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Hellenic Bioinformatics 10 Hellenic Bioinformatics 10 AGENDA + ABSTRACTS HB-10 6-9 SEPTEMBER, 2017 HERAKLION, GREECE CONTENS CONFERENCE ANNOUNCEMENT Page 2 CONFERENCE POSTER Page 3 PRE-CONFERENCE WORKSHOPS Page 4 PRE-CONFERENCE TUTORIALS AND OPENING SESSION Page 5 ORGANIZERS Page 6 INVITED SPEAKERS Page 7 CONFERENCE AGENDA BY NUMBERS Page 8 CONFERENCE AGENDA AT A GLANCE Page 9 CONFERENCE AGENDA Page 11 SPONSORS Page 16 SPEAKER ABSTRACTS Page 17 POSTER ABSTRACTS Page 63 AUTHOR INDEX Page 79 HB-10 1 HB-10 The 10th Conference of Hellenic Bioinformatics September 6-9, 2017 Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH) Heraklion, Crete, Greece Bioinformatics and its applications in Health, Biodiversity and the Environment about Elixir • biodiversity • bioinformatics • bioprospecting • computational biology • enzyme discovery • genomics • metabolic engineering • microbiome • pharmacogenomics • phylogeny • structural genomics • synthetic biology • systems biology • text mining • functional proteomics HB-10 2 HB-10 3 PRE-CONFERENCE WORKSHOPS Tuesday, September 5, 2017 Hall Alkiviades Payatakis Chair Michalis Aivaliotis 08:30-09:00 Registration & Coffee Workshop I Proteomics Workshop – Hands-on Proteomics Bioinformatics: From raw MS-data to knowledge Chair: Michalis Aivaliotis Michalis Aivaliotis: Introduction to proteomics 09:00-09:15 o Brief history of MS-based proteomics o State-of-the-art proteomics M. Aivaliotis, N. Kountourakis, K. Psatha, C. Seitanidou: Bioinformatics I – MS-Raw data processing 09:15-10.30 o Proteome Identification and quantitation using commercial available and free bioinformatic platforms Functional proteome annotation o Quality control and filtering of proteomics data M. Aivaliotis, N. Kountourakis, K. Psatha, C. Seitanidou: Bioinformatics II – Meta-data analysis and visualization o Comparative proteomics analysis 10:30-13:00 o Functional proteome annotation o GO terms and pathways enrichment analysis o Protein-protein interaction networks o Visualization of proteomics data 13.00-14.00 ☕ Coffee break Workshop II RNA-Seq and ChIP-Seq data analysis – Hands-on Advanced RNA-Seq and ChIP-Seq data analysis – Hands-on Chair: Pantelis Topalis Pantelis Topalis: Introduction to RNA-Seq and ChIP-Seq 14:00-14:15 o Experimental Design and Data analysis o Quality Control P. Topalis, E. Dialynas, G. Papagiannakis: RNA-Seq Data Analysis o De novo transcriptome assembly 14:15-16:00 o Differential Gene Expression o Everything you always wanted to know about batch effects P. Topalis, E. Dialynas: ChIP-Seq Data Analysis o Peak finding (Transcription Factors, Histone modifications, Super Enhancers) 16:00-18:00 o Irreproducible Discovery Rate (IDR) pipeline o Peak annotation Important Notes: - Number of maximum participants 35. - A digital textbook and references will be provided to all participants in advance. - All the participants need to have their own laptops. No computers will be provided by the organizers HB-10 4 PRE-CONFERENCE TUTORIALS & OPENING SESSION Wednesday, September 6, 2017 Hall Orfanoudakis Chair Alexandros Stamatakis 08:30-09:00 Registration & Coffee Session I Metagenomics Chair: Folker Meyer 09:00-10:30 Alex Mitchell ➧ Introduction to EBI Metagenomics 10:30-11.00 ☕ Coffee break Folker Meyer ➧ MG-RAST version 4.0 This tutorial will demonstrate the features of MG-RAST v4.0 for data management and 11:00-12:30 process as well as analysis. Depending on the time available the tutorial can include cmd-line as well as web interface components. The tutorial will cover metagenome, metatranscriptome and amplicon metagenome analysis. 12.30-13.30 ☕ Coffee break Session II Phylogenomics Chair: Alexandros Stamatakis Alexandros Stamatakis ➧ Phylogenomic inference methods: inferring species trees from 13:30-15:00 whole-genome alignments 15:00-15:30 ☕ Coffee break Bastien Bousseau ➧ Reconciliation methods: interpreting gene trees given species 15:30-17:00 trees 17:00-17:30 ☕ Coffee break and end of Tutorials OPEN SESSION Session III Data Integrity Chair: Vasiliki Petousi Co-organized by project DEFORM (H2020) 18:00-18:30 Ioannis Ioannidis ➧ Predating data: Integrity of methods and statistics Gemma Galdon Clavell ➧ Misconduct and data: privacy, accountability and responsibility in 18:30-19:00 (big) data in social science Nektarios Tavernarakis ➧ The European Research Council position on Data Integrity and 19:00-19:30 Scientific Misconduct 19:30-20:00 Discussion 20::00-22:00 Reception / Conference Gala dinner HB-10 5 HB-10 ORGANIZERS PRESIDENT VICE PRESIDENT Ioannis Iliopoulos Michalis Aivaliotis Faculty of Medicine, IMBB, FORTH University of Crete SCIENTIFIC PROGRAM COMMITTEE Ioannis Vasilis Michalis Iliopoulos Promponas Aivaliotis University of University of IMBB, FORTH Crete Cyprus Nikos Kyrpides