Institute of Bioinformatics WWU Münster

Name:	Marcin Tomasz Jakalski
Status:	Ph.D. student
Email:	jakalssj3[at]uni-muenster[dot]de
Room:	2650.110.204
Phone:	+49 251 835300-2

evolution of mitochondrial outer membrane beta-barrels
RNA-based gene duplication and retrogene's evolution in green algae
Transcriptomics of Apicomplexa parasites
Genomics and transcriptomics of Trypanosoma congolense

2009-2017: Ph.D. in Bioinformatics at Univeristy of Muenster, Muenster, Germany.
- Advisor: Wojciech Makalowski
2007-2009: M.Sc. in Biology with a specialization in Bioinformatics, at Adam Mickiewicz University, Poznan, Poland.
- Thesis: Comparative analysis of overlapping genes in 12 Drosophila species (PDF - in Polish, English summary).
- Advisor: Izabela Makalowska
2004-2007: B.Sc. in Biology with a specialization in Bioinformatics, at Adam Mickiewicz University, Poznan, Poland.
- Thesis: Comparative characteristics of bioinformatics methods for analysis of unstructured regions in proteins.
- Advisor: Janusz M. Bujnicki

2015.08.16-20: 25th International Conference of the World Association for the Advancement of Veterinary Parasitology (WAAVP), Liverpool, United Kingdom.
- Participant with an oral presentation
- Title: NGS-based resequencing and reannotation of the Trypanosoma congolense genome and trancriptome
2013.06.12-13: 3rd annual Muenster Graduate School of Evolution Symposium, Muenster, Germany.
- Poster presentation
- Title: Analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii
2013.05.07-11: The Biology Of Genomes, Cold Spring Harbor, USA.
- Poster presentation
- Title: Analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii
2011.02.18-19: Interdisciplinary Graduate Students' Symposium, Muenster, Germany.
- Participant with poster and oral presentations
- Title: Phylogenetic analysis of mitochondrial outer membrane beta-barrel channels (poster)
2010.09.21-24: 14th Evolutionary Biology Meeting at Marseilles, Marseilles, France.
- Participant with an oral presentation
- Title: Evolutionary history of the mitochondrial outer membrane channels of a predicted beta-barrel topology (abstract, slides)
2010.05.23-28: 16th Annual European Meeting of PhD Students in Evolutionary Biology, Wierzba, Poland.
- Participant with an oral presentation
- Title: Evolution of the mitochondrial import machinery in Dictyostellium discoideum (slides)
2009.10.2-4: II Convention of the Polish Bioinformatics Society, joined with 7th Workshop on Bioinformatics, Bedlewo, Poland.
- Participant with an oral presentation
- Title: Evolution of overlapping genes in Drosophila genomes (slides)
2009.05.21-23: I Scientific-Didactic Conference of the Faculty of Biology of the Adam Mickiewicz University, Poznan, Poland.
- Participant with a poster presentation
- Title: Evolution of overlapping genes in Drosophila genomes (abstract, poster)
2008.08.23: "Teaching crystallography in the 21st Century" at the XXI Congress and General Assembly of the International Union of Crystallography, Osaka, Japan.
- Presentation co-author (with prof. Mariusz Jaskolski, Andrzej Zielezinski and Julia Nosalska)
- Title: Accuracy and precision of PDB entries (and biology majors)
2008.04.6-9: The 6th TID Workshop on "Structural Biology with Synchrotron Radiation, Poznan, Poland.
- Participant

2015-2016: Bioinformatics 1 course supervisor (winter semester).
- sequence alignments, BLAST
2013.08.18-23: 10th Poznan Summer School of Bioinformatics, Poznan, Poland.
- sequence alignments, BLAST, calculation of selection pressure, MEGA5
2012-2013: Bioinformatics 1 course supervisor (winter semester).
- Gene prediction
2011.07.11-15: 9th Poznan Summer School of Bioinformatics, Poznan, Poland.
- Ensembl, BioMart, Galaxy
2010.07.5-10: 8th Poznan Summer School of Bioinformatics, Poznan, Poland.
- Phylogenetic analyses, BLAST, protein structure prediction
2009-2010: Bioinformatics 2 course supervisor (summer semester).

Jakalski M, Takeshita K, Deblieck M, Koyanagi KO, Makalowska I, Watanabe H, Makalowski W.
Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.
Biology Direct 2016; doi:10.1186/s13062-016-0138-1.
Suganuma K, Sarwono AE, Mitsuhashi S, Jakalski M, Okada T, Nthatisi M, Yamagishi J, Ubukata M, Inoue N.
Mycophenolic Acid and Its Derivatives as Potential Chemotherapeutic Agents Targeting Inosine Monophosphate Dehydrogenase in Trypanosoma congolense.
Antimicrob Agents Chemother. 2016; doi: 10.1128/AAC.02816-15.
Jakalski M, Wakaguri H, Kischka TG, Nishikawa Y, Kawazu S, Matsubayashi M, Kawahara F, Tsuji N, Cao S, Sunaga F, Xuan X, Okubo K, Igarashi I, Tuda J, Mongan AE, Eshita Y,Maeda R, Makalowski W, Suzuki Y, Yamagishi J.
DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.
Nucl. Acids Res. 2014; doi: 10.1093/nar/gku1240.
Makalowski W, Jakalski M, Makalowska I.
Bioinformatics (version 2.0).
In: eLS. John Wiley & Sons Ltd, Chichester.
Janice J, Jakalski M, Makalowski W.
Surprisingly high number of Twintrons in vertebrates.
Biology Direct 2013, 8:4. PubMed PMID: 23356793.
Wojtkowska M, Jakalski M, Pienkowska JR, Stobienia O, Karachitos A, Przytycka TM, Weiner J 3^rd, Kmita H, Makalowski W.
Phylogenetic Analysis of Mitochondrial Outer Membrane β-barrel Channels.
Genome Biol Evol. 2011 Dec 8. PubMed PMID: 22155732.
Majorek K, Kozlowski L, Jakalski M, Bujnicki JM
First steps of protein structure prediction.
In "Prediction of Protein Structures, Functions and Interactions".
Editor: Bujnicki JM. Wiley & Sons 2008

Screencast: Protein crystallization
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