News&Blog

Computational Biology // Massey University

News&Blog


[ 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

[ 04 Apr 2018 | NEWS ]  New publication: Molecular Biology and Evolution

Mammalian evolution has seen a rapid proliferation of various types of non-coding RNAs, including members of both spliceosomal RNAs and small nucleolar RNAs. The significance of this remarkable expansion however remains obscure. While ncRNA copy number expansions have been linked in some instances to functionally tractable effects, such as increased regulatory complexity driven by microRNAs, other examples suggest that such events may equally likely be neutral as a result of random retrotransposition. Hindering progress in our understanding of such observations...

publication

[ 26 Jan 2018 | NEWS ]  PhD scholarship available in bioinformatics

PhD position in computational biology/bioinformatics

We have a PhD position, including scholarship covering fees and living expenses, available in our group in Auckland, New Zealand. The prospective candidate will analyse transcriptomics and genomics data sets from high-throughput experiments in mammalian systems with a focus on gene regulation and non-coding RNAs. Please have a look at our recent publications to get an idea on what topics we work on. However, if you have specific interests within the wider scope...

team

[ 24 Oct 2017 | NEWS ]  New publication: Epigenetics & Chromatin

We are very happy about this one. The first paper from work led by my PhD student Elena! Congrats! Link to open access article here: https://doi.org/10.1186/s13072-017-0158-9

Abstract below:

Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for...

publication

[ 15 Sep 2017 | NEWS ]  New publication: Sci Rep

Our proof-of-principle study of colorectal cancer subtype microbiomes got published today at Scientific Reports. We are currently busy scaling the study up to include many more patients to get a more general picture of the microbiomes of New Zealand colorectal cancer subtypes. In the future we hope we will be able to translate this research into clinical applications. Watch this space!

publication

[ 06 Sep 2017 | BLOG ]  A list of journals

After giving the task of choosing the “right” journal for a manuscript to a student, I started to think a bit more about the nature of science publishing. A lot has been written and discussed about predatory publishers/journals and publishers taking advantage of their power over Universities. So, I wanted a list of “good” journals as an initial starting point and guide for students?

I initially thought of two criteria that can be applied to narrow the field...

journals publishing science

[ 26 Jul 2017 | NEWS ]  Invited guest lecture at the SBS, University of Auckland

Sebastian was invited to the School ol Biological Sciences, University of Auckland, to give a guest lecture on “Epigenome profiling” to 4th year students.

teaching talk

[ 15 Jul 2017 | NEWS ]  New preprint: Transcribed macrophage enhancers at bioRxiv.

Genome-wide profiling of transcribed enhancers during macrophage activation

Background Macrophages are sentinel cells that play essential role in tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M1 (IFNγ) and M2 (IL-4/IL-13) phenotypes are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression, with recent studies highlighting their importance in macrophages.

Results...

preprint enhancer regulation macrophages

Contact

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

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

Publications // latest

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Scientific Reports, 2018, 8:6758

An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Molecular Biology and Evolution, 2018, msy046

Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 2017, 10:50

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