Personal:
Rozkład jazdy PKS Poznań
Mapa Poznania
Era - BOA
Rozkład jazdy PKP
Rozkład jazdy MPK Poznań
Lukas Bank - strona banku
Rozkład jazdy PKS Poznań
Commercial Union - strona domowa Towarzystwa
Pogoda ICM
Bioinfobank Library
Napisy do filmow
Allegro - serwis aukcjny
Bioinformatics:
An Automated Comparative Protein Modelling Server
NCBI
PubMED
ENTREZ
PSI-BLAST
Protein Data Bank (RCSB)
SCOP
Czasopisma on-line
Institute of Bioorganic Chemistry
Genome News Network
CASP - Submition
T-COFFEE
BioPERL
SWISS MODEL
CMC Modelling Guide
Verify 3D
Enzyme Database - BRENDA
Kyoto Encyclopedia of Genes and Genomes
Dali
Protein Structure Prediction Center
Dunbrack's Culling PDB's
Kinemage Home Page
GlobPlot
Genome Browser
mfold
Biblioteka Wirtualna ICM
PRIDE
TOPS
Primer3
My own services:
Dark Music Portal
Bioinformatics Laboratory UAM
Interdyscyplinary Computing Center
Fundacja Badań Nad Rakiem
Personal Bioinformatic Tools:
Gi Reretrieval
Gene Name Formateer
BiB Alignment View
GI number cleener
Friends homepages:
Erik Delber
Dylan Chivian
Yuzhen Ye
Lukas the Silvan Archmage
Marcin - Biologia molekularna
Darman - Fizyka
Jachu - Dystanse genetyczne
Scotty - góry i NBA
Lucjan - Genomika
Marcin von Grotthuss - Klastrowanie zwiazków chem.
Wojciech Lasociński
Uciekinierka - strona domowa
Mateusz - fotografia
Ewa Stachowiak
Marcin Feder
Linux:
WLAN
LinuxSky
Samba Domain Control
ASUS A1000
Ruch Na Rzecz Wolnego Oprogramowania
wlan2
wep3
WLAN
LinuxSky
Samba Domain Control
ASUS A1000
Ruch Na Rzecz Wolnego Oprogramowania
wlan2
wep3
Programing:
C++ Manual
Refleksja na temat bezpieczeństwa serwisów internetowych ;)
PHP Manual
PERL Manual
(My)SQL Manual
Fortran 77
Linux C programing
Magic Software
Slideshow
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My sites
About Me
CV
PROFESSIONAL EXPERIENCE
I 2008 – III 2008 - University Of Catania - The application of graph theory and high performance computing medical diagnostics and nanotechnology.
X 2007 - Present - Polytechnic University of Bucharest- High performance computing for nano-electronic design automation.
XI 2005 - II 2006 - Max Planck Institute for Molecular Genetics, Departamet Of Bioinformatics, Searching for snoRNA of H/ACA type in human genome.
I 2005 – X 2007 - Adam Mickiewicz University, Laboratory of Bioinformatics, High throughput computing.
II 2004 – Present Institute of Biooorganic Chemistry, Poznan, Laboratory of tRNA biochemistry. Molecular Docking & protein modelng.
I 2003 – X 2007 - BioInfo Bank Institute. Research Scientist. Computer programming & protein structure prediction.
IX 2002 - XII 2002 - Burnham Institute, San Diego, Departament of Bioinformatics & Systems Biology. Improving FFAS alignments using T-Cofee.
VI 2002 - IX 2002 - University of Washington, Seattle, Department of Biochemistry. Creating fragment database for ROSETTA - ab inito protein tetriary structure prediction method.
III 2001 - IX 2001 - National Research Institute of Animal Production Poultry Research Branch at Zakrzewo near Poznan. Creating genomic fingerprints using Random Amplified Polymorphic DNA (RAPD) methods.
