HBio 2016 CONFERENCE AGENDA
November 18th, Friday (at CERTH)
Pre-Conference workshop
Theme: Tutorials
● 08:30-09:30 Registrations and coffee
● 09:30-11:00 Nikos Kyrpides ➧ Genome & Metagenome analysis with IMG
● 11:00-12.30 Claudine Médigue ➧ Genome annotation with MicroScope
● 12:30-13:30 Lunch Break
● 13:30-15:00 Alex Mitchell ➧ Introduction to EBI Metagenomics
● 15:00-15:15 Break
● 15:15-16:45 Folker Meyer ➧ Metagenome analysis with MG-RAST
● 16:45-17:00 Break
● 17:00-18:30 Victoria Newman ➧ Ensembl tutorial
● 19:00-22:00 Speakers dinner November 19th, Saturday (at NOESIS)
Theme: Systems 08:00-09:00 Registrations
09:00-10:15 HBio Welcome and Opening talks Chair: Zacharias Scouras and Lefteris Angelis 09:05-09:10 Maria Kollia-Tsaroucha (Minister for Macedonia and Thrace) 09:10-09:15 Ioannis Pantis (Secretary General, Ministry of Education) 09:15-09:20 Pericles Mitkas (Rector, AUTH) 09:20-09:30 Athanasios Konstantopoulos (Director General, CERTH) 09:30-09:45 Nektarios Nasikas (Ministry of Education, Res., & Rel. Affairs) 09:45-10:00 Georgios Chourdakis (Ministry of Education, Res., & Rel. Affairs) 10:00-10:05 Nikos Kyrpides, co-chair (DOE-JGI) 10:05-10:15 Christos Ouzounis, chair (CERTH)
10:15-10:30 Coffee break
10:30-12:30 Session 1: Genome Analysis Chairs: Ilias Kappas and Sofia Morfopoulou 10:30-11:00 Hans-Peter Klenk: Impact of genome analyses on taxonomy and systematics Challenges & problems in phylogenetic inference and bioinformatics 11:00-11:30 Alexandros Stamatakis : Challenges & problems in phylogenetic inference and bioinformatics 11:30-11:45 Lucas Czech: Do phylogenetic tree viewers correctly display support values? 11:45-12:00 Argyris Nicolaidis: A quantum approach to the DNA functioning 12:00-12:15 Stella Tamana: Standard operating procedure for computing compositionally biased pan-genomes 12:15-12:30 Panagiotis Ioannidis: Genomic features of the damselfly Calopteryx splendens, representing primitively-winged insect clades
12:30-13:30 Lunch
13:30-15:30 Session 2: Pathways & Networks Chairs: Ioannis Vizirianakis and Stella Tamana 13:30-14:00 Costas Maranas: Optimization methods in metabolic networks analysis and redesign 14:00-14:30 Osman Ugur Sezerman: Identification of disease related pathways in complex diseases using multi omics data 14:30-14:45 Theodora Farmaki: Cross-talk between proteostatic mechanisms and signaling pathways in plants 14:45-15:00 Charikleia Seitanidou: Integrative network analysis of lymphoma proteomics & transcriptomics data 15:00-15:15 Anastasia Politou: LBR over-expression upsets the transcriptional profile of mouse embryonic stem cells: implications for totipotency/pluripotency 15:15-15:30 Vasilis Promponas: A comparative and functional genomics approach for elucidating virulence determinants in Pseudomonas
15:30-16:15 Coffee break and Posters
16:15-17:45 Session 3: Community resources Chairs: Theodora Farmaki and Anastasios Chanalaris 16:15-16:45 Claudine Medigue: Accurate microbial genome annotation using an integrated system for community expertise of gene functions 16:45-17:15 Guy Cochrane: Sequence data handling: From global repository to local workbench 17:15-17:30 Michalis Aivaliotis: Analysis, visualization & integration of (prote)omics data 17:30-17:45 Christos Arvanitidis: Construction and operation of the LifeWatchGreece Research Infrastructure (ESFRI): examples of virtual laboratories
17:45-18:15 Group Photo (Main Entrance, Lobby)
18:15-18:30 Nektarios Tavernarakis: HBio-2017
18:30-20:00 Session 4: Role of Greek Bioinformatics in Elixir Roundtable discussion Chairs: Babis Savakis & Nektarios Tavernarakis (short introduction followed by discussion) Participants: ● Babis Savakis (Greece) ● Christos Ouzounis (Greece) ● Anna Tramontano (Italy) ● Guy Cochrane (UK) ● Claudine Medigue (France) ● Nikos Kyrpides (USA)
