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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Programme Overview 


Download a PDF version of the programme here.

Jump to programme on Monday, 09 September 2019
Jump to programme on Tuesday, 10 September 2019
Jump to programme on Wednesday, 11 September 2019
Jump to programme on Thursday, 12 September 2019

Monday, 09 September 2019 

09.00 - 16.00: Tutorials and workshops at the University of Basel (how to get there)


  • 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 (cancelled)
  • 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 (Keynote lecture)
    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
    "From GWAS to Function: interpreting GWAS results in biological context"
  • 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
    "Machine learning approaches for elucidating complex gene-environment interactions"
  • 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 (Keynote lecture)
    Vasant Narasimhan
    , Novartis, CH
    "Reimagining medicine: The power of data science and digital technologies"


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)


Industry Symposia

Label-free 3D Live Cell Imaging in Drug Discovery: Introducing the CX-A, saying good bye to phototoxicity and end point assays

Wednesday, 12:45 - 13:45 (Room Samarakand)

Organised by:

Alex Jones, PhD (CCO, Nanolive)
Hugo Moreno, MSc (Applications Scientist, Nanolive)

Nanolive provides high quality live cell images, label-free and in 3D, for these reasons this imaging technique is well suited for testing the effects of drugs on cell's morphological and sub-cellular organisation. To further support drug discovery applications we have developed our new automated system, the CX-A, which we are showing for the first time at MipTec / Basel Life. We will further report on recent imaging experiments where we perform a range of perturbations with various drugs in long-term time-lapse approaches demonstrating the practicality of the technology in a drug testing context. These experiments provide stunning video of cells evolving in a perturbed or unperturbed context. This process demonstrated that automatizing our technology should be a advantage for laboratories, both in time, cost, and the new unperturbed biological insight observed. Providing not only the possibility to evaluate drugs in prospective steps but to parallelise the process of drug effect evaluation with non-invasive, label-free power. We can now show that it is possible to use Nanolive Imaging technology for automatized drug effect evaluation in multi-well setup.


Open Science and/or Compliance – What future do you want for Computational Biology?

Thursday, 13:15 - 14:15 (Room Sydney)

Organised by:
Markus Wyss (DSM), Axel Braun (F. Hoffmann-La Roche Ltd), Jan Lucht (scienceindustries)

Markus Wyss (DSM)
Christin Peters (ZHAW Wädenswil, Group leader Biosystems Technology, Institute of Chemistry and Biotechnology & School of Life Sciences and Facility Management)

The Nagoya Protocol is a supplementary agreement to the Convention on Biological Diversity (CBD), and entered into force in 2014. The Nagoya Protocol is supposed to provide a transparent legal framework for the fair sharing of benefits arising out of the utilization of biological resources, thereby contributing to the conservation and sustainable use of biodiversity. It imposes obligations on all users of biological resources (both academic and industrial) to secure that access to biological resources and benefit sharing are done in full compliance with all applicable Access and Benefit Sharing (ABS) laws.

In the international negotiations around the CBD and the Nagoya Protocol, it is currently hotly debated whether also published information on biological resources (subsumed under the term “Digital Sequence Information”) should be formally included in the scope of the ABS obligations. This would have far-reaching consequences for research and innovation, and in particular for computational biology.

The symposium aims:

  • To present the current “state of affairs”, re. the opportunities and risks of the Nagoya Protocol in general, and of the inclusion of “Digital Sequence Information” in the formal scope of ABS obligations.
  • To provide both an academic and an industrial perspective on the potential implications for research and innovation.
  • To trigger interest and engagement in the international debates on the future scope of ABS obligations.

Within two short presentations, the speakers will provide an academic (Christin Peters) and an industrial (Markus Wyss) perspective on the opportunities and risks of the Nagoya Protocol for life science R&D and innovation with a main focus on Digital Sequence Information. The presentations are followed by an open discussion with the audience.

Sponsored by:




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Swiss Biotech Association

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Scientific Committee

The scientific committee 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 scientific committee and different session chairs are:

The tutorial and workshop programme is organised by:


ISB Travel Fellowships 

Congratulations to Qaaifah Gillani Syed and Zannatun Nayema, who have been selected for the [BC]2 Travel Fellowships provided by the ISB International Society for Biocuration!

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  • Qaaifah Gillani Syed (University of Kashmir, IN)
    Qaaifah Gillani Syed is a PhD student in the group of Shaida Andrabi in the Department of Biochemistry at the University of Kashmir in India. Her research is focusing on Cancer Biology and by using different bioinformatics tools, she is studying the mitotic and oncogenic role of different kinases.

    Why did you decide to attend [BC]2 and BASEL LIFE?
    "I decided to attend [BC]2 and BASEL LIFE because I believe being a part of this prestigious event will be a great platform to present my work to a diverse scientific audience, and to interact with eminent scientists and other researchers, who can make me look at my work through a different perspective. In particular, I am interested in increasing my understanding of the different bioinformatic approaches to study the unknown functions of my proteins of interest. Through this event, I can update myself about the latest trends and advancements in this field, which I can then implement in my research. Attending [BC]2 and BASEL LIFE will allow me to meet other researchers from similar fields and it may give me an opportunity to advance my knowledge through future collaborations as well. Since I am currently pursuing the last year of my PhD, the conference may also help me find a post-doc position, thus allowing me to carry my research further."

    If you would like to learn more about Qaaifah’s research project, join the [BC]2 and EMBO flash talk session and listen to her presentation on how “PCTAIRE1 kinase overcomes PolST induced mitotic arrest and cell death”.
    The [BC]2 and EMBO Flash Talk Session will be on 10 September 2019, from 3:30 – 4:30 pm.

  • Zannatun Nayema (Kanazawa University, JP)
    Zannatun Nayema is a first-year PhD student in the group of Atsushi Tajima in the Department of Bioinformatics and Genomics at the Kanazawa University in Japan. Her main research focus is on the analysis of Genome Wide Association Studies connected to the Metabolic syndrome (a cluster of conditions that increases the risk of heart disease, stroke and diabetes) and polygenic risk score analyses.

    Why did you decide to attend [BC]2 and BASEL LIFE?
    “As a first-year student in the field of Bioinformatics, it is imperative for me to meet and network with other researchers. By bringing together scholars from multi-valued logic and especially from my related field of interest, [BC]2 has become one of my first choices to apply for. I believe this conference will provide me not only with networking opportunities, but will also enable me to learn about cutting-edge research in Bioinformatics and Computational Biology which will upgrade my research ideas and thinking.“

    If you would like to learn more about Zannatan’s research project, visit her poster entitled “Genome-wide association study in Japanese cohort identifies variants near amylase genes associated with serum amylase level”.
    The Poster Session takes place on Tuesday, 10 September 2019, from 5:30 – 7 pm.



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

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