Challenges in Data-Driven Genomic Computing

Workshop in Como, Villa del Grumello – March 6-8 2019

Organized by the Advanced ERC Project 693174 “GeCo” – data-driven Genomic Computing

The Workshop brings together researchers who are contributing to genomic computing from different perspectives, combining computer science, biology and medical science, with a strong interdisciplinary approach. Participants are hosted in the historical Villa Grumello, facing lake Como, for three intense days of presentations and discussions.  The workshop takes place at halfway of the five-year Advanced ERC Project “data-driven Genomic Computing” (GeCo); it provides to the GeCo group at Politecnico di Milano an opportunity for consolidating existing collaborations or starting new ones.




Wednesday, March 6

9:30 – Welcome Coffee

10:00 – 13:00 Session 1:  Foundations of Genomic Computing

10:00 Val Tannen (University of Pennsylvania) – Language design and data provenance

10:45 Stefano Ceri (Politecnico di Milano) – Data and language abstractions in GeCo

11:15 Pietro Pinoli, Luca Nanni, Marco Masseroli (Politecnico di Milano) – GMQL in action to solve biological and clinical problems

12:15 Limsoon Wong (National University Singapore): Towards a new language for genomic computing

12:30 General discussion

13:00 Lunch

14:15 – 18:00 Session 2: Biological and Cancer Applications for Genomics

14:15 Giovanni Ciriello (University Lausanne) and Elisa Oricchio (EPFL) – Exploring cancer genomes in 3D

15:00 Colin Logie (Univ. Neijmegen) – Epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages

15:30 Cliff Meyer (Harvard University) – Determinants of transcription factors regulatory range

Coffee Break

16:30 Giulio Pavesi (Univ. Statale Milano) – Long-distance enhancer-promoter interactions

17:00 Rosario Piro (Free University Berlin) – Identification of the mutational signatures active in individual cancers

17:30 Limsoon Wong (National University Singapore) – From bewilderment to enlightenment in cancer research… hopefully?


Thursday, March 7

9 – 13:30 Session 3: Genomics for Personalized Secondary Prevention and Prognosis in Cancer

9:00 Stefano Ceri: Welcome

9.15 Giovanni Apolone (Istituto Nazionale Tumori) – Keynote on personalized secondary prevention and prognosis in cancer

10:00 Nadia Zaffaroni (Istituto Nazionale Tumori) – Prostate Cancer: identification of biomarkers discriminating indolent from aggressive tumors to improve the selection of patients suitable for active surveillance

10:30 Mattia Boeri (Istituto Nazionale Tumori) – Lung Cancer: Circulating microRNAs for early lung cancer detection

Coffee Break

11:30 Sergio Marchini (Istituto Mario Negri) – Ovarian Cancer: An integrated signature classifier for stage 1 epithelian ovarian cancer

12:00 Isabella Castiglioni (CNR/Bicocca) – Radiomics and radiogenomics for cancer

12:30 Paolo Verderio (Istituto Nazionale Tumori) – On data quality for omics datasets

13:00 Maddalena Fratelli (Istituto Mario Negri) – Beyond canonical gene expression in transcriptomics

13:30 Lunch

14:30 – 16:30 Session 4 – Parallel groups on Prostate, Lung, Ovarian cancer (with participation of expert clinicians/bioinformatics from the three cancer types) + other special interests groups — using the entire Villa for “spontaneous / semi-organized” groups.

17:00 Wrap-up: short summaries from the groups

17:30 Social Program

Transfer to funicolare Como-Brunate, meet at the basis at 18:30 and catch the train running up, then walk about 30-40 mins (150 meters up) to vista point and “Locanda del dolce basilico” – if needed or bad weather we’ll arrange a bus for 18 people, the rest will be brave walkers. To inspire the walk, it was done in a rainy day some 30 years ago with three perspective ACM Turing Awards: Barbara Liskov, Jim Gray, Mike Stonebraker.

19:30-22:00 Dinner

22.00 – walk down to catch the last train to Como at 22:30 (alternative – pleasant walk along the street, digesting food & drinks).

Friday, March 8

10:00 – 13:00 Session 5: (Big) Data Challenges

10:00 Angelos Anadiotis (EPFL) – Thinking “big” in science and genomics

10:30 Jan Ramon Troncoso-Pastoriza (EPFL) – Responding to the security and privacy challenges raised by precision medicine

Coffee Break

11:30 Anna Bernasconi, Arif Canakoglu (Politecnico di Milano) – Metadata reconciliation in genomics

12:00 Sara Foresti (Univ. Statale Milano) – Data protection abstractions in genomics

12:30 Raffaele Calogero (Univ. Torino) – A path to moderate the reproducibility in bioinformatics

13:00 Enzo Medico (Univ. Torino) – 3D big data interactive visualization for cancer genomics and precision medicine

13:30 Lunch

14:30 – 17:00 Session 6: Research challenges in genomics

ALL: Gong show: 5 minutes and max one slide, responding to the question: “what is most exciting in data-driven genomics?”

17:00 – PhD OralStefano Perna