Monthly Archives: November 2016

Seminar Dr Mario Guarracino “Unveiling the challenges of a happy marriage between Biology and Informatics”

Biomedical Science Seminar Series – Monday 28th November 2016, 12 noon

Conference Room, A Floor, Alfred Denny Building

Dr Mario Guarracino
Laboratory for Genomics, Transcriptomics and Proteomics
National Research Council of Italy
Unveiling the challenges of a happy marriage between Biology and Informatics
Next generation sequencing (NGS) technologies are widely used to characterize the genomic map of organisms. Since their advent, high-throughput experiments have produced a burst in knowledge and understanding of genomic, transcriptomic and epigenomic mechanisms and their altered states.
NGS workflows might be divided into three main phases: the first produces raw data through base calling and quality assessment; the second, which is application specific, aims at converting the sequence data into biological information (e.g. gene list, variant list), primarily through the alignment to the reference genome or de novo assembly; finally, the so called tertiary analysis concerns with the extrapolation of the biological meaning and the integration of different approaches to exhaustively investigate the data.
Although standard procedures have not yet been defined so far, many tools and pipelines have already been developed to perform the primary and secondary NGS analyses.
The third phase is particularly sensitive to interdisciplinarity. The exchange of knowledge between computational researcher and experimental researcher plays a pivotal role to interpret and gain new biological knowledge from data analysis. Furthermore, the fast evolution of technologies for quantitative biology requires the design of new data analysis methods that are able to keep up with such fast changes.
In this talk I will give a brief introduction of NGS technologies and describe some of the methods and tools used for analysis. I will be focusing on methods for DNA variants annotation and filtering, the detection of contaminating sequences in NGS data. I will also describes approaches for data integration.
I will also describe applications we have been developed and optimised on the identification of miRNA-target interactions through the data integration of miRNA, mRNA and protein expression profiles, tools for annotation and enrichment of novel transcripts and methods for reconstruction of genetic regulatory networks.

Host: Dr Marta Milo

All Welcome

For a full list of forthcoming speakers – please see the Departmental
web site:

Spare room Dec – Feb

Two MRes students from Silwood, Sophie and Filipa, will be visiting the lab for a couple of months to work on the sparrow project and are in need of accommodation. They’ll be starting in the lab on 5th December. If you might be able to help, please let me know. Thanks!

Natalie   (

Postdoc: Life in a cold climate: the adaptation of cereals to new environments and the establishment of agriculture in Europe

University of Manchester vacancy S&E-09130


Two phd projects – trans-generational effects; Imperial Silwood Park

Offering two PhD studentships, one with a more theoretical focus and one with an empirical research focus, on trans-generational effects. The current speed at which environmental conditions change is unprecedented, endangering vulnerable populations and species. A cool idea for how organisms can sustainably respond to rapid environmental changes are environmentally induced adaptations that are heritable. Such trans-generational, potentially epigenetic effects can, with high precision mediate evolutionary rescue of populations that experience rapidly changing environments. These advantages put TAGs at the forefront of mechanisms leading to adaptations to global change. These projects will use a wild population of passerines, and experiments in captivity, to disentangle phenotypic plasticity induced during development from epigenetic TAGs. We will use long-term data and behavioural observations to test the hypotheses. The theoretical project will use population modelling and individual-based simulations infer evolutionary consequences of TAGs.

For both projects, you should have solid foundation in quantitative biology. Experience in advanced statistical methods using R is an advantage for both projects. The empirical project requires a student willing to conduct fieldwork in the UK during the breeding season of each year. A bird ringing license (BTO) is not required, but a big advantage. Students applying for the theoretical project should be highly quantitative and have at least some programming experience.

The Silwood Park Campus is a vibrant graduate campus one hour by train from London City with more than 120 graduate students from countries all over the world.

Silwood’s academics are world-class scientists, and we offer a range of graduate courses to improve hard and soft skills.

To apply, please send your CV, a motivation letter detailing your relevant expertise, and contact information for two references to:


To be eligible for a full award a student must have:

•         Settled status in the UK, meaning they have no restrictions on how long they can stay,

•         Been ‘ordinarily resident’ in the UK for 3 years prior to the start of the studentship.

•         This means they must have been normally residing in the UK (apart from temporary or occasional absences)

•         Not been residing in the UK wholly or mainly for the purpose of full-time education. (This does not apply to UK or EU nationals).

For FAQs and to apply please visit:

Have you got Whole Genome Sequence Data and you’re not sure what to do with it? This Triple A Winter School is for you.

Date: 15-20th January 2017

Where: Monte Veritá, Switzerland

Triple A Winter School is a intensive workshop on how to Assemble, Annotate and Analyse Whole Sequence Data – with a focus on de novo whole genome assembly and analysis of complex genomes. The Winter School will combine lectures with computer based practicals, and will be most valuable to those who have or will soon have whole genome sequence data.


Instructors include:

Monica Monuz-Torres from Lawrence Berkeley National Laboratory, USA.

