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T-Reg Comparator

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Tomasz Zemojtel

Dr. sc. hum.
Dipl. Ing. (TU) Computer Science

Max Planck Institute for Molecular Genetics
Ihnestr. 73
14195 Berlin, Germany

Phone: + 49 30 8413-1147
Fax: + 49 30 8413-1152
Email: zemojtel@molgen.mpg.de

Research interests

· Genetic diagnostics

§ Inherited diseases

§ X-linked and autosomal recessive intellectual disability and related disorders

§ Applications of next generation sequencing (NGS) – based diagnostics

· Genomic impact of transposable elements (TEs)

§ TEs as seeds spreading transcription factor binding sites

§ Exonization of TEs

§ Alternative promoters within sequences of TE

§ Identification of active transposons in mammalian genomes
LINE-1 retrotransposons
http://l1base.molgen.mpg.de/
http://l1xplorer.molgen.mpg.de/

……

· Evolution of gene regulatory elements

Secondary interests

· Small G-proteins

· Nitric Oxide signaling pathway

Curriculum Vitae

2004.02- Staff Scientist, Max Planck Institute for Molecular Genetics, Dep. of Computational Molecular Biology, Berlin, Germany
Prof. Martin Vingron

2002.06- 2004.01. Assistant Professor, Univ. of Wuerzburg, Germany, Dep. of Bioinformatics

Prof. Thomas Dandekar, Prof. Joerg Schultz

2002.10 - 2003.11 Scientific Visitor, Boehringer Ingelheim Fellowship, EMBL, Heidelberg, Biocomputing unit,

Dr. Rebecca Wade Group

2002.06 - 2002.07 ESF fellow, Max Born Institute, Berlin

Dr. Nibbering Group

2001.08 - 2002.06 Research associate, Univ. of Freiburg, Germany, Institute for Mol. Med. and Cell Research,
Prof. Thomas Dandekar, Biocomputing Group

1999.10 - 2001.08 Research associate, Dep. of Biochemistry, Univ. of Califiornia San Diego, USA

Prof. Magde and Prof. Sharma groups

1999.09 –2002 Research associate, Innere Medizin I, Hematology/Oncology, Univ. of Freiburg, Germany

1998 - 1999 Teacher Assistant, Medical Academy of Gdansk, Poland

1998 Programmer, University of Gdansk, Poland

Degrees

2002-2005                   Doctor scientiarum humanarum, Medical Faculty, University of Heidelberg, Germany
                                    Summa cum Laude (2005)
                                    Supervisor: Prof. Dr. Thomas Dandekar, University of Würzburg, Germany

1994-1999 Dipl. Ing. (M.Sc.) Computer Science and Engineering,
Faculty of Electronics, Telecommunications and Informatics, Technical University of Gdansk, Poland

Publications (h-index: 11)
26	Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics. 2012 Feb 1.




25	Zemojtel T, Badge R.M. Active L1s in human brains. Science* 2011; E-letter:

24	Zemojtel T*, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M.
	CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol. 2011;3:1304-11.

23	Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, Püttmann L, Vahid LN, Jensen C, Moheb LA, Bienek M, Larti F, Mueller I, Weissmann R, Darvish H, Wrogemann K, Hadavi V, Lipkowitz B, Esmaeeli-Nieh S, Wieczorek D, Kariminejad R, Firouzabadi SG, Cohen M, Fattahi Z, Rost I, Mojahedi F, Hertzberg C, Dehghan A, Rajab A, Banavandi MJ, Hoffer J, Falah M, Musante L, Kalscheuer V, Ullmann R, Kuss AW, Tzschach A, Kahrizi K, Ropers HH.
	Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature. 2011; 478(7367):57-63.

22	Kolanczyk M, Mautner V, Kossler N, Nguyen R, Kühnisch J, Zemojtel T, Jamsheer A, Wegener E, Thurisch B, Tinschert S, Holtkamp N, Park SJ, Birch P, Kendler D, Harder A, Mundlos S, Kluwe L.
	MIA is a potential biomarker for tumour load in neurofibromatosis type 1. BMC Med. 2011; 9:82. PMID:21726432

21	Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R.
	Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene. 2011 Mar 1;473(2):139-49. PMID:21156198
20	Kolanczyk M, Pech M, Zemojtel T*, Yamamoto H, Mikula I, Calvaruso MA, van den Brand M, Richter R, Fischer B, Ritz A, Kossler N, Thurisch B, Spoerle R, Smeitink J, Kornak U, Chan D, Vingron M, Martasek P, Lightowlers RN, Nijtmans L, Schuelke M, Nierhaus KH, Mundlos S
	NOA1 is an essential GTPase required for mitochondrial protein synthesis. Mol Biol Cell. 2011 Jan 1;22(1):1-11.