IX 2000 - Bioinformatic Unit at International Institute Of Biochemistry and Molecular Biology, Warsaw. Training Period - "Bioinormatic methods in molecular research"
IV 2000 - VI 2000 - Scottish Agricultural College, Edinburgh, Training period. Molecular study of phospoglycerate kinase gene of arbuscular mycorrrhizal Fungi.
WORKSHOPS
VII 2004 - Protein Modeling Summer School, Poznan, Poland.
V 2003 - ELM Coding Camp - EMBL, Heidelberg, Germany.
XII 2002 - Critical Assessment of Techniques for Protein Structure Prediction Student Addendum Conference, Asilomar, U.S.A.
X 2001 - The 1st Summer School on "Parallel Computing in Biomolecular Simulations", Gdansk, Poland.
GRANTS
"Rational engineering of lipid metabolism in flax to produce branched-chainfatty acids, unusual fatty acids with potent biolubricant properties". Projekt Europejski QLK3-2000-00349
“The Eukaryotic Linear Motif resource, ELM: A new European bioinformatics facility for revealing functional sites in modular proteins Projekt Europejski”. QLRI-CT-2000-00127
“Exploiting genomics to engineer an environmentally friendly microorganism for bioremediation purposes. Projekt Europejski”. QLK3-CT-2000-00170
„Charakterystyka genów kodujących niektóre enzymy szlaku fenylopropanoidów w łubinie żółtym” Badawczy własny 3 P06A 021 25
Wyszukiwanie i analiza roli małych jąderkowych RNA (sno RNA) klasy H/ACA w genomie człowieka" Promotorski 2 P05A 057 27
„In-Silico Prediction of gene function, GeneFun”
Projekt Europejski. LSHG-CT-2004-503567
„BioSapiens Network of Excellence”
Projekt Europejski, FP6-LIFESCIHEALTH
„Post-genomic datamining of enzymes for the synthesis of chiral pharmaceutical intermediates, DataGenome”
Projekt Europejski, LSHB-CT-2003-503017
EDUCATION:
II 2004 - present Institute of Bioorganic Chemistry. Laboratory Of tRNA Biochemistry. PhD study (“Searching for noncoding RNA in human genome”)
X 1996 – V 2001 Poznan University of Life Sciences. Grduate with distinction on “Structural and sequential analysis of proteins related to metabolism of BcFA (methyl branched-chain fatty acids)”
IX 1992 – VI 1996 Jozef Wybicki Secondary School. Facultet of Biology. Matriculation.
Languages:
Polish, English, Russian
SKILLS
Advanced skills as computer system operator/administrator and of office - applications,
Operating Systems:
UNIX (Solaris, IRIX, Linux), Mac OS, Windows
Advanced system administration and network configuration
Adwanced operating of PC, SUN, SGI machines.
Internet/Intranet solution installing and configuration on UNIX / Windows. System & network administration, Webmastering with CGI spport. Cluster system and high throughput computing.
Databeses instaling / operating.
Programing languages:
C, C++, Perl, PHP, Visual Basic, Delphi, Javascript, Java, SQL
Bioinformatic tools operating:
Insight, Bioedit, Clustal, Phylip, RASMol, Swiss SPDB Viewer, Autodock, MEGA, Artemis
Easy interpersonal contacts
Good work organisation skills
Obstinacy in endeavour to goal
Punctuality, sense of duty
INTEREST
Music, Computer science and technology, trekking,
MEMBERSHIP
Polish Biochemical Society, Mars Society Polska, Polish Linux Users Group, IEEE, Fundation For Cancer Research
CONFERENCES
Pas J.,Barciszewski J.
"Structure prediction and evolution of CHASE domain" - oral presentation
Cytokinin 2004, Metabolism, Signaling and Function
07/10/2004 Berlin, Germany
Gougeon S., Prost I., Brigé A., Roussy I., Robin C., Vong P.C., Bourgaud F., Devreese B., Pas J., Rychlewski L., Portais J. C., Wilmer J., Thomasset B., Gontier E.
