Big Data in Molecular Medicine

This year’s thematic focus is on the use of big data in molecular medicine. The conference will feature presentations of latest research results, workshops, tutorials, poster sessions, and keynote lectures by international experts providing a prime opportunity to learn about cutting-edge research in computational biology and bioinformatics, and to network with other members of our community.

The main [BC]2 conference will take place September 10-11 at the Congress Centre in Basel as an integral part of the BASEL LIFE congress, giving [BC]2 attendants access to all of BASEL LIFE’s activities, including the EMBO conference. The [BC]2 workshops and tutorials are on Monday, September 9 at the University of Basel.

[BC]2 at BASEL LIFE is organized by the SIB Swiss Institute of Bioinformatics. The scientific committee is chaired by Erik van Nimwegen (University of Basel & SIB) and Niko Beerenwinkel (ETH Zurich & SIB). All members of the scientific committee are Group Leaders at SIB.


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The registration for [BC]2 has to be performed via the Basel Life registration platform. The registration gives access to all pillars of Basel Life and allows particpants to not only attend the [BC]2 conference, but to also join all other sessions of the Basel Life congress.


  Students (incl. PhD)  Academic and industry 

Early bird registration
until 12 Jun

190 CHF 300 CHF
Intermediate registration
13 Jun - 15 Aug
230 CHF 370 CHF
Late registration
16 Aug - 12 Sep
270 CHF 470 CHF
Daycards 100 CHF 160 CHF
Tutorials and workshops 120 CHF 120 CHF
Opening ceremony 60 CHF 60 CHF


Programme Overview 


Download a PDF version of the programme here.


Monday, 09 September 2019

09.00 - 16.00: Tutorials and workshops at the University of Basel


  • T1: Using the Ensembl REST APIs to programmatically access genomic data. More details
  • T2: Genomic epidemiology and phylodynamics with Nextstrain. More details
  • T3: Introduction to Machine Learning: opportunities for advancing omics data analysis. More details
  • T4: Interpretability for deep learning models in computational biology. More details
  • T5: Bioinformatics Pipelines for the Analysis of Viral NGS Data. More details
  • T6: Introduction to research data management with openBIS. More details
  • T7: Analysis of multi-sample multi-condition scRNA-seq datasets. More details


  • WS1: EMBO Young Investigator Workshop on Evolutionary and Computational Biology. More details
  • WS2: Annotation and curation of computational models in biology. More details

16.45 - 18.00: Opening lecture at the Basel Town Hall

  • 16.45 - 17.00
    Lukas Engelberger
    , Basel Stadt, CH
  • 17.00 - 18.00
    Thomas Stocker
    , University of Bern, CH
    "Climate Crisis: How much can we bear?"

18.00 - 19.00: Welcome reception


Tuesday, 10 September 2019

10.00 - 11.45: Single-cell Data plenary session
Chairs: Manfred Claassen (ETH Zurich & SIB), Mark Robinson (University of Zurich & SIB)

  • 10.00 - 10.45 (Keynote lecture)
    Peter Kharchenko, Harvard Medical School, US
    "Joint analysis of heterogeneous single-cell dataset collections"
  • 10.45 - 11.05
    Christof Seiler,
    Maastricht University, NL
    "Uncertainty Quantification in Multivariate Mixed Models for Mass Cytometry Data"
  • 11.05 - 11.25
    Will Mcnair,
    University of Zurich & SIB, CH
    "psupertime: supervised pseudotime inference for single cell RNA-seq data with sequential labels"
  • 11.25 - 11.45
    Anna Klimovskaia,
     Facebook AI Research, FR
    "Hyperbolic geometry as a tool for analysis of complex hierarchies from single-cell data"

11.45 - 13.15: Lunch break

13.15 - 15.00: Evolutionary Medicine plenary session
Chairs: Anna-Sapfo Malaspinas (University of Lausanne & SIB), Richard Neher (University of Basel & SIB)

