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Events: Seminars - EBI External Seminars
External seminars are open to the campus and usually take place on Mondays from 13:30 in the shared facilities room C209/210 of the Genome Campus. Ideas for speakers are warmly welcomed. Please send suggestions to Kathryn Hardwick .
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
19th Feb 2010 10:30 to 19th Feb 2010 12:00 |
| Speaker |
Prof. Sydney Brenner Crick-Jacobs Center Brenner Laboratory, Salk Institute |
Abstract/
Additional Info |
The first part of the talk will be to outline a new theory of the
dynamics of genomes and how the problem of isochores can be finally
resolved. The second part will deal with how cell types, especially in
the brain, might be specified and what we can learn from the study of
"krikologs" (linked duplications) in the human genome.
|
| Venue |
Francis Crick Auditorium |
| Host |
Janet Thornton
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
2nd Feb 2010 14:00 to 2nd Feb 2010 14:45 |
| Speaker |
Aoife McLysaght Genetics Dept. of Trinity College Dublin, Ireland |
Abstract/
Additional Info |
The origin of new genes is extremely important to evolutionary
innovation. Most new genes arise from existing genes through duplication
or recombination. The origin of new genes from noncoding DNA is
extremely rare, and very few eukaryotic examples are known. We present
evidence for the de novo origin of at least three human protein-coding
genes since the divergence with chimp. Each of these genes has no
protein-coding homologs in any other genome, but is supported by
evidence from expression and, importantly, proteomics data. The absence
of these genes in chimp and macaque cannot be explained by sequencing
gaps or annotation error. High-quality sequence data indicate that these
loci are noncoding DNA in other primates. Furthermore, chimp, gorilla,
gibbon, and macaque share the same disabling sequence difference,
supporting the inference that the ancestral sequence was noncoding over
the alternative possibility of parallel gene inactivation in multiple
primate lineages. The genes are not well characterized, but
interestingly, one of them was first identified as an up-regulated gene
in chronic lymphocytic leukemia. This is the first evidence for entirely
novel human-specific protein-coding genes originating from ancestrally
noncoding sequences. We estimate that 0.075% of human genes may have
originated through this mechanism leading to a total expectation of 18
such cases in a genome of 24,000 protein-coding genes. |
| Venue |
Courtyard room, EBI |
| Host |
Nick Goldman
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
3rd Nov 2009 14:00 to 3rd Nov 2009 15:00 |
| Speaker |
Victor Kunin Environmental Ecology Group, DOE Joint Genome Institute, CA, USA |
Abstract/
Additional Info |
Title:
Accurate estimation of microbial community using pyrotags.
Abstract:
Pyrosequencing of small subunit ribosomal RNA amplicons (pyrotags) is
rapidly gaining popularity as the method of choice for profiling
microbial communities. It has revealed that the extent of rare microbial
populations in several environments, the “rare biosphere”, is orders of
magnitude higher than previously thought. However, the large amount of
data, and errors associated with the sequencing technology present
significant analytical challenges. I will show how sequencing errors can
potentially inflate diversity estimates. I will describe PyroTagger – a
fast, scalable computational pipeline designed to ensure accurate
estimates of microbial diversity.
Title:
The Open Journal – social network, journal club and peer-reviewed
journal with automated editors and production.
Abstract:
The Open Journal combines social network and a peer-reviewed journal.