Robert Waterhouse from Université de Genéve and the Swiss Institute of Bioinformatics, Switzerland.

Emmanuelle Lerat from Chargé de recherche – CNRS, France.

Peter Fields from Universität Basel, Switzerland.

TOTAL COST: 610 CHF + travel to Locarno (Switzerland)
Covers tuition, accommodation (shared double room) and all meals (breakfast, lunch, dinner, and coffee breaks).

REGISTRATION CLOSES: 30th November 2016
Spaces are limited to 40 participants. See our webpage for more details.

Dr Jessica Stapley, ETH Zürich; Dr Stuart Dennis, EAWAG; Dr Stefan Zoller, GDC ETH Zürich and Professor Alex Widmer ETH Zürich.

Does your university pay fair?

See how fair the University of Sheffield is

Postdoc lunch Thu 17 Nov – Common Room

Dear PostDocs / Early Career Researchers,

Come and meet your fellow PostDocs over lunch, which the APS PostDoc Society will provide on Thursday November 17th in the common room. To avoid food waste, please let us know whether you’re joining us (link).

We’ll start at 12:00 and we’ve promised to give the common room back by 14:00. Can’t make it? We’re still interested in your views! You can fill in our 100% optional and anonymous questionnaire attached to the lunch sign-up form.

The PostDoc Society aims to facilitate social interactions between PostDocs by organizing social events, facilitate training and career development and give PostDocs a stronger voice within APS and the University of Sheffield. We’d love to hear your views on PostDoc representation in APS and the faculty of sciences, which events you’d like to see organised, and the answer to the ultimate question of life, the universe, and everything.
If you have time to fill in the (optional & anonymous) questionnaire attached to the lunch sign-up form that would make you absolutely awesome, but you can also just chat with us over lunch.
The lunch will also double as an AGM (don’t worry, you’ll hardly notice), so we won’t have to bother you with that separately.

Hope to see you soon,
The APS PostDoc Society Committee

Celine is fundraising by training 14hours this Saturday (12/11)

Dear all,

I am fundraising for the National Autistic Society by training 14 hours this Saturday. If you’d like to support the NAS (or encourage me to keep going through the 14 hours!), please donate on our JustGiving page!

Thank you!


Room in January

A postdoc from Gothenburg who works with us on Littorina, Marina Rafajlovic, will visit Sheffield from about 7 to 14 January. If anyone has a room that she might use for the week, please let me know.



Postdoctoral opportunities: Evolution of Sensory Systems & Evolutionary Genetics of Diversification

Two postdoctoral positions are available in the laboratory of Dr. Janette Boughman for projects funded by
NSF. I am looking for highly motivated, creative scientists to join my group on two research projects.
One position emphasizes the evolution of sensory systems, including the selective forces (e.g., ecology,
predation) that shape vision, olfaction, and mechanosensory systems. Experience with any aspect of
sensory biology or communication, and experience doing field work in challenging locales highly
desirable. Additional experience in quantitative genetics, or with genetics or genomics would be a plus.
The other position emphasizes evolutionary and landscape genetics. Experience in genomics and analysis
(e.g., admixture mapping, fitness mapping, landscape genomics, population genomics) highly desirable,
as is experience with bioinformatics. Additional experience in evolution of sensory systems or evolution
of behavior and/or other aspects of phenotypic evolution a definite plus.
For both positions:
Experience generating and analyzing phenotypic and fitness data on morphology, color, behavior, or
other adaptive phenotypes. The positions require excellent analytical skills. Demonstrated ability to
publish good quality papers is necessary. Good writing and communication skills are highly prized. The
positions provide additional opportunities for independent research for motivated postdoctoral scientists.
Initial appointments are for 1 year, with possibility of renewal for up to 3 years.
The Boughman lab studies the evolutionary process of diversification, including speciation. We study the
interplay between sexual and natural selection in diversification; the creative and destructive role of
hybridization; the evolution of behavior, communication, cognition, and sensory systems; and the
consequences this trait evolution has for speciation. We use the charismatic threespine stickleback system
because of its extraordinary power for addressing evolutionary questions. Plus, the fish are fun to work
with and inherently intriguing. Ongoing research is in British Columbia and Iceland, and we run many
experiments in my very fine fish lab on the MSU campus.
MSU provides a dynamic intellectual environment for motivated evolutionary biologists through the
Ecology, Evolutionary Biology & Behavior Program ( – ranked 4th in the country),
and the BEACON Center for the Study of Evolution in Action ( ). You
can get more information about my lab at ( ). However, my website is
not fully updated, so you can contact me for more information as well.
Ph.D. required in a related field of biology. Salary and benefits are competitive. Review of applications
will begin immediately. All applications submitted before November 15 will receive full consideration. I
encourage women and members of minorities to apply. Michigan State University is an Affirmative
Action / Equal Opportunity Employer.
To apply, please send CV, letter of interest, contact information for 3 referees, and 1 or 2 of your papers
to: Jenny Boughman at .