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Conference program

The program of the CIBB 2017 International Conference is out! Check it here!

Thursday, 7th September 2017

OPENING & REGISTRATION (9:00 - 9:30)
SESSION #1: Invited talk (9:30 - 10:30)
Manja Marz
Crosstalk between viruses and high-throughput technologies
COFFEE BREAK (10:30 - 11:00)
SESSION #2: Classification, Prediction & Exploration
11.00-11.25
Wojciech Wieczorek and Olgierd Unold.
GP-based grammatical inference for classification of amyloidogenic sequences
11.25-11.50
Marco Notaro, Max Schubach, Marco Frasca, Marco Mesiti, Peter N. Robinson and Giorgio Valentini.
Ensembling Descendant Term Classifiers to Improve Gene – Abnormal Phenotype Predictions
11.50-12.15
Samuele Fiorini, Federico Tomasi, Margherita Squillario and Annalisa Barla.
Adenine: a HPC-oriented tool for biological data exploration
12.15-12.40
Angela Serra, Maria Domenica Guida, Pietro Liò and Roberto Tagliaferri.
Multi-View patient sub-typing with a hierarchical block matrix based methodology
LUNCH BREAK (12:40 - 14:00)
SESSION #3: Modeling and simulation methods for Systems Biology and Systems Medicine (Chair: Chiara Damiani)
14.00-14.20
Daniele Ramazzotti, Alex Graudenzi, Giulio Caravagna and Marco Antoniotti.
Inference of temporal orderings for cumulative biological phenomena
14.20-14.40
Davide Maspero, Claudio Isella, Marzia Di Filippo, Alex Graudenzi, Sara Erika Bellomo, Marco Antoniotti, Giancarlo Mauri, Enzo Medico and Chiara Damiani.
Metabolic enrichment through functional gene rules
14.40-15.00
Antonia Perrella, Michele Sorelli, Leonardo Bocchi, Lorenzo Frassineti and Francesco Giardini.
Wavelet phase coherence between breathing and the microvascular pulse contour: a preliminary study
15.00-15.20
Valentina Mameli, Debora Slanzi and Irene Poli.
Evolutionary experimental design for optimization based on bootstrap group penalties regression models
15.20-15.40
Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, Marco Salvatore Nobile and Paolo Cazzaniga.
Estimation of kinetic reaction constants: exploiting reboot strategies to improve PSO’s performance
COFFEE BREAK (15:40 - 16:10)
SESSION #4: Inference & Learning
16.10-16.35
Teppei Shimamura, Yusuke Matsui, Taisuke Kajino, Satoshi Ito, Takashi Takahashi and Satoru Miyano.
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics
16.35-17.00
Marco Frasca, Jean Fred Fontaine, Giorgio Valentini, Marco Mesiti, Marco Notaro, Dario Malchiodi and Miguel Andrade-Navarro.
Disease–Genes must Guide Data Source Integration in the Gene Prioritization Process
SOCIAL EVENT (20.00 - 22.00)
Reception at "Ghetto Centro Comunale d'Arte e Cultura - Cagliari" (link)
Till midnight you can also enjoy the many events organized in the historical areas of Cagliari (program)


Friday, 8th September 2017

SESSION #5: Invited talk (9:40 - 10:40)
Alessandra Carbone
One-dimensional and three-dimensional protein spaces and protein evolution
COFFEE BREAK (10:40-11:10)
SESSION #6: En route to the synthesIs of artificial cells (Chair: Pasquale Stano)
11.10-11.30
Emiliano Altamura and Fabio Mavelli.
Towards the implementation of photo-autotrophic synthetic cells
11.30-11.50
Maria Raposo, Andreia Duarte, Paulo Gomes, Paulo Ribeiro, Marli Moraes and Roland Steitz.
Structural features of a DPPG liposome layer adsorbed on a rough surface
11.50-12.10
Andrea Antunes, Mardey S. Silva, Cristiano A. Guarany and Maria Raposo.
Investigation of thermal degradation of chitosan scaffolds
12.10-12.30
Pasquale Stano, Roberto Marangoni and Fabio Mavelli.
Lipid vesicles diversity and its role in free or immobilized synthetic cell populations models
LUNCH BREAK (12:30 - 14:00)
SESSION #7: Sequences, Variants and Mutations
14.00-14.25
German Tischler.
Haplotype and Repeat Separation in Long Reads
14.25-14.50
Ilio Catallo, Eleonora Ciceri, Stefania Stenirri, Stefania Merella, Paola Carrera and Sauro Vicini.
An open-source tool for managing time-evolving variant annotation
14.50-15.15
Veronica Tozzo and Annalisa Barla.
Cancer mutational signatures identification with sparse dictionary learning
COFFEE BREAK (15:15 - 15:45)
SESSION #8: Molecular docking & image processing
15.45-16.10
Yusuke Matsui, Satoru Miyano and Teppei Shimamura.
Tumor subclonal progression model for cancer hallmark acquisition
16.10-16.35
Mattia Gastaldello, Tiziana Calamoneri and Marie-France Sagot.
Extracting Few Representative Reconciliations with Host-Switches
16.35-17.00
Daniele Pepe and Tomasz Burzykowski.
The distribution equivalence problem in Mendelian randomization models
BUSINESS MEETING (17.00 - 18.00)


