Author: berlinbioinf

Meeting 2016 September

~ berlinbioinf

Useful bash one-liners – continued

Correction of Confounding in Genome-Wide Association Studies

  • Florian Wenzel, HU Berlin
  • Slides

Genomation: an R package to summarize, annotate and visualize genomic intervals

  • Katarzyna Wreczycka, MDC Berlin

Bioinformatics Social Meetup May 30, 2017

~ berlinbioinf

Dear all,

 

we would like to invite you to the special summer Bioinformatics Social Meeting in May 2017. The next meeting will be on Tuesday, May 30, 2017and start at 18:00h in the Maud Menten Hall at the IRI Life Sciences, 3rd floor (Campus of HU Berlin, see here https://goo.gl/Vmcny5).

 

The Bioinformatics Social Meeting is an informal, bimonthly meeting aimed at PhD students and Postdoctoral researchers working in Bioinformatics and related fields (Biostatistics, Computational Biology etc.). The meeting usually consists of talks of scientific and technical nature and discussions of Bioinformatics problems that people face (e.g., “does anyone know of a good tool for X?”). The meeting takes place in the last week of every second month.

 

The next meeting will have the following topics:

 

  • “A Real-time Approach for Privacy Protection in Next Generation Sequencing” — Tobias Loka, RKI Berlin
  • “Using Bioconda for software installation and packaging” — Manuel Holtgrewe, BIH Berlin
  • “Creating Galaxy packages” — Dilmurat Yusuf, MDC Berlin
  • “Prelude of Emerging Topics in Bioinformatics” — The Organisers

 

Afterwards this session we will change the standard procedure and start having a BBQ in the backyard of IRI. The organisers will provide the barbecue grill and everyone else is responsible for her/his own drinks and food for the barbecue. Let’s cross the fingers that the weather will be nice.

 

Please also forward this invitation to your Bioinformatics friends and colleagues in Berlin. In particular, Bioinformaticians embedded in wet lab or clinical groups can benefit greatly from discussions in a broader group.

 

You can subscribe to our mailing list here:

 

https://lists.fu-berlin.de/listinfo/compbio-social

 

The mailing list is for asking questions, having discussions, and sharing information beneficial to other bioinformaticians (such as job offers, PhD grants etc.)

 

Cheers,

Manuela Benary, Philipp Drewe, Manuel Holtgrewe, Stefan Konigorski, Florian Uhlitz, Tobias Loka and Max Schubach

Meeting 2016 July

~ berlinbioinf

Mendelian randomization

  • Katharina Nimptsch, MDC Berlin
  • References
    • Methodological papers and reviews
      • Ebrahim, Davey Smith: Mendelian Randomization: can genetic epidemiology help redress the failures of observational epidemiology? Hum Genet (2008)
      • Palmer, Lawlor et al.: Using multiple genetic variants as instrumental variables for modifiable risk factors. Stat Meth Med Res (2012)
      • Brion, Shakhbazov, Visscher: Calculating statistical power in Mendelian Randomization. Int J Epi (2013)
      • Burgess: Sample size and power calculations in Mendelian randomization with a single instrumental variable and a binary outcome. Int J Epi (2014)
      • Palmer, Sterne et al.: Instrumental variable estimation of causal risk ratios and causal odds ratios in Mendelian randomization analyses. Am J Epi (2011)
    • Book
      • Burgess, Thompson: Mendelian Randomization – Methods for Using Genetic Variants in Causal Estimation. CRC Press Taylor&Francis Group. Boca Raton 2015

Useful bash one-liners

  • Max Schubach, Florian Uhlitz, Manuel Holtgrewe
  • Slides

Meeting 2016 March

~ berlinbioinf

The following material was presented. We try to provide the list of references for each talk, publication of slides is in the speaker’s discretion.

Beyond SNP-zygosities and tandem repeats: can Cancer Cell Line samples be reliably identified by reshaping and weighting their heterogenous and incomplete NGS small variant genotype-data?
10,001 Dalmatians – how to build (and analyze) a bio-bank of isolated populations
  • Inga Patarcic, MDC Berlin
  • References
    • Kauffmann, F.; Cambon-Thomsen, A. (2008). “Tracing Biological Collections: Between Books and Clinical Trials”. JAMA: the Journal of the American Medical Association 299 (19): 2316–2318.doi:10.1001/jama.299.19.2316 PMID 18492973
    • Vitart V, Rudan I, Hayward C, Gray NK, Floyd J, Palmer CN, Knott SA, Kolcic I, Polasek O, Graessler J, Wilson JF. SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. Nature genetics. 2008 Apr 1;40(4):437-42.
    • Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M. Genes mirror geography within Europe. Nature. 2008 Nov 6;456(7218):98-101.
    • Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014 Sep 18;513(7518):409-13.
    • Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 2015 Mar 2.

Processing and Analysis of Hi-C Data

  • Henriette Miko, MDC Berlin
  • References
    • 3C:
      • Dekker et al., “Capturing Chromosome Conformation”, Science (2002)
    • Hi-C
      • Lieberman-Aiden et al., “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome”, Science (2009)
    • Reviews
      • Lajoie et al., “The Hitchhiker’s guide to Hi-C analysis: Practical guidelines”, Methods (2015)
      • Ay and Noble, ”Analysis methods for studying the 3D architecture of the genome”, Genome Biology (2015)