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).


Programme Overview


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

18.00 - 19.00: Welcome reception


Tuesday, 10 September 2019

10.00 - 11.45: Single-cell data plenary session
Chairs: Manfred Claassen, Mark Robinson

  • 10.00 - 10.45: Keynote lecture
    Peter Kharchenko, Harvard Medical School, US
    "Joint analysis of heterogeneous single-cell dataset collections"
  • 10.45 - 11.05: Selected oral presentation
  • 11.05 - 12.25: Selected oral presentation
  • 11.25 - 11.45: Selected oral presentation

11.45 - 13.15: Lunch break

13.15 - 15.00: Evolutionary medicine plenary session
Chairs: Anna-Sapfo Malaspinas, Richard Neher

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

    "Predicting antibiotic resistance"
  • 14.00 - 14.20: Selected oral presentation
  • 14.20 - 14.40: Selected oral presentation
  • 14.40 - 15.00: Selected oral presentation

15.00 - 15.30: Coffee break

15.30 - 16.30: [BC]2 & EMBO poster flash talks
Chairs: Sven Bergmann, Philipp Bucher

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, Niko Beerenwinkel

  • 09.00 - 9.45: 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, Matthew Robinson

  • 10.00 - 10.45: Keynote lecture
    Danielle Posthuma
    , Vrije Universiteit Amsterdam, NL
  • 10.45 - 11.05: Selected oral presentation
  • 11.05 - 11.25: Selected oral presentation
  • 11.25 - 11.45: Selected oral presentation

11.45 - 13.15: Lunch break

13.15 - 15.00: Systems biology of disease plenary session
Chairs: Giovanni Ciriello, Mihaela Zavolan

  • 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: Selected oral presentation
  • 14.20 - 14.40: Selected oral presentation
  • 14.40 - 15.00: Selected oral presentation

15.00 - 15.30: Coffee break

15.30 - 17.15: Multi-level data integration plenary session
Chairs: Karsten Borgwardt, Julia Vogt

  • 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: Selected oral presentation
  • 16.34 - 16.55: Selected oral presentation
  • 16.55 - 17.15: Selected oral presentation

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, 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, The Weizmann Institute, IL
  • 09.50 - 10.15: Julien Gagneur, Technical University of Munich, DE

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, 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)


Open calls - deadlines

Call for Oral and Poster Presentations: 21 May 2019

Abstracts can be submitted in the following three categories: oral presentation, poster + flash talk and and poster only. Abstracts that are not accepted as oral presentation or flash talk can present posters instead. Abstract submission guidelines 

Call for participation at WS1: 21 May 2019

The "EMBO Young Investigator Workshop on Evolutionary and Computational Biology" workshop is adressed to early-career researchers aspiring to progress toward independence. Please submit a brief statement on your career stage, why you would like to participate, and what you are expecting from the workshop using the following application form.

Call for ISB travel fellowship2 June 2019

The ISB International Society for Biocuration will provide 2 travel fellowships to current ISB members aiming to attend [BC]2. Students, junior curators, curators from low-income countries, and curators from countries suffering from natural disasters are encouraged to apply. Applicants are asked to send a motivation letter to This email address is being protected from spambots. You need JavaScript enabled to view it. before Sunday 2 June 2019 and must have submitted an abstract for an oral or poster presentation (deadline 21 May!) to [BC]2.

Call for abstract submission to WS2: 20 June 2019

The "Annotation and curation of computational models in biology" has scheduled several presentations based on submitted abstracts. Abstract submissions for oral presentations should be sent to the following addresses anna.niaraki[at], thelikar2[at], Laurence.Calzone[at], with the indication: [BC]2_2019 Workshop Submission.


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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