Saturday, 9th September 2017

SESSION #9: Invited talk (9:00-10:00)
Valentina Boeva
Identification of distinct neuroblastoma identity types through the analysis of transcriptomics and epigenetics data
COFFEE BREAK (10:00-10:30)
SESSION #10: on Molecular Communication (Chair: Pietro Liò)
10.30-10.48
Giordano Rampioni, Francesca D'Angelo, Alessandro Zennaro, Livia Leoni and Pasquale Stano.
Synthetic biology: exchanges of chemical signals between liposome-based cell-like compartments and biological cells as an approach to bio-chemical information and communication technologies
10.48-11.06
Peng He, Yuming Mao, Pietro Lio’, Qiang Liu and Kun Yang.
Co-channel Interference Analysis of Synaptic Channels in Molecular Communication
11.06-11.24
Luca Felicetti, Mauro Femminella and Gianluca Reali.
A nano communication system for CTC detection in blood vessels
11.24-11.42
Alessio Mancini, Filmon Eyassu, Maxwell Conway, Annalisa Occhipinti, Sandra Pucciarelli, Claudio Angione and Pietro Liò.
Tetrahymena thermophila, a complex ecosystem of organelles for studying multi compartment metabolism.
11.42-12.00
Pietro Liò and Andrea Bracciali.
Formal multi-scale analysis of comorbidity for predictive medicine
Tutorial (12.00-13.00)
Francesco Masulli
An Introduction to the Well-Being Technology
LUNCH BREAK (13:00 - 14:00)
SESSION #11: Evolution
14.00-14.25
Ahmad Husein Alkaff, Mochammad Arfin Fardiansyah Nasution and Usman Sumo Friend Tambunan.
Screening of Natural Products Conjugated to HIV-1 Tat peptide as Inhibitor of Ebola Virus Glycoprotein-Mediated Cell Entry through Flexible Molecular Docking Simulation
14.50-15.15
Majid Mohammad Sadeghi, Emin Kececi, Kerem Bilsel and Ayşe Aralaşmak.
Biomedical image processing software development for shoulder arthroplasty: Shoulderart
SESSION #12: k-mers and Alignments, NGS
15.15-15.40
Filippo Utro, Daniel Platt and Laxmi Parida.
A quantitative and qualitative characterization of k-mer based alignment-free phylogeny construction
15.40-16.05
Teresa Maria Rosaria Noviello, Antonella Di Liddo, Giovanna Maria Ventola, Salvatore D'Aniello, Antonietta Spagnuolo, Michele Ceccarelli and Luigi Cerulo.
Detecting long non-coding RNA orthology with n-gram similarity metrics
16.05-16.30
Federico Tomasi, Margherita Squillario, Alessandro Verri, Davide Bagnara and Annalisa Barla.
ICING: large-scale inference of immunoglobulin clonotypes
CLOSING (16.30-17.00)


Invited talks

Here you can find the list of the invited speakers of the CIBB 2017 International Conference. It also provides an abstract of their respective keynotes and a short bio.

Keynote 1: Identification of distinct neuroblastoma identity types through the analysis of transcriptomics and epigenetics data

Speaker: Valentina Boeva

Valentina Boeva is a group leader at the Institut Cochin/Inserm/CNRS, Paris. The research objective of her team is to understand the link between genetic and epigenetic changes in cancer and decipher the role of epigenetic modifications. Valentina and her group designed and implemented bioinformatics tools in two main areas: (i) Analysis of copy number alterations and structural variants in cancer genomes: FREEC/Control-FREEC, SVDetect, SV-Bay, ONCOCNV; and (ii) Analysis of ChIP-seq data: MICSA, HMCan, HMCan-diff and Nebula (link). The team also develops computational techniques for integration of high-throughput data applied to cancer research.


Abstract. Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neural crest cells (NCC). Neuroblastoma genomes are characterized by relatively few recurrent driver mutations. The most frequently mutated neuroblastoma-related gene, ALK, is found to be altered in less than 15% of cases at diagnosis. This scarcity of identified driver mutations in neuroblastoma leaves a possibility of the “driving” role of non-genetic, i.e. epigenetic changes in oncogenic processes of this pediatric cancer. Indeed, latest studies have demonstrated that tumorigenesis of many cancers is associated with considerable epigenetic modifications: changes in the chromatin states and DNA methylation. Changes in chromatin states in cancer include, in particular, formation of de novo enhancers and super-enhancers (i.e. long active chromatin regions encompassing tens of Kb and comprising a dozen of enhancer elements) and enhancer hijacking.

