Szymon M. Kiełbasa

szymon.kielbasa at gmail.com, s.m.kielbasa at  lumc.nl

Curriculum vitae

[Education] * [Employment] * [Publications] * [Internships] * [Talks/Posters] * [Experience]

Education

2006

Dr. rer. nat. (in Biophysics, from Humboldt University in Berlin, Germany). The thesis, entitled “Bioinformatics of Eukaryotic Gene Regulation”  was prepared in Institute for Theoretical Biology, Humbolt University, Berlin, under supervision of prof. Hanspeter Herzel.

1998

M. Sc. (in Physics, from Jagiellonian University, Kraków, Poland). Diploma thesis title: “A strong semiconductor laser for analysis of gas properties at dielectric surfaces”. Supervised by prof. Tomasz Dohnalik.

Employment

Oct. 2011
- now

Assistant professor at Bioinformatics Center of Expertise, Leiden University Medical Center.

15. Jun. 2011
- Sep. 2011

Postdoctoral researcher in Computational Biology Group of dr. med. Peter N. Robinson at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin.

Mar. 2005
- 14. Jun. 2011

Postdoctoral researcher in the group of prof. Martin Vingron (Computational Molecular Biology) at Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany.

Nov. 1999
- Dec. 2004

PhD student in the group of prof. Hanspeter Herzel (Molecular and Cellular Evolution) at Institute of Theoretical Biology, Humbolt University, Invalidenstr. 43, D-10115 Berlin, Germany.

Dec. 2001
- Jun. 2003

Bioinformatican in MicroDiscovery GmbH, Marienburger Str. 1, D-10405 Berlin, Germany.

Sep. 1998
- Oct. 1999

Research assistant in the group of prof. Tomasz Dohnalik at Institute of Physics, Jagiellonian University, Reymonta 4, PL-30059 Kraków, Poland.

Publications

(Boldface, when first or shared first authorship; ➤ denotes main research area)

25.

Two Plasmodium 6-Cys family-related proteins have distinct and critical roles in liver-stage development.

Annoura T, van Schaijk BC, Ploemen IH, Sajid M, Lin JW, Vos MW, Dinmohamed AG, Inaoka DK, Rijpma SR, van Gemert GJ, Chevalley-Maurel S, Kielbasa SM, Scheltinga F, Franke-Fayard B, Klop O, Hermsen CC, Kita K, Gego A, Franetich JF, Mazier D, Hoffman SL, Janse CJ, Sauerwein RW, Khan SM.

(FASEB J. 2014 Feb 7)

(PERL)

24.

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.

Meyer P, Siwo G, Zeevi D, Sharon E, Norel R; DREAM6 Promoter Prediction Consortium (Siwo G, Rider AK, Tan A, Pinapati RS, Emrich S, Chawla N, Ferdig MT, Tung YA, Chen YS, Chen MJ, Chen CY, Knight JM, Sahraeian SM, Esfahani MS, Dreos R, Bucher P, Maier E, Saeys Y, Szczurek E, Mysicková A, Vingron M, Klein H, Kielbasa SM, Knisley J, Bonnell J, Knisley D, Kursa MB, Rudnicki WR, Bhattacharjee M, Sillanpää MJ, Yeung J, Meysman P, Rodríguez AS, Engelen K, Marchal K, Huang Y, Mordelet F, Hartemink A, Pinello L, Yuan GC), Segal E, Stolovitzky G.
(Genome Res., 2013)

(Oracle/QMAKE, D, R)

23.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium (Agius P, Arvey A, Bucher P, Callan CG Jr, Chang CW, Chen CY, Chen YS, Chu YW, Grau J, Grosse I, Jagannathan V, Keilwagen J, Kiełbasa SM, Kinney JB, Klein H, Kursa MB, Lähdesmäki H, Laurila K, Lei C, Leslie C, Linhart C, Murugan A, Myšičková A, Noble WS, Nykter M, Orenstein Y, Posch S, Ruan J, Rudnicki WR, Schmid CD, Shamir R, Sung WK, Vingron M, Zhang Z), Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

(Nat. Biotechnol., 2013)

(Oracle/QMAKE, D, R)

22.

