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 Mdigue 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 Earths Virome
15:30-15:45 Sofia Morfopoulou: Metagenomics-based diagnostics for brain
infections
15:45-16:00 Christos Ouzounis:Developing computational biology at Meridian
23 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