News from the group:
CAMDA'17 Conference
ISMB/ECCB Track
22-23 July 2017,
Prague, Czech Republic
(read more)
Outstanding Presentation Prize
for PP Łabaj
at CAMDA'15 (photo)
OeAW APART fellowship
for PP Łabaj
(photo)

Sequencing Quality Control (SEQC) project,
MAQC Consortium 2011–2014 (read more)
Host–parasite interactions in biocontrol, WWTF grant 2010–2013 (read more)

Power and limitations of RNA-Seq,
FDA SEQC, Nature Biotechnology (read more)
Characterization and improvement of RNA-Seq precision,
Bioinformatics (read more)
Impact of heavy tails in microarray analysis, Bioinformatics (read more)
Novel conserved repeats in sorting signals,
FEBS Journal (read more)
Sound sensation gene,
Nature communications
(read more)
RNA interference in ageing research,
Gerontology (read more)
State-of-the-art applications and integrated analyses
We have applied established state-of-the-art tools to a variety challenging biological questions.

Fluorescence Microscopy of Interphase Nuclei (follow link for full Supplement) Most plants and animals have two copies of each chromosome in the normal chromosome set. Unbalanced numerical changes resulting from gains or losses of individual chromosomes (aneuploidy) usually have deleterious consequences. For example, Down syndrome in humans is caused by an extra (triplicate) copy of chromosome 21. Human tumor cells usually display numerous alterations in chromosome number and structure. Little is known about how changes in chromosome number influence gene activity and chromosome integrity, thereby perturbing physiology and development. The current literature, moreover, seems to be divided regarding the question whether in an organism with an extra chromosome most of the genes on the extra chromosome reflect the dosage M(A) plot of the systemic increase of expression for chromosome-5 genes in the trisomic plants, as a function of the average gene expression level (on the x-axis). Transcripts on chromosome 5 are coloured green, and the intensity dependent trend plus/minus standard deviation is plotted in magenta. (follow link for full figure and legend) increase. In such assessments, classical analyses face the problem that a large number of genes change in an asymmetric way, invalidating most commonly used normalization approaches. Using appropriate transforms, however, we could show in Huettel et al. (2008) that most genes indeed reflect the dosage increase, with only a small percentage being regulated differentially from this trend.

In Kanno et al. (2008), we could identify and, by way of domain-based sequence analysis, discuss a novel protein involved in RNA-directed DNA methylation. The protein is interesting in that it contains the SMC hinge but no other SMC domains.

References

  1. Huettel B,* Kreil DP,* Matzke M, Matzke AJ (2008) Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet. 4, e1000226. (read more | Supplement)
  2. Kanno T, Bucher E, Daxinger L, Huettel B, Böhmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet. 40, 670–5 (preprint on request)
[*=joint first]

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