The social network part has profiles of scientists including education,
research interests, work history and publications. Journal club allows
exchanging opinions on publications. The peer-reviewed journal lets
authors upload papers and have a complete control over the peer review
process. Authors choose potential referees and the system automatically
verifies that referees have appropriate qualifications and no conflicts
of interests. The reviewer identities are public, ensuring both
acknowledgment and accountability for referees. The production process
is fully automated, rendering journal-formatted articles in HTML and pdf
formats directly from authors’ submission. Beyond accountability,
transparency and open access, the system is designed for speedy
publication process at low cost. |
| Venue |
A202-3, shared facilities |
| Host |
Aswin Sai Narain Seshasayee
|
| Target Audience |
All are wellcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
13th Oct 2009 14:00 to 13th Oct 2009 15:00 |
| Speaker |
Andrew Firth Recoding Lab, University College, Cork, Ireland |
Abstract/
Additional Info |
Overlapping genes (whereby the same nucleotide sequence codes for two or
more proteins in different reading frames), and genes translated via
non-canonical mechanisms (such as programmed ribosomal frameshifting,
stop codon read-through, leaky scanning, non-AUG initiation, IRESs, and
ribosomal shunting), are particularly common in RNA viruses, where they
allow the virus to optimize the coding potential of a compact genome,
regulate gene expression, and circumvent the host cell's canonical -
though not ubiquitous - rule of 'one functional protein per mRNA'. Such
genes can be difficult to detect with traditional gene-finding software,
especially when they are very short. We have been using a number of
comparative bioinformatic methods in order to systematically identify
'difficult' genes that have been persistently overlooked in virus
genomes. Recent discoveries include short but highly-conserved
overlapping genes in the potyviruses, the alphaviruses, and the Japanese
encephalitis group of flaviviruses - all three of which are translated
via programmed ribosomal frameshifting. The identification of these and
other 'hidden' genes is leading to the characterization of a number of
novel sequence motifs capable of stimulating ribosomal frameshifting and
other non-canonical translation events. The bioinformatic methods and
the novel translation motifs identified are relevant to the search for
and annotation of 'hidden' genes in cellular genomes. |
| Venue |
C209-10, Shared facilities |
| Host |
Gregory Jordan
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
2nd Oct 2009 11:00 to 2nd Oct 2009 12:00 |
| Speaker |
Christophe Dessimoz Institute of Computational Science, ETH Zürich |
Abstract/
Additional Info |
The alignment of biological sequences is of chief importance to most
evolutionary and comparative genomics studies, yet the two main
approaches used to assess alignment accuracy have flaws: reference
alignments are derived from the biased sample of proteins with known
structure, and simulated data lack realism.
In the talk, I present two novel tree-based tests of alignment accuracy.
Not only are they based on large and representative samples of real
biological data, but they also enable the evaluation of gap placement
accuracy (which is notoriously difficult with existing methods).
I compare the performance of common multiple sequence alignment
strategies/methods, assess the effect of excluding gaps and variable
regions, and show that state-of-the-art alignment/tree methods neglect a
considerable amount of phylogenetic signal in alignments.
This study provides the broad community relying on sequence alignment
with practical recommendations, sets novel standards for assessing
alignment accuracy, and paves the way for the development of
phylogenetic inference methods of significantly higher resolution. |
| Venue |
C209-10, Shared facilities |
| Host |
Nick Goldman
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
22nd Sep 2009 10:00 to 22nd Sep 2009 11:00 |
| Speaker |
David Wallace Newton Institute, Cambridge |
Abstract/
Additional Info |
The Isaac Newton Institute for Mathematical Sciences www.newton.ac.uk runs themed research programmes of one to six months, with 40 or more visitors from around the world at any one time. Topics span mathematics and all its applications. The talk will describe how the Institute works, including proposal of programmes and participation. Recent and planned programmes include stochastic computation in the biosciences, phylogenetics, modelling the heart, and genome resequencing. The short talk will be followed by discussion aimed at exploring the potential interests in bio and medical sciences, and at stimulating possible future proposals to the Institute. |