20:00-22:00 HBio Members Dinner (by invitation only) November 20th, Sunday (at NOESIS)
Theme: Omics 09:00-11:00 Session 5: Structural genomics Chairs: Anastasia Politou and Christos Arvanitidis 09:00-09:30 Anna Tramontano: The computational analysis of protein structures: the case of antibodies 09:30-10:00 Manuela Helmer Citterich: High-throughput analysis of RNA secondary structure: focus on protein-RNA interaction 10:00-10:15 Minos Matsoukas: A multi-pharmacophore virtual screening methodology and the discovery of novel compounds targeting pharmacological targets 10:15-10:30 George Papamokos: Linking QSAR and Mode of Action data to improve the prediction of carcinogens 10:30-10:45 Dimitrios Zisis: Comparison of computational methods for 4C-seq NGS data analysis 10:45-11:00 Kovacevic, Jovana: One structured output learning method for protein function prediction
11:00-11:30 Coffee Break
11:30-13:00 Session 6: Metagenomic Technologies Chairs: George Tsiamis and Nikos Kyrpides 11:30-12:00 Rob Finn: Shedding light on billions of metagenomics sequences: challenges, pitfalls and discovery 12:00-12:30 Folker Meyer: Metagenomic analysis — new requirements and resolutions for the next 5 years 12:30-12:45 Jacques Lagnel: HCMR HPC bioinformatics platform facilitates the marine and aquaculture genomics research in Greece (?) 12:45-13:00 Ilias Lagkouvardos: IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies
13:00-14:00 Lunch
14:00-16:00 Session 7: Metagenomic analysis Chairs: Vasilis Promponas and Michalis Aivaliotis 14:00-14:30 Pilar Francino: Microbial succession in the infant's gut 14:30-15:00 Kostas Konstantinidis : Beyond Ribosomal RNA genes: Community Tools for Analysis of Whole-Genomes and Metagenomes 15:00-15:15 Elias Asimakis: Identification of putative horizontal gene transfer events between B. cucurbitae and Wolbachia 15:15-15:30 Nikos Kyrpides: Uncovering Earth’s Virome 15:30-15:45 Sofia Morfopoulou: Metagenomics-based diagnostics for brain infections 15:45-16:00 Christos Ouzounis:Developing computational biology at Meridian 23º – eastwards
16:00-17:00 Coffee Break and Posters
17:00-19:00 Session 8: HBio Society Matters ● HBio Society overview ● HBio elections
20:00-22:00 HBio Committees Dinner (by invitation only)
November 21st, Monday (at CERTH)
Theme: Technologies
09:00-11:00 Session 9: Text mining & Ontologies Chairs: Pantelis Topalis and Giorgos Kotoulas 09:00-09:30 Fay Christodoulou : microRNAs as biomarkers: from literature buzz to clinical applications 09:30-10:00 George Garrity: Ground-truthing prokaryotic genomes 10:00-10:15 Anastasios Nentidis: BioASQ : A challenge in large-scale biomedical semantic indexing and question answering 10:15-10:30 Evangelos Pafilis: EXTRACT 2.0: interactive extraction of environmental and biomedical contextual information 10:30-10:45 Theodosios Theodosiou: Uniprot Related Documents (UniReD): Predict protein-protein interactions from PubMed documents relationships 10:45-11:00 Ioannis Vizirianakis: Harnessing pharmacological knowledge in the era of precision cancer therapeutics
11:00-11:30 Coffee Break
11:30-13:30 Session 10: Meta-analysis Chairs: Yiannis Kourmpetis and Ilias Lagkouvardos 11:30-12:00 John Ioannidis: Improving Reproducible Research Practices 12:00-12:15 Alexandros Kanterakis: MutationInfo: A tool to infer chromosomal positions from HGVS mutations 12:15-12:30 Anastasios Chanalaris: Utilising transcriptomics to understand post-traumatic osteoarthritis 12:30-12:45 Theodora Katsila: ePGA: An integrated electronic Pharmacogenomics Assistant for Personalized Medicine 12:45-13:00 Sophia Ananiadou : Bespoke text mining workflows based on federated tools: Applications in the biodiversity and metabolomics domains
13:00-14:00 Lunch