  • 13.15 - 14.00 (Keynote lecture)
    Roy Kishony,
    Israel Institute of Technology, IL

    "Predicting antibiotic resistance"
  • 14.00 - 14.20
    Emma Hodcroft,
    University of Basel & SIB, CH
    "The Next Step for Nextstrain: Tracking Pathogen Evolution and Transmission"
  • 14.20 - 14.40
    Yuval Tabach
    , The Hebrew University, IL
    "Comparative genomics of 1600 species reveals new insights regarding 'superpowers', breast cancer, and genetic diseases"
  • 14.40 - 15.00
    Pierre Barrat-Charlaix,
     University of Basel & SIB, CH
    "How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins"

15.00 - 15.30: Coffee break

15.30 - 16.30: [BC]2 & EMBO poster flash talks
Chairs: Sven Bergmann (University of Lausanne & SIB), Philipp Bucher (EPFL & SIB)

For a detailed list of all flash talk presenters and titles, please click here.

16.30 - 17.45: SIB Bioinformatics Awards ceremony

  • 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: Poster session and networking apéro


Wednesday, 11 September 2019

09.00 - 09.45: [BC]2 keynote lecture
Chairs: Erik van Nimwegen (University of Basel & SIB), Niko Beerenwinkel (ETH Zurich & SIB)

  • 09.00 - 9.45 (Keynote Lecture)
    Susan Holmes
    , Stanford School of Medicine, US

    "Hidden Variables: quantifying our uncertainties in the analyses of human microbiome data"

10.00 - 11.45: Clinical Population Genomics plenary session
Chairs: Zoltán Kutalik (CHUV, University of Lausanne & SIB), Matthew Robinson (University of Lausanne & SIB)

  • 10.00 - 10.45 (Keynote lecture)
    Danielle Posthuma
    , Vrije Universiteit Amsterdam, NL
  • 10.45 - 11.05
    Olivier Delaneau,
    University of Lausanne & SIB, CH
    "Integrative haplotype estimation with sub-linear complexity"
  • 11.05 - 11.25
    Liza Darrous,
     University Center for Primary Care and Public Health Lausanne & SIB, CH
    "Simultaneous Estimation of Heritability, Genetic Confounding, and Bi-directional Causal Effect from GWAS Summary Statistics"
  • 11.25 - 11.45
    Daniel Trejo-Banõs,
    University of Lausanne & SIB, CH
    "Bayesian inference for large human medical genetic datasets"

11.45 - 13.15: Lunch break

13.15 - 15.00: Systems Biology of Disease plenary session
Chairs: Giovanni Ciriello (University of Lausanne & SIB), Mihaela Zavolan (University of Basel & SIB)

  • 13.15 - 14.00 (Keynote lecture)
    Thomas Kepler
    , Boston University School of Medicine, US

    "Cellular and clonal dynamics in humoral immunity"
  • 14.00 - 14.20
    Gasper Tkacik,
    IST Austria, AT
    "An ab-initio derivation of the Drosophila gap gene system from an optimization principle"
  • 14.20 - 14.40
    David Gfeller,
    University of Lausanne & SIB, CH
    "Deciphering HLA-I motifs across HLA peptidomes improves epitope predictions and reveals novel properties of HLA-I molecules"
  • 14.40 - 15.00
    Anna Niarakis,
    Université Evry Val-d'Essonne & Université Paris-Saclay, FR
    "Automated inference of Boolean dynamics from molecular interaction maps. Application on Rheumatoid Arthritis."

