Updated Instructions for Authors

Molecular Systems Biology has recently completed a major update of its Instructions for Authors. Of particular importance, this new document now fully incorporates information about our policies regarding transparency in scientific publishing. Molecular Systems Biology, along with the other EMBO Publications journals, has made a strong commitment to promoting transparency in the editorial process, and recently began publishing a Review Process File, containing anonymous reviewers’ reports, authors’ rebuttal letters, and the editor’s decisions, with accepted manuscripts. In addition, we have been working to promote greater availability, transparency, and re-usability for scientific data associated with published works. For more details on these efforts please see our editorial, “From bench to website.”  … Read more

Editors’ Conference Agenda – 2011

Here is a preliminary list of conferences that the Molecular Systems Biology editors will be attending in 2011. We are looking forward seeing a lot of the Alps this year, with meetings in Innsbruck, Geneva, and Vienna. And, of course, we also looking forward to meeting Molecular Systems Biology’s readers and authors; if you are attending one of these conferences or workshops, we would be quite happy to chat with you and learn about your research.  Read more

[Research highlight] Transcription in action

In a work just published at Nature, Churchman and Weissman (2011) describe a new method for directly capturing and sequencing elongating, or nascent, RNA transcripts. The authors then use this method to provide a detailed look at the transcriptional process in action, revealing a histone modification-dependent mechanism that constrains genome-wide antisense transcription, and pervasive transcriptional pausing and backtracking throughout genes.  Read more

[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

[Research highlight] Laws of microbial growth

In a work recently published in Science, Scott et al reveal a series of microbial “growth laws” that describe simple relationships between translation, nutrition, and cellular growth. They show that these laws hold across different experimental perturbations and E. coli strains, and, ultimately, provide a phenomenological model describing the delicate balancing act cells maintain when deciding how much of their proteome to allocate to ribosome-related processes.  Read more

[Research highlight] NF-kappaB signaling goes digital

In a report published this week at Nature, Tay et al. reveal that populations of mouse 3T3 cells exposed to TNF-α show a digital NF-κB response, where increasing TNF-α concentrations lead to a higher proportion of cells with nuclear localized NF-κB — an effect that depends, in part, on pre-existing heterogeneity within the cell population. These results provide another compelling example of the way that studies using single cell measurements are transforming our understanding of cellular signaling mechanisms. Interestingly, these results seem to contrast with another recent single-cell-based study of NF-κB dynamics (Giorgetti et al. 2010), which observed a relatively uniform population-level NF-κB response to TNF-α in human HCT116 cells, indicating that there is still much to learn about the dynamics of NF-κB signaling.  Read more

[Research highlight] Cis-regulatory evolution, not so mysterious after all?

Animal genomes are littered with conserved non-coding elements (CNEs)—most of which represent evolutionarily constrained cis-regulatory sequences—however, it is often not clear why these sequences are so exceptionally conserved, since anecdotal examples have shown that orthologous CNEs can have divergent functions in vivo (Strähle and Rastegar 2008; Elgar and Vavouri 2008). In an article recently published in Molecular Biology & Evolution, Ritter et al. compare the functional activities of 41 pairs of orthologous conserved non-coding elements (CNEs) from humans and zebrafish (2010). Interestingly, sequence similarity was found to be a poor predictor of which CNEs had conserved function. In contrast, the authors found that measuring transcription factor binding site change, instead of simple sequence divergence, improves their ability to predict functional conservation.  Read more

Editors’ conference agenda

I spent May 14-15th at the Symposium on Integrative Network Biology and Cancer, hosted by the Institute of Cancer Research in London. The organizers, Chris Bakal and Rune Linding, managed to attract a stellar speakers list, and I had great discussions with many of the attendees. Inspired by this, I thought it could be useful to share a tentative list of conferences in 2010 that will be attended by the Molecular Systems Biology editors. If you happen to be at one these conferences, we would be delighted to meet you in person and hear about your research.  Read more