Computational Biology // Massey University


[ 28 May 2019 | NEWS ]  Recent funding successes.

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...

funding projects

[ 20 Mar 2019 | NEWS ]  New publication: Frontiers in Immonology

“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.


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.

publication, tuberculosis, microRNA

[ 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.


  • 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.


  • 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.

[ 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...


[ 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 The slides of the seminar are available at figshare (

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


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

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

Publications // latest

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing. PLoS One, 2020, accepted.

Molecular subtyping improves prognostication of Stage 2 colorectal cancer. BMC Cancer, 2019, 19, 1155

DeePEL: Deep learning architecture to recognize p-lncRNA and e-lncRNA promoters. In proceedings: IEEE International Conference on Bioinformatics and Biomedicine, 2019, B516, accepted.

News&Blog // latest

[ 20190528 | news ] Recent funding successes.

[ 20190319 | news ] New publication: Frontiers in Immonology

[ 20190122 | news ] New publication: BMC Genomics

[ 20181230 | news ] New publication: Molecular Phylogenetics and Evolution

[ 20180703 | news ] New publication: Nature Methods

Tweets // latest