Medhat Mahmoud PostDoc

Research

I am a computational Biologist focusing on method developing for sequencing applications.
In general, my interests focus on three key areas:

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)

Education

M.Sc In Genetic Enginerring and Biotechnology, Bioinformatics department, 2011
Ph.D in Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań Poland 2018

Work experience

08/2007-01/2008: Internship
- The European Molecular Biology Laboratory
- Duties included: Method development for cryo electron microscopy
- Supervisor: Achilleas Frangakis
11/2008-12/2012: PhD student
- Cibiv - Max F. Perutz Laboratories
- Duties included: Method development for NGS and SVs detection
- Supervisor: Arndt von Haeseler
01/2013-12/2014: PostDoc
- Cibiv - Max F. Perutz Laboratories
- Duties included: Method development for NGS and SVs detection
- Supervisor: Arndt von Haeseler
12/2014-12/2015: Computational Sci. Analyst I
- Simons Center for Quantitative Biology - Cold Spring Harbor Laboratories
- Duties included: Method development for NGS and SVs detection
- Supervisor: Michael C. Schatz
12/2015-04/2017: PostDoc
- Department of Computer Science - Johns Hopkins University
- Duties included: Method development for NGS and SVs detection
- Supervisor: Fritz J Sedlazeck
09/2018-present: PostDoc
- HGSC, Baylor College of Medicine
- Duties included: Method development for NGS and SVs detection
- Supervisor: Michael C. Schatz

Publications

Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis

H.Q. Dinh, M. Dubin*, F.J. Sedlazeck*, N. Lettner, O. Mittelsten Scheid, and A. von Haeseler (2012). "Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis." Genome Research. 22, 1468-1476.

Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets

F.J. Sedlazeck, P. Talloji, A. von Haeseler, and A. Bachmair (2012). "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.

Updating benchtop sequencing performance comparison

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." Nature Biotechnology. 31, 294-296.

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

F.J. Sedlazeck∗, P. Rescheneder∗, and A. von Haeseler (2013). "NextGenMap: fast and accurate read mapping in highly polymorphic genomes." Bioinformatics. 29, 2790-2791.

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs

C. Vesely, S. Tauber, F.J. Sedlazeck, M. Tajaddod,A. von Haeseler, M.F. Jantsch (2014). "ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain." Nucleic Acids Research. 42, 2155-12168.

Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study

M. Krunic, R. Ertle, B. Hagen, F.J. Sedlazeck, R. Hofmann- Lehmann, A. von Haeseler and D. Klein (2012). "Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study." BMC Veterinary Research. 11, 90.

Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus)

J. Cheng, F.J. Sedlazeck, J. Altmüller, A.W. Nolte (2015). "Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus)." Proceedings B. 282, 20150746.

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways

M. Tscherner, F. Zwolanek, S. Jenull, F.J. Sedlazeck, I.E. Frohner, N. Chauhan, A. von Haeseler and K. Kuchler (2012). "The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways." PLOS Pathogen. 11, e1005218.

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

M. Smolka, P. Rescheneder, M.C. Schatz, A. von Haeseler, F.J. Sedlazeck (2015). "Teaser: Individualized benchmarking and optimization of read mapping results for NGS data." Genome Biology. 16, 235.

The pineapple genome and the evolution of CAM photosynthesis

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(2012). "The pineapple genome and the evolution of CAM photosynthesis," Nature Genetics. 47, 1435-1442.

