Functional Genomics
- Wintersemester 2017/2018 -

 


 

- last update: 10.12.2017 -

December 04
09.00-10:45 a.m., Seminar room 2, ground floor, Max Planck Institute for Biology of Ageing
Introduction
(Martin Denzel)


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Bibliography

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  • Encode explained (2012) Nature News & Views 489
  • Lander ES (2011) Initial impact of the sequencing of the human genome. Nature 470: 187-197.

  • Guidelines for seminars 
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  • Seminar papers 
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  • Seminar schedule 
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December 04
11 - 12.45 a.m., Seminar room 2, ground floor, Max Planck Institute for Biology of Ageing
Introduction to laboratory safety
(Christoph Geisen)

 

 
December 05
9.00 - 10.45 a.m., Seminar room 2, ground floor, Max Planck Institute for Biology of Ageing

Using genetic tools to understand the neuronal control of feeding (Sophie Steculorum)



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Bibliography
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  • Sternson SM et al (2016) An Emerging Technology Framework for the Neurobiology of Appetite. Cell Metabolism
  • Chen Y et al (2016) Making sense of the sensory regulation of hunger neurons. Bioessays 38: 316–324
  • Ruud J et al (2016) Neuronal control of peripheral insulin sensitivity and glucose metabolism DOI: 10.1038/ncomms15259

December 11

9.00 - 10.45 a.m., Seminar room 2, ground floor, Max Planck Institute for Biology of Ageing

A short introduction into genetic screens (Martin Denzel)



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Bibliography
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  • Elling U et al (2011) Forward and reverse genetics through derivation of haploid mouse embryotic stem cells. Cell Stem Cell 9: 563-574.
  • Hansen M et al (2005) New genes tied to endocrine, metabolic and dietary regulation of lifespan from a Caenorhabditis elegans genomic RNAi screen. Plos Genet 1: 0119-0128.
  • Jorgensen EM, Mango SE (2002) The art and design of genetic screens: Caenorhabditis elegans. Nat Rev Genet 3: 356-369.
December 12
9.00 - 10.45 a.m., Auditorium, Max Planck Institute for Biology of Ageing
Systematic Interaction Mapping - the Genetic and Metabolic Exploration of Cellular Functions
(Martin Graef)

Bibliography
  • Bassik MC et al (2013) A systematic mamalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 152: 909-922.
  • Orvedahl A et al (2011) Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature 480: 113-117.
  • Costanzo M et al (2010) The genetic landscape of a cell. Science 327: 425-431.
December 18
9.00 - 10.45 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Using forward and reverse genetics to study mouse embryonic development
(Hisham Bazzi)

Bibliography
  • Horii T and Hatada I (2016) Production of genome-edited pluripotent stem cells and mice by CRISPR/Cas. Endocrine Journal 2016, 63 (3), 213-219
  • Anderson KV (2000)Finding the genes that direct mammalian development - ENU mutagenesis in the mouse.TIG March 2000, volume 16, No. 3
  • Sung YH et al (2004) Functional Genomics Approach Using Mice. Journal of Biochemistry and Moledular Biology, Vol 37, No. 1, January 2004, pp. 122-132
December 19
9.00 - 10.45 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Genomic eng(e/i)neering using site specific recombinase systems
(Thomas Wunderlich)

Bibliography
  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21: 381-395.
  • Petesch SJ, Lis JT (2012) Overcoming the nucleosome barrier during transcript elongation. Trends Genet 28: 285-294.
December 21
15.00 - 17.00 p.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Student seminars I
January 08
9.00 - 10.45 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Quantitative and population genetics: from genotypes to phenotypes and backwards
(Dario Valenzano)

Bibliography
  • Barroso-Batista et al (2015) Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nature Communications DOI: 10.1038/ncomms9945
  • Capellini TD et al (2017) Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nature Genetics doi:10.1038/ng.3911
  • Enge M et al (2017) Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell http://dx.doi.org/10.1016/j.cell.2017.09.004
January 09
9.00 - 10.45 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Using synthetic biological approaches to study lysine-acylation
(Michael Lammers)

Bibliography
  • Chin JW (2014) Expanding and Reprogramming the Genetic Code of Cells and Animals. Annu. Rev. Biochem. 2014. 83:379–408
  • Knyphausen P et al (2015) Lysine-acetylation as a funcamental regulator of Ran function: Implications for signaling of proteins of the Ras-superfamily. Small GTPases 6:4, 189--195; October/November/December 2015
  • Wittinghofer A and Vetter IR (2011) Structure-Function Relationships of the G Domain, a Canonical Switch Motif. Annu. Rev. Biochem. 2011. 80:943–71
January 10
15.00 - 17.00 p.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Student seminars II
January 12
15.00 - 17.00 p.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Student seminars III
January 15
9.00 - 10.45 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Chromatin plasticity and transcriptional regulation
(Peter Tessarz)

Bibliography
  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21: 381-395.
  • Petesch SJ, Lis JT (2012) Overcoming the nucleosome barrier during transcript elongation. Trends Genet 28: 285-294.
January 16
9.00 - 10.45 a.m., Seminar room 1, First floor, Max Planck Institute for Biology of Ageing
3D genome (re)organization in homeostasis and disease
(Argyris Papantonis)

Bibliography
  • Denker A and Wouter L (2016) The second decade of 3C technologies: detailed insights into nuclear organization. http://www.genesdev.org/cgi/doi/10.1101/gad.281964
  • Rao et al (2014) A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. http://dx.doi.org/10.1016/j.cell.2014.11.021
  • Papantonis A (2013) Transcription Factories: Genome Organization and Gene Regulation. dx.doi.org/10.1021/cr300513p | Chem. Rev. 2013, 113, 8683−8705
January 19
15.00 - 17.00 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Student seminars IV
January 22
9.00 - 10.45 a.m., Seminar room 1, First floor, Max Planck Institute for Biology of Ageing
Transcriptional regulation in development and disease
(Alvaro Rada-Iglesias)

Bibliography
  • Heinz S et al (2015) The selection and function of cell type-specific enhancers. Nat Rev Mol Cel Biol 16: 144-154.
  • Smith E, Shilatifard A (2014) Enhancer biology and enhanceropathies. Nat Struct Mol Biol 21: 210-219.
  • Won H et al (2016) Chromosome conformation elucidates regulatory relationships in developing human brain. Nature doi:10.1038/nature19847
  • Lupianez et al (2015) Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions http://dx.doi.org/10.1016/j.cell.2015.04.004
January 23
9.00 - 10.45 a.m., Seminar room 1, First floor, Max Planck Institute for Biology of Ageing
Functional annotation of the non-coding Genome
(Leo Kurian)

Bibliography
  • Montalbano A et al (2017) THigh-Throughput Approaches to Pinpoint Function within the Noncoding Genome. Mol Cell http://dx.doi.org/10.1016/j.molcel.2017.09.017
  • Engreitz et al (2016) Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nature doi:10.1038/nrm.2016.126
  • Kim J (2016) Genome editing comes of age. Nature Protocols doi:10.1038/nprot.2016.104
  • Barrangou R and Doudna JA (2016) Applications of CRIRISPR technologies in research and beyond. Nature Biotech doi:10.1038/nbt.3659
January 26
15.00 - 17.00 a.m., Seminar room 1, ground floor, Max Planck Institute for Biology of Ageing
Student seminars V
February 01
13.00 - 15.00 p.m., Seminar room 2, ground floor, Max Planck Institute for Biology of Ageing
Written exam
TBD Deadline Protocol

 

 

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last modification: December 10, 2017