Welcome to BrykLab.

Announcing Programming for Evolutionary Biology Conference

UPDATE 20th July 2018 Thanks to generous funding from our supporting organisations, The Genetics Society and The Company of Biologists, we are able to keep the registration open. If you still thinking of applying, please send us an email, we may be able to accommodate you!

The Genetics Society logo The Company of Biologists logo

As you might have heard elsewhere ;-), this Autumn we are organising a PGR and ECR-led conference: Programming for Evolutionary Biology Conference. From September 2-6 we are taking over an entire YHA Hostel in Buttermere in the Lake District for four days of talks and workshops. Here is the excerpt from the conference website:

The Programming for Evolutionary Biology (PEB) conference brings together scientists broadly interested in applying bioinformatic tools to answer evolutionary and ecological questions. Unlike other conferences featuring mostly talks and poster sessions, it aims to serve as a platform for discussing common programming pitfalls encountered during research and features workshops to further develop participants’ bioinformatic skills.

The conference is informal and cheap (£275 all inclusive except travel), so go ahead and apply :-):

Next generation biologists workshop

And here we go again! Our “Next Generation Biologists” workshop - this time it’s number four - takes place on June 18-20 at the University of Huddersfield. Application procedure and more information is available at nextgenbiologists.org. Application deadline is on May 25th. Apply away!

Next generation biologists workshop

Just to remind everyone that the deadline for our “Next Generation Biologists” workshop in on this Wednesday, 7th March. Application procedure and more information is available at nextgenbiologists.org.

Hello, Alex!

We are very happy to welcome the third member (!) of our merry band, Alexandra Siddall, who joins us from the wrong other side of the Pennines for her year-long research placement at the University of Huddersfield. Alex is a current student at Huddersfield, inexplicably drawn to all things synthetic biology ;-) and so she decided to take over my UNIGEMS project and support NCBE at the University of Reading in the development of the few missing parts in the Wellcome kits.

Welcome, Alex :-)

Hello, Rohan!

We are very happy to welcome Rohan Raval, a new PhD student in Huddersfield, who came to Huddersfield from the depths of the Silwood Park in the faraway lands of somewhere west of London. Not only he used to do a lot of field work with Apodemus, but he also did his Masters in Computational Methods in Ecology and Evolution at Imperial College London, studying genomic signature of sexual dimorphism in Drosophila. He will be working on genetics and genomics of metabolic rates in A. flavicolis.

Welcome, Rohan :-)

One more time - next generation biologists workshop

Aaaand we are back! I am happy to announce that the registration for the second workshop (to take place at the University of Huddersfield on 13-15th December) in our Next Generation Biologists project is open!

As previously, the details about the workshops, including preliminary programme and application details (deadline 21st November) are available on the project’s website: nextgenbiologists.org. You can also contact us directly at @jarekbryk or @nextgenbiol.

Next generation biologists workshop

UPDATE 18th August 2017 The workshop #2 was postponed until December 2017. More information at nextgenbiologists.org.

I am happy to announce that the registration for the second workshop in our Next Generation Biologists project is open! As previously, the details about the workshops, including preliminary programme and application details (deadline 23rd August) are available on the project’s website: nextgenbiologists.org. You can also contact us directly at @jarekbryk, @evol_molly or @nextgenbiol.

Next generation biologists workshops

I am happy to announce that Mary O’Connell, Martin Callaghan and me are going to run a series of 10 workshops for life scientists planning to work or working on high-throughput data. The entire training series is run in partnership between University of Leeds and University of Huddersfield and is funded by the BBSRC’s Strategic Training Awards for Research Skills’ programme – so BBSRC-funded scientists, as well as students and staff from both organising institutions, can attend for free.

All the details about the workshops, including preliminary programme and application details (deadline 15th July) are available on the project’s website: nextgenbiologists.org. You can also contact us directly at @jarekbryk, @evol_molly or @nextgenbiol.

Fully-funded PhD position on comparative genomics of Apodemus

The BrykLab has* a fully-funded PhD position available to continue and expand our work on Apodemus genomics, from phylogeography to genome-wide scans for positive selection. The position is officially adverstised on findaphd.com and the deadline in on March 26th (!).

(*The university announced 15 projects in total but only 8 studentships, and only projects that will attract the best candidates overall will be awarded the positions.)

Below is a slightly modified text of the announcement that will go live any day now on evoldir.

Rodents from the genus Apodemus are the most common mammals in the Palearctic and an attractive subject for evolutionary and molecular studies: they are likely to be under multitude of selective pressures in different habitats, they contribute to the spread of Lyme disease and tick–borne encephalitis and harbour extra (“B”) chromosomes. However, the genomic and genetic resources for their studies remain very limited.

