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 ➧ 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 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 () ● 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

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