9–12 September 2019

Congress Center Basel

Programme Overview

Monday, 09 September 2019

09.00 – 16.00

16.45 – 18.00

Welcome and Opening lecture at the Basel Town Hall

Chair: Michael Hall(University of Basel, CH)

Lukas Engelberger (Basel Stadt, Basel, CH)

Opening Lecture - Climate Crisis: How much can we bear?
Thomas Stocker (University of Berne, Berne, CH)

18.00 – 19.00

Welcome reception

Tuesday, 10 September 2019

10.00 – 11.45


[BC]2 Plenary session 1: Single-cell data

Manfred Claassen (ETH Zurich, CH & SIB)
Mark Robinson (University of Zurich, Zurich, CH & SIB)

10.00 - 10.45
Joint analysis of heterogeneous single-cell dataset collections

Peter Kharchenko (Harvard Medical School, Boston, United States)

10.45 - 11.05
Uncertainty quantification in multivariate mixed models for mass cytometry data
Christof Seiler (Maastricht University, Maastricht, Netherlands)

11.05 - 11.25
Psupertime: supervised pseudotime inference for single cell RNA-seq data with sequential labels
Will Macnair (University of Zurich, Zurich, Switzerland) 

11.25 - 11.45
Hyperbolic geometry as a tool for analysis of complex hierarchies from single-cell data
Anna Klimovskaia (Facebook AI Research, Paris, France)

11.45 – 13.15

Lunch break

13.15 – 15.00

[BC]2 Plenary session 2: Evolutionary medicine

Anna-Sapfo Malaspinas (University of Lausanne, Lausanne, CH & SIB)
Richard Neher (University of Basel, Basel, CH & SIB)

13.15 - 14.00
Predicting antibiotic resistance
Roy Kishony (Israel Institute of Technology, Israel)

14.00 - 14.20
The next step for Nextstrain: tracking pathogen evolution and transmission
Emma Hodcroft (Biozentrum University of Basel & SIB Swiss Institute of Bioinformatics, Basel, Switzerland)

14.20 - 14.40
Comparative genomics of 1600 species reveals new insights regarding “superpowers”, breast cancer, and genetic diseases
Yuval Tabach (The Hebrew University-Hadassah Medical School, Jerusalem, Israel)

14.40 - 15.00
How pairwise coevolutionary models capture the collective residue variability in proteins
Pierre Barrat-Charlaix (University of Basel & Swiss Institute of Bioinformatics, Basel, Switzerland)

15.30 – 16.30

EMBO & [BC]² Flashtalks on the stage

Sven Bergmann (University of Lausanne, Lausanne, CH & SIB)
Philipp Bucher (EPFL, Lausanne, CH & SIB)

16.30 – 17.45

[BC]2 Session – SIB Bioinformatics Awards

16.30 - 16.55
SIB Early Career Bioinformatician Award

16.55 - 17.20
SIB Best Swiss Bioinformatics Graduate Paper Award

17.20 - 17.45
SIB Bioinformatics Resource Innovation Award

17.30 – 19.00

Networking event & Poster session for EMBO and [BC]2 Presenters

Sven Bergmann (University of Lausanne, Lausanne, CH & SIB)
Philipp Bucher (EPFL, Lausanne, CH & SIB)

Wednesday, 11 September 2019

09.00 – 09.45

[BC]2 Keynote lecture: Hidden Variables: quantifying our uncertainties in the analyses of human microbiome data

Susan Holmes (Stanford University, Stanford, USA)

Erik van Nimwegen (University of Basel, Basel, CH)
Niko Beerenwinkel (ETH Zurich, Zurich, CH & SIB)

10.00 – 11.45

[BC]2 Plenary session 3: Clinical population genomics

Zoltán Kutalik (CHUV, University of Lausanne, Lausanne, CH & SIB)
Matthew Robinson (University of Lausanne, Lausanne, CH & SIB)

10.00 - 10.45
From GWAS to Function: interpreting GWAS results in biological context

Danielle Posthuma (Vrije Universiteit (VU) Amsterdam & VU University Medical Center Amsterdam (VU), Amsterdam, NL)

10.45 - 11.05
Integrative haplotype estimation with sub-linear complexity
Olivier Delaneau (University of Lausanne, Lausanne, Switzerland)

11.05 - 11.25
Simultaneous estimation of heritability, genetic confounding, and bi-directional causal effect from GWAS summary statistics
Liza Darrous (University Center for Primary Care and Public Health, Lausanne, Switzerland)

11.25 - 11.45
Bayesian inference for large human medical genetic datasets
Daniel Trejo-Banõs (University of Lausanne, Lausanne, Switzerland)

11.45 – 13.15

Lunch break

13.15 – 15.00

[BC]2 Plenary session 4: Systems biology of disease

Giovanni Ciriello (University of Lausanne, Lausanne, CH & SIB)
Mihaela Zavolan (University of Basel, Basel, CH & SIB)

13.15 - 14.00
Cellular and clonal dynamics in humoral immunity
Thomas Kepler, Boston University School of Medicine, US

14.00 - 14.20
An ab-initio derivation of the Drosophila gap gene system from an optimization principle
Gasper Tkacik (IST Austria, Klosterneuburg, Austria)

14.20 - 14.40
Deciphering HLA-I motifs across HLA peptidomes improves epitope predictions and reveals novel properties of HLA-I molecules
David Gfeller (University of Lausanne, Lausanne, Switzerland)

14.40 - 15.00
Automated inference of Boolean dynamics from molecular interaction maps. Application on rheumatoid arthritis
Anna Niarakis (UEVE, Univ Paris-Saclay, Paris, France)

15.30 – 17.15

[BC]2 Plenary session 5: Multi-level data integration

Karsten Borgwardt (ETH Zurich, Zurich, CH & SIB)
Julia Vogt (University of Basel, Basel, CH & SIB)

15.30 - 16.15
Bayesian matrix factorization and deep learning data fusion for drug-target interaction prediction
Yves Moreau, KU Leuven, BE

16.15 - 16.35
Selected oral presentation

16.35 - 16.55
The molecular basis and genetic control of local gene co-expression
Diogo M. Ribeiro (University of Lausanne, Lausanne, Switzerland)

16.55 - 17.15
Automated analysis of large-scale NMR data generates metabolomic signatures and links them to candidate metabolites
Bita Khalili (UNIL, Lausanne, Switzerland)

17.15 - 17.30

Closing remarks

Thursday, 12 September 2019

09.00 – 10.15

Joint session [BC]2/EMBO

Plenary session 6: Computational biology, artificial intelligence and machine learning in precision medicine

Chair: Jan Korbel (Genome Biology Unit EMBL, Heidelberg, DE)

09.00 - 09.25
Machine learning approaches for elucidating complex gene-environment interactions
Oliver Stegle (European Bioinformatics Institute, Hinxton, UK)

09.25 - 09.50
Understanding chronic blood diseases using millions of electronic health records and single cell genomics
Amos Tanay (The Weizmann Institute of Science, Rehovot, ISR)

09.50 - 10.15
Pinpointing disease-causing regulatory genetic variants by multi-omics and machine learning
Julien Gagneur (Fakultät für Informatik, Technische Universität München, Munich, DE)

12.30 – 13.45

Lunch break

16.00 – 16.45