Jakub Paś

Jakub Paś (born September 27, 1977, in Śrem) is a Polish scientist and developer. He is a doctor of chemistry at the Faculty of Chemistry of Adam Mickiewicz University in Poznań.

Jakub Pas
Jakub Paś
Born27 September 1977 (1977-09-27) (age 46)
Śrem, Poland
Alma materAdam Mickiewicz University in Poznań
Scientific career
Fields
ThesisApplication and implementation of probabilistic profile-profile comparison methods for protein fold recognition (2013)

Early years

Pas was born in 1977 in Śrem, a small town near Poznan. He attended No. 4 Primary School in Śrem and the Józef Wybicki High School in Śrem; at that time, he succeeded as a laureate of Polish Mathematics Olympiad. In 2001, he was awarded the MSc in Biotechnology title at the Faculty of Biochemistry of Adam Mickiewicz University in Poznań; his thesis Sequential and structural analysis of proteins related to the BcFA (methyl branched-chain fatty acids), supervised by Leszek Rychlewski, was awarded distinction in of that year. In 2013, he defended his PhD thesis in chemistry, Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition[1][2][3] (under the supervision of Marcin Hoffmann). He also completed IT Project Management postgradual study on WSB School of Banking Poznan with thesis Transformation of the IT department and change of the technological process while maintaining the continuity of the product

Academic career

Already during his MSc course, Pas took an Socrates-Erasmus internship at the University Of Edinburgh under Lucy A Harrier supervision worked on bionformatics project explaining genomics of arbuscular mycorrhizal fungi. During his master's Pas worked on REFLAX[4] European project (for Rational Engineering of FLAX) that aimed at the integration of metabolic, physiological, molecular biological, genetical, structural biological, proteomics and bioinformatics studies to provide a basis for the rational engineering of oilseeds towards the production of BcFAs. Part of that research was included in his MSc thesis. Upon receiving his PhD degree, he was employed as research scientist in Bioinfobank Institute, Sanford Burnham Prebys Medical Discovery Institute and Howard Hughes Medical Institute. He also worked on fellowship in Max Planck Institute for Molecular Genetics and University of Catania. In 2007 Pas was granted Marie Curie Fellowship at Politehnica University of Bucharest where he received International Supercomputing Conference Poster Award for work GPGPU Accelerated Sparse Linear Solver for Fast Simulation of On-Chip Coupled Problems. In 2009 he received Marie Curie Reintegration Grant. As of 2018 Jakub Pas is employed at GSK plc.

Scientific activity

Pas research focuses on the application of computational methods for protein structure prediction, fold recognition and phylogeny, investigation of the structure of molecules[5] and the interactions between them.[6] During his work in Bioinfobank Institute Jakub Pas was involved in multiple European project such as ELM, SEPSDA, NARCISUS, DATAGENOME or BIOSAPIENS.[7] His applied work focuses on automation in pharmaceutical research, Continuous Integration / Continuous Development (CI/CD) and test automation in highly regulated industry. The results of his scientific research include:

  • Explanation of the mechanism of interaction between SARS coronavirus helicase/ATPase and ATP and design of potential inhibitors of this enzyme.[8]
  • ELM: the status of the 2010 eukaryotic linear motif [9]
  • ORFeus: detection of distant homology using sequence profiles and predicted secondary structure [10]
  • Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases [11]
  • Ligand. Info small-molecule meta-database [12]
  • Application of 3D-Jury, GRDB, and Verify3D in fold recognition [13]
  • Ligand-Info, searching for similar small compounds using index profiles [14]
  • Structure prediction, evolution and ligand interaction of CHASE domain [15]
  • Lead toxicity through the leadzyme [16]
  • Comparison of proteins based on segments structural similarity [17]
  • How unique is the rice transcriptome? [18]
  • Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum [19]
  • 3D-Hit: fast structural comparison of proteins[20]
  • The PDB-Preview database: a repository of in-silico models of ‘on-hold’PDB entries[21]
  • Two sequences encoding chalcone synthase in yellow lupin (Lupinus luteus l.) may have evolved by gene duplication[22]
  • GRDB - Gene Relational DataBase[23]
  • Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition [24]

These and other studies resulted in authorship and co-authorship of ca. 20 publications (21 according to Google Scholar), including highly prestigious scientific journals, such as Science, Nucleic Acid Research and Gene. His papers are increasingly cited year after year (totalling 1050 - Google Scholar), which yields 11 citations per publication and the h-index of 11.[25]

Educational activity

Since 2002, Pas has been actively training phylogeny and bioinformatics. He was also leading course molecular modeling and prediction of spatial structure of proteins. In 2004 Pas was leading Summer modeling school at Laboratory of Bioinformatics, Institute of Physics on Adam Mickiewicz University.