15.00 - 15.30: Coffee break

15.30 - 17.15: Multi-level Data Integration plenary session
Chairs: Karsten Borgwardt (ETH Zurich & SIB), Julia Vogt (University of Basel & SIB)

  • 15.30 - 16.15 (Keynote lecture)
    Yves Moreau
    , KU Leuven, BE

    "Bayesian matrix factorization and deep learning data fusion for drug-target interaction prediction"
  • 16.15 - 16.35
    Monique Zahn, SIB Swiss Institute of Bioinformatics, CH
    “Exploring neXtProt data and beyond: a SPARQLing solution”
  • 16.34 - 16.55
    Diogo M. Reibeiro, University of Lausanne & SIB, CH
    "The molecular basis and genetic control of local gene co-expression"
  • 16.55 - 17.15
    Bita Khalili,
    University of Lausanne & SIB, CH
    "Automated analysis of large-scale NMR data generates metabolomic signatures and links them to candidate metabolites"

17.15 - 17.30: Closing remarks


Thursday, 12 September 2019

Although the main [BC]2 conference is on 9-11 September, all [BC]2 participants have free access to the talks and sessions scheduled on this day.

09.00 - 10.15: Computational biology, artificial intelligence and machine learning in precision medicine - joint session by [BC]2 and EMBO 

  • 09.00 - 09.25
    Oliver Stegle
    , European Bioinformatics Institute, GB
  • 09.25 - 09.50
    Amos Tanay
    , Weizmann Institute of Science, IL
    "Understanding chronic blood diseases using millions of electronic health records and single cell genomics"
  • 09.50 - 10.15
    Julien Gagneur, Technical University of Munich, DE
    "Pinpointing disease-causing regulatory genetic variants by multi-omics and machine learning"

10.15 - 16.00: EMBO sessions and parallel events

16.00 - 16.45: Joint keynote lecture by [BC]2 and EMBO

  • 16.00 - 16.45
    Vasant Narasimhan
    , Novartis, CH


Keynote speakers

[BC]2 keynote speakers

  • Susan Holmes (Stanford School of Medicine, US)
    Susan Holmes' work focusses on the analysis of large heterogeneous multi-layer data sets in a variety of different biological contexts trying to better understand the underlying biology. She is an expert in data exploration and visualisation and will give the [BC]2 keynote lecture. Find out more about Susan's work on her webpage.
  • Peter Kharchenko (Harvard Medical School, US)
    Peter Kharchenko studies tumour heterogeneity, as well as the interactions between tumour cells and their microenvironment. He is featured in the “Single-cell Data” plenary session. Find out more about Peter's work on his webpage.
  • Roy Kishony (Technion - Isareal Institute of Technology, IL)
    Roy Kishony combines experimental and theoretical approaches the evolution of pathogens and antibiotics resistance. He will discuss his work in the “Evolutionary Medicine” plenary session. Find out more about Roy's works on his webpage.
  • Danielle Posthuma (Vrije Universiteit Amsterdam, NL)
    Danielle Posthuma is a behaviour and psychiatric geneticists, who is specialised in statistical genetics. She will give the opening lecture of the “Clinical Population Genomics” plenary session. Find out more about Danielle's work on her webpage.
  • Thomas Kepler (Boston University School of Medicine, US)
    Thomas Kepler develops and applies novel mathematical models and statistical methods to research the biology of our immune system. He presents his work at the “Systems Biology of Disease” plenary session. Find out more about Thomas' work on his webpage.
  • Yves Moreau (KU Leuven, BL)
    Yves Moreau works in the field of systems biology, trying to understand how the genetic variation in a person’s genome can influence the risk or severity of a disease. He will present in the “Multi-level Data Integration” plenary session. Find out more about Yves' work on his webpage.

Keynote speakers joint between [BC]2 and EMBO

  • Computational biology, artificial intelligence and machine learning in precision medicine
    (Thursday, 12 September, 09.00 - 10:15)
  • Joint keynote lecture by [BC]2 and EMBO
    (Thursday, 12 September, 16.00 - 16.45)


Scientific committee

The scientific committe is co-chaired by SIB Group Leader Erik van Nimwegen (University of Basel & SIB) und Niko Beerenwinkel (ETH Zurich, D-BSSE & SIB). Further members of the scientitifc committee and different session chairs are:

The tutorial and workshop programme is organised by:



We would like to thank all our sponsors supporting the [BC]2 conference!

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