News&Blog

Computational Biology // Massey University

News&Blog


[ 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):

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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

[ 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

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

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

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

Tweets // latest