Polish scientist and entrepreneur (born 1977)
Jakub Pas
Born 27 September 1977 (1977-09-27 ) (age 46) Alma mater
Adam Mickiewicz University in Poznań Scientific career Fields
Thesis Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition (2013)
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 .
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
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 .
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]
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 .
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]
^ Jakub, Paś.
"Jakub Paś PhD desideration" (PDF) . AMUR - Adam Mickiewicz University Repository .
^ Paś, Jakub.
"Jakub Paś PhD review" (PDF) . Adam Mickiewicz University Faculty of Chemistry .
^
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 )
^ Pas, Jakub.
"REFLAX" . Bioinfo.Pl . Retrieved 26 April 2023 .
^ Samayoa, Josue.
Utilizing Rosetta and NMR Data in a Homology-based Modeling Approach . p. 41.
^ Wang, Nian (2016). Virulence Mechanisms of Plant-Pathogenic Bacteria (1 ed.). APS Publications. pp. 107–124.
ISBN
978-0-89054-449-5 .
^ Rychlewski, Leszek.
"BioinfoBank European Projects" .
^ 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 .
^ 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.
^
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 .
^
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 .
^ 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 .
^
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 .
^ 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 .
^ 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 .
^ 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 .
^
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 .
PMID
15094837 .
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 .
^ 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 .
^
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 .
^ 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 .
^ 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 .
^ 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.
^ Pas, Jakub; Stępniak, Piotr; Wyrwicz, Lucjan; Ginalski, Krzysztof; Rychlewski, Leszek (2011). "GRDB - Gene Relational DataBase". BioInfoBank Library Acta . 11 (1): 2659.
^ Pas, Jakub (2013). "Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition". Adam Mickiewicz University.
^
Jakub Paś publications indexed by
Google Scholar
^ Popis-Witkowska, Anna (2009).
Castle Party : muzyka, ludzie, zjawiska . Greg, Marta Jakubowska, Scriptoris. Olsztyn: Scriptoris.
ISBN
978-83-929888-7-8 .
OCLC
922175645 .
^ Mościcka, Ewa (2006). "Dotyk Gotyku". Popcorn . November 2006. Warsaw: Axel Springer: 72–73.
ISSN
1230-8137 .
^ Pawłowski, Adam (2008). "Ludzie z ciemnej strony planety". Głos Wielkopolski (in Polish). Poznan: Polska Press: 27.
ISSN
1898-3154 .
^ Baczyński, Jerzy (2008). "Sekator na szatana". Polityka (2(2666)/2008). Warsaw: POLITYKA Sp. z o.o.
ISSN
0032-3500 .