Boa tarde a todos,

Teremos na próxima semana, na sexta-feira, dia 7 de Abril, o próximo
evento do THOR, que decorre no âmbito de um projecto em curso e em
que alguns de nós participam. Notem o dia e o local excepcionais,
estão todos convidados pelo João Carriço a visitar o IMM. Deixo-vos
o anuncio oficial:

It is my great pleasure to announce the extra CBBS seminar indicated
below. Can is collaborating with us in a FTC-TUBITAK (Turkish
Science Foundation) project and agreed to give us a seminar of one
of his latest work. He has authored in several high impact papers
on human genome sequencing and he is particularly interested in
copy number variation and genome organisation.  If any of you want
to meet him for lunch let me know.

With my very best regards
João André Carriço

Computational Biology and Bioinformatics Seminar (CBBS) 

Room: Auditorio David Ferreira (Room 52) 
Date and time: 7 April 2017 10:30-11:30

Discovery of large genomic inversions using long range information
Can Alkan
Dept. Computer Engineering, Bilkent University, Ankara, Turkey

Although many algorithms are now available that aim to characterize
different classes of structural variation, discovery of balanced
rearrangements such as inversions remains an open problem. This is
mainly due to the fact that breakpoints of such events typically
lie within segmental duplications or common repeats, which reduces
the mappability of short reads. The algorithms developed within the
1000 Genomes Project to identify inversions are limited to relatively
short inversions, and there are currently no available algorithms
to discover large inversions using high throughput sequencing
technologies.

Here we propose a novel algorithm, Valor, to discover large inversions
using new sequencing methods that provide long range information
such as 10X Genomics linked-read sequencing, pooled clone sequencing,
or other similar technologies that we commonly refer to as long
range sequencing. We demonstrate the utility of Valor using both
pooled clone sequencing and 10X Genomics linked-read sequencing
generated from the genome of an individual from the HapMap project
(NA12878). We also provide a comprehensive comparison of Valor
against several state-of-the-art structural variation discovery
algorithms that use whole genome shotgun sequencing data.
           
We show that Valor is able to accurately discover all previously
identified and experimentally validated large inversions in the
same genome with a low false discovery rate. Using Valor, we also
predicted a novel inversion, which we validated using fluorescent
in situ hybridization.

Short Bio: Can Alkan is currently an Assistant Professor at the
Department of Computer Engineering at Bilkent University since
January 2012. He graduated from Bilkent University Dept. of Computer
Engineering in 2000, and received his Ph.D. in Computer Science
from Case Western Reserve University in 2005 after a brief visit
to Simon Fraser University. During his Ph.D. he worked on the
evolution of centromeric DNA, RNA-RNA interaction prediction and
RNA folding problems. He then joined the Department of Genome
Sciences of the University of Washington as a postdoctoral fellow.
Since then his work includes computational prediction of human
genomic structural variation, and characterization of segmental
duplications and copy-number polymorphisms using next generation
sequencing data. More information in the Bioinformatics and
Computational Genomics Group webpage:
http://donut.cs.bilkent.edu.tr/index.htmland
http://www.researcherid.com/rid/D-2982-2009.