New article on arXiv: Scaling of PWM scores

I’m happy to announce that our second year PhD student Xiaoyan has deposited her first article on arXiv prior to publication.

arXiv:1503.04992  Reliable scaling of Position Weight Matrices for binding strength comparisons between transcription factors

What started as a nuisance that many bioinformaticians face every day turned into an [...]

New publication

Our paper “Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.” has been out for more than half a year, but I had not remembered putting up a brief post about it – probably because it was more of a review rather than the [...]

New publication

Our manuscript “Estimating binding properties of transcription factors from genome-wide binding profiles” has now been accepted in Nucleic Acids Research. For more scientific background, see the blog post about the pre-published in arXiv version.

It was a long, painful uphill battle to get this piece published. But it was also one [...]

New publication

After about four years in the making, we’ve finally published our paper “A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL” (the title, I know!!!). Please find the PDF here.

This has been an exciting journey. About four [...]

Last bits of Boris’ PhD published!

Better late than never, one might think. Once upon a time when I spent time in Tien Hsu’s lab, back in 2001 at the Medical University of South Carolina, I conducted a 2-hybrid experiment with the fly von Hippel-Lindau (VHL) tumor suppressor. Amongst a few other candidates, we found the nm23 tumour suppressor [...]

New article on arXiv: TF copy number estimation

We are very happy to announce the submission of another article to arXiv prior to publication in a peer-reviewed open access journal:

arXiv:1404.5544: Estimating transcription factor abundance and specificity from genome-wide binding profiles

This is a rather curious story, as we had actually been working on something else! If [...]

Pushing the limits of biology

It’s not always big news that excites us. In their recent newsletter, the Prime-XS Consortium features an article Pushing the limits of biology. It’s an introduction into the cutting-edge proteomics that the Functional Genomics Centre Zurich does for their Prime-XS partners. Under the heading Next-generation proteomics they report about their work with [...]

Final post for 2013

One of our most exciting stories that we’ve worked on for the past couple of months was Daphne Ezer’s project on physical constraints in bacterial promoter architecture. We analysed E. coli promoters and looked at the influence of TF affinity, TF concentration, and the relative location of TF binding sites (orientation, distance between) [...]

New publication

Our manuscript “The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity” has now been published in PLoS ONE. We summarised the main findings in a few other blog posts, and it’s not a long one, so why don’t you have a quick read of the abstract at PLoS. [...]

New publication

Our manuscript “The effects of transcription factor competition on gene regulation“ was just published in Frontiers in Systems Biology in the special issue on The origins of biological noise after a whooping 36 days between first submission and acceptance. We discuss the influence of TF abundance on the arrival time of TFs on [...]