Displaying posts categorized under


Blogosphere catches: Marco Island, finding Ada and blog carnivals

Some interesting events cropped up recently. The Marco Island Advances in Genome Biology and Technology meeting was heavily tweeted and blogged about.  Pacific Biosciences unveiled their third generation sequencer. Ostensibly, it can sequence reads of 20,000 length, but the fraction of actual long reads in a run, and their quality is still a bit hazy. […]

Ancient Greenlander’s DNA reveals ugly mullet

Seriously, this is what I first thought when I saw the cover of this week’s Nature, and the associated drawings  in the press.  The dude’s haircut seems like it was even bad in the ’80s… 2080 BCE that is, which is when his body is dated. Approximately. A large group of researchers were involved in […]

Filling in the evolutionary blanks, genome by genome

After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of […]

Videos on sequencing

A few cool vids on sequencing. Company infomercials, but still entertaining and informative. Thanks to my student, David Ream, for finding these. Pyrosequencing: Helicos: SOLiD: BASETM nanopore sequencing:

Photosynthesis, phages and structures: there’s treasure everywhere!

Here’s a really cool work, published this September in Nature.. Why did I choose this work?  Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and […]

The Genomic Ark: 10,000 vertebrate genomes

The first bioinformatics meeting I went to was in 1996 at the  Nachsholim resort,  north of Tel Aviv. I received a fellowship for the duration, and shared a room with the brilliant Golan Yona, then a grad student at the Hebrew University. I was doing biochemistry at the time and knew next to nothing about […]

Short Bioinformatics Hacks: Glimmer Splitter

Glimmer is a program that predicts ORFs in bacterial and archeal genomes. The input is the assembled genome FASTA file, the output are several files of the predictions in different stages. The terminal output file is the .predict file. which looks something like this: >NODE_1_length_38001_cov_935.551880 orf00001 481      362  -2     1.45 orf00002      451      567  +1     0.59 […]

The medium-rare biosphere

All the roots hang down Swing from town to town They are marching around Down under your boots All the trucks unload Beyond the gopher holes There’s a world going on Underground — Tom Waits, “Underground” Our picture of the microbial biosphere is heavily skewed towards what we can see, culture, and are interested in. […]

Weekly Poll: will you have your own genome sequenced?

CLARIFICATION: the events described here have not happened. Yet. We are a few years into the future. Whole human genomes can be sequenced relatively cheaply and accurately. Direct to Consumer Genomics companies offer true genomic analyses now, not just marker analyses. They BLAST* your sequence against known genotype & disease databases, looking for known genotypic […]

Science 2.0: things that work and things that don’t

Open Notebook What is it? Open Notebook means “no insider information” You lab notebook is on a wiki, out there for everyone to see. Negative results & all.  You share your research process with the world as you go along. There are many shades to this process: you may share some of your data, edit […]

A Flurry of Red and Green

UPDATE: I submitted this post to the National Evolutionary Synthesis Center’s sponsored contest for a travel award to ScienceOnline2010. Let’s see how it goes… #scio10 In a previous post about Hatena we saw what might very well be the beginning of a (beautiful?) [:ttip=”symbiosis where one partner lives inside the cell of the other” id=”10″]endosymbiotic[:/ttip] […]

The Incredible Shrinking Genome

Mass Extinctions and Genomics The geological signs for mass extinctions are very distinct: the photo shows the boundary of the Cretaceous-Tertiary KT extinction that happened ~65 million years ago (Mya), and killed some 70% of the species on Earth, most famously the dinosaurs. This was the last mass extinction, and its effects on Earth’s life […]

Metagenomics Metadata and Metaanalysis

I am a co-organizer of this… see for yourself. Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. If you are coming to ISMB/ECCB 2009, consider coming to the M3 SIG. Link to announcement 1-page poster, because you really want to tack this to your departmental […]