| Venue |
M203 Cairns Pavilion |
| Host |
Janet Thornton
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
27th Aug 2009 16:00 to 27th Aug 2009 17:00 |
| Speaker |
Dave Ussery Microbial Genomics Group Leader, Technical University of Denmark |
Abstract/
Additional Info |
Currently, there are 27 different strains of E. coli that have been
completely sequenced and are in GenBank, with about twice as many
strains that are in various stages of completion. This relatively large
number of sequenced genomes of the same species allows the possibility
to construct an E. coli core- and pan-genome, and to compare the genes
in these two categories. Further, we estimate the upper limit of the
total number of E. coli gene families to be in the range of 50,000, or
more than the number of genes in the human genome. The diversity within
individual E. coli genomes is quite large, with many E. coli genomes
sharing only around half of their gene families in common with other
sequenced E. coli genomes. Pan-genome family trees can be used to
cluster closely related strains, and discern larger families of various
types of E. coli genomes, based on shared gene families from the
pan-genome. |
| Venue |
C209-10, Shared facilities |
| Host |
Aswin Seshasayee
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
1st Jul 2009 14:00 to 1st Jul 2009 15:00 |
| Speaker |
Philippe Laflamme McGill University and Genome Quebec Innovation Center |
Abstract/
Additional Info |
Developed at the McGill University and Genome Quebec Innovation Centre,
GenoByte is an Open Source Java API for storing and analysing of very
large sets of genotyping data. Out of the box, the GenoByte API supports
transactional operations, frequency analysis, genotype inconsistency
identification, case-control analysis for genome-wide association
studies and allows plugging custom genotype analysis algorithms.
Currently in production at the Innovation Centre, GenoByte is used to
store and analyse more than 16B genotypes produced by 8 different
genotyping technologies. GenoByte is currently freely available as part
of OBiBa: an Open Source Software development project targeted at
biobanks and supported by the Public Population Project in Genomics
(P3G) consortium.
|
| Venue |
C209-10, Shared facilities |
| Host |
Mario Caccamo
|
| Target Audience |
All are wellcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
6th Apr 2009 11:00 to 6th Apr 2009 12:00 |
| Speaker |
Thomas Rattei Department of Genome Oriented Bioinformatics, Technische Universität München |
Abstract/
Additional Info |
Amino acid sequences are the most important source of evolutionary and
functional information in bioinformatics. In order to facilitate the
computationally intensive tasks of sequence analysis, the Similarity
Matrix of Proteins (SIMAP) database provides a comprehensive and
up-to-date dataset of the pre-calculated sequence similarity matrix and
sequence-based features like InterPro domains for all proteins contained
in the major public sequence databases. This includes all metagenomes
deposited in NCBI Genbank. As of March 2009, SIMAP covers ~43 million
protein entries and more than 21 million non-redundant sequences
(including metagenomes) and provides a complete annotation based on
InterPro 19.
Important technical aspects of the SIMAP implementation comprise the
incremental update procedures for sequence similarities as well as
InterPro domains and the rapid calculation of FASTA and HMMer through
the volunteer computing grid BOINC.
In order to structure the sequence space of known proteins, SIMAP
provides an integrated clustering that is based on sequence homology as
well as domain architectures. Clusters are calculated using a
hierarchical algorithm consisting of generation of non-redundant sets of
sequences, Tribe-MCL and sub clustering based on the presence and order
of InterPro domains. Mapping of Gene Ontology Annotations (GOA) to these
clusters provides reasonable protein function predictions for large
parts of the protein sequence space.
|
| Venue |
C209-10, Shared facilities |
| Host |
Sarah Hunter
|
| Target Audience |
All are wellcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
2nd Mar 2009 11:00 to 2nd Mar 2009 12:00 |
| Speaker |
Dr Rune Linding Teamleader Cellular & Molecular Logic Team Integrative Network Biology initiative |
Abstract/
Additional Info |
Directionality in protein signalling networks is due to modulated
protein-protein interactions
and is fundamental for proper signal progression and response to
external and
internal cues. This property is in part enabled by linear motifs
embedding post-translational
modification sites. These serve as recognition sites, guiding
phosphorylation by kinases and
subsequent binding of modular domains (e.g. SH2 and BRCT).