We analyzed the enhancer and super-enhancer landscape of neuroblastoma, integrated it with gene expression data and detected transcription factors that constitute the core neuroblastoma regulatory circuitries and drive expression of genes determining cell identity in neuroblastoma and affecting cell phenotype. For this study, we used 20 neuroblastoma cell lines and two patient-derived mouse xenografts. We demonstrated that integrative analysis of ChIP-seq profiles for the acetylation of lysine 27 of the histone H3 and gene expression data can point to the key transcriptional regulators of neuroblastoma. We also defined two neuroblastoma identity subtypes. To analyze ChIP-seq data we used a method we specifically develop to process ChIP-seq profiles generated from cancer cells: HMCan [Ashoor et al, 2013]. HMCan takes into account copy number alterations ubiquitously present in cancer cells; it also corrects for the library size and GC-content bias. To predict super-enhancer regions based on the H3K27ac profiles in cancer cell lines and xenograft samples we used our unpublished tool – LILY (boevalab.com/LILY/). LILY takes into account copy number alterations, which distort the H3K27ac signal in cancer cells, and provides accurate annotations of super-enhancers in regions of copy number loss and gain. To detect possible drivers of the super-enhancer landscape in neuroblastoma, motif discovery with the i-cisTarget method was applied to regions corresponding to valleys of H3K27ac peaks located in super-enhancers.

Keynote 2: Crosstalk between viruses and high-throughput technologies

Speaker: Manja Marz

Manja Marz got a Full Professorship for "High Throughput Sequencing Analysis" at the Friedrich Schiller University, Jena, and since 2015 she is a group leader at Leibniz Institute for Age Research – Fritz Lipmann Institute. She is also a founding and board member of FIFI (Fördervereinverein des Instituts für Informatik), and a board member of ZAJ (Aging Research Center Jena).
She is also a founding member of MSCJ (Michael Stifel Zentrum Jena for Data-Driven and Simulation Science) and a founding member of ZAJ (Aging Research Center Jena). From 2010 to 2012, she was also a group Leader of "RNA Bioinformatics" at Philipps-University, Marburg.


Abstract. In the last years we have witnessed both the emergence of new viral diseases (e.g. MERS, SARS) and the re-emergence of known diseases in new geographical areas (e.g. Zika, Dengue and Chikungunya). Virologists have traditionally concentrated on studying viruses that cause disease in humans, animals or plants. However, there has been estimated around 1031 viruses in the biosphere and only a minuscule fraction has been identified, yet. On the other hand, the power of new genome sequencing technologies, associated with new tools to handle “big data”, provide unprecedented opportunities to address fundamental questions in virology. We would like to emphasize that many of the common questions raised in virology require specific bioinformatics support and for the need to bring together the expertise of bioinformaticians and virologists.

For this mission, the European Virus Bioinformatics Center (EVBC) was founded on 8th March 2017 in Jena, Germany. The EVBC has about 100 founding members from over 50 research institutions distributed across 13 European countries. The EVBC is intended to bring together virologists and bioinformaticians across Europe and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. I will present first attempts to tackle with virus-specific programs open questions in (co- )phylogeny, high-throughput sequencing data analysis, virus detection, virus-host interaction, and host barriers .

Keynote 3: One-dimensional and three-dimensional protein spaces and protein evolution

Speaker: Alessandra Carbone

Alessandra Carbone is Distinguished Professor of Computer Science at UPMC and she has led the Analytical Genomics team since 2003 and is the director of the Department of Computational and Quantitative Biology since 2009. Her group works on computational problems concerning the functioning and evolution of biological systems. Mathematical methods coming from statistics and combinatorics, as well as algorithmic tools are employed to study fundamental principles of the cellular functioning starting from genomic data. The projects are all aimed at understanding the basic principles of evolution and co-evolution of molecular structures in the cell. They concern sequence evolution of entire genomes as well as protein evolution. Alessandra Carbone received the Prix Joliot-Curie in 2010 from the Ministère de la Recherche et de l’Enseignement Supérieur and from the EADS Foundation, and she was distinguished in 2012 with the Grammaticakis-Neuman Prize of the Académie des Sciences for "Integrative Biology". Since 2013 she is a senior member of the Institut Universitaire de France.


Abstract. Biology entered a new era, with computational biology producing biological data that are impossible nowadays to obtain with wet experiments. Tackling biological questions with advanced engineering, new computer algorithms and novel computational approaches is a challenge that will lead to revolutionize biology and medicine through deeper, ubiquitous use of DNA information.

A fundamental question is the extraction of evolutionary information from DNA sequences. We consider protein sequences here and we shall describe how a precise mapping between the one-dimensional representation of a protein (its sequence) and its three-dimensional representation (its structure) revealed important biological information on protein-protein binding sites and on mechanical and allosteric properties of proteins. Fine combinatorial readings of the conservation and co-evolution signals between residues in sequences can be used to identify protein- protein interaction (PPI) networks and describe them at the molecular level. In particular, these analyses apply to vertebrate and viral protein families.

PPI are at the heart of the molecular processes governing life and constitute an increasingly important target for drug design. Given their importance, it is vital to determine which protein interactions have functional relevance and to characterize the protein competition inherent to crowded environments. Suitable mathematical approaches appear necessary to properly address these questions and, in the talk, we shall highlight the new computational challenges.