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NIH scaling back on model organism database funding: what you can do

TL;DR: NIH are scaling back funding on model organism databases, which will degrade annotation quality.  This can have far-reaching implications in many aspects of biology and computational biology. There’s a letter you can sign electronically, please do.  <http://www.genetics-gsa.org/MODsupport> I am hoping to write a more detailed post on why this is important, but for the […]

I’m Moving and Hiring

Starting June 1, 2015, my lab is moving to Iowa State University in Ames, Iowa, and I’m very excited about this. I’ll be joining a growing cohort of researchers as part of a presidential “big data” hire the university has started a year ago. The research environment is superb, and there are some great bioinformaticians and genomics […]

A Simple Genome Annotator?

A question to genome annotators out there. I need a simple genome annotator for annotating bacteriophage genomes in an undergraduate course. Until now, we used DNAMaster but for various reasons  I would like to move away from that. Here’s what  I need for class: 1. Annotate a single assembled linear chromosome, about 50,000 bp, 80-120 genes, no […]

Sequencing the frog that can save lives

TL; DR:  The genome sequence of the North American Wood Frog will tell us a lot about the genetic control of freezing and reanimating whole organisms. My friend and colleague, Dr. Andor Kiss is crowdfunding this project. If you would like to help, please go to experiment.com. You will get acknowledged by name in the paper. To […]

The genome of nerds

What makes a nerd a nerd? The stereotype is that of someone with a high intelligence, coupled with  social awkwardness and a wardrobe that may alert the fashion police. Now scientists think they may found the genomic links to these traits. There was always a strong suspicion of a genetic component in people that are […]

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 […]

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 […]

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 […]

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 […]

The power of single-cell genomics: the mysterious SR1 bacteria have a unique genetic code

Thanks to Mitch Balish for calling my attention to this one. SR1 bacteria are not exactly a household name, even among microbiologists. They were first discovered in contaminated aquifers,  and since then they were found to be also in animal and insect guts, as well as in human mouths. They are even suspected of being […]

Some omics words we would like to see

Advertisomics: environmental sequencing aimed at obtaining popular press coverage with little or no scientific value. Samples obtained from an environment otherwise not of microbiological interest. “Hey, did you hear they swabbed  the car wheels in the building’s parking lot and found that the microbes all cluster by tire brand name?” Celebromics: sequencing the genome or […]

Critical Assessment of Genome Interpretation, 2013

From the organizers of CAGI 2013. I have been to the Critical Assessment in 2010 and 2011, and even participated as an assessor. It’s a fun meeting, and if your work involves prediction of phenotypes from genotypes, there is still time (just about) to accept some of the challenges. The Critical Assessment of Genome Interpretation […]

Life Stands on the shoulders of Giants (Viruses)

Back to ancient life, what exactly defines life, and where does life end and non-life begin. One of my favorite subjects, and one of which I am the least knowledgeable. Doesn’t stop me writing about it though. Viruses are… well… not really life. Or so says common wisdom. They have some elements of life: a […]

DIGging into Images and Genomes

Our lab has a new project and website up. The project is BioDIG: Biological Database of Images and Genomes.  BioDIG lets you combine image data and genome data of, well, just about anything which you can make images and have a genome, or partial genomic information. You can upload your image, annotate (tag) parts of […]