Characterisation of such
modification-modulated interactions on a proteome-wide scale requires
extensive
computational and experimental analysis. In my talk I will review our
latest advances in
methods for unravelling phosphorylation mediated cellular interaction
networks. In particular I
will discuss how the combination of quantitative mass-spectrometric
technologies and
computational algorithms (NetworKIN [1] and NetPhorest [2]) together are
enhancing
mapping of these largely uncharted dynamic networks. By combining
quantitative
measurements of phosphorylation events with computational approaches I
will discuss how
systems level models will help to decipher complex diseases through the
ability to predict
cellular systems trajectories. Recently, we have utilised these
algorithms in combination with
quantitative genetic screens to model the regulatory networks
surrounding JNK kinase in
Drosophila [3]. I will show how this new integrative approach is crucial
for gaining new insight
into phosphorylation driven molecular gating and cellular decision
processes..
1: Linding et al., Cell 127, 2007.
2: Miller et al., Science Signaling, 1, 2nd September, 2008.
3: Bakal, Linding, Llise et al., Science, October, 2008.
|
| Venue |
C209-210 |
| Host |
Rolf Apweiler
|
| Target Audience |
All are welcome |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
18th Feb 2009 14:00 |
| Speaker |
Prof Jamie Prilusky and Eran Hoddis Weizmann Institute |
Abstract/
Additional Info |
Rather than relying on text to provide the understanding of biomacromolecular structures, a collaborative website called Proteopedia provides a new resource by linking written information and 3D structural information. The wiki web resource, http://www.proteopedia.org, displays protein structures and other biomacromolecules interactively -- they can be rotated and zoomed. These interactive images are surrounded by descriptive text containing hyperlinks that change the appearance (such as orientation, zoom, representations, colors or labels) of the adjacent 3D structure to reflect the concept explained in the text. This makes the complex structural information readily accessible and comprehensible, even to non-structural biologists. Using Proteopedia, anyone can easily create descriptions of biomacromolecules linked to their 3D structure, e.g.:
· HIV-1 protease: http://proteopedia.org/wiki/index.php/HIV-1_protease
· Yeast poly(A) polymerase: http://www.proteopedia.org/wiki/index.php/2q66
· Acetylcholinesterase with bound inhibitor Huperzine: http://www.proteopedia.org/wiki/index.php/1vot
· Lac repressor: http://www.proteopedia.org/wiki/index.php/Lac_repressor
Aside from content added by the hundreds of registered users of Proteopedia, pages on each of the more than 55,000 entries in the Protein Data Bank have been automatically created, already useful and primed for expansion by users. Pages can be viewed by anyone with an Internet browser (e.g. Internet Explorer, Firefox, Safari) and members of the scientific community are invited to request a user account to edit existing pages and to create new ones. |
| Venue |
C209/10 |
| Host |
James Watson
|
| Target Audience |
All welcome |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
15th Dec 2008 11:00 to 15th Dec 2008 12:00 |
| Speaker |
Christoph Best EMBL-EBI,Macromolecular Structure Database Group |
Abstract/
Additional Info |
Cryo-electron microscopy of subcellular structures and macromolecular
complexes is one of the most promising technologies both to study the
structural bases of cellular function and the interplay of
macromolecular complexes in the living cell.
The Electron Microscopy Data Bank (EMDB), established at EBI in 2002 in
the Macromolecular Structural Database group, is the internationally
established repository for three-dimensional high-resolution images from
electron microscopy in structural biology, similar to the Protein Data
Bank (PDB) for macromolecular structures.
It contains both high-resolution density maps of macromolecular
complexes derived by averaging large number of individual images for
resolution improvements, and tomographic maps of three-dimensional
subcellular structures obtained from tilted image series of cellular
sections embedded in vitreous ice. Both technologies are expected to
expand rapidly both in power and in volume, with single-particle
averaging reaching towards atomic resolution, and tomography allowing to
study cellular processes in high detail.
