New Directions in Single Cell Analysis

Technologies, data analytical approaches and biomedical / clinical applications.

Organisers: Wolfgang Huber, Niko Beerenwinkel, John Marioni and Oliver Stegle

Dates

28 and 29 August: Scientific Workshop
27 August, 13:00h – 18:00h: satellite meeting for the SOUND consortium

Venue

BioQuant
Im Neuenheimer Feld 267
Ruprecht-Karls-Universität Heidelberg
Heidelberg

How to get to BioQuant
By car:
Coming from the motorway (A 656): Turn left towards “Chirurgie” at the end of the Autobahn. Having crossed the Neckar on Ernst-Waltz-Brücke follow Berliner Straße. At the 2nd traffic light (“Shell” gas station & “Bunsengymnasium”) turn left towards Neuenheimer Feld (BioQuant 267).

By public transport:
From main railway station (Hauptbahnhof): Take either the tram number 24 (direction Handschuhsheim) or the number 21 (direction Technologiepark) and get off at the “Bunsengymnasium” stop.
From Heidelberg downtown (Bismarckplatz): Take the bus number 31 towards “Neuenheim, Chirurgische Klinik” and get off at the “Bunsengymnasium” bus stop.

Confirmed speakers

  • Simon Anders, ZMBH Heidelberg
  • Tim Becker, Broad Institute of MIT and Harvard, Cambridge
  • Michael Boutros, DKFZ Heidelberg
  • Laleh Haghverdi, EMBL Heidelberg
  • Thomas Höfer, DKFZ Heidelberg
  • Smita Krishnaswamy, Yale School of Medicine, USA
  • Aaron Lun, Cancer Research UK Cambridge Institute
  • Svetlana Ovchinnikova, ZMBH Heidelberg
  • Lucas Pelkmans, University of Zurich
  • Wolf Reik, Babraham Institute Cambridge
  • Charlotte Soneson, University of Zurich
  • Oliver Stegle, EMBL Heidelberg
  • Barbara Treutlein, Max Planck Institute for Evolutionary Anthropology, Leipzig
  • Britta Velten, EMBL Heidelberg
  • Lars Velten, EMBL Heidelberg

Registration

Registration for this workshop is closed and the event is fully booked. Spontaneous registrations on site are not possible.

Programme

Tuesday, 28 August 2018

09:00 – 09:10 Welcome. Organisers
09:10 – 9:50 Multiplexed protein maps link subcellular organization to cellular states. Lucas Pelkmans
9:50 – 10:30 Manifold learning yields insight into complex cellular state space.
Smita Krishnaswamy
10:30 – 11:00 Coffee break
11:00 – 11:40 Extendable benchmarks and reproducible exploration for scRNA-seq data. Charlotte Soneson
11:40 – 12:20 From Targeting Diseases to Characterizing Asthma. Tim Becker
12:20 – 13:20 Lunch
13:20 – 14:00 Reconstructing cellular transitions using single cell transcriptomics.
Barbara Treutlein
14:00 – 14:40 Combining somatic heterogeneity with scRNA-sew. Oliver Stegle
14:40 – 15:00 Coffee break
15:00 – 15:40 Batch correction in scRNA-seq data. Laleh Haghverdi
15:40 – 15:50 Break
15:50 – 17:00 Tutorial: Visual interactive exploration of omics data.
Simon Anders and Svetlana Ovchinnikova
17:00 – 19:00 Free time
19:00 Dinner (for the SOUND consortium and invited speakers only)

Wednesday, 29 August 2018

9:00 – 9:40 Single cell epigenome landscape of mammalian development and ageing. Wolf Reik
9:40 – 10:20 Mapping context-dependent genetic circuits of cells. Michael Boutros
10:20 – 10:50 Coffee break
10:50 – 11:30 DNA barcoding to decode hematopoietic development. Thomas Hoefer
11:30 – 12:10 Spatial transcriptomics reveals design principles of the haematopoietic stem cell niche. Lars Velten
12:10 – 13:15 Lunch
13:15 – 16:00 Tutorial: End-to-end workflow for single cell RNA-Seq analysis. Aaron Lun
15:00 – 15:30 Coffee break
16:00 – 17:00 Tutorial: Multi-Omics Factor Analysis. Britta Velten
17:00 End of the workshop