Other activities

Jakub Pas is currenttly working as Principal Automation Engineer in GSK plc. He is involved in open source software development and organizing Linux user group meetings. He is also a member of Project Management Institute and author of articles about contemporary music.[26][27][28][29]

References
  1. Jakub, Paś. "Jakub Paś PhD desideration" (PDF). AMUR - Adam Mickiewicz University Repository.
  2. Paś, Jakub. "Jakub Paś PhD review" (PDF). Adam Mickiewicz Unieversity Faculty of Chemistry.
  3. Wydział Chemii Uniwersytetu im. Adama Mickiewicza w Poznaniu : 1981-2016 : wydanie jubileuszowe. Henryk Koroniak, Andrzej Burewicz, Uniwersytet im. Adama Mickiewicza. Wydział Chemii, Uniwersytet im. Adama Mickiewicza. Wydawnictwo Naukowe. Poznań: Wydawnictwo Naukowe Uniwersytetu im. Adama Mickiewicza. 2016. ISBN 978-83-232-3094-6. OCLC 982589276.{{cite book}}: CS1 maint: others (link)
  4. Pas, Jakub. "REFLAX". Bioinfo.Pl. Retrieved 26 April 2023.
  5. Samayoa, Josue. Utilizing Rosetta and NMR Data in a Homology-based Modeling Approach. p. 41.
  6. Wang, Nian (2016). Virulence Mechanisms of Plant-Pathogenic Bacteria (1 ed.). APS Publications. pp. 107–124. ISBN 978-0-89054-449-5.
  7. Rychlewski, Leszek. "BioinfoBank European Projects".
  8. Plewczynski, D.; Hoffmann, M.; von Grotthuss, M.; Ginalski, K.; Rychewski, L. (April 2007). "In silico prediction of SARS protease inhibitors by virtual high throughput screening". Chemical Biology & Drug Design. 69 (4): 269–79. doi:10.1111/j.1747-0285.2007.00475.x. PMC 7188353. PMID 17461975.
  9. Gould, Cathryn M; Diella, Francesca; Via, Allegra; Puntervoll, P\aal; Gemünd, Christine; Chabanis-Davidson, Sophie; Michael, Sushama; Sayadi, Ahmed; Bryne, Jan Christian; Chica, Claudia; others (2010). "ELM: the status of the 2010 eukaryotic linear motif resource". Nucleic Acids Research. 39 (suppl_1): –167–D180.
  10. Ginalski, Krzysztof; Pas, Jakub; Wyrwicz, Lucjan S; Grotthuss, Marcin von; Bujnicki, Janusz M; Rychlewski, Leszek (2003). "ORFeus: detection of distant homology using sequence profiles and predicted secondary structure". Nucleic Acids Research. 31 (13): 3804–3807. doi:10.1093/nar/gkg504. PMC 168911. PMID 12824423.
  11. Feder, Marcin; Pas, Jakub; Wyrwicz, Lucjan S; Bujnicki, Janusz M (2003). "Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases". Gene. 302 (1–2): 129–138. doi:10.1016/S0378-1119(02)01097-1. PMID 12527203.
  12. Grotthuss, Marcin v; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek (2004). "Ligand. Info small-molecule meta-database". Combinatorial Chemistry & High Throughput Screening. 7 (8): 757–761. doi:10.2174/1386207043328265. PMID 15578937.
  13. Grotthuss, Marcin von; Pas, Jakub; Wyrwicz, Lucjan; Ginalski, Krzysztof; Rychlewski, Leszek (2003). "Application of 3D-Jury, GRDB, and Verify3D in fold recognition". Proteins: Structure, Function, and Bioinformatics. 53 (S6): 418–423. doi:10.1002/prot.10547. PMID 14579330. S2CID 6105634.
  14. von Grotthuss, Marcin; Pas, Jakub; Rychlewski, Leszek (2003). "Ligand-Info, searching for similar small compounds using index profiles". Bioinformatics. 19 (8): 1041–1042. doi:10.1093/bioinformatics/btg117. PMID 12761071. Pas, Jakub; Wyszko, Eliza; Rolle, Katarzyna; Rychlewski, Leszek; Nowak, Stanis\law; Żukiel, Ryszard; Barciszewski, Jan (2006). "Analysis of structure and function of tenascin-C". The International Journal of Biochemistry & Cell Biology. 38 (9): 1594–1602. doi:10.1016/j.biocel.2006.03.017. PMID 16698307.
