Scientific Program

Scientific Program


21 May, 2013

9:00 - 12:30 Workshop on Variathon v0.1

Participants can attend the Workshop for free. More information can be found at http://bioinf.dimi.uniud.it/variathon/workshop. In case of participation, please send an e-mail to fnadalin@appliedgenomics.org.

13.00 - 14:00 Registration and poster hang-up
14.00 - 14:20 Welcome

Prof. Furio Honsell (mayor of Udine)
Prof. Leonardo Alberto Sechi (pro-rector University of Udine)
Prof. Raffaele Testolin (president of the Institute of Applied Genomics)

14:20 - 15:10 Keynote Lecture - Preparata Lecture

Mauno Vihinen
Accurate prediction of pathogenic variants - preliminaries and requirements

15:10 - 15:50 Joint Session with Variathon Workshop

Sirén J, Välimäki N, Longi K, Mäkinen V
Indexing Graphs for Path Queries with Applications in Genome Research

Cereda M, Peterlongo P, Radice P, Barile M, Bonanni B, Ciccarelli FD
Identification of variants associated with risk for familial breast cancer using whole exome sequencing 

16:10 - 16:20 Coffee break
16:20 – 16:40 Session - Genomics

De Pascale F, Vezzi A, Telatin A, Corteggiani Carpinelli E, Schiavon R, Valle G
NGS Linkage Mapping

16:40 – 18:20 SPECIAL SESSION - Algorithmic and statistical analysis of high throughput sequencing data

Highlight Lecture: Alberto Apostolico
Algorithmic Challenges in NGS

Kishore K, Ronchi A, Lister R, Ecker JR, Pelizzola M
methylPipe: an R package for the integrative analysis of DNA methylation data 

Zammataro L, DeMolfetta R, Ceol A, Muller H
Classification of human cancer samples from somatic mutation spectra 

Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A
EricScript to identify gene fusions in paired-end RNA-seq data 

Magi A, Tattini L, Benelli M, Palombo F, Pippucci T
H3M2: a novel algorithm for the detection of Runs of Homozygosity from second generation sequencing data 

18:30 BITS - Members Assembly


22 May, 2013

8:30 - 9:00 Poster hang-up
09.00 - 09.50 Keynote Lecture

Alvis Brazma
Using high-throughput sequencing to understand human transcriptome

09.50 - 10.30 Poster session (with coffee)
10.30 - 11.50 Session - Transcriptomics

Merella S, Stupka E, Provero P
Statistical methods for the analysis of gene expression in family studies of genetic and complex disease

Picardi E, Pesole G
REDItools: efficient detection of RNA editing changes by deep sequencing data

Riccardo F, Arigoni M, Iezzi M, Buson G, Longo DL,  Carrara M, Fiore A, Calogero RA, Quaglino E and Cavallo F
Characterization of a genetic mouse model of lung cancer: a promise  to identify oncoantigens associated with different stages of NSCLC progression

Martini P, Sales G, Chiogna M, Romualdi C
timeClip: viewing the pathway along time

11.50 - 12.50 Discussion: Training and education in bioinformatics within Italian universities
12.50 - 13:50 Lunch
13.50 - 14.30 Session - Systems Biology

Ollino L, Caselle M, Bussolino F, Cora' D.
CircuitsDB_2: integrating lncRNAs into the cancer genes regulatory network

Cordero F, Slyskova J, Naccarati A, Pardini B, Korenkova V, Levy M, Pitule P, Buchler T, Paparella A, Vodicka P
Systems biology strategies to address DNA repair dynamics in colorectal cancer patients

14:30 - 15:40 SPECIAL SESSION - Multicellular and Multiscale Models of Biological Systems

Highlight Lecture: Marco Scianna
Multiscale developments of the cellular Potts model

Di Stefano M, Rosa A, Belcastro V, di Bernardo D, Micheletti C
Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19

Graudenzi A, Caravagna G, De Matteis G, Antoniotti M
Investigating intestinal crypt homeostasis through multiscale modeling 

Short discussion with all speakers 

15:40 - 16:10 Poster session (with coffee)
16:10 - 16:30 Session - Molecular Evolution

Simone D, Bay DC, Turner RJ
Evolution of the TatC protein family

16:30 - 17:30 Session - Algorithms for Bioinformatics

Falda M, Fontana P, Barzon L, Toppo S, Lavezzo E
keeSeek: a tool for distant k-mer generation

Del Fabbro C, De Paoli E, Prezza N, Celii M, Morgante M, Policriti A
ERNE-BS5: Aligning BS-treated sequences by multiple hits on a 5-letters alphabet

Cangelosi D, Muselli M, Parodi S, Blengio F, Koster J, Schramm A, Gambini C and Varesio L
Data discretization and Logic Learning Machine defined a novel simplified gene expression signature improving Cancer Patients. Outcome prediction

17:40 - 20:00 Social tour
20:00 - 23.00 Social Dinner (at Hotel Astoria, in the historical centre)


23 May, 2013

09.00 - 09.50 Keynote Lecture

Mario Caccamo Sarah Ayling
De novo assemblies for complex crop genomes 

09.50 - 10.20 Poster session (with coffee)
10.20 - 12.30 SPECIAL SESSION - Protein-protein interactions joint to Session: Protein structure and function

Highlight Lecture: Guido Capitani
Protein interface classification by evolution and geometry: principles and applications

Carlon A, Eduati F, Di Camillo B, Toffolo G
A comprehensive rule-based model of insulin signaling pathway

Walsh I, Sirocco F, Minervini G, Di Domenico T, Ferrari C, Tosatto SCE
Mining and automatic classification of repeat protein structures with RAPHAEL

Vangone A, Cavallo L, Oliva R
CONSRANK: ranking multiple docking solutions based on the conservation of inter-residue contacts

Alocci D, Bernini A, Spiga O, Niccolai N
Atom depth analysis delineates mechanisms of protein intermolecular interactions

Round Table - discussion with Chairs and speakers

12.30 - 13.00 Discussion: BITS Regional Meetings
13.00 - 14.00 Lunch 
14.00 - 14:40 Session - Next Generation Sequencing

Palluzzi F, Venco F, Dahal S, Masseroli M, Ceri S
Integration Oriented Modelling of Next Generation Sequencing Data

Marinoni A, Rizzo E, Limongelli I, Gamba P, Bellazzi R
A kinetic information model to classify NGS short reads by their allele origin

14.40 - 15.00 Closing remarks and announcements of Awards
15.00 - 17.00 Tutorial

Bud Mishra
Prometheus Bound: From Genomics to Stringomics

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