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, pysichians, scientists and friends of the NCT run “to opose cancer with a positive note.” An EMBL team supports this initiative every year.
See more (in German only)

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

New paper: Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

Abstract: Hypothesis weighting improves the power of large-scale multiple testing. We describe independent hypothesis weighting (IHW), a method that assigns weights using covariates independent of the P-values under the null hypothesis but informative of each test’s power or prior probability of the null hypothesis: www.bioconductor.org/packages/IHW. IHW increases power while controlling the false discovery rate and is a practical approach to discovering associations in genomics, high-throughput biology and other large data sets.

Read more

Welcome Arne Smits

Arne has a PhD degree from the Radboud University (Nijmegen, The Netherlands). His previous research in the laboratory of Prof. Michiel Vermeulen focused on the identification and quantification of protein-protein and DNA-protein interactions using quantitative proteomics. As a EIPOD postdoctoral fellow at EMBL, he is studying the systems-wide effects of drug treatment in collaboration with Cellzome and the Steinmetz 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

Congratulations Sophie Rabe

Sophie studied Molecular Biotechnology at the University of Heidelberg. She joined the Huber Group in Spring 2014 as student research assistant and worked on genomic biomarkers of drug sensitivity in primary blood cancer cells. For her PhD thesis, Sophie is now joining the group of Sascha Dietrich at NCT Heidelberg, where she will work on the SYMPATHY project, an integrated system medicine approach to personalized and targeted therapy in leukaemia and lymphoma. This multidisciplinary project is intended to have direct clinical impact on patient care in blood cancers.

Welcome Karsten Bach

Karsten Bach has a B.Sc. in Biology from the University of Bonn. He joined the Huber group in March 2016. At EMBL, he is finishing up his M.Sc. in Molecular Biotechnology and working on quantitative proteomics together with Dorothee Childs and Nikos Ignatiadis.