News&Blog

Computational Biology // Massey University

News&Blog


[ 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

[ 08 Apr 2017 | NEWS ]  New publication: RNA Biology.

Today RNA Biology published a manuscript “DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.” A project together with our friends at the King Abdullah University of Science and Technology. DES-ncRNA is a information extraction system to gather knowledge on microRNAs and lncRNAs from published literature.

publication

[ 20 Mar 2017 | NEWS ]  Invited research seminar at the Otago Medical School

Sebastian was invited to the Department of Medicine of the University of Otago, Christchurch to give a research seminar. The Seminar talk was entitled: “The macrophage enhancer lanscape during cytokine stimulation and tuberculosis infection.” The talk was well received and the discussion and question&answer session after the talk extended way past lunch time. Sebastian also met with collaborators to discuss current and future projects.

travel research talk

[ 08 Mar 2017 | NEWS ]  PhD scholarship available!

We have a open PhD position with a full scholarship available in our group. The successful candidate will investigate the mutational and genetic basis for the biological phenotypes seen in evolved wild yeast lines. We are seeking a candidate with experience in handing next generation sequencing data, assembling genomes, calling variants, and functional genomics. Read more here.

team position PhD

[ 08 Mar 2017 | NEWS ]  Media coverage: Nature publication.

The New Zealand Herald featured an article about our latest work in published in Nature. The publication was also covered among others in ScienceDaily, TheScientist, and GEN Genetic Engineering & Biotechnology News.

press media

[ 01 Mar 2017 | NEWS ]  New publication: Long non-coding RNA atlas published in Nature!

Today, the FANTOM collaboration published their latest work in Nature. Elena and Sebastian were fortunate enough to be able to work together with a great team of researchers on this exciting project. Here, we studied a poorly understood and highly controversial class of genes, known as long non-coding RNAs (lncRNAs). There is a long standing debate in the scientific community questioning if most of these lncRNAs are functional. Here, we generated a comprehensive collection of ~28000 lncRNAs and summarised,...

publication

[ 17 Feb 2017 | BLOG ]  Sent "server down" information to Slack channel

The other day we had a power-cut. I was forewarned, so I was able to shut down my server in time. Before I did so, I was sending messages to my team via Slack, so that they could finish up their work before the server went down. This got me thinking. I thought it would be neat to have a message automatically appearing in a Slack channel if some server of interest could not be reached anymore, so...

python coding slack linux

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

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology, 2017, 10.1080/15476286.2017.1312243.

An atlas of human long non-coding RNAs with accurate 5' ends. Nature, 2017, 543:199–204.

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Research, 2017, 45(D1): D145-D150, doi: 10.1093/nar/gkw1007

Workshops // upcoming

[ Nov 2017 ] Software Carpentry Workshop, Massey University Auckland

Tweets // latest