CHiCAGO is released!

We are finally ready to release CHiCAGO, our pipeline for Capture HiC analysis. Led by Jonathan, Paula and Mikhail, and a result of two years of work, this package features a new statistical model and a bespoke multiple testing procedure for calling significant interactions in these challenging data. A preprint describing the algorithm in detail will be available in the next few weeks, but the software and documentation are ready to use!

Phoebe joins the lab as a summer student

Phoebe is joining us for her final project as part of the MPhil Computational Biology course. She will be combining single-cell and population-level RNAseq data to study vascular smooth muscle cell biology and then will fly back to the her native USA for a PhD.

Welcome Phoebe!

Erin joins the lab for a rotation project

Erin joins us as part of her BBSRC DTP studentship. Erin hails from a computer science background with an MEng from UCL and will study lineage plasticity using single-cell RNA-seq data during her rotation. Welcome!

The group goes Ape!

We’re off to a group retreat tomorrow, starting with science discussions in the morning at Jesus College (hosted by Jo). After lunch in town, we then head to Thetford Forest for GoApe.

Update: We’ve survived!

Jo is staying in the lab for her PhD

Having successfully completed her rotation project with us, Jo has chosen our lab for her PhD. Needless to say, we are very happy with Jo’s choice!

Mikhail’s article is published in BioEssays

Mikhail’s opinion piece “Spurious transcription factor binding: Non-functional or genetically redundant?” is out in open access on BioEssays website and will become part of the August issue of the journal.

Hashem’s DNAse-seq benchmarking paper is out

Hashem’s paper “A Comparison of Peak Callers Used for DNase-Seq Data” is out in PLOS ONE. Hashem started this work while with Tim Hubbard at Sanger Institute and continued working on it in collaboration with Mikhail after moving to Babraham. Congratulations to Hashem!

Jo starts her rotation in our lab

Jo has joined us, initially for 10 weeks, as part of her 4-year PhD programme at Cambridge University funded by BBSRC. Welcome!

The medaka population genomics paper is out

Mikhail’s paper on the population genetics parameters of wild medaka fish is out in G3. This was part of a large collaboration involving the teams of Ewan Birney at EMBL-EBI, Jochen Wittbrodt and his very talented student Tom Auer at Uni Heidelberg, Felix Loosli in Karlsruhe, and last but not least Kiyoshi Naruse at NIBB (Okasaki, Japan). This work lays the foundation for establishing a population genomics resource in medaka fish (similar to DGRP in Drosophila and 1000 genomes in humans).

Ewan Birney wrote a nice guest blog post on this project at Haldan’s Sieve when we submitted the first preprint of our story to ArXiv.

Hashem joins us

Hashem Koohy has joined the group, moving on from a postdoc with Tim Hubbard at Sanger Institute and two (!) PhD studies (one in pure maths and one in bioinformatics). Hashem will be co-supervised by Peter Fraser and other PIs from the Nuclear Dynamics ISP. Hashem’s main focus will be on the Systems Biology of Ageing Programme that is carried out jointly by our ISP, but he also has plans for some other exciting projects on the side. Welcome!