In this talk, I will give an overview of what electron microscopy can
provide in data for structural, cellular, and systems biology, which
informatics challenges arise in obtaining and reconstructing these
highly noisy images, and how the information is processed, stored, and
presented in the Electron Microscopy Data Bank now and in the future.
|
| Venue |
C209-10 |
| Host |
Janet Thornton
|
| Target Audience |
All are welcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
8th Dec 2008 |
| Speaker |
Leena Peltonen |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
1st Dec 2008 11:00 to 1st Dec 2008 12:00 |
| Speaker |
Dr Matthieu Louis EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona |
Abstract/
Additional Info |
Chemotaxis involves directed navigation toward attractive stimuli and
away from aversive stimuli. Although this process is critical for the
survival of all motile animals, the mechanisms by which higher organisms
with complex nervous systems navigate through chemical gradients remain
poorly described. We are studying this problem in Drosophila larvae
which represent a powerful paradigm to investigate the principles of
odor coding. To characterize the navigation strategies of larvae, we
developed a novel chemotaxis assay where odorant conditions can be both
measured and controlled. Using high-resolution computerized analysis of
individual animal trajectories, we showed that Drosophila larvae advance
up an odorant gradient by constantly aligning their direction of motion
with that of the local odorant gradient.
We manipulated the larval olfactory system to generate animals with an
altered repertoire of odorant receptors. Animals possessing only a
single pair of functional olfactory sensory neurons - one on each side
of the head - were generated and showed robust chemotaxis. The
complexity of the system was further reduced by genetically engineering
larvae with a single olfactory neuron in either the right or left side
of the head. Our behavioral results provide evidence that, while
bilateral olfactory input is not essential for larval chemotaxis, it
enhance the accuracy of the chemotactic navigation by increasing the
signal-to-noise ratio in odor detection. |
| Venue |
C209-210 |
| Host |
Nicolas Le Novère
|
| Target Audience |
All are welcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
24th Nov 2008 11:00 to 24th Nov 2008 12:00 |
| Speaker |
Mr Ian Grieve Physiological Genomics & Medicine, MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Imperial College |
Abstract/
Additional Info |
Expression quantitative trait loci (eQTLs) represent genetic control
points of gene expression and can be categorized as cis- or
trans-acting, reflecting local and distant regulation of expression.
eQTLs were mapped in four tissues from a panel of recombinant inbred rat
strains, and thousands of cis- and trans-eQTLs were identified.
I describe a genome-wide correlation analysis of the expression profiles
of eQTL transcripts and the genotypes at their peaks of linkage.
Consistent differences in the patterns of statistically significant
correlation were observed between cis- and trans-eQTLs across all four
tissues. Genes underlying trans-eQTL clusters - groups of trans-eQTLs
linked to a common region of the genome - were found consistently to be
co-expressed and frequently also functionally related. I discuss the
implications of all of these findings as they relate to large-scale
analyses of eQTL data.
I correlated physiological trait measurements obtained in the
recombinant inbred strains with the expression profiles of cis-eQTLs in
relevant tissue(s). I detail the findings relating to one trait in
particular, left ventricular mass (LVM), and their significance in the
eventual implication of Ogn as a key regulator of LVM. |
| Venue |
C209-10 |
| Host |
Paul Flicek
|
| Target Audience |
All are welcome |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
20th Nov 2008 |
| Speaker |
Robert Hoffmann |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
3rd Nov 2008 11:00 to 3rd Nov 2008 12:00 |
| Speaker |
Prof. Mauno Vihinen Institute of Medical Technology, University of Tampere, Finland. |
Abstract/
Additional Info |
Gene defects are relatively easy to identify, but obtaining information
about the effects of sequence variation and elucidation of the detailed
molecular mechanisms of genetic disease will be the next major efforts
in mutation research. We have analysed the structural and functional
effects of disease-causing mutations and elucidated the molecular basis
for a number of hereditary diseases. Amino acid substitutions may have
diverse effects on protein structure and function, thus a detailed
analysis of the mutations is essential. Experimental study of the
molecular effects of mutations is laborious, while useful and reliable
information about the effects of amino acid substitutions can readily be
obtained by theoretical methods. We have used experimentally defined
structures and molecular modelling as a basis for interpretation of the
mutations. The effects of missense mutations can be analysed even when
the 3D structure of the protein has not been determined, although
structure-based analyses are more reliable. Analyses of sequence
conservation and protein structural disorder and aggregation
propensities can be performed at the sequence level. Structural analyses
include studying the contacts between residues, their implication for
the stability of the protein and the effects of the introduced residues.