We are a young and small research group that has recently embarked on establishing phylogenetic and phylogeographic relationships between Apodemus populations in Europe based on whole-genome genotypes. Thanks to collaboration with researchers in Poland, Germany and Belgium we are presently acquiring and analysing whole-genome high-density genotyping data (ddRAD-seq) from hundreds of individuals across Europe. Analysis of this data will inform future directions of our studies: phylogeography of sylvaticus and flavicolis, diversity and divergence of their populations, SNP-based genetic maps and whole-genome scans for signatures of positive selection.

We are looking for an independent candidate with keen interest in evolution and computational approaches to study genetic variation on a population scale. Familiarity with UNIX/Linux, command line or R is a plus, as is research experience, preferably on a master’s level, but strong B.Sc. graduates are also encouraged to apply. Majority of the project involves computational analyses of large datasets, but it has a small wet-lab component, such as preparation of DNA and/or RNA sequencing libraries.

The PhD student will be associated with the Evolutionary and Environmental Genomics Group at the Department of Biological Sciences and embedded with PhD students in the Leverhulme Doctoral Training Centre who work on human and cattle phylogeography, archaeoentomology, yeast transposable elements and evolution of choanoflagellates using genomic approaches. The studentship requires candidates to undertake small teaching duties during the PhD. For more information about us and our work, please go to bryklab.net/research/ and Jarek Bryk’s staff profile. Candidates are encouraged to contact the project’s supervisor, Dr Jarek Bryk, directly with informal questions and requests.

To apply, send an email outlining your motivation and experience to j.bryk@hud.ac.uk (CC’d to f.cross@hud.ac.uk), including a CV and the names of two referees. You also need to complete an on-line application. For more details about the application process please go to the official announcement on findaphd.com.

My talk at Yorkshire Wildlife Trust

Yorkshire Wildlife Trust Cake and Nature talks banner

I was recently invited by Kara Jackson from the Yorkshire Wildlife Trust (YWT) to give a talk on our research and/or evolutionary biology. I wasn’t aware of the YWT before, but it turns out they own a big farm over at Berry Brow, which they maintain to showcase agricultural practice that respects and enable wildlife to flourish. It’s called Stirley Community Farm and it includes a community centre, where they recently launched “Cake and Nature” series of talks—hence my visit.

The talk will take place on 16th February at 7pm (map) and I will be talking on how we use DNA to study evolution. The full abstract of my talk is below:

In the last decade, biological sciences have undergone a revolution: due to breakthrough developments in sequencing technologies—the capability to read DNA—it is now possible to obtain complete genetic information on a population scale. Apart from more mainstream application of these advances, such as genealogy or identification of disease–causing mutations, one of the most exciting is our ability to study patterns of genetic variation in wild populations of almost any species. This ability, coupled with studies of the genetics material of long–extinct organisms, allows unprecedented insight into the evolutionary history of many species.

I will provide an overview of how we study molecular basis of evolutionary change by looking at DNA of modern and extinct species through several examples, from metabolism of bacteria and wings of peppered moths through the beaks of Darwin’s finches to the fur of beach mice and others, including the most self-obsessed of the apes, humans.

These advances are being developed on the background of our ability to also synthesize DNA of a desired sequence and modify DNA in situ to an extraordinary degree. Overall, they have turned biology into a sophisticated, statistics–based and data–driven discipline not unlike high-energy physics, justifying the expectations that the XXI century will be the age of biology.

See you there!

New undergraduate research projects are live

Today is the day when the research projects’ topics for the final year students are going online. You can now have a look at what BrykLab has to offer this year (hint: lots of weasels :-). Good luck.

This website is moving

Just to let you know that for the next few weeks bryklab.net might look funny or not show up at all. I am transferring this website over to Github and I expect bumps and mishaps as I am learning how to do it as I go along.

If everything goes fine, by the end of July bryklab.net will point to a new location as Github Pages, powered by Jekyll. Fingers crossed.

Update on 3rd August: it works!

Hello, Marisa!

I am very happy to welcome Marisa Martín Cerezo, a new PhD student in Huddersfield, with whom I will be working on the Apodemus and Mustela projects. Marisa came to The North from Madrid, where she did her Masters on mtDNA-based phylogeography of snails from the Caenogastropoda clade, and subsequently worked on extremophilic lichens Circinaria gyrosa (in outer space!). She also studied invasive biology of fire ants Solenopsis geminata at Galapagos Islands (!). Unfortunately, she supports the other club from Madrid, but hey, nobody’s perfect.

Marisa in the lab

Welcome, Marisa :-)

Hello, world!

Update in February 2018

Welcome to the website of a single-person two-person three-person research group of Dr Jarek Bryk at the University of Huddersfield in the north of England.