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Profile summary

Scientific publications (peer reviewed)

Professional experience

Education

Awards, scholarships, fellowships

Book chapters

Invited talks and tutorials


Contact:

Biocomputing Group
Department of Physics
Sapienza - University of Rome
P.le A. Moro 5 - 00185 Rome - Italy

jan.kosinski@uniroma1.it
jan.kosinski@gmail.com

jan

Profile summary:

Highly experienced bioinformatician with over 10 years experience and 18 peer-reviewed publications in bioinformatics and molecular biology. Possess a unique expertise integrating experimental biology, bioinformatics and advanced computer programming. Mastered a wide variety of bioinformatics techniques to study evolution, structure, dynamics, and function of proteins and their complexes. Obtained several awards and fellowships. Experienced in writing fellowship and grant applications. Supervised students, gave courses and lectures in bioinformatics for both bioinformaticians and other biologists.

 

Scientific publications (peer reviewed):
  1. Kosinski, J., Barbato, A., Tramontano, A. "MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships" (2013) Bioinformatics, in press
  2. Barbato A., Benkert P., Schwede T., Tramontano A. and Kosinski J. "Improving your target-template alignment with MODalign" (2012) Bioinformatics  28(7):1038-9
  3. Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM. "REPAIRtoire--a database of DNA repair pathways" (2011) Nucl. Acids Res. 39 (suppl 1)
  4. Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G. "Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair" (2010) Hum Mutat. Aug;31(8):975-82
  5. Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG. "Physiological truncation and domain organization of a novel uracil-DNA-degrading factor" (2010) FEBS J. 277(5):1245-59
  6. Kosinski, J., Plotz, G., Guarné, A., Bujnicki, J.M. and Friedhoff P. “The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family” (2008) J Mol Biol 382(3):610-27

  7. Liu, Y., Li, Z., Lin, Q., Kosinski, J., Seetharaman, J., Bujnicki, J.M., Sivaraman, J. and Hew, C.L. “Structure and Evolutionary Origin of Ca2+-Dependent Herring Type II Antifreeze Protein” (2007) PLoS ONE 2(6):e548

  8. Kosinski, J., Kubareva, E. and Bujnicki, J.M. “A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.” (2007) Proteins 68(1):324-36

  9. Miyazono, K., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J.M., Endo, Y., Tanokura, M. and Kobayashi, I. “Novel protein fold discovered in the PabI family of restriction enzymes” (2007) Nucleic Acids Res 35(6):1908-18.

  10. Chovancova, E., Kosinski, J., Bujnicki, J.M. and Damborsky, J. “Phylogenetic analysis of haloalkane dehalogenases” (2007) Proteins 67(2):305-16

  11. Ahrends, R., Kosinski, J., Kirsch, D., Manelyte, L., Giron-Monzon, L., Hummerich, L., Schulz, O., Spengler B. and Friedhoff, P. “Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry” (2006) Nucleic Acids Res 34(10):3169-80

  12. Zegers, I., Gigot, D., van Vliet, F., Tricot, C., Aymerich, S., Bujnicki, J.M., Kosinski, J. and Droogmans, L. “Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase” (2006) Nucleic Acids Res 34(6):1925-34

  13. Skowronek, K.J., Kosinski, J. and Bujnicki, J.M. “A theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis” (2006) Proteins 63(4):1059-68

  14. Armalyte, E., Bujnicki, J.M., Giedriene, J., Gasiunas, G., Kosinski, J., Lubys, A. “Mva1269I: a monomeric type IIS restriction endonuclease from micrococcus varians with two EcoRI- and FokI-like catalytic domains.” (2005) J Biol Chem 280(50):41584-94

  15. Kosinski, J., Gajda, M.J., Cymerman, I.A., Kurowski, M.A., Pawlowski, M., Boniecki, M., Obarska, A., Papaj, G., Sroczynska-Obuchowicz, P., Tkaczuk, K.L., Sniezynska, P., Sasin, J.M., Augustyn, A, Bujnicki, J.M. and Feder, M. "FRankenstein becomes a cyborg: on the automation of the method for protein structure prediction by recombination and realignment of Fold-Recognition models and its application in CASP6" (2005) Proteins; 61 Suppl 7:106-13.

  16. Kosinski, J., Steindorf, I., Bujnicki, J.M., Giron-Monzon, L. and Friedhoff, P. “Analysis of the quaternary structure of the MutL C-terminal domain” (2005) J Mol Biol 351(4):895-909

  17. Kosinski, J., Feder, M. Bujnicki, J.M. “The PD-(D/E)xK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function” (2005) BMC Bioinformatics 6:172

  18. Kosinski, J., Cymerman, I.A., Feder, M., Kurowski, M.A., Sasin, J.M. oraz Bujnicki, J.M. (2003). "A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation." Proteins 53 Suppl 6: 369-79.