Chromosomal- Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

S. Vij, H. Kuh, I. S. Kuznetsova, A. Komissarov, A. A.Yurchenko, P. V. Heusden, S. Singh, N. M. Thevasagayam, P.S.R. Sridatta, K. Purushothaman, J.M. Saju1, J. Jiang, S.K. Mbandi, M. Jonas, A.H.Y. Tong, S. Mwangi, D. Lau, S.Y. Ngoh, W.C. Liew, X. Shen, L.S. Hon, J.P. Drake, M. Boitano, R. Hall, J. Chin, R. Lachumanan, J. Korlach, V. Trifonov, M. Kabilov, A. Tupikin, D. Green, S. Moxon, T. Garvin, F.J. Sedlazeck, G.W. Vurture, G. Gopikrishna, V.K. K, T.H. Noble, V. Scaria, S. Sivasubbu, D.R. Jerry, S.J. O’Brien, M.C. Schatz, T. Dalmay, S. Turner, S. Lok, A. Christoffels, L. Orbán(2012). "Chromosomal- Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding" Plos Genetics. 12(4): e1005954.

Phased diploid genome assembly with single-molecule real-time sequencing

C.S. Chin, P. Peluso, F.J. Sedlazeck, M. Nattestad, G.T. Con- cepcion, A. Clum, C. Dunn, R.O. Malley, R. Figueroa-Balderas, A. Morales-Cruz, G.R. Cramer, M. Delledonne, C. Luo, J.R. Ecker, D. Cantu, D.R. Rank, M.C. Schatz (2016) "Phased diploid genome assembly with single-molecule real-time sequencing." Nature Methods. 22, 1468-1476.

The genomic basis of circadian and circalunar timing adaptations in a midge

T.S. Kaiser, B. Poehn, D. Szkiba, M. Preussner, F.J. Sedlazeck, A. Zrim, T. Neumann, L. Nguyen, A.J. Betancourt, T. Hummel, H. Vogel, S. Dorner, F. Heyd, A. von Haeseler, K. Tessmar- Raible (2016). "The genomic basis of circadian and circalunar timing adaptations in a midge." Nature. 540, 69–73.

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

D.C. Jeffares, C. Jolly, M. Hoti, D. Speed, L. Shaw, C. Rallis, F. Balloux, C. Dessimoz*, J. Bähler*, F.J. Sedlazeck* (2017). "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast." Nature Communications. 14061.

GenomeScope: fast reference-free genome profiling from short reads

G. Vurture*, F.J. Sedlazeck*, M. Nattestad, C. Underwood, H. Fang, J. Gurtowski, M.C. Schatz, (2017). "GenomeScope: fast reference-free genome profiling from short reads." Bioinformatics. 33 (14): 2202-2204.

DangerTrack: A scoring system to detect difficult-to-assess regions

I. Dolgalev*, , F.J. Sedlazeck* , B. Busby (2017). "DangerTrack: A scoring system to detect difficult-to-assess regions." F1000 Research. 6:443.

Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin

S. Dennenmoser, F.J. Sedlazeck, E. Iwaszkiewicz, X. Li, J. Alt- müller, A.W. Nolte (2017). "Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin." Molecular Ecology.

LRSim: A Linked-Reads Simulator generating insights for better genome partitioning.

R. Luo, FJ. Sedlazeck, CA. Darby, SM. Kelly, MC. Schatz (2017). "LRSim: a Linked Reads Simulator generating insights for better genome partitioning" Computational and Structural Biotechnology Journal.

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.

FJ. Sedlazeck, H. Lee, CA. Darby, MC. Schatz (2018). "Piercing the dark matter: bioinformatics of long-range sequencing and mapping." Nature Genetics Reviews.

Accurate detection of complex structural variations using single-molecule sequencing.

FJ. Sedlazeck, P. Rescheneder, M. Smolka, H. Fang, M. Nattestad, A. Haeseler, MC. Schatz (2018). "Accurate detection of complex structural variations using single-molecule sequencing." Nature Methods.

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

M. Nattestad, S. Goodwin, K. Ng, T. Baslan, FJ. Sedlazeck, P. Rescheneder, T. Garvin, H. Fang, J. Gurtowski, E. Hutton, E. Tseng, J. Chin, T. Beck, Y. Sundaravadanam, M. Kramer, E. Antoniou, J. McPherson, J. Hicks, WR. McCombie, MC Schatz. (2018). "Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line." Genome Research.