About

PhD Thesis

Rafał Wóycicki - Sequencing, assembly and annotation of cucumber (Cucumis sativus L. cv. Borszczagowski) nuclear genome

MSc Thesis

Publications

Pawełkowicz, M., Zieliński, K., Zielińska, D., Pląder, W., Yagi, K., Wojcieszek, M., Przybecki, Z. 2015. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. - Plant Science  doi:10.1016/j.plantsci.2015.07.025

Yagi K. Siedlecka E. Pawełkowicz M. Wojcieszek M. Przybecki Z. Tagashira N. Hoshi Y. Malepszy S. Pląder W. 2014 Karyotype Analysis and Chromosomal Distribution of Repetitive DNA Sequences of Cucumis metuliferus Using Fluorescence in situ Hybridization - Cytogenet Genome Res 2014;144:237-242  (DOI:10.1159/000369183)

Osipowski P., Pawełkowicz M. Przybecki Z,  2014. Computational structural variation discovery in genomes state of the art and challenges - Proc of SPIE vol. 9290,(J), doi: 10.1117/12.2074136 

Pawełkowicz M., Nowak R., Osipowski P., Rymuszka J., Świerkula K., Wojcieszek M., Przybecki Z.  2014. The discrepancies in the results of bioinformatics for genomic structural annotation - Proc of SPIE vol. 92901 (L) doi: 10.1117/12.2074396

Wojcieszek M., Pawełkowicz M., Nowak R., Przybecki Z.,  2014. Genomes correction and assembling - present methods and tools - Proc of SPIE vol. 92901 (X) doi: 10.1117/12.207562

Kowalczuk C., Pawełkowicz M, Chądzyńska K, Paziewska A, Wóycicki R, Ostrowski J, Cebula J, Przybecki Z, Evaluation of reference genes transcription stabillity in generative whorls of cucumber flower (Cucumis sativus. L), Biotechnology and Plant Breeding perspectives, published by Agrobios, 2014 str. 275 – 286.

Pawełkowicz M, Osipowski P, Wojcieszek M. Wóycicki M, Witkowicz J, Hincha D, Przybecki Z. Identification and characterization of genes connected with flower morphogenesis in cucumber. BioTechnologia vol 93 (2) 2012 pp 123 – 134.

Wojcieszek M; P. Róż; M. Pawełkowicz ; R. Nowak and Z. Przybecki, Development of genome viewer (Web Omics Viewer) for managing databases of cucumber genome. Proc. SPIE 8454, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2012, 84541Y (October 15, 2012); doi:10.1117/12.2000236;

Wóycicki R, Witkowicz J, Gawronski P, Dabrowska J; Lomsadze A, Pawelkowicz M, Siedlecka E, Plader W, Seroczynska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpinski S, Malepszy S, Przybecki Z. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. 2011 PlosOne

Malepszy S.,Przybecki Z., Kowalczuk C., Filipecki M., „ Genome sequencing makes a significant progress in plant breeding ”, Kosmos 2012

Malepszy S., „ Sekwecjonowanie genomów dla hodowli roślin. ”, Hodowla Roslin i Nasiennictwo 2011; 3 i 4; 21 - 24

Gutman W., Pawełkowicz M., Woycicki R., Piszczek E. and Przybecki Z., „ The construction and characteristics of a BAC library for Cucumis sativus L. ‘B10 ”, Cellular Molec Biol Lett, Volume 13 (2008) pp 74-91

Presentations

Osipowski P. Progress in Assembling the Cucumber Borszczagowski (B10) Line Genome Using Long Reads XIth Eucarpia Cucurbitaceae 2016, July 24-28, 2016, Warsaw, Poland

Skarzyńska A. Bioinformatics pipeline for functional identification and characterization of proteins. 25-31.05.2015 XXXVI-th IEEE-SPIE Joint Symposium Wilga 2015

Osipowski P. Progress in cucumber genome assembly using NGS technologies 25-31.05.2015 XXXVI-th IEEE-SPIE Joint Symposium Wilga 2015

Wojcieszek M. Genome structural annotation enhancement with RNAseq data25-31.05.2015 XXXVI-th IEEE-SPIE Joint Symposium Wilga 2015

Woycicki R., Borodovsky M., Przybecki Z., „ Assembly and structural annotation of cucumber genome ”, internal lecture, 8 June 2009, Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw, Poland

Malepszy, S., Wóycicki, R., Przybecki, Z., „Sekrety ogórka nareszcie ujawnione – genom zsekwencjonowany”, Cucumber’s secrets disclosed: the investigation on nuclear genome sequence completed. Oral presentation, Conference: „ Wyzwania współczesnej biologii komórki – genetyka molekularna, biologia systemów, bioinformatyka ”(The Challenges of Contemporary Cell Biology – Molecular Genetics, SystemBiology, Bioinformatics), 20-21 April 2009, Łódź, Poland.

Woycicki R., Gutman W., Pawelkowicz M., Plader W., Siedlecka E., Smiech M., Witkowicz J., Malepszy S., Przybecki Z., „ Cloning of the sex genes of cucumber (Cucumis sativus L.): first insights into the organization of a cucumber genome by analyzing BAC END sequences”, oral presentation, II Ogólnopolska Konferencja: Genetyka i Genomika w doskonaleniu roślin uprawnych – od rośliny modelowej do nowej odmiany,  (Second Polish Conference: Genetics and Genomics in Crops Improvement – from model plant to the new variety), 24-26 November 2008, Poznań, Poland

Posters

Wojcieszek M., Osipowski P., Pawełkowicz M., Skarzyńska A., Pląder W., Borodovsky M., Przybecki Z. Transcriptome based annotation for new version of C. sativus genome 17th European Biotechnology Congress. 3-6 July 2016, Kraków Poland

Pawelkowicz M. Pryszcz L. Wojcieszek, M. Osipowski P. Plader W. Przybecki Z. (2015, January). Comparative Analysis of Transcriptomes Connected with Sex Expression in Cucumber. In Plant and Animal Genome XXIII Conference. Plant and Animal Genome.

Osipowski, P. Wojcieszek M. Pawelkowicz M. Yagi K. Plaąder W. Przybecki Z. (2015, January). High Quality Short Read Assembly of B10 Cucumber Line Genome. In Plant and Animal Genome XXIII Conference. Plant and Animal Genome.

Pawełkowicz, M., Krzywkowski, T., Kowalczuk, C., Wóycicki, R., Osipowski, P.,  Przybecki, Z. Comparative analysis of novel CsABI1 and CsABI2 genes in the male and female flowers of cucumber.

Woycicki R., Witkowicz J., Pawelkowicz M, Siedlecka E., Gutman W., Plader W., Seroczynska A., Smiech M., Niemirowicz-Szczytt K., Karpinski S, Malepszy S., Przybecki Z.,  „ Sequencing of the Cucumber (Cucumis sativus L.) Genome ”, poster session, XVII Pl. and Anim. Meeting, 09-14 January 2009, San Diego, CA, USA

Woycicki R., Gutman W., Przybecki Z., „ BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations”, poster session, EMBnet CONFERENCE 2008 20th Anniversary Celebration - Leading applications and technologies, 18-20 September 2008, Martina Franca, Italy