Mutations in PIGO, a Member of the GPI-Anchor-Synthesis Pathway, Cause Hyperphosphatasia with Mental Retardation.

Krawitz PM, Murakami Y, Hecht J, Krüger U, Holder SE, Mortier GR, Delle Chiaie B, De Baere E, Thompson MD, Roscioli T, Kielbasa S, Kinoshita T, Mundlos S,Robinson PN, Horn D.

(Am J Hum Genet., 2012)

(SGE/QMAKE, PERL, D, R)

21.

CpG deamination creates transcription factor binding sites with high efficiency.

Żemojtel T, Kiełbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M.

(Genome Biol Evol., 2011)

(SGE/QMAKE, R, PERL, D)

20.

Adaptive seeds tame genomic sequence comparison. 

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC

(Genome Res., 2011)

(MAKE, SGE/QMAKE, R, BLAST/BLAT, C++/C, Suffix Arrays)

19.

What it takes to understand and cure a living system: Computational Systems Biology and a Systems-Biology driven PharmacoKinetics-PharmacoDynamics platform.

Swat M, Kiełbasa SM, Polak S, Olivier B, Bruggeman F, Tulloch MQ, Snoep JL, Westerhoff HV

(Biosim Focus Issue: Advancing Systems Medicine and Therapeutics through Biosimulation, 2011)

URL: http://www.sbpkpd.org

(Java/GWT, JavaScript, PERL, R)

18.

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells.

Jürchott K, Kuban RJ, Krech T, Blüthgen N, Stein U, Walther W, Friese C, Kiełbasa SM,  Ungethüm U, Lund P, Knösel T, Kemmner W, Morkel M, Fritzmann J, Schlag PM, Birchmeier W, Krueger T, Sperling S, Sers C, Royer HD, Herzel H, Schäfer R

(PLoS Genetics, 2010)

(PERL/contributed-library)

17.

TransFind--predicting transcriptional regulators for gene sets.

Kiełbasa SM, Klein H, Roider HG, Vingron M, Blüthgen N.

➤ Nucleic Acids Res. 2010 Jul 1;38 Suppl:W275-80. Epub 2010 May 28.

URL: http://transfind.sys-bio.net

(C++/Boost, MAKE, SGE/QMAKE, Joomla!, PHP)

16.

Targetfinder.org: a resource for systematic discovery of transcription factor target genes.

Kiełbasa SM, Blüthgen N, Fähling M, Mrowka R.

➤ Nucleic Acids Res. 2010 Jul 1;38 Suppl:W233-8. Epub 2010 May 11.

URL: http://www.targetfinder.org

(C++/Boost, MAKE, Joomla!, PHP)

15.

Regulation of clock-controlled genes in mammals.

Bozek K, Relógio A, Kielbasa SM, Heine M, Dame C, Kramer A, Herzel H.

PLoS One. 2009;4(3):e4882. Epub 2009 Mar 16.

(PERL/contributed-library)

14.

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts.

Blüthgen N, Legewie S, Kielbasa SM, Schramme A, Tchernitsa O, Keil J, Solf A, Vingron M, Schäfer R, Herzel H, Sers C.

FEBS J. 2009 Feb;276(4):1024-35. Epub 2009 Jan 12.

(PERL)

13.

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale.

Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M.

➤ Trends Genet. 2009 Feb;25(2):63-6. Epub 2008 Dec 26.

(PERL, MAKE, C++, R)

12.

Transcriptional autoregulatory loops are highly conserved in vertebrate evolution.

Kiełbasa SM, Vingron M.

➤ PLoS One. 2008 Sep 15;3(9):e3210.

(PERL, C++, MAKE, R)

11.

DisLex: a transformation for discontiguous suffix array construction.

Horton P, Kielbasa SM, Frith MC.

Proc. of the Workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI), pages 1–11. 2008.

(C++)

10.

Promoter analysis of Mammalian clock controlled genes.

