News&Blog

Computational Biology // Massey University

News&Blog


[ 23 Jan 2019 | NEWS ]  New publication: BMC Genomics

“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.
publication, tuberculosis, enhancers, ncRNAs

[ 31 Dec 2018 | NEWS ]  New publication: Molecular Phylogenetics and Evolution

“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.
publication

[ 04 Jul 2018 | NEWS ]  New publication: Nature Methods

“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...

publication

[ 29 Jun 2018 | NEWS ]  Workshop: Towards reproducible computational biology

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):

teaching workshop reproducibility

[ 01 Jun 2018 | NEWS ]  Invited research seminar at the Medical University of Graz

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.

travel research talk

[ 25 May 2018 | NEWS ]  Elena defended her PhD thesis.

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!

students PhD

[ 24 May 2018 | NEWS ]  Recent funding success.

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

We got awarded two grants to further our projects on colorectal cancer (CRC) in collaboration with Rachel Purcell and Frank Frizelle at Department of Surgery, University of Otago. We were granted a Maurice and Phyllis Paykel Trust Grant to investigate how to harness the gut microbiome to predict the response to radiotherapy in rectal cancer. In addition,...

funding projects

[ 18 Apr 2018 | NEWS ]  New preprint: Transcribed enhancers during M.tb infection at bioRxiv.

Transcribed enhancers in the macrophage immune response to Mycobacterium tuberculosis infection

Tuberculosis (TB) remains a major public health threat and cause of death worldwide. Macrophages are immune cells that compose the first line of an organism’s defence against Mycobacterium tuberculosis (M.tb), the causative agent of TB. Interactions between macrophages and M.tb define the infection outcome. Enhancers are cis-regulatory DNA elements that activate transcription of target genes and mediate various responses in macrophages. To what extent the host’s genetic response...

preprint tuberculosis enhancer ncRNA

Contact

Dr. Sebastian Schmeier
Research Group Leader
Senior Lecturer in Bioinformatics/Genomics

Massey University
Auckland, New Zealand
+64 9 414 0800 (ext: 43538)

Publications // latest

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics, 2019, 20:71

Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes. Molecular Phylogenetics and Evolution, 2018, 10.1016/j.ympev.2018.12.031.

Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 2018, 15:475–476

Tweets // latest