Notes Meeting 2016 March - berlinbioinformatics/berlinbioinformatics.github.io GitHub Wiki

The meeting takes place in June 29, 2016 at 18:00 in Maude Menten Hall, at HU Berlin.

Presentations

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)