Our paper “Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila” (see older post) has now been published by the Journal of Computational Biology.
We published a paper describing the Lemon-Tree software in the PLOS Computational Biology Software article collection:
Bonnet E, Calzone L, Michoel T. (2015) Integrative multi-omics module network inference with Lemon-Tree. PLoS Comput Biol 11(2): e1003983.
Our work in collaboration with the Cardiovascular Genomics group on expression quantitative trait loci (eQTLs) across 7 tissues sampled from coronary artery bypass surgery patients has been published in Circulation Cardiovascular Genetics. Our main finding is that eQTLs acting across increasing numbers of tissues are increasingly enriched for coronary artery disease risk and reside at regulatory hot spots in the genome. Read more in the paper Expression quantitative trait loci acting across multiple tissues are enriched in inherited risk of coronary artery disease.
Our paper Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila has been accepted for a talk at the Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, and will be published in a special issue of the Journal of Computational Biology.
We contributed to a paper by Kerstin Rönsch and Andreas Hecht titled “SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer” and published in Molecular Oncology. Congrats to Kerstin, Andreas and all others involved!
We posted a preprint titled “Integrative multi-omics module network inference with Lemon-Tree” on the arXiv. The preprint describes the current status of our module networks inference software Lemon-Tree and demonstrates how it can be used to identify cancer driver genes from large-scale copy number variation and gene expression datasets such as generated by The Cancer Genome Atlas. All of this is joint work with Eric Bonnet.
We posted a preprint titled “Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila” on the arXiv. In this paper we use gene expression data measured during early embryonic development in six Drosophila species and networks of ChIP-chip and ChIP-seq interactions for developmental transcription factors in five species to demonstrate that the integration of data from comparable experiments in multiple species improves the inference of gene regulatory networks.
Source code and test data accompanying our paper Natural coordinate descent algorithm for L1-penalised regression in generalised linear models are now available from Google code.
We contributed to a paper by Ming-Mei Shang, Josefin Skogsberg and Johan Björkegren from the Cardiovascular Genomics group on “Lim domain binding 2 – a key driver of transendothelial migration of leukocytes and atherosclerosis” and published in Arteriosclerosis, Thrombosis, and Vascular Biology. Congrats to Ming-Mei who led the study!
We contributed to a paper by Maarten Houbraken and colleagues at IBCN titled “The Index-Based Subgraph Matching Algorithm with General Symmetries (ISMAGS): Exploiting symmetry for faster subgraph enumeration” and published in PLoS One. This paper introduces a novel subgraph matching algorithm which realises important speed-up compared to other methods by taking into account subgraph symmetries. Congrats to Sofie who did the work on our side and Maarten who led the study!