Category Archives: Seminar

Talk on naturalist Carl Linnaeus, Tue 16/10 7pm

The Centre for Nordic Studies’ first talk this semester will be given by Dr Eva Robards (York) at 7pm in the Humanities Research Institute on Tuesday 16 October. Her talk is on, ‘The Swede who organised the world: naturalist Carl Linnaeus’.

For further information, contact Dr Colin Roth by e-mailing

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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:

Seminar today (Friday 15th July) – Common Room 1PM

Clive Darwell (Okinawa Institute of Science and Technology Graduate University) will give a talk on:
Community Assembly in South-East Asian fig wasps.

Extra Seminar, Simon Griffith TOMORROW Friday 24th June 2pm

There will be an extra EEE seminar this FRIDAY (24th June) at 2pm in the common room.

Simon Griffith, Macquarie University

A global perspective on conflict and cooperation in animal mating systems

If you are interested in having a chat with Simon contact Terry (

special seminar this Thurs: >40 years of butterfly host shifts

Dear All,

There will be a special seminar this Thursday (1oth) from 1-2pm in the D-floor common room, by Professor Mike Singer. Mike is nothing short of a living legend, having studied butterfly ecology and evolution in California for >40 years. It should be a refreshing display of integration of ‘old school’ and modern approaches to biology. Title etc. below.

Hope to see you there.

cheers, Patrik

Patterns in space and time: a geographic mosaic of host association and six independent host shifts by a Californian butterfly

Mike Singer, Plymouth University

Bioinformatics webinars next week

Balti and Bioinformatics On Air: 21st January 2015

Including another chance to see Dave Lunt’s talk on ReproPhylo if you missed it at PopGroup last week.

Statistics of Blast by its author Stephen Altschul
The Statistics of Local Pairwise Sequence Alignment, part I – Jan 22nd

The Statistics of Local Pairwise Sequence Alignment, part II – Jan 29th

Special seminar on genomics of speciation, this Thursday August 7th

Hello All,

A candidate for a post-doctoral position in our lab will be visiting APS this Thursday, August 7th. She has worked on empirical analyses of genome variation in hybrid zones (e.g., in Populus with Christian Lexer) and on theoretical models of genomic architecture and speciation (e.g., with Alex Buerkle). She will be giving a 30 minute seminar on her research at 4pm in the common room (this Thursday). All all welcome so spread the news. Drinks to follow in the pub around 5pm.



Special seminar on phenotypic plasticity and evolution in plants

Hello All,

A candidate for a post-doctoral position in my lab is visiting Sheffield this Friday and Saturday and will give a 30 minute seminar on his work on phenotypic plasticity and evolution in Arabidopsis at 4pm this Friday, July 4th in the Common Room. All are welcome and encouraged to attend. We will head to the pub then at 5pm.

cheers, Patrik

How to get published in Nature seminar 30/7, Medical School

Visit of Dr Ritu Dhand – Chief Biological Sciences Editor at Nature
Date: Tuesday 30th July 2013

10:30-11:30         Tea, Coffee and Seasonal Cakes with Ritu – Post Docs and Post Graduate Students
Venue: Heritage Room (B Floor, Medical School) please notify that you will be attending

12:00-12:45         Sandwich Lunch – Academics
Venue: Heritage Room (B Floor, Medical School) please notify that you will be attending

13:00-14:00         Seminar – Nature: the journal, review process and publishing group This seminar is open to all.
Venue: LT3, F Floor, Medical School

Deborah ( will also be arranging one to one sessions through-out the day for anyone who would like to meet Ritu,  please get in contact to book your place.

Talk in APS on evolution of Japanese stickleback

Hello All,

A postdoctoral fellow who is visiting APS for the course next week will give a talk on Thursday about his work on the evolution of Japanese stickleback. He is also aiming to apply for a Marie Curie fellowship to work between Japan and my lab on this system.

Time: noon-1pm, Date: March 21st, Place: B52

title and abstract below, all are welcome, cheers,


Ecological speciation and adaptive radiation in Japanese sticklebacks

Mark Ravinet
Queen’s University Belfast, UK; National Institute of Genetics, Mishima Japan

When species colonize new environments, they often undergo remarkable
diversification, occupying unexploited niches and evolving remarkable
adaptive phenotypic variation. Adaptive radiations driven by divergent
natural selection between habitats can therefore play a major role in
the evolution of biodiversity. Yet why is it that some species are
more prone to adaptive radiation than others? Over the last 10 years,
the stickleback species complex has become an evolutionary
‘supermodel’ for the study of rapid phenotypic adaptation and
speciation. Two highly divergent Japanese stickleback species occur
across the Japanese archipelago. The Japan Sea and Pacific Ocean forms
are unique in that they are the only known example of an anadromous
species pair and furthermore they experience near-complete
reproductive isolation. Curiously, only one lineage, the Pacific
Ocean, is able to colonize freshwater and therefore diversify
phenotypically. The Japanese stickleback system therefore provides an
excellent opportunity to study the role that ecological divergence has
played in shaping both speciation and the extent of adaptive