Investigation of the steric and stereochemical consequences of
substitutions provides insight on the molecular fit of the introduced
residue. Mutations that change the electrostatic surface potential of a
protein have wide-ranging effects. Analyses of the effects of mutations
on interactions with ligands and partners have been performed for
elucidation of functional mutations. We have employed numerous methods
or predicting the effects of amino acid substitutions, and a portal
providing easy access into the tools and methods useful in the analysis
is under development. The applicability of these methods in the analysis
of genes, proteins, and diseases to reveal protein structure-function
relationships and disease genotype-phenotype correlations will be discussed.
|
| Host |
Janet Thornton
|
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
31st Oct 2008 11:00 to 31st Oct 2008 12:00 |
| Speaker |
Dr Chris Lipinski Melior Discovery |
Abstract/
Additional Info |
In drug discovery what is a good target? In part the answer is based on technology and in part the answer depends on the skill sets of the person asking the question. In dealing with academic drug discovery groups the question often devolves down to the very different training and world views of biologists and chemists. In the US, at least, one of the biggest impediments to success in academic drug discovery is the disconnect between the beautiful biology found in academia and the beautiful medicinal chemistry found in the pharmaceutical industry. The sensible application of rules and filters to chemistry structures has a role in bridging this divide. Target tractability from a chemistry viewpoint shows progress in some areas, eg. ligands for protein – protein interactions but overall to date there is not very much evidence of chemistry progress in improving developability as opposed to druggability. With respect to chemical biology as opposed to drug discovery I believe that a proportion of ligands exhibiting lack of selectivity can be traced to artifactual purely chemistry related issues. |
| Venue |
M203 - Cairns Pavilion |
| Host |
John Overington
|
| Target Audience |
All are welcome. |
| Event Category |
Seminars |
| Event Subcategory |
EBI External Seminars |
| Date |
27th Oct 2008 11:00 to 27th Oct 2008 12:00 |
| Speaker |
Amy Schmid Institute for Systems Biology, Seattle, WA, USA |
Abstract/
Additional Info |
Previous gene regulatory network studies in a model prokaryote have
resulted in a mathematical model which accurately predicts the
transcriptional behavior for 80% of the genome in response to
environmental perturbation. However, mRNA expression is often not
predictive of protein and phenotypic level changes. It is therefore
imperative to include information about posttranscriptional processing
to increase predictive accuracy. To address this issue, we have
investigated the transcriptional and posttranscriptional regulatory
circuitry involved in energy generation in archaea. In particular, we
have measured the response to oxygen and nutrient availability using
high throughput approaches such as quantitative proteomics and
genome-scale transcription factor location analysis. Under fluctuating
oxygen concentrations, the organism employs several posttranscriptional
mechanisms which regulate the appropriate timing of cellular response.
In addition, we have characterized the function and mechanism of a novel
transcriptional regulator that was initially excluded from the gene
regulatory network model. This nutrient-responsive regulator coordinates
the system-wide expression of diverse metabolic pathways. Using these
new data as constraints, we are working to refine the existing network
model. Predictions from this model will be used in cell re-engineering
studies for diverse applications from bioenergy to preventative medicine.
|
| Venue |
C209-10 |
| Host |
Wolfgang Huber
|
|
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