Ilias Kappas Christos DOE Joint Aristotle Ouzounis Genome University of CPERI, Institute, USA Thessaloniki CERTH ORGANIZING COMMITTEE • Michalis Aivaliotis, Greece • Christos Ouzounis, Greece • Sophia Ananiadou, UK • Evangelos Pafilis, Greece • Christos Arvanitidis, Greece • Pavlos Pavlidis, Greece • Ioannis Iliopoulos, Greece • Yiota Poirazi, Greece • Dimitris Kafetzopoulos, Greece • George Potamias, Greece • Ilias Kappas, Greece • Vasilis Promponas, Cyprus • Christos Karapiperis, Greece • Alexandros Stamatakis, Germany • George Kotoulas, Greece • Nektarios Tavernarakis, Greece • Yiannis Kourmpetis, Switzerland • Pantelis Topalis, Greece • Nikos Kyrpides, USA • Ioannis Tsamardinos, Greece • Tereza Manousaki, Greece • George Tsiamis, Greece • Christophoros Nikolaou, Greece • Ioannis Vizirianakis, Greece LOCAL ORGANIZING COMMITTEE • Christos Arvanitidis • Anastasis Oulas • Anastasis Chalanaris • Evaggelos Pafilis • Emmanouil Dialinas • Eleftherios Panteris • Ioannis Grigoriadis • Nikolas Papanikolaou • Nikolaos Grigoriadis • Charikleia Seitanidou • John Kouklinos • Theodosis Theodosiou HB-10 6 HB-10 INVITED SPEAKERS Daniele Daffonchio, Rob Finn, KAUST, Saudi Arabia EBI, UK Maria Pilar Francino, Carolin Frank, CSISP, Spain UC Merced, USA Lars Jensen, John Ioannidis, University of Copenhagen, Stanford University, USA Denmark Peter Karp, Yiota Poirazi, SRI, USA IMBB, Greece Daniel Lundin, Hector-Garcia Martin, SciLifeLab, Sweden Joint Bioenergy Institute, USA Folker Meyer, Yves Moreau, Argonne National Laboratory, University of Leuven, Belgium USA Periklis Papadopoulos, Evangelia Petsalaki, San Jose State University, USA EBI, UK Panos Roussos, Lynn Schriml, Mount Sinai, NY, USA University of Maryland, USA Ewa Szczurek, David Ussery, University of Warzawa, Poland University of Arkansas, USA Alfonso Valencia, Eleftheria Zeggini, Spanish National Cancer Sanger Center, UK Research Centre, Spain HB-10 7 HB-10 CONFERENCE AGENDA BY NUMBERS CONFERENCE STRUCTURE 5 KEYNOTES 11 SESSIONS 1 ROUND TABLE 1 SOCIETY ALL HANDS MEETING CONFERENCE VIEW BY SPEAKERS KEYNOTE SPEAKERS 5 INVITED SPEAKERS 15 SPEAKERS SELECTED FROM ABSTRACTS 25 SPEAKERS BY COUNTRY 1. GREECE 21 2. USA 11 3. UK 3 4. CYPRUS 2 5. SPAIN 2 6. BELGIUM 1 7. DENMARK 1 8. GERMANY 1 9. POLAND 1 10. SAUDI ARABIA 1 11. SWEDEN 1 HB-10 8 HB-10 CONFERENCE AT A GLANCE Thursday, September 7, 2017 THEME: HEALTH John Ioannidis, Stanford University, USA Keynote 1 Title: Credibility and utility of big data Session 1 Medical Genomics Eleftheria Zeggini, Sanger Center, UK Title: Progress in understanding the genomic etiology of osteoarthritis Evangelia Petsalaki, EBI, UK Title: Integrative study of the role of RhoGAP/GEFs in the Rho protein signaling network Session 2 Neuro-Genomics Panos Roussos, Mount Sinai, NY, USA Title: Big Data Analysis and Genetic Liability to Common Neuropsychiatric Traits Yiota Poirazi, IMBB, Greece Title: Learning and remembering with dendrites: lessons from computational models Session 3 Cellular Networks and Modeling Ewa Szczurek, University of Warsaw, Poland Title: Statistical and mathematical models in computational oncology Hector-Garcia Martin, Joint Bioenergy Institute, USA Title: Mathematical modeling of -omics data for biofuel production through synthetic biology Session 4 Roundtable: Role of Greek Bioinformatics in Elixir Alfonso Valencia, Spanish National Cancer Research Centre, Spain Keynote 2 Title: Networks based approaches in epigenomics, evolution and biomedicine Friday, September 8, 2017 THEME: ENVIRONMENT Peter Karp, SRI, USA Keynote 3 Title: The Omics Dashboard for Interactive Exploration of High-Throughput Data Session 5 Human Microbiome HB-10 9 Lynn Schriml, University of Maryland, USA Title: GSC metadata standards in action: MetaSUB and ISD Maria Pilar Francino, CSISP, Spain Title: Microbiota development in the gut of infants, children and adolescents Session 6 Computational Metagenomics Folker Meyer, ANL, USA Title: A novel pipeline for high quality amplicon analysis integrated into MG- RAST Rob Finn, EBI, UK Title: Expanding the scope and reproducibility of analysis in EBI metageno- mics Session 7 Environmental Microbiome Daniele Daffonchio, KAUST, Saudi Arabia Title: Soil development and rhizosphere effect in a High Arctic desert chronosequence Carolin Frank, UC Merced, USA Title: Nitrogen fixation by the foliar conifer microbiome Session 8 Society Matters Saturday, September 9, 2017 THEME: BIODIVERSITY Yves Moreau, Leuven, Belgium Keynote 4 Title: Bayesian matrix factorization with side information and application to drug-target activity prediction Session 9 Phylogenomics Daniel Lundin, SciLifeLab, Sweden Title: The evolution of ribonucleotide reduction Session 10 Comparative Genomics David Ussery, University of Arkansas,
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