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Max F. Perutz Laboratories
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Philipp Rescheneder


Short Vita:

Education:

  • 2012 - present: Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Phd.
  • 2009 - 2012: Medical University of Vienna, Medical Informatics, MSc.
  • 2006 - 2009: University of Applied Sciences Hagenberg, Bioinformatics, BSc.
  • 1999 - 2004: HTL Wien Donaustadtstraße, Department for Applied Computer Science and Economics

Professional Experience:

  • 2015: Visiting PhD student at Cold Spring Harbor Labs (Schatz group)
  • 2012 - present: PhD student at the Center for Integrative Bioinformatics Vienna
  • 2010 - 2012: Master student at the Center for Integrative Bioinformatics Vienna
  • 2009: Internship at the Stockholm Bioinformatics Center (Sonnhammer group)

Degree:

  • 'Dipl.-Ing.' (2012), Vienna, Austria
  • 'B.Sc.' (2009), Hagenberg, Austria

Publications

2016
  • K. Gessone, P. Reschenedere, M.P. Skoruppa, A. von Haeseler, T. Dechat, and R. Foisner (2016) A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha. Genome Res., 26, in press. (DOI: 10.1101/gr.196220.115, PMID: 26798136)
    e contributed equally
2015
  • M. Smolka, P. Rescheneder, M. Schatz, A. von Haeseler and F.J. Sedlazeck (2015)
    Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol., 16, 235. (DOI: 10.1186/s13059-015-0803-1, PMID: 26494581, PMCID: PMC4618857, Teaser webpage)

  • Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS (2015)
    The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation. PLoS Pathog 11(9): e1005160. doi:10.1371/journal.ppat.1005160
2014
  • Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M. (2014)
    Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biology, 11:83 - 82.
2013
  • F.J. Sedlazecke, P. Reschenedere, and A. von Haeseler (2013)
    NextGenMap: Fast and accurate read mapping in highly polymorphic genomes. Bioinformatics, 29, 2790-2791. (DOI: 10.1093/bioinformatics/btt468, PMID: 23975764)
    e contributed equally
2012
  • Rescheneder P., von Haeseler A. and J. Sedlazeck F. (2012)
    MASon: MILLION ALIGNMENTS IN SECONDS - A Platform Independent Pairwise Sequence Alignment Library for Next Generation Sequencing Data. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, pages 195-201. (DOI: 10.5220/0003775701950201)

Poster

  • NextGenMap-LR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis
    Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19.09.-2.09.2016. (poster)

  • NextGenMap-LR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis
    Genome Informatics 2015, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 28.10.-31.10.2015. (poster)

  • NextGenScores: Fast Alignment-based Estimation of Intragenomic Sequence Similarities
    ISMB 2014, John B. Hynes Memorial Convention Center, Boston, Massachusetts, USA, 13.7.-15.7.2014. (poster)

  • NextGenMap: An ultra fast and sensitive tool for aligning Next Generation Sequencing reads
    Genome Informatics 2012, Robinson College, Cambridge, UK, 6.9.-9.9.2012. (program)

Tools

  • NextGenMap-LR
    NextGenMap-LR is a long-read mapper desigend to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was desigend to correctly align reads stemming from (complex) structural variations. NextGenMap-LR uses an SV aware k-mer search to find approximate mapping locations for a read and a banded Smith-Waterman alignment algorithm with a non-affine gap model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows NextGenMap-LR to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from (complex) structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling NextGenMap-LR to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions). Currently NextGenMap-LR takes about 60 minutes (on a AMD Opteron 6348) and 10 GB RAM for aligning 1Gbp of Pacbio Reads when using 10 threads.
  • SlamDunk
  • NextGenMap
    NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.
  • Teaser
    Teaser analyzes the performance of read mappers based on a data set provided by you. After you enter key characteristics such as read length and reference genome, Teaser will simulate read data including the gold standard alignment. After the simulation, Teaser automatically runs and evaluates each mapper for the selected parameters and summarizes the results in a report. Teaser also supports benchmarking mappers on real data or custom simulations, as well as testing new mappers and custom parameter sets. You can start using Teaser right now using this web application, or download and install it to unlock all advanced features.

Addresses

Philipp Rescheneder

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University, and Medical University, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2
A-1030 Wien, Austria
Phone: +43 1 4277-74324
Email: philipp(DOT)rescheneder(AT)univie.ac.at

Postal Address:

Center for Integrative Bioinformatics Vienna (CIBIV)
Max F. Perutz Laboratories (MFPL)
Dr. Bohr Gasse 9
A-1030 Wien, Austria



Philipp Rescheneder - Last Change: 01.Nov.2016 .