanding their function and their impact on Life – all these are challenges that will remain with us for a long time, and which have revolutionized biology into the […]

New Links between Bacteria and Cancer

Microbiology and Cancer Cancer and microbiology have been closely linked for over 100 years. Cancer patients are usually immunosuppressed due to chemotherapy, requiring special treatment and conditions to prevent bacterial infection. Bladder cancer is typically treated with inactivated tuberculosis bacteria to induce an inflammatory response which turns against remaining cancer cells, with remarkably effective results.  Also, viruses are […]

SCOTUS: DNA is information, not a chemical

Should DNA be subject to copyright law, rather than patent law? Section 101 of Title 35 U.S.C. sets out the subject matter that can be patented: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the […]

The allure of the superficial

A new paper from my lab and Patsy Babbitt’s lab in UCSF has recently been published  in  PLoS Computational Biology. It is something of a cautionary tale for quantitative biologists, especially  bioinformaticians and system biologists. Genomics has ushered biology into the  data rich sciences. Bioinformatics, developing alongside genomics, provided the tools necessary to decipher genomic […]

Bats use blood to reshape tongue for feeding

Great bit of research showing the amazing adaptation of bat tongues to nectar feeding.   Harper, C., Swartz, S., & Brainerd, E. (2013). Specialized bat tongue is a hemodynamic nectar mop Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1222726110  

#DNA60

It has not escaped Twitter’s notice that the Watson & Crick paper is 60 years old today . Sorry, too busy to be really creative, so here is a repost from 2009. Think of it as a transposon. Short quiz and a movie for DNA day. 1) We celebrate DNA day because: a) Congress said so […]