Uni Münster Med. Fakultaet
NewickTreeModifier: a simple web page to prune and modify Newick trees
"The complete sequence of a human Y chromosome” by T2T Consortium has been published by Nature
"The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research” by Felix Manske, Lynn Ogoniak, Norbert Grundmann and Wojciech Makałowski has been published by Nucleic Acids Research.
"A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes” by Reza Halabian and Wojciech Makałowski has been published by Biology.
"paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences" by Lynn Ogoniak, Norbert Grundmann and others
"Mobilome of Apicomplexa Parasites" by Rodriguez and Makalowski has been published by Genes.
"Software evaluation for de novo detection of transposons" by Rodriguez and Makalowski has been published by Mobile DNA.
"From telomere to telomere: The transcriptional and epigenetic state of human repeat elements” by T2T consortium has been published by Science.
"Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing” by GRAID consortium that IoB is part of has been published by BMC Research Notes.
Congratulations to Reza and Matias on the excellent contribution on TE-driven DNA transductions in the human genome
"Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer" was published by MDPI

Victoria Shabardina

Victoria Shabardina
Dr. rer. nat. Victoria Shabardina
postdoctoral researcher
  • graduated from Moscow State University in 2010, Department of Biology, Bioorganic Chemistry
  • postgraduate studies completed in 2015 at ZMBE, Institute for Medical Biochemistry, University of Muenster supervisor Prof. Volker Gerke
Main experience
  • cell culture, molecular cloning and expression of recombinant proteins
  • biochemical chrachterisation of proteins: binding and localization in the cell, conformation, physical properties
  • confocal fluorescent microscopy, spectrometry, FRET, QCM
  • high throughput sequencing and the data analysis, analysis of RNAseq data, molecular phylogeny, comparative transcriptomics
Current projects
  • phylogenetic analysis of ERM (ezrin, radixin, moesin) cytoskeletal proteins in Metazoa
  • development of the pipeline for the analysis of ONT MinION sequencing data
  • side projects: genome and transcriptome analysis of Tardigrades; searching for specific SNVs in the uORF regions in cancer patients genomic data
Completed projects
  • comparing genome and transcriptome structures of the two amoeba species with the different ecological background
Teaching experience
  • Conducting practicals and delivering part of the lecture course for the bachelor students of Universuty of Muenster
  • Conducting workshops on bioinformatics analysis of MinION sequencing data at the summer schools "The MinION sequencing and its applications" in 2017 (Bankgkok, Thailand) and 2018 (Manado, Indonesia), and Bioinformatics Summer School 2017 in Poznan, Poland
List of publications
  • Mode of ezrin-membrane interaction as a Function of PIP2 binding and pseudophosphorylation, Biophys J. 2016 by Shabardina V., Kramer C., Gerdes B., Braunger J., Cordes A., Schaefer J., Mey I., Grill D., Gerke V., Steinem C. See here
  • Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis, Int J Biol Sci. 2018 by Shabardina V., Kischka T., Kmita H., Suzuki Y., Makalowski W. See here
  • The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup, BMC Genomics 2017 by Wojtkowska M.,\ Buczek D., Suzuki Y., Shabardina V., Makalowski W., Kmita H. See here
  • Chapter for "Bioinformatics", Makalowski W., Shabardina V., Makalowska I., 2018, eLS, John Wiley & Sons Ltd, Chichester
  • NanoPipe, an interactive tool for MinION sequencing analysis, GigaScience 2019, in print by Shabardina V., Kischka T., Manske F., Grundmann N., Frith M.C., Suzuki Y., Makalowski W.
2019-01-25 15:31