Bozek K, Kiełbasa SM, Kramer A, Herzel H.

Genome Inform. 2007;18:65-74.

(PERL/contributed-library)

9.

Regulatory elements of marine cyanobacteria.

Kiełbasa SM, Herzel H, Axmann IM.

➤ Genome Inform. 2007;18:1-11.

(PERL, MAKE, GnuPlot)

8.

Measuring similarities between transcription factor binding sites.

Kielbasa SM, Gonze D, Herzel H.

➤ BMC Bioinformatics. 2005 Sep 28;6:237.

(C++, MAKE, R)

7.

Inferring combinatorial regulation of transcription in silico.

Blüthgen N, Kiełbasa SM, Herzel H.

➤ Nucleic Acids Res. 2005 Jan 12;33(1):272-9. Print 2005.

(C++, MAKE, GnuPlot)

6.

HuSiDa--the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells.

Truss M, Swat M, Kielbasa SM, Schäfer R, Herzel H, Hagemeier C.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D108-11.

(PHP, MySQL, R)

5.

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W235-41.

(Java)

4.

HOMGL-comparing genelists across species and with different accession numbers.

Blüthgen N, Kiełbasa SM, Cajavec B, Herzel H.

Bioinformatics. 2004 Jan 1;20(1):125-6.

(C++, MySQL, MAKE)

3.

Prediction of cis-regulatory elements of coregulated genes.

Kiełbasa SM, Blüthgen N, Sers C, Schäfer R, Herzel H.

➤ Genome Inform. 2004;15(1):117-24.

(C++, MAKE)

2.

Combining frequency and positional information to predict transcription factor binding sites.

Kiełbasa SM, Korbel JO, Beule D, Schuchhardt J, Herzel H.

➤ Bioinformatics. 2001 Nov;17(11):1019-26.

(C++, MAKE)

1.

Interatomic potentials of cadmium-argon B1(3sigma+) and X0+(1sigma+) states based on near-dissociation expansion and 'hot' bands observed in the B1 <-- X0+ excitation spectrum.

Koperski J, Kiełbasa SM, Czajkowski M.

Spectrochim Acta A Mol Biomol Spectrosc. 2000 Jul;56A(8):1613-26.

(C)

Internships

Sep.-Oct. 2009, Sep.-Oct. 2007

Computational Biology Research Center, Advanced Industrial Science and Technology, Tokyo, Japan

Oct. 2004,
Oct. 2003

Boston University, USA

Selected Talks/Posters/Events

Mar. 2011

poster

MASH6 method and applications (EuTRACC, Transcription Networks Symposium; Berlin, Germany)

Nov. 2010

DREAM5 challenge,
poster

own method “MASH6: Predicting transcription factor-DNA binding affinity using best k-mer contribution model”,  ranked 4/13 in the DREAM5 Challenge (RECOMB; New York, USA)

Aug. 2010

talk

co-authored manuscript “LAST – an efficient algorithm

for comparing large, repeat-rich sequences” presented at workshop “What are the best strategies for analyzing Next Generation Sequencing data?” (Berlin, Germany)

Jul. 2010

workshop (organizer),
talk

organization of joint workshop of  Depts. of prof. Vingron and prof. Tiuryn; presentation of own method “TransFind — predicting transcriptional regulators for gene sets”  (Sopot, Poland)

Jul. 2009

talk

“Are Autoregulatory Loops Conserved in Transcriptional Regulatory Networks?” (CBRC, AIST, Tokyo, Japan)

Feb. 2009

co-authored talk

“Methylation and deamination of CpGs generates p53 binding sites on a genomic scale” (Asilomar, CA, USA)

2007

talk

Conference talk “Regulatory Elements of Marine Cyanobacteria” (IBSB 2007, Tokyo, Japan)

2002, 2003

teaching

two one-semester courses of bioinformatics for students (Humbolt University)

Experience

Bioinformatics (own methods):

Bioinformatics (external methods/libraries/databases):

These programs I have integrated in my C++/PERL library (approx. 350 classes):

Programming/IT:
Other: