Jakub Paś (born 27 September 1977) is a Polish

scientist A scientist is a person who Scientific method, researches to advance knowledge in an Branches of science, area of the natural sciences. In classical antiquity, there was no real ancient analog of a modern scientist. Instead, philosophers engag ...

and developer. He is a doctor of chemistry at the Faculty of Chemistry of

Adam Mickiewicz University in Poznań The Adam Mickiewicz University (; Latin: ''Universitas Studiorum Mickiewicziana Posnaniensis'') is a research university in Poznań, Poland. Due to its history, the university is traditionally considered among Poland's most reputable institution ...

Early years

Paś was born in 1977 in

Śrem Śrem () is a town on the Warta river in central Poland. It is the seat of Śrem County in the Greater Poland Voivodeship. As of 1995, the population of Śrem was 29,800. Śrem is to the south of Poznań, a local road junction on the road from ...

. 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

; his

thesis A thesis (: theses), or dissertation (abbreviated diss.), is a document submitted in support of candidature for an academic degree or professional qualification presenting the author's research and findings.International Standard ISO 7144: D ...

''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 A Doctor of Philosophy (PhD, DPhil; or ) is a terminal degree that usually denotes the highest level of academic achievement in a given discipline and is awarded following a course of graduate study and original research. The name of the deg ...

thesis in chemistry, ''Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition'' (under the supervision of Marcin Hoffmann). He also completed IT Project Management postgradual study on WSB School of Banking Poznań 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, Paś took an Socrates-Erasmus internship at the

University Of Edinburgh The University of Edinburgh (, ; abbreviated as ''Edin.'' in Post-nominal letters, post-nominals) is a Public university, public research university based in Edinburgh, Scotland. Founded by the City of Edinburgh Council, town council under th ...

under Lucy A Harrier supervision worked on bioinformatics project explaining genomics of arbuscular mycorrhizal fungi. During his master's Paś worked on REFLAX 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 A Doctor of Philosophy (PhD, DPhil; or ) is a terminal degree that usually denotes the highest level of academic achievement in a given discipline and is awarded following a course of graduate study and original research. The name of the deg ...

, he was employed as research scientist in Bioinfobank Institute, Sanford Burnham Prebys Medical Discovery Institute and

Howard Hughes Medical Institute The Howard Hughes Medical Institute (HHMI) is an American non-profit medical research organization headquartered in Chevy Chase, Maryland with additional facilities in Ashburn, Virginia. It was founded in 1953 by Howard Hughes, an American busin ...

. He also worked on fellowship in Max Planck Institute for Molecular Genetics and

University of Catania The University of Catania () is a university located in Catania, Sicily. Founded in 1434, it is the oldest university in Sicily, the 13th oldest in Italy, and the 29th oldest in the world. With over 38,000 enrolled students, it is the largest uni ...

. In 2007, Paś was granted Marie Curie Fellowship at

Politehnica University of Bucharest Politehnica University of Bucharest () is a technical university in Bucharest, Romania founded in 1818.International Supercomputing Conference The ISC High Performance, formerly known as the International Supercomputing Conference, is a yearly conference on supercomputing which has been held in Europe since 1986. It stands as the oldest supercomputing conference in the world. History ...

Poster Award for work

GPGPU General-purpose computing on graphics processing units (GPGPU, or less often GPGP) is the use of a graphics processing unit (GPU), which typically handles computation only for computer graphics, to perform computation in applications traditiona ...

Accelerated Sparse Linear Solver for Fast Simulation of On-Chip Coupled Problems. In 2009 he received Marie Curie Reintegration Grant. As of 2018, Jakub Paś is employed at

GSK plc GSK plc (an acronym from its former name GlaxoSmithKline plc) is a British Multinational corporation, multinational Pharmaceutics, pharmaceutical and biotechnology company with headquarters in London. It was established in 2000 by a Mergers an ...

Scientific activity

Paś research focuses on the application of computational methods for

protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ...

, fold recognition and

phylogeny A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or Taxon, taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, M ...

, investigation of the structure of molecules and the interactions between them. During his work in Bioinfobank Institute Jakub Paś was involved in multiple European project such as ELM, SEPSDA, NARCISUS, DATAGENOME or BIOSAPIENS. His applied work focuses on automation in pharmaceutical research, Continuous Integration / Continuous Development (

CI/CD In software engineering, CI/CD or CICD is the combined practices of continuous integration (CI) and continuous delivery (CD) or, less often, continuous deployment. They are sometimes referred to collectively as continuous development or contin ...

) and test automation in highly regulated industry. The results of his scientific research include: * Explanation of the mechanism of interaction between

SARS coronavirus Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), previously known as severe acute respiratory syndrome coronavirus (SARS-CoV), is a strain of coronavirus that causes severe acute respiratory syndrome (SARS), the respiratory illn ...

helicase Helicases are a class of enzymes that are vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic double helix, separating the two hybridized ...

ATPase ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, ATP hydrolase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or ...

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

publications To publish is to make Content (media), content available to the general public.Berne Conv ...

(21 according to

Google Scholar Google Scholar is a freely accessible web search engine that indexes the full text or metadata of Academic publishing, scholarly literature across an array of publishing formats and disciplines. Released in Beta release, beta in November 2004, th ...

), including highly prestigious

scientific journal In academic publishing, a scientific journal is a periodical publication designed to further the progress of science by disseminating new research findings to the scientific community. These journals serve as a platform for researchers, schola ...

s, such as

Science Science is a systematic discipline that builds and organises knowledge in the form of testable hypotheses and predictions about the universe. Modern science is typically divided into twoor threemajor branches: the natural sciences, which stu ...

, Nucleic Acid Research and

Gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

. His papers are increasingly cited year after year (totalling 1050 -

), which yields 11 citations per publication and the

h-index The ''h''-index is an author-level metric that measures both the productivity and citation impact of the publications, initially used for an individual scientist or scholar. The ''h''-index correlates with success indicators such as winning t ...

of 11.

Educational activity

Since 2002, Paś has been actively training

and bioinformatics. He was also leading course

molecular modeling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scienc ...

and prediction of spatial structure of proteins. In 2004, Paś was leading Summer modeling school at Laboratory of Bioinformatics, Institute of Physics on

Adam Mickiewicz University Adam is the name given in Genesis 1–5 to the first human. Adam is the first human-being aware of God, and features as such in various belief systems (including Judaism, Christianity, Gnosticism and Islam). According to Christianity, Adam si ...

Other activities

Jakub Paś is currently working as Principal Automation Engineer in

. He is involved in

open source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

development and organizing

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

user group meetings. He is also a member of

Project Management Institute The Project Management Institute (PMI, legally Project Management Institute, Inc.) is a U.S.-based not-for-profit professional organization for project management. Overview PMI serves more than five million professionals including over 680,0 ...

and author of articles about contemporary music.

References

External links

*
Biography on Linkedin

Official website

Open Source projects on Github
{{DEFAULTSORT:Pas, Jakub Living people 1977 births Academic staff of Adam Mickiewicz University in Poznań Adam Mickiewicz University in Poznań alumni People from Śrem Polish biochemists Polish computer scientists