  15. Pas, Jakub; von Grotthuss, Marcin; Wyrwicz, Lucjan S; Rychlewski, Leszek; Barciszewski, Jan (2004). "Structure prediction, evolution and ligand interaction of CHASE domain". FEBS Letters. 576 (3): 287–290. doi:10.1016/j.febslet.2004.09.020. PMID 15498549. S2CID 45662511.
  16. Barciszewska, Miroslawa Z; Szymanski, Maciej; Wyszko, Eliza; Pas, Jakub; Rychlewski, Leszek; Barciszewski, Jan (2005). "Lead toxicity through the leadzyme". Mutation Research/Reviews in Mutation Research. 589 (2): 103–110. doi:10.1016/j.mrrev.2004.11.002. PMID 15795164.
  17. Plewczynski, Dariusz; Pas, Jakub; Von Grotthuss, Marcin; Rychlewski, Leszek (2004). "Comparison of proteins based on segments structural similarity". Acta Biochimica Polonica. 51 (1): 161–172. doi:10.18388/abp.2004_3608. Von Grotthuss, Marcin; Wyrwicz, Lucjan S; Pas, Jakub; Rychlewski, Leszek; Bradley, Phil; Kuhlman, Brian; Dantas, Gautam; Baker, David (2004). "Predicting protein structures accurately". Science. 304 (5677): 1597–1599. doi:10.1126/science.304.5677.1597b. PMID 15192202. S2CID 29787060.
  18. Wyrwicz, Lucjan S; von Grotthuss, Marcin; Pas, Jakub; Rychlewski, Leszek (2004). "How unique is the rice transcriptome?". Science. 303 (5655): 168–169. doi:10.1126/science.303.5655.168b. PMID 14715990. S2CID 38165567.
  19. Wyszko, Eliza; Nowak, Monika; Pospieszny, Henryk; Szymanski, Maciej; Pas, Jakub; Barciszewska, Miros\lawa Z; Barciszewski, Jan (2006). "Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum". The FEBS Journal. 273 (22): 5022–5031. doi:10.1111/j.1742-4658.2006.05497.x. PMC 7163940. PMID 17032353.
  20. Plewczyński, D; Paś, J; Von Grotthuss, M; Rychlewski, L; others (2002). "3D-Hit: fast structural comparison of proteins". Applied Bioinformatics. 1 (4): 223–225. PMID 15130838.
  21. Fischer, Daniel; Paś, Jakub; Rychlewski, Leszek (2004). "The PDB-Preview database: a repository of in-silico models of 'on-hold'PDB entries". Bioinformatics. 20 (15): 2482–2484. doi:10.1093/bioinformatics/bth262. PMID 15073011.
  22. Narożna, Dorota; Pas, Jakub; Schneider, Jolanta; Mądrzak, Cezary J (2004). "Two sequences encoding chalcone synthase in yellow lupin (Lupinus luteus l.) may have evolved by gene duplication". Cellular & Molecular Biology Letters. 9 (1): 95–105.
  23. Pas, Jakub; Stępniak, Piotr; Wyrwicz, Lucjan; Ginalski, Krzysztof; Rychlewski, Leszek (2011). "GRDB - Gene Relational DataBase". BioInfoBank Library Acta. 11 (1): 2659.
  24. Pas, Jakub (2013). "Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition". Adam Mickiewicz University. {{cite journal}}: Cite journal requires |journal= (help)
  25. Jakub Paś publications indexed by Google Scholar
  26. Popis-Witkowska, Anna (2009). Castle Party : muzyka, ludzie, zjawiska. Greg, Marta Jakubowska, Scriptoris. Olsztyn: Scriptoris. ISBN 978-83-929888-7-8. OCLC 922175645.
  27. Mościcka, Ewa (2006). "Dotyk Gotyku". Popcorn. Warsaw: Axel Springer. November 2006: 72–73. ISSN 1230-8137.
  28. Pawłowski, Adam (2008). "Ludzie z ciemnej strony planety". Głos Wielkopolski (in Polish). Poznan: Polska Press: 27. ISSN 1898-3154.
  29. Baczyński, Jerzy (2008). "Sekator na szatana". Polityka. Warsaw: POLITYKA Sp. z o.o (2(2666)/2008). ISSN 0032-3500.
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