Monday 27 August 2018

SOUND Consortium Meeting (15’ presentation + 5’ discussion)

12:00 Registration and sandwich lunch
13:00 Welcome. Wolfgang Huber
13:10 – 13:30 WP 8 and 10. Martin Morgan (RPCCC)
13:30 – 13:50 WP 9. Alexander Bertram (BDD)
13:50 – 14:10 WP 4. Niko Beerenwinkel (ETH Zurich)
14:10 – 14:25 Break
14:25 – 14:45 WP 4. Susana Vinga (IDMEC)
14:45 – 15:05 WP 2. Daniele Biasci (UCAM)
15:05 – 15:35 Coffee break
15:35 – 15:55 WP 6. Mitch Levesque and Phil Cheng (USZ)
15:55 – 16:15 WP 5. Thorsten Zenz (DKFZ and USZ)
16:15 – 16:35 WP 1. Junyan Lu and Jennifer Hüllein (EMBL)
16:35 – 17:15 Discussion and wrap-up. All
17:15 – 19:00 Free time
19:00 Dinner (for the SOUND consortium and invited speakers only)

For inquiries related to the registration, scientific program and organisation, please contact Simone Bell, simone.bell(at)embl.de at European Molecular Biology Laboratory (EMBL), Heidelberg.

CSAMA 2018 – Statistical Data Analysis for Genome Scale Biology

CSAMA 2018 (16th edition)
Statistical Data Analysis for Genome Scale Biology
Bressanone-Brixen, Italy (South Tyrol Alps)
July 8-13, 2018

Lecturers:

  • Vincent J. Carey, Harvard Medical School
  • Laurent Gatto, University of Cambridge
  • Robert Gentleman, 23andMe, Mountain View
  • Laleh Haghverdi, European Molecular Biology Laboratory (EMBL), Heidelberg
  • Wolfgang Huber, European Molecular Biology Laboratory (EMBL), Heidelberg
  • Michael I. Love, University of North Carolina-Chapel Hill
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo
  • Johannes Rainer, European Academy of Bozen (EURAC)
  • Charlotte Soneson, University of Zurich
  • Levi Waldron, CUNY School of Public Health at Hunter College, New York

Teaching Assistants:

  • Simone Bell, EMBL, Heidelberg
  • Vladislav Kim, EMBL, Heidelberg
  • Lori Shepherd, RPCCC, Buffalo
  • Mike L. Smith, EMBL, Heidelberg

The one-week intensive course Statistical Data Analysis for Genome-Scale Biology teaches statistical and computational analysis of multi-omics studies in biology and biomedicine. It covers the underlying theory and state of the art (the morning lectures) and practical hands-on exercises based on the R / Bioconductor environment (the afternoon labs). At the end of the course, you should be able to run analysis workflows on your own (multi-)omic data, adapt and combine different tools, and make informed and scientifically sound choices about analysis strategies.

Topics include:

  • Introduction to R and Bioconductor
  • The elements of statistics: hypothesis testing, multiple testing, regression, regularization, clustering and classification, parallelization and performance (machine learning), visualisation
  • RNA-Seq data analysis
  • Computing with sequences and genomic intervals
  • Working with annotation – genes, genomic features, variants, transcripts and proteins
  • Gene set enrichment analysis
  • Mass spec proteomics and metabolomics
  • Basis of microbiome analysis
  • Experimental design, batch effects and confounding
  • Reproducible research and workflow authoring with R markdown
  • Package development, version control and developer tools (incl. git, github, RStudio)
  • Working with large data: performance parallelisation and cloud computing

The course consists of

  • morning lectures: 20 x 45 minutes: Monday to Friday 8:30h – 12:00h
  • 4 practical computer tutorials in the afternoons (13:30h – 16:30h) on Monday, Tuesday, Thursday and Friday

Visit the course’s website at: http://www.huber.embl.de/csama

Fifth Consortium Meeting


Date: 15th November 2017
Venue: EMBL Heidelberg
Room: 202
Meyerhofstr. 1
69117 Heidelberg

