News&Blog

Computational Biology // Massey University

News&Blog


[ 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

[ 10 Jul 2017 | NEWS ]  Invited research seminar at the SBS, University of Auckland

Sebastian was invited to the School ol Biological Sciences, University of Auckland, to give a research seminar. The Seminar talk was entitled: “The regulatory impact of enhancers on macrophage polarization.” Sebastian also met with collaborators to discuss current and future projects.

research talk

[ 06 Jul 2017 | NEWS ]  New preprint: CRC subtype microbiomes at bioRxiv.

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes....

preprint cancer

[ 23 May 2017 | NEWS ]  Daniel finished his MSc in Genetics.

Daniel has handed in his final thesis after only minor emendations and will graduate soon. The referees were impressed with his work and he will receive a MSc in Genetics with First Class Hons. Congratulations Daniel! Well done!

team graduation

[ 14 Apr 2017 | NEWS ]  Software Carpentry workshop at Massey University Auckland

We organised and taught another Software Carpentry hands-on computational workshop at Massey University Auckland on the 10th and 11th of April. We had around 25 people eager to learn new computational skills. At the first day we had Tina teaching task automation using the Unix command-line followed by Asher teaching all about version control with git. The complete second day was dedicated to making use of the statistical language R to analyse data. Elena was teaching this session. We...

teaching swc

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

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

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports, 2017, doi: 10.1038/s41598-017-11237-6

Consensus molecular classification of colorectal cancer and association with the colonic microbiota. Diseases of the Colon & Rectum, 2017, 60(6):E90-E91 (In proceedings: Annual Meeting of the American Society of Colon and Rectal Surgeons)

Workshops // upcoming

[ Nov 2017 ] Software Carpentry Workshop, Massey University Auckland

Tweets // latest