"Biochemical preliminary study of Acyltransferase and ß-Ketoacyl Synthase subdomains bovis BCG Mycocerosic Acid Synthase: Incorporation of 14C methylmalonyl into lipid fractions using isolated" - poster.
16th International Plant Lipid Symposium
07/1-4/ 2004 Budapest, hungary
Plewczynski D., Pas J.,Grotthuss M., Rychlewski L.,
"3D-Hit, Fast Structural Comparison of Proteins" - poster.
10th International conference on intelligent Systems For Molecular Biology
08/03-07/2002 Edmonton, Canada
PUBLICATIONS
1: Wyszko E, Nowak M, Pospieszny H, Szymanski M, Pas J, Barciszewska MZ,
Barciszewski J [PubMed]
Leadzyme formed in vivo interferes with tobacco mosaic virus infection in
Nicotiana tabacum
FEBS J. 2006 Oct 9
2: Pas J, Wyszko E, Rolle K, Rychlewski L, Nowak S, Zukiel R, Barciszewski J [PubMed]
Analysis of structure and function of tenascin-C
Int J Biochem Cell Biol. 2006;38(9):1594-602. Epub 2006 Apr 18.
3: Barciszewska MZ, Szymanski M, Wyszko E, Pas J, Rychlewski L, Barciszewski J [PubMed]
Lead toxicity through the leadzyme
Mutat Res. 2005 Mar;589(2):103-10. Epub 2004 Dec 23. Review.
4: von Grotthuss M, Koczyk G, Pas J, Wyrwicz LS, Rychlewski L [PubMed]
Ligand.Info small-molecule Meta-Database
Comb Chem High Throughput Screen. 2004 Dec;7(8):757-61. Review.
5: Pas J, von Grotthuss M, Wyrwicz LS, Rychlewski L, Barciszewski J [PubMed]
Structure prediction, evolution and ligand interaction of CHASE domain
FEBS Lett. 2004 Oct 22;576(3):287-90.
6: von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L [PubMed]
Predicting protein structures accurately
Science. 2004 Jun 11;304(5677):1597-9; author reply 1597-9. No abstract
available.
7: Plewczynski D, Pas J, von Grotthuss M, Rychlewski L [PubMed]
3D-Hit: fast structural comparison of proteins
Appl Bioinformatics. 2002;1(4):223-5.
8: Plewczynski D, Pas J, Von Grotthuss M, Rychlewski L [PubMed]
Comparison of proteins based on segments structural similarity
Acta Biochim Pol. 2004;51(1):161-72.
9: Fischer D, Pas J, Rychlewski L [PubMed]
The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB
entries
Bioinformatics. 2004 Oct 12;20(15):2482-4. Epub 2004 Apr 8.
10: Narozna D, Pas J, Schneider J, Madrzak CJ [PubMed]
Two sequences encoding chalcone synthase in yellow lupin (Lupinus luteus l.)
may have evolved by gene duplication
Cell Mol Biol Lett. 2004;9(1):95-105.
11: Wyrwicz LS, von Grotthuss M, Pas J, Rychlewski L [PubMed]
How unique is the rice transcriptome
Science. 2004 Jan 9;303(5655):168; author reply 168. No abstract available.
12: von Grotthuss M, Pas J, Wyrwicz L, Ginalski K, Rychlewski L [PubMed]
Application of 3D-Jury, GRDB, and Verify3D in fold recognition
Proteins. 2003;53 Suppl 6:418-23.
13: Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L [PubMed]
ORFeus: Detection of distant homology using sequence profiles and predicted
secondary structure
Nucleic Acids Res. 2003 Jul 1;31(13):3804-7.
14: von Grotthuss M, Pas J, Rychlewski L [PubMed]
Ligand-Info, searching for similar small compounds using index profiles
Bioinformatics. 2003 May 22;19(8):1041-2.
15: Feder M, Pas J, Wyrwicz LS, Bujnicki JM [PubMed]
Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose
2'-O-methyltransferases
Gene. 2003 Jan 2;302(1-2):129-38.
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