Archive by category | Genome-wide

[Research highlight] modENCODE releases extensive functional investigation of fly and worm genomes

Recently, a series of publications by members of the modENCODE consortium were released online at Science, Nature, and Genome Research. These works collectively describe a massive effort to functionally characterize and annotate the Drosophila melanogaster and Caenorhabditis elegans genomes, including in-depth analyses of genes and transcripts, epigenetic marks, transcription factor binding, and replication timing, across a range of developmental and tissue sources.  Read more

Keystone Symposium – Omics Meets Cell Biology (II)

Keystone Symposium – Omics Meets Cell Biology (II)

Before I carry on with a summary of the second part of the Keystone Symposium ‘Omics Meets Cell Biology’, I should clarify that this post and the previous one dedicated to this conference are not intended to provide an comprehensive account of all the talks but rather to communicate some general (and subjective) impressions of the meeting. To keep these posts reasonably short (and sometimes due to a lack of memory…), I had to omit several of the excellent presentations given at this meeting. The full program and complete list of speakers is available at the Keystone Symposium website.  Read more

Keystone Symposium – Omics Meets Cell Biology (I)

Keystone Symposium – Omics Meets Cell Biology (I)

At the Keystone Symposium ‘OMICS Meets Cell Biology’, held this week in Breckenridge, Colorado, attendees had initially to face two major challenges: the first was to survive the cocktail mixing jet lag and altitude sickness and the second one—oh, it hurts!— was to resist the temptation to just forget all about science and focus exclusively on the concepts revolving around snow, slopes and fun sports…  … Read more

SciFoo: scientific fireworks

SciFoo: scientific fireworks

In his list of eight ‘generative’ values (Better Than Free), Kevin Kelly includes ’embodiment’–the actual physical realization of an item or event which could be otherwise freely distributed over the web. While we are all ‘hyperlinked’ on the Internet, the value of those unique qualities that cannot be generated or “copied” on the web is dramatically increased. The type of intense emulation and shared excitement sparked at the recent Science Foo Camp (SciFoo 2008), organized by Nature, Google and O’Reilly, gave a wonderful example of the unique value of direct human exchange during an exclusive event bringing together roughly 200 top scientists, ‘geeks’ and other technologists at the Googleplex in Mountain View, California.  Read more

Fascinating correlations or elegant theories?

Chris Anderson, Editor-in-Chief of Wired , wrote a few weeks ago a provocative piece “”http://www.wired.com/science/discoveries/magazine/16-07/pb_theory”>The End of Theory: The Data Deluge Makes the Scientific Method Obsolete“, arguing that in our Google-driven data-rich era (”The Petabyte Age”) the good old “approach to science —hypothesize, model, test — is becoming obsolete”, leaving place to a purely correlative vision of the world. There is a good dose of provocation in the essay and it was quite successful in spurring a flurry of skeptical reactions in the blogosphere, FriendFeed-land and lately in Edge’s Reality Club.  Read more

Top-down mapping of gene regulatory pathways

Top-down mapping of gene regulatory pathways

In a very recent lecture (see full video from NIH VideoCasting) given for the NIH Systems Biology Special Interest Group, Trey Ideker presents a great overview of the various strategies his group has been developing in the recent years in order to integrate multiple types of large scale datasets. While one of the most pervasive ‘meme’ about high-throughput measurement is that they are “notoriously unreliable” (see Hakes et al, 2008, for a recent example), Trey beautifully illustrates how predictive computational models and novel biological insights can be generated by sophisticated data integration strategies. Three types of applications are presented in his talk:  … Read more

Transcription paused and poised for regulation

Transcription paused and poised for regulation

For eukaryotes, it is widely thought that transcription is primarily regulated through recruitment of the essential machinery to transcription start-sites. Previous hints challenging this paradigm have been confirmed by recent analyses showing that transcription regulation of a large number of genes actually occurs after recruitment. Mechanistically, such studies have gone furthest in Drosophila melanogaster (Muse et al, 2007; Zeitlinger et al, 2007). Here, conservative estimates indicate that more than 10% of genes are regulated through promoter-proximal pausing. On such genes, RNA polymerase II is recruited and initiates transcription, but then pauses around 50 bp downstream of the transcription start-site where it awaits further signals to resume elongation and complete transcription proper.  Read more

Personal genomics for a fistful of dollars

Personal genomics for a fistful of dollars

The wave of personal genomics is progressing rapidly. A string of four papers appeared recently (Porreca et al, 2007, Albert et al, 2007, Okou et al 2007, Hodges et al, 2007) reporting on microarrray-based technologies that enable the enrichment of selected genomic fragments in a single massively multiplexed reaction, thus greatly facilitating subsequent resequencing of pre-defined portions of the human genome (eg all coding exons). These technologies are expected to reduce dramatically the cost of targeted resequencing of individual genomes.  Read more