The Huber Group on the 6th NCT Run

The race event of the National Center for Tumor Diseases (NCT) Heidelberg took place for the 6th time last Friday, 7 July 2017. More than 4.500 participants including patients and their families, physichians, scientists and friends of the NCT run “to opose cancer with a positive note” joined the event this year. An EMBL team supports this initiative every year.
See more (in German)

NCT Run - Huber Group

From the left to the right: Simone Bell, Olena Yavorska, Vladislav Kim, Frederik Ziebell, Almut Lütge and Britta Velten from the Huber Group.

EMBL Charity Cycle Challenge

On 30 June 2017 a group of 14 EMBL cyclists set off on an epic ride from Heidelberg to EMBL Grenoble over five days. Their goal is to raise money for the Kinderplanet, a charity that supports the families of children treated at the Heidelberg University Hospital. As the Kindergarten relies solely on donations in order to operate, their mission is to help Kinderplanet in supporting families of sick children.

30 June – 4 July 2017
5 days – 850 km distance – 16.500 m ascent
By completing this physically and mentally demanding cycling challenge they hope to spread the word about Kinderplanet charity and encourage our colleagues, friends and family members to donate for a great cause.

Almut Lütge and Mike Smith from the Huber Group are taking part in this epic ride!

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CSAMA 2017 – Statistical Data Analysis for Genome Scale Biology

CSAMA 2017 (15th edition)
Statistical Data Analysis for Genome Scale Biology
Bressanone-Brixen, Italy (South Tyrol Alps)
June 11-16, 2017

Lecturers:

  • Jennifer Bryan, RStudio and UBC
  • Vincent J. Carey, Harvard Medical School
  • Laurent Gatto, University of Cambridge
  • Wolfgang Huber, European Molecular Biology Laboratory (EMBL), Heidelberg
  • Martin Morgan, Roswell Park Cancer Institute, 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, RPCI, 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

CSAMA 2016 – we were there

The 14th edition of the course Statistical Data Analysis for Genome Scale Biology took place in July 2016 in Bressanone-Brixen. More than 70 participants spent a fantastic week studying in a mix of lectures and practical computer tutorials, learning from the lecturers Wolfgang Huber, Martin Morgan, Vincent Carey, Charlotte Soneson, Simon Anders, Michael Love, Levi Waldron and Jennifer Bryan. Senior scientists, Postdocs and students from the Huber group participated to this course as well. Additionally, everybody enjoyed biking and hiking in the high-alpine regions. One of the highlights of that week was a wonderful hiking tour into the Plose Mountain.

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Wolfgang Huber, Mike Smith, Alejandro Reyes and Levi Waldron enjoyed a mountain bike tour in the late afternoon after the course.

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Wolfgang Huber, Karsten Bach and Nils Kurzawa on another mountain bike tour on Saturday after the course.

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The 2017 course will take place from 11 to 16 June.

Photos from Brixen by Junyan Lu.

The Huber Group on the 5th NCT Run

The race event of the National Center for Tumor Diseases (NCT) Heidelberg took place for the 5th time last Friday, 8 July 2016. Tousands of participants including patients and their families, physichians, scientists and friends of the NCT run “to opose cancer with a positive note” participated this year. An EMBL team supports this initiative every year.
See more (in German only)

NCTrun_hubergroup_s

From the left to the right: Annika Gable, Mike Smith, Britta Velten, Karsten Bach, Junyan Lu, Nils Kurzawa and Alejandro Reyes from the Huber Group.

CSAMA 2016 Statistics and Computing in Genome Data Science

CSAMA 2016 (14th edition)
Statistics and Computing in Genome Data Science
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 Statistics and Computing in Genome Data Science 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: hypothesis testing, multiple testing, regression, regularization, clustering and classification (machine learning), visualization
  • Computing with sequences and genomic intervals
  • Integrating multiple layers of ‘omic data
  • Working with annotation – genes, genomic features and variants
  • RNA-Seq data analysis and differential expression
  • Single-cell RNA-Seq
  • Proteomics primers
  • Interactive displays with Shiny

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

The registration for CSAMA 2016 closed on June 15th 2016

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

SOUND second consortium meeting

The second consortium meeting of the SOUND project, which is led by Wolfgang Huber, was hosted by our colleagues from IDMEC Lisbon. Principal investigators, postdocs and PhD students attended the meeting and presented recent results and progress in the work packages. All partners are well on track with their project aims and the atmosphere of sharing research developments was quite enthusiastic. Junyan Lu held a talk on “Mechanistic study of drug response using ex-vivo drug testing and multi-omics technology“ and Małgorzata Oleś provided a presentation on “Modulators of drug response identified by multivariate lasso regression”. Wolfgang Huber gave a lecture on “Data driven hypothesis weighting and false discovery rates”.

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SOUND consortium

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Photos from Lisbon by Junyan Lu.

Group Retreat 2015

The group retreat 2015 took place in the end of September in the beautiful Black Forest. In a joint event bringing together the groups of Wolfgang Huber and Judith Zaugg, 22 scientists spent a fantastic time together exchanging their research approaches and results. Additionally, they enjoyed developing and discussing “Blue Sky” science projects in small groups, presented in a “back to basics” way using hand-drawn posters. The retreat was closed with a wonderful hiking tour on the third day.

Huber Group

Huber Group

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Registration open: CSAMA 2015 (13th ed.) Statistics and Computing in Genome Data Science

CSAMA 2015 (13th edition)
Statistics and Computing in Genome Data Science
Bressanone-Brixen, Italy (South Tyrol Alps)
June 14-19, 2015

Registration for CSAMA 2015 is now open
http://www.huber.embl.de/csama

Lecturers:

  • Martin Morgan, Fred Hutchinson Cancer Research Center (USA)
  • Wolfgang Huber, European Molecular Biology Laboratory
  • Vincent J. Carey, Channing Laboratory, Harvard Medical School (USA)
  • Michael Love, Dana Farber Cancer Institute and the Harvard School of Public Health (USA)
  • Simon Anders, European Molecular Biology Laboratory
  • Mark Robinson, University of Zurich (CH)
  • Laurent Gatto, University of Cambridge (UK)
  • Paul Pyl, University of Copenhagen (DK)

The one-week intensive course “Statistics and Computing in Genome Data Science” 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 (“preprocessing”) of high-throughput sequencing based assays in functional genomics (transcriptomics, epigenetics, etc.) as well as 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: hypothesis testing, multiple testing, regression, regularization, clustering and classification (machine learning), visualization
  • Computing with sequences and genomic intervals
  • RNA-Seq data analysis and differential expression
  • ChIP-Seq and epigenetics
  • Integrating DNA variant calls with functional data, and large-scale efficient computation with genomic intervals
  • Working with annotation – genes, genomic features and variants
  • Metagenomics and proteomics primers
  • Single-cell RNA-Seq primer
  • Interactive displays with Shiny

The course consists of

  • morning lectures: 20 x 45 minutes: Monday to Friday 8:30am – 12:00am
  • 4 practical computer tutorials in the afternoons (2pm – 5pm) on Monday, Tuesday,Thursday and Friday

For registration visit our website at: http://www.huber.embl.de/csama