14:00-16:00 Session 11: Industrial applications Chairs: Ioannis Iliopoulos and Theodora Katsila 14:00-14:30 Nicolas Tsesmetzis: Unravelling the microbial subsurface conversions: A metagenomics perspective 14:30-15:00 Spiros Likothanassis: InSyBio- Suite: A Platform Identifying Biomarkers that Enable Personalized Medicine 15:00-15:15 Pantelis Angelidis: Bioinformatics Innovation Excellence in Greek SMEs 15:15-15:30 Stella Bezergianni: Towards Sustainable HEFAs for Aviation 15:30-15:45 Sarlikioti Vaia: Applications of hyperspectral remote sensing in agriculture 15:45-16:00 Yiannis Kourmpetis: The role of Bioinformatics in Patent Searching and Analytics
16:00-16:30 Coffee Break
16:30-17:30 Session 12: Bioinformatics as a growth engine for Greece Roundtable discussion Chairs: Christos Ouzounis & Pantelis Angelidis (short introduction followed by discussion) Participants: ● Pantelis Angelidis ● Christos Ouzounis ● Nicolas Tsesmetzis ● Yiannis Kourmpetis ● other sponsors
17:30-18:00 HBio-2017 Handoff, Closing Remarks and Awards List of Speakers
Speaker Affiliation Country
Aivaliotis, Michalis IMBB-FORTH Greece
Ananiadou, Sophia The University of Manchester UK
Angelidis, Pantelis Thessaloniki Innovation Zone Greece
Arvanitidis, Christos IMBBC-HCMR Greece
Asimakis, Elias University of Patras Greece
Bezergianni, Stella Institute of Applied Biosciences-CERTH Greece
Chanalaris, Anastasios University of Oxford UK
Chourdakis, Georgios Ministry of Education, Research & Religious Greece Affairs, Sector for Research &Innovation
Christodoulou, Fay Miroculus USA
Cochrane, Guy European Bioinformatics Institute UK
Czech, Loucas Heidelberg Institute for Theoretical Studies Germany
Farmaki, Theodora Institute of Applied Biosciences-CERTH Greece
Finn, Rob European Bioinformatics Institute UK
Francino, Pilar Center for Public Health Research Spain
Garrity, George Michigan State University USA
Helmer-Citterich, Manuela University of Rome Tor Vergata Italy
Ioannidis, John Stanford University USA
Ioannidis, Panagiotis University of Geneva Switzerland
Kanterakis, Alexandros Institute of Computer Science, FORTH Greece
Katsila, Theodora University of Patras Greece
Klenk, Hans-Peter Newcastle University UK
Konstantinidis, Kostas Georgia Institute of Technology USA
Kourmpetis, Yiannis Nestle Switzerland
Kovacevic, Jovana Belgrade University Serbia
Kyrpides, Nikos DOE Joint Genome Institute USA
Lagkouvardos, Ilias Technical University of Munich Germany
Lagnel, Jacques IMBBC-HCMR Greece Likothanassis, Spiros University of Patras Greece
Maranas, Costas Penn State University USA
Matsoukas, Minos University of Patras Greece
Medigue, Claudine CNRS & CEA France
Meyer, Folker Argonne National Laboratory USA
Mitchell, Alex European Bioinformatics Institute UK
Morfopoulou, Sofia University College London UK
Nasikas, Nektarios Ministry of Education, Research & Religious Greece Affairs, Sector for Research &Innovation
Nentidis, Anastasios NCSR Dimokritos Greece
Newman, Victoria European Bioinformatics Institute UK
Nicolaidis, Argyris Physics Department, University of Thessaloniki Greece
Ouzounis, Christos CREPI, CERTH Greece
Pafilis, Evangellos IMBBC-HCMR Greece
Papamokos, Georgios University of Ioannina Greece
Politou, Anastasia University of Ioannina Greece
Potamias, George Institute of Computer Science, FORTH Greece
Promponas, Vasilis University of Cyprus Cyprus
Sarlikioti, Vaia Gamaya Switzerland
Savakis, Charalambos BSRC Alexander Fleming Greece
Seitanidou, Charikleia IMBB-FORTH Greece
Sezerman, Osman Ugur Acibadem University Turkey
Stamatakis, Alexandros Heidelberg Institute for Theoretical Studies Germany
Tamana, Stella University of Cyprus Cyprus
Tavernarakis, Nektarios IMBB-FORTH Greece
Theodosiou, Theodosios TETRAKTYS INTELLIGENCE Greece
Tramontano, Anna Sapienza University Italy
Tsesmetzis, Nicolas Shell International USA
Vizirianakis, Ioannis Aristotelian University of Thessaloniki, School of Pharmacy Greece
Zisis, Dimitrios Institute of Plant Genetics, Polish Academy of Sciences Poland