Research Interests:

• Sequence Analysis:
  
  Method development to analyze Next Generation Sequencing (NGS) data
  Detection of Structural Variations
  Assessment of the variability of genomes
  
• High performance computing:
  
  Programming on GPU Graphics Cards (CUDA, OpenCL)
  Programming on CPUs (SSE, AVX)
  Programming on Grid Engine (SGE, Slurm)
  

Short Vita:

Professional Experience:

• December 2014 - present : Computational Sci. Analyst I at the Schatz Lab, Cold Spring Harbor Laboratories (CSHL)
• December 2012 - December 2014 : Post Doc at the Center for Integrative Bioinformatics Vienna (CIBIV)
• September 2008 - December 2012: PhD at the Center for Integrative Bioinformatics Vienna (CIBIV)
• September 2007 - June 2008: EMBL Heidelberg, Frangakis Group

Education:

• 2012: Dr. rer. nat. Bioinformatics
• 2008: Diplom (FH) Bioinformatics
• 2003: Abitur

Degree:

• 'Ph.D' in Molecular Biology (Dr. rer. nat.), Vienna, Austria, 2012
  Thesis: Benchtop sequencing on benchtop computers.
• DI (FH) (2008), Hagenberg
  Thesis: Correlative Cryo-Fluorescence and cryo-Electron Microscopy.

Fellowships, Fundings, and Awards:

• Vienna Biocenter PhD Award (2013)
• Leonardo da Vinci II Traineeship (2007)

Publications

2015
• R. Ming, R. VanBuren, C.M. Wai, H. Tang, M.C. Schatz, J.E. Bowers, E. Lyons, M. Wang, J. Chen, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, Z. Lin, H. Wang, H. Zhou, W.C. Yim, H.D. Priest, C. Zheng, M. Woodhouse, P.P. Edger, R. Guyot, H. Guo, H. Guo, G. Zheng, R. Singh, A. Sharma, X. Min, Y. Zheng, H. Lee, J. Gurtowski, F.J. Sedlazeck, A. Harkess, M.R. McKain, Z. Liao, J. Fang, J. Liu, X. Zhang, Q. Zhang, W. Hu, Y. Qin, K. Wang, L. Chen, N. Shirley, Y. Lin, L. Liu, A.G. Hernandez, C.L. Wright, V. Bulone, G.A. Tuskan, K. Heath, F. Zee, P.H. Moore, R. Sunkar, J. H. Leebens-Mack, T. Mockler, J.L. Bennetzen, M. Freeling, D. Sankoff, A.H. Paterson, X. Zhu, X. Yang, J.A.C. Smith, J.C. Cushman, R.E. Paull, Q. Yu (2015) The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. (DOI: 10.1038/ng.3435)
• 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)
• M. Tscherner, F. Zwolanek, S. Jenull, F.J. Sedlazeck, A. Petryshyn, I.E. Frohner, J. Mavrianos, N. Chauhan, A. von Haeseler, and K. Kuchler (2015) The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog., 11, e1005218. (DOI: 10.1371/journal.ppat.1005218, PMID: 26473952)
• J. Cheng, F. Sedlazek, J. Altmüller, and A. Nolte (2015) Ectodysplasin signalling genes and typic evolution in sculpins (Cottus). Proc. R. Soc. B, 282, 20150746. (DOI: 10.1098/rspb.2015.0746, PMID: 26354934)
• M. Krunic^e, R. Ertl^e, B. Hagen, F.J. Sedlazeck, R. Hofmann-Lehmann, A. von Haeseler and D. Klein (2015) Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. BMC Vet. Res., 11, 90. (DOI: 10.1186/s12917-015-0378-9, PMID: 25879730)
2014
• C. Vesely, S. Tauber, F. Sedlazeck, M. Tajaddod, A. von Haeseler, and M. Jantsch (2014) ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res., in press. (DOI: 10.1093/nar/gku844, PMID: 25260591)
2013

• F.J. Sedlazeck^e, P. Rescheneder^e, 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).

• S. Jünemann, F.J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye and D. Harmsen (2013) Updating benchtop sequencing performance comparison. Nat. Biotechnol., 31, 294-296. (DOI: 10.1038/nbt.2522, PMID: 23563421)

• F.J. Sedlazeck, P. Talloji, A. von Haeseler, and A. Bachmair (2013) Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics, 101, 204-209. (DOI: 10.1016/j.ygeno.2012.12.001, PMID: 23246509)
2012

• H.Q. Dinh, M. Dubin^e, F.J. Sedlazeck^e, N. Lettner, O. Mittelsten Scheid, and A. von Haeseler (2012) Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis. PLoS ONE, 7, e41528. (DOI: 10.1371/journal.pone.0041528, PMCID: PMC3401099)

• P. Rescheneder, A. von Haeseler, and F.J. Sedlazeck (2012) MASon: Million Alignments In Seconds - A Platform Independent Pairwise Sequence Alignment Library for Next Generation Sequencing Data. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012), 195-201, SciTePress, Setubal, Portugal. (DOI: 10.5220/0003775701950201)

• C. Vesely^e, S. Tauber^e, F.J. Sedlazeck, A. von Haeseler, and M.F. Jantsch (2012) Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res., 22, 1468-1476. (DOI: 10.1101/gr.133025.111, PMID: 22310477)

^e contributed equally

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