Sid’s paper Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections has been published in PLOS Neglected Tropical Diseases. Congrats again to Sid and everyone who contributed!
Category: News
EMBO symposium Chennai
I’ll be at the EMBO symposium on regulatory epigenomics next week. Looking forward to it!
Welcome Ammar!
A warm welcome to Ammar Malik who has joined the group as a PhD student. Ammar has a degree in Computer Engineering and brings with him a lot of experience in machine learning. Welcome!
Postdoc position available
A postdoc position is available in my group, to develop machine learning methods for inferring causal gene networks from genome, epigenome and transcriptome sequencing data. For more information and application instructions, see here.
Bayesian network preprint
A new preprint, “High-dimensional Bayesian network inference from systems genetics data using genetic node ordering”, is available on bioRxiv. Bayesian networks are statistical models for gene regulatory networks, and their inference from large-scale omics data is a major problem in systems genetics. In this paper we present an algorithm to solve this problem that uses causal inference, topological sorting and variable selection, and that is much more efficient than traditional Markov chain Monte Carlo algorithms. The algorithm is implemented in the Findr and lassopv software packages.
4 PhD positions in computer science
Four PhD positions in computer science are available at the Department of Informatics. These positions can be held in any of the department’s research areas (algorithms, bioinformatics, machine learning, optimization, programming theory, security, and visualization). Applicants with an interest in computational biology and machine learning are welcome to contact me prior to submitting their application.
For more details and application instructions, see here.
NeurIPS poster
The pdf of my NeurIPS2018 poster is available here.
VIB Omics talk
I will give a talk at the VIB training event
Challenges within and between omics data integration.
NeurIPS paper
My paper “Analytic solution and stationary phase approximation for the Bayesian lasso and elastic net” has been accepted to NeurIPS. A great excuse to visit the largest conference in machine learning and AI!
VSG Pacbio preprint
It’s been a long time in the making, but Sid’s work on using long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections has finally been posted on bioRxiv!
In this collaboration with Liam Morrison, we applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from mice infected with T. brucei. We found that long read sequencing is reliable for resolving allelic differences between VSGs, that there is significant expressed diversity (449 VSGs detected across 20 mice) and that there is a striking semi-reproducible pattern of expressed diversity across the timeframe of study.
Well done Sid and everyone else who contributed to this study!