  19. Ye, X., O`Neil P.K., Gorenstein N.M., Foster A.N., Gajda, M.J. Kosinski J., Kurowski M.A., Bujnicki J.M., Friedman A.M., Bailey-Kellogg C. (2004). “Probabilistic Cross-Link Analysis and Experiment Planning for High-Throughput Elucidation of Protein Structure” Protein Science 13: 3298-331

Professional experience:

  • 2009, December - present: Postdoctoral researcher in Biocomputing Group at the Department of Biochemical Sciences, "Sapienza" University, Rome, Italy
  • 2009, October – 2009, November: research assistant in the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology, Warsaw

  • 2005, June – 2009, September: Ph.D. student in the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology, Trojdena 4, 02-190 Warsaw, Poland (supervisor – dr. habil. Janusz M. Bujnicki)

  • 2006, September: participation in EMBO practical course on "Bioinformatics for Mass Spectrometry in Proteomics", Les Diablerets, Switzerland

  • 2006, May – August: participation in 7th edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7)

  • 2006, March – June: Ph.D internship – Institute of Biochemistry, University of Giessen, Germany (supervisor – dr. Peter Friedhoff)

  • 2005, November: visitig scientist – Organic Chemistry Department, Masaryk University, Brno, Czech Republic (Dr. J. Damborsky group)

  • 2005, October: participation in EMBO practical course on “Combination of Electron Microscopy and X-ray Crystallography in Structure Determination”, Gif-sur-Yvette, France

  • 2005, July – September: Ph.D internship – Institute of Biochemistry, University of Giessen, Germany (supervisor – dr. Peter Friedhoff)

  • 2004, September – December: student internship - Institute of Biochemistry, University of Giessen, Germany (supervisor – dr. Peter Friedhoff)

  • 2004, July – September: participation in 6th edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP6) as a member of one of the winner groups - Genesilico.pl Group

  • 2003, July – September: student internship - Institute of Biochemistry, University of Giessen, Germany (supervisor – dr Peter Friedhoff).

  • 2002, July – September: participation in 5th edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP5) as a member of one of the winner groups - Genesilico.pl Group

  • 2001 – 2005: undergraduate student in the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology, Trojdena 4, 02-190 Warsaw, Poland

Education:

  • 2009Ph.D. degree in biological sciences; thesis “Dissecting molecular basis of dysfunction of protein complexes involved in DNA mismatch repair by characterization of their structure and mutual interactions, and their mechanism of action”; awarded by Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-106 Warszawa, Poland; Supervisor of a Ph.D. thesis: prof. dr. habil. Janusz M. Bujnicki

  • 2005 – 2009; Ph.D student in Postgraduate School of Molecular Medicine, Pasteura 3, 02-093 Warsaw, Poland (http://www.smm.edu.pl/)

  • 2005 – M.Sc. in Biotechnology molecular biology; thesis “Protein structure prediction using the „FRankenstein’s monster approach” in CASP5 and CASP6” at the Faculty of Biology, University of Warsaw, Poland

  • 2004 – B.Sc. degree in molecular biology; thesis “Phylogenetic and structural analysis and identification of new members of the DNA:m5C methyltransferases family” at the Faculty of Biology, University of Warsaw, Poland

  • 2001 – 2005 student of Centre for Interfaculty Individual Studies in Mathematical and Natural Sciences (MISMaP) at the University of Warsaw

Awards, scholarships, fellowships:


  • 2010-2012: EMBO Long-Term Fellowship

  • 2010: Polish Prime Minister Award for PhD thesis

  • 2010: Polish Bioinformatics Society for the best bioinformatic PhD thesis in 2009

  • 2009, December - 2010, February: fellowship funded from KAUST Global Research Partnership award to Anna Tramontano

  • 2009: Mazovian Doctoral Scholarship for the best students in Mazovia region in the frame of Integrated Regional Operational Programme.

  • 2007 – 2009: START Programme stipend from Foundation of Polish Science

  • 2005 – present: PhD Scholarship from the Postgraduate School of Molecular Medicine

  • 2004, September – December: awarded an Exchange Grant from the European Science Foundation (ESF) 'Integrated Approaches for Functional Genomics' program

  • 2003 – 2004: PZU Życie S.A. scholarship for talented students of University of Warsaw

  • 2002 – 2004: academic scholarship for excellent results in education

Book chapters:

  1. Kosinski, J., Tkaczuk, K.L., Kasprzak, J. and Bujnicki, J.M. “Template based prediction of three-dimensional protein structures: Fold recognition and comparative modeling” In "Prediction of Protein Structures, Functions and Interactions". Editor: Bujnicki JM. Wiley & Sons 2009

Popular science articles:

  1. Bujnicki, J.M., Ginalski, K., Koliński, A. and Kosiński, J. „Odgadywanie struktur życia” (2006) Świat Nauki 2(174) (publication in Polish version of Scientific American)

Invited talks and tutorials:

  • Kosinski J. Practical course "Protein structure manipulation and basics of structure prediction" on Poznan Summer School of Bioinformatics, July 2009, Poznan, Poland
  • Kosinski J. Theoretical tutorial "Comparative structural modeling of proteins and protein-DNA complexes: What can and what can’t be predicted" on the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference in Computational Biology and Bioinformatics, Stockholm, Sweden, June/July 2009
  • Kosinski J. Theoretical tutorial "From sequence to structure and function: Structural modeling of proteins and protein-DNA complexes by comparative methods" on European Conference in Computational Biology and Bioinformatics 2008 (ECCB08), Cagliari, Sardinia-Italy, September 2008
  • Kosinski J. Lecture "Protein structure prediction" and practical course: "Modeling of protein structures by comparative methods". Bionformatics in Torun 2008 Conference; Torun, Poland, June 2008.
  • Kosinski J. Practical course "Modeling of protein-DNA complexes by comparative methods". „DNA Enzymes” Workshop (6FP MC-RTN grant); Warsaw, Poland, October 2007.
  • Feder, M. and Kosinski J., "Protein structure prediction with Dr FRankenstein" CASP6 meeting, Gaeta, Italy, December 2004

 







 

Last Updated ( Thursday, 14 February 2013 15:54 )