How to go there: https://www.embl.de/aboutus/contact/travel/index.html

Tuesday, 14th November 2017


18:00 s.t. EMBL shuttle departs from the ATC main entrance towards Bismarckplatz
19:45 Dinner at Oskar Restaurant und Vinothek. Haspelgasse 5, Heidelberg

 

Wednesday, 15th November 2017


08:30 Registration and coffee
08:50 Welcome. Wolfgang Huber

Session I, scientific presentations


(15’ presentation + 5’ discussion)

09:00 – 09:20 Talk 1. Christian Mertes and Daniela Simancas (TUM)
09:20 – 09:40 Mitochondrial Genetic Disorders. Robert Kopajtich (TUM-MED)
09:40 – 10:00 Renjin: Update. Alexander Bertram (BDD)
10:00 – 10:30 Coffee break
10:30 – 10:50 Precision Oncology in Melanoma. Phil Cheng (USZ)
10:50 – 11:10 Network-based integration of multi-omics data for cancer gene prioritization. Christos Dimitrakopoulos (ETH Zurich)
11:10 – 11:20 Break
11:20 – 11:40 DegreeCox – Estimating structured sparse survival models. André Veríssimo (IDMEC)
11:40 – 12:00 Talk 7. Daniele Biasci (UCAM)
12:00 – 13:00 Lunch and group photo (meet at 12:45h in front of the ATC for the photo)

Session II, scientific presentations


13:00 – 13:20 Tools and methods for high-throughput perturbation assays and integrative analysis. Junyan Lu (EMBL)
13:20 – 13:40 Genomics of Drug Sensitivity of Primary Cancer Cells. Thorsten Zenz (DKFZ and USZ)
13:40 – 14:00 Coffee break
14:00 – 14:50 Discussion. All
15:00 End of the meeting
15:00 – 16:00 Distinguished Lecture with David Baker, University of Washington.
Large Operon
15:40 s.t. EMBL shuttle departs from the ATC main entrance towards Heidelberg main train station

 

Workshop on Tools for Molecular Diagnostic Boards


Date: 5th December 2016
Venue: ETH Zurich
Department of Biosystems Science and Engineering (D-BSSE)
Euler Meeting Room P.60 (ground floor)
Mattenstrasse 26
4058 Basel

How to go there: https://www.bsse.ethz.ch/department/locations.html

Monday, 5th December 2016


12:15 Sandwich lunch
13:00 – 13:10 Welcome. Wolfgang Huber

Data producers


(8’ presentation + 2’ discussion)

13:10 – 13:20 xx.Niko Beerenwinkel (ETH)
13:20 – 13:30 xx.Mitch Levesque (UHZ)
13:30 – 13:40 xx.Holger Prokisch (TUM-MED)
13:40 – 13:50 xx.Julien Gagneur (TUM)
13:50 – 14:00 xx.Benedikt Brors (DKFZ)
14:00 – 14:10 xx.Peter Horak (NCT Heidelberg)
14:10 – 14:20 Supporting Swiss clinics in comprehensive cancer diagnostics.
Daniel Stekhoven (ETH)

Data processors


14:20 – 14:30 xx.Parham Solaimani and Alexander Bertram (BDD)
14:30 – 15:00 Coffee break
15:00 – 15:10 xx.Martin Morgan (RPCI)
15:10 – 15:20 xx.Wolfgang Huber (EMBL)
15:20 – 17:00 Round-table discussion

 

Clinical Bioinformatics as a Service – ECCB 2016 workshop

ECCB 2016 is the 15th edition of the European Conference on Computational Biology. It will take place in The Hague (Netherlands) between September 3 and 7, 2016. The event hosts two days of workshops and tutorials prior to the actual conference starting on September 5.

CALL FOR TALKS AT WORKSHOP

We are welcoming contributions to our workshop «Clinical Bioinformatics as a Service». The deadline for submissions is May 29, 2016. There are two formats available: contributed talks (15+5 minutes) and flash talks (2 minutes). Submit your abstracts online.

