User profiles for P. Rescheneder

Philipp Rescheneder

Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of …
Verified email at univie.ac.at
Cited by 3164

Accurate detection of complex structural variations using single-molecule sequencing

FJ Sedlazeck, P Rescheneder, M Smolka, H Fang… - Nature …, 2018 - nature.com
… Using the Illumina data and a P value threshold of 0.01 (two-sided, one-sample t-test), we
confirmed 3,415 (PacBio) and 3,879 (Oxford Nanopore) deletions and 2,685 (PacBio) and …

Thiol-linked alkylation of RNA to assess expression dynamics

…, B Reichholf, T Neumann, P Rescheneder, P Bhat… - Nature …, 2017 - nature.com
… We observed a significant increase in relative mRNA stability for targets of the miR-291a
family when compared with transcripts without target site (KS test, P < 10 −15 and P < 10 −4 for …

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

FJ Sedlazeck, P Rescheneder, A Von Haeseler - Bioinformatics, 2013 - academic.oup.com
When choosing a read mapper, one faces the trade off between speed and the ability to
map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate …

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

…, C Umkehrer, J Jude, C Wieshofer, P Rescheneder… - Science, 2018 - science.org
Defining direct targets of transcription factors and regulatory pathways is key to
understanding their roles in physiology and disease. We combined SLAM-seq [thiol(SH)–linked …

A-type lamins bind both hetero-and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha

K Gesson, P Rescheneder, MP Skoruppa… - Genome …, 2016 - genome.cshlp.org
Lamins are components of the peripheral nuclear lamina and interact with heterochromatic
genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1 being …

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

…, K Ng, T Baslan, FJ Sedlazeck, P Rescheneder… - Genome …, 2018 - genome.cshlp.org
The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which
affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although …

[HTML][HTML] The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation

…, M Lybecker, N Popitsch, P Rescheneder… - PLoS …, 2015 - journals.plos.org
… burgdorferi recovery from starvation, we starved 32 P-labeled cells for 6 h in RPMI before
returning them to BSK + RS for 10 min (Fig 1A, lane 4) or 2 h (Fig 1A, lane 5). (…

[HTML][HTML] Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

…, J Zuber, SL Ameres, P Rescheneder - BMC …, 2019 - Springer
… a labeling time long enough that all transcripts are labeled (p SU =1) for all 3' intervals to
retrieve P T→C . Since we assume that P T→C is constant for a given experiment we obtain …

Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation

I Bilusic, N Popitsch, P Rescheneder, R Schroeder… - RNA biology, 2014 - Taylor & Francis
… Moreover, DicF was enriched with the p-value just above the threshold (p adj = 0.052),
while 3 other sRNAs were not enriched. SroC, a sRNA shown to bind Hfq in SalmonellaCitation …

[PDF][PDF] Natural RNA polymerase aptamers regulate transcription in E. coli

N Sedlyarova, P Rescheneder, A Magan, N Popitsch… - Molecular cell, 2017 - cell.com
In search for RNA signals that modulate transcription via direct interaction with RNA
polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding …