News&Blog

A long overdue post. Together with our collaborators we were successful in several funding rounds, which will help us progress some exciting projects.

First we got awarded a Maurice Wilkins Centre Flexible Research Programme grant to advance our project on long non-coding RNA identification in colorectal cancer. This grant will help us to validate some of the prediction from our identification pipeline.

We received a Massey University Research Fund Grant which will help Arielle to fund a stay at University...

“Differential Targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 Promotes the Intracellular Growth of Mycobacterium tuberculosis in Alternatively IL-4/IL-13 Activated Macrophages.” has been published in Frontiers in Immunology.

Highlights

Our work reports a host detrimental role of miR-143 and miR-365 during Mtb infection and highlight the role and miRNA-mediated regulation of c-Maf, Bach-1, and Elmo-1 in Mtb-infected M(IL-4/IL-13) macrophages.

“Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection.” has been published in BMC Genomics.

Highlights

• Transcribed enhancer landscape in macrophages infected with Mycobacterium tuberculosis.
• We identified in particular a set of enhancers that establish new transcriptional activity upon infection
• These enhancers are highly specific to not only the tissue but also the process.

“Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes.” has been published in Molecular Phylogenetics and Evolution.

Highlights

• KRTAP1 gene repeats in mammals show a concerted evolution pattern.
• KRTAP1 gene flanking regions strongly contrast: show a divergent pattern of evolution.
• Contrast in patterns results from gene conversion events in KRTAP1 coding regions.
• Selective or non-selective processes may produce KRTAP1 coding region-specific events.

“Bioconda: sustainable and comprehensive software distribution for the life sciences” has been published in Nature Methods.

While this one has been out a while on bioRxiv, I am very happy to see this published in Nature Methods today! Great effort by many great people to keep Bioconda up to date and populated with relevant software for the life sciences! One of the most exciting developments in recent years!

See full correspondence here or free read access...

Sebastian gave a seminar followed by a hands-on session with the title “Towards reproducible computational biology” at the ResBaz conference in Auckland. He discussed life science package managers, workflow management system, as well as containerization and how this can be used to produce reproducible bioinformatics data analysis workflows. The workshop tutorial material is available at https://reproducible.sschmeier.com. The slides of the seminar are available at figshare (https://doi.org/10.6084/m9.figshare.6726416.v1):

• Schmeier, Sebastian (2018):...

Sebastian was invited to the the Institute of Hygiene, Microbiology and Environmental Medicine at the Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz in Austria. The seminar was entitled “Towards reproducible computational biology: A case study on cancer transcriptomics.” and discussed tools and processes that one can use to facilitate reproducible computational research. He also met with several scientists and discussed their research themes.

On Friday, Elena defended her PhD thesis entitled “Transcriptional regulation in mouse macrophages: the role of enhancers in macrophage activation and infection”. The referees were impressed with her work and she passed without any required emendations. Congratulations and well done!