WORKSHOP IN CLINICAL BIOINFORMATICS AS A SERVICE

There is an increasing need for bioinformatics provided in clinics as a service. Examples include omics-informed precision oncology, rare genetic diseases, infectious diseases, gene therapy, etc. The field is young and rapidly evolving, such that there is much uncertainty about best practices, tools are unstable, and much re-invention or duplication is happening. This workshop aims to bring together leading researchers and practitioners in this area to exchange latest approaches, experiences, tool benchmark results, protocols and best practice guidelines for reporting molecular-based evidence to clinicians and patients. Visit the workshop website.

TIME & DATE

The workshop takes place on September 4, 2016, 09:00 – 17:00 (CEST) at the World Forum in The Hague, Netherlands. This is the same venue as the ECCB 2016 main conference starting directly after the workshop with the welcome reception. Find a complete schedule here.

INVITED SPEAKERS

DEADLINES

  • May 29, 2016: Submission Deadline for Contributions to Workshop
  • July 29, 2016: Early Bird Registration for Conference closes
  • August 19, 2016: Online Registration for Conference closes

ORGANIZERS

  • Niko Beerenwinkel, ETH Zurich, Basel, Switzerland
  • Wolfgang Huber, EMBL, Heidelberg, Germany
  • Simon Tavaré, CRUK, Cambridge, U.K.
  • Daniel Stekhoven, ETH Zurich, Zurich, Switzerland

CSAMA 2016 – Statistical Data Analysis for Genome Biology

CSAMA 2016 (14th edition)
Statistical Data Analysis for Genome Biology
Bressanone-Brixen, Italy (South Tyrol Alps)
July 10-15, 2016

Lecturers:

  • Simon Anders, Institute for Molecular Medicine, Helsinki
  • Jennifer Bryan, University of British Columbia, Vancouver
  • Vincent J. Carey, Channing Laboratory, Harvard Medical School
  • Wolfgang Huber, European Molecular Biology Laboratory (EMBL), Heidelberg
  • Michael Love, Dana Farber Cancer Institute and the Harvard School of Public Health
  • Martin Morgan, Roswell Park Cancer Institute, Buffalo, New York.
  • Charlotte Soneson, University of Zurich
  • Levi Waldron, CUNY School of Public Health at Hunter College, New York

Teaching Assistants:

  • Simone Bell, EMBL, Heidelberg
  • Alejandro Reyes, EMBL, Heidelberg
  • Mike L. Smith, EMBL, Heidelberg

The one-week intensive course Statistical Data Analysis for Genome Biology teaches statistical and computational analysis of multi-omics studies in biology and biomedicine. It covers the underlying theory and state of the art (the morning lectures), and practical hands-on exercises based on the R / Bioconductor environment (the afternoon labs). The course covers the primary analysis of high-throughput sequencing based assays in functional genomics and integrative methods including efficiently operating with genomic intervals, statistical testing, linear models, machine learning, bioinformatic annotation and visualization. At the end of the course, you should be able to run analysis workflows on your own (multi-)omic data, adapt and combine different tools, and make informed and scientifically sound choices about analysis strategies.

Topics include:

  • Introduction to Bioconductor
  • Elements of statistics: hhypothesis testing, multiple testing, regression, regularization, clustering and classification, parallelization and performance (machine learning), visualisation
  • Reproducible research and R authoring with markdown and knitr
  • RNA-Seq data analysis and differential expression
  • New workflows for RNA-seq
  • Computing with sequences and genomic intervals
  • End-to-end RNA-Seq workflow
  • Experimental design, batch effects and confounding
  • Working with annotation – genes, genomic features and variants
  • Visualization, the grammar of graphics and ggplot2
  • Use of Git and GitHub with R, RStudio, and R Markdown
  • Gene set enrichment analysis

The course consists of

  • morning lectures: 20 x 45 minutes: Monday to Friday 8:30h – 12:00h
  • 4 practical computer tutorials in the afternoons (14:00h – 17:00h) on Monday, Tuesday, Thursday and Friday

Visit the course’s website at: http://www.huber.embl.de/csama