19	Zemojtel T, Duchniewicz M, Zhang Z, Paluch T, Luz H, Penzkofer T, Scheele JS, Zwartkruis FJ. Retrotransposition and mutation events yield Rap1 GTPases with differential signalling capacity. BMC Evol Biol.* 2010;10:55. PMID:20170508 Scheele JS, Kolanczyk M, Gantert M, Zemojtel T, Dorn A, Sykes DP, Möbest DC, Kamps MP, Räpple D, Duchniewicz M. The Spt-Ada-Gcn5-acetyltransferase complex interaction motif of E2a is essential for a subset of transcriptional and oncogenic properties of E2a-Pbx1. Leuk Lymphoma. 2009; 50(5):816-28. PMID: 19399691


18

17	Lee JW, Zemojtel T, Shakhnovich E.
	Systems-level evidence of transcriptional co-regulation of yeast protein complexes. J Comput Biol. 2009;16(2):331-9. PMID: 19193150

16	Jürgens AS, Kolanczyk M, Moebest DC, Zemojtel T, Lichtenauer U, Duchniewicz M, Gantert MP, Hecht J, Hattenhorst U, Burdach S, Dorn A, Kamps MP, Beuschlein F, Räpple D, Scheele JS.
	PBX1 is dispensable for neural commitment of RA-treated murine ES cells. In Vitro Cell Dev Biol Anim. 2009; 45(5-6):252-63. PMID: 19148706

15	Zemojtel T*, Kielbasa SM, Arndt PF, Chung HR, Vingron M.
	Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends in Genetics 2009; 25(2):63-6. PMID: 19101055

14	Raepple D, von Lintig F, Zemojtel T, Duchniewicz M, Jung A, Lübbert M, Boss GR, Scheele JS.
	Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation. Ann Hematol. 2009; 88(4):319-24. PMID: 18784923

13	Zemojtel T*, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M.
	Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics 2007; 8(1):392. PMID: 17963496

12	Lichtenauer UD, Duchniewicz M, Kolanczyk M, Hoeflich A, Hahner S, Else T, Bicknell AB, Zemojtel T*, Stallings NR, Schulte DM, Kamps MP, Hammer GD, Scheele JS, Beuschlein F.
	Pre-B-cell transcription factor 1 and steroidogenic factor 1 synergistically regulate adrenocortical growth and steroidogenesis. Endocrinology 2007; 148(2):693-704. PMID: 17082260

11	Zemojtel T*, Fröhlich A, Palmieri MC, Kolanczyk M, Mikula I, Wyrwicz LS, Wanker EE, Mundlos S, Vingron M, Martasek P, Durner J.
	Plant nitric oxide synthase: a never-ending story? Trends in Plant Science 2006; 11(11):524-5. PMID: 17030145

10	Duchniewicz M and Zemojtel T*, Kolanczyk M, Grossmann S, Scheele JS, Zwartkruis FJ.
	Rap1A-deficient T and B cells show impaired integrin-mediated cell adhesion. Mol Cell Biol. 2006 ; 26(2):643-53. PMID: 16382154

9	Zemojtel T* and Kolanczyk M, Kossler N, Stricker S, Lurz R, Mikula I, Duchniewicz M, Schuelke M, Ghafourifar P, Martasek P, Vingron M, Mundlos S.
	Mammalian mitochondrial nitric oxide synthase: characterization of a novel candidate. FEBS Lett. 2006 Jan 23;580(2):455-62. PMID: 16380119

8	Zemojtel T*, Penzkofer T, Duchniewicz M, Zwartkruis FJ.
	HRap1B-retro: a novel human processed rap1B gene blurs the picture? Leukemia. 2006; 20(1):145-6; author reply 146-7. PMID: 16307016

7	Penzkofer T, Dandekar T, Zemojtel T*.
	L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res. 2005; 33(Database issue):D498-500. PMID: 15608246

6	Ginalski K and Zemojtel T*.
	ECEPE proteins: a novel family of eukaryotic cysteine proteinases. Trends Biochem Sci. 2004; 29(10):524-6. PMID: 15450606

5	Zemojtel T*, Penzkofer T, Dandekar T, Schultz J.
	A novel conserved family of nitric oxide synthase? Trends Biochem Sci. 2004; 29(5):224-6. PMID: 15130557

4	Zemojtel T*, Rini M, Heyne K, Dandekar T, Nibbering ET, Kozlowski PM.
	NO-bound myoglobin: structural diversity and dynamics of the NO ligand. J Am Chem Soc. 2004; 126(7):1930-1. PMID: 14971914

3	Zemojtel T*, Wade RC, Dandekar T.
	In search of the prototype of nitric oxide synthase. FEBS Lett. 2003; 554(1-2):1-5. PMID: 14596904

2	Zemojtel T and Scheele JS, Martasek P, Masters BS, Sharma VS, Magde D.
	Role of the interdomain linker probed by kinetics of CO ligation to an endothelial nitric oxide synthase mutant lacking the calmodulin binding peptide (residues 503-517 in bovine). Biochemistry. 2003; 42(21):6500-6. PMID: 12767233

1	Scheele JS, Bruner E, Zemojtel T, Martasek P, Roman LJ, Masters BS, Sharma VS, Magde D.
	Kinetics of CO and NO ligation with the Cys(331)-->Ala mutant of neuronal nitric-oxide synthase. J Biol Chem. 2001; 276(7):4733-6. PMID: 11067850