I joined the University of Muenster in January 2007. Prior to moving here, I worked at the Pennsylvania State University, USA (2001-2007), the National Center for Biotechnology Information (NCBI), NIH, USA (1994-2001), and the University of Montreal, Canada (1991-1993). My Ph.D. is from the Adam Mickiewicz University, Poznan, Poland (1991), and I also have a Master degree of Biology (1983) and a Master degree of Philosophy (1988) from the same university.

Telephone: +49 251 835 3006
Email: wojmak@uni-muenster.de

I am a molecular biologist with strong interest in evolution. My main research aims at understanding evolution at the genome level with special focus on transposable elements and their influence on a host genome. I am also interested in history and philosophy of science. In past I have been involved in large scale projects, e.g. sequencing and analysis of twelve drosophila genomes and H-inv project of annotating the human genome. Recently, my group joined the Telomere-to-Telomere (T2T) consrotium (https://sites.google.com/ucsc.edu/t2tworkinggroup) which completed a human genome and now is working on several primate genomes. Please email me if you are interested in joining my exciting research group or wish to discuss specific areas of my research program.

• Transposable Elements and gene transcription regulation.
• TE-driven genomic transduction in health and disease.
• Upstream open reading frames (uORFs) and cancer.
• Transcriptomics of Amoebozoa with special focus on mitochondrial import apparatus.
• Evolutionary genomics of apicomplexa parasites.
• Bioinformatics software development with focus on nanopore sequencing.

• Dr. Michele Boiani, Max-Planck Institute for Molecular Medicine, Muenster, Germany
• Prof. Georg Fuellen, University of Rostock, Rostock, Germany
• Prof. Martin Frith, University of Tokyo, Kashiwa, Japan
• Prof. Juergen Gadau, University of Muenster, Muenster, Germany
• Prof. Hanna Kmita, Adam Mickiewicz University, Poznań, Poland
• Dr. Juergen Schmitz, University of Muenster
• Prof. Yutaka Suzuki, University of Tokyo, Kashiwa, Japan
• Dr. Klaus Wethmar, University of Muenster, Muenster, Poland
• Dr. Junya Yamagishi, Hokkaido University, Sapporo, Japan

Deutscher Akademischer Austauschdienst (DAAD)
2023 The role of transposable elements in shaping structural and transcriptional variation of Arabidopsis thaliana genome (Collaborative project with Institute of Bioorganic Chemistry, Polish Academy of Sciences).

Deutsche Forschungsgemeinschaft (DFG)
2022 - 2025 The evolution of genome compartmentalization in the ant genus Cardiocondyla Lukas Schrader (University of Muenster), W. Makalowski (University of Muenster)

Deutsche Forschungsgemeinschaft (DFG)
2022 - 2024 The apportionment of zygotic totipotency: Origins, intermediaries and implications for natural and assisted reproduction in the mouse model M. Boiani (Max Planck Institute), W. Makalowski (University of Muenster), G. Fuellen (Rostock University Medical Center)

• 176 published papers
• Over 9,900 total citations (according to Google Scholar) (Web of Science citations - 6,088)
• H-index = 45 (Web of Science H-index - 36)

• Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM (2023) The complete sequence of a human Y chromosome. Nature volume 621, pages 344–354. doi: 10.1038/s41586-023-06457-y.
• Manske F, Ogoniak L, Jürgens L, Grundmann N, Makałowski W, Wethmar K. (2023) The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. Nucleic Acids Res. 51(D1):D328-D336. doi: 10.1093/nar/gkac899.
• Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O'Neill RJ. (2022) From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science. 376(6588):eabk3112. doi: 10.1126/science.abk3112
• Rodriguez M, Makałowski W. (2022) Software evaluation for de novo detection of transposons. Mob DNA. 13(1):14. doi: 10.1186/s13100-022-00266-2.
• Bohn J, Halabian R, Schrader L, Shabardina V, Steffen R, Suzuki Y, Ernst UR, Gadau J, Makałowski W. (2021) Genome assembly and annotation of the California harvester ant Pogonomyrmex californicus. G3 (Bethesda). 2021 Jan 18;11(1):1-9. doi: 10.1093/g3journal/jkaa019.
• Juergens L, Manske F, Hubert E, Kischka T, Floetotto L, Klaas O, Shabardina V, Schliemann C, Makalowski W, Wethmar K (2021) Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer. Biomedicines 2021; 9(6):618. doi: 10.3390/biomedicines9060618.
• Shabardina V, Kashima Y, Suzuki Y, Makalowski W. (2020) Emergence and Evolution of ERM Proteins and Merlin in Metazoans. Genome Biol Evol. 12(1):3710-3724. doi: 10.1093/gbe/evz265.
• Wünnemann F, Ta-Shma A, Preuss C, Leclerc S, van Vliet PP, Oneglia A, Thibeault M, Nordquist E, Lincoln J, Scharfenberg F, Becker-Pauly C, Hofmann P, Hoff K, Audain E, Kramer HH, Makalowski W, Nir A, Gerety SS, Hurles M, Comes J, Fournier A, Osinska H, Robins J, Pucéat M; MIBAVA Leducq Consortium principal investigators, Elpeleg O, Hitz MP, Andelfinger G. (2020) Loss of ADAMTS19 causes progressive non-syndromic heart valve disease. Nat Genet. 52(1):40-47. doi: 10.1038/s41588-019-0536-2. Epub 2019 Dec 16.
• Makałowski W, Shabardina V. (2020) Bioinformatics of nanopore sequencing. J Hum Genet. 65(1):61-67. doi: 10.1038/s10038-019-0659-4. Epub 2019 Aug 26.
• Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L. (2019) An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo. Sci Rep. 16;9(1):13356. doi: 10.1038/s41598-019-49817-3.
• Makałowski W, Gotea V, Pande A, Makałowska I. (2019) Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics. Methods Mol Biol. 2019;1910:177-207. doi: 10.1007/978-1-4939-9074-0_6.
• Shabardina V, Kischka T, Manske F, Grundmann N, Frith MC, Suzuki Y, Makalowski W (2019) NanoPipe - a web server for nanopore MinION sequencing data analysis. GigaScience, giy169, doi: 10.1093/gigascience/giy169
• Kellner M, Makalowski W (2018) Transposable Elements Significantly Contributed to the Core Promoters in the Human Genome. SCIENCE CHINA Life Sciences. doi: 10.1007/s11427-018-9449-0
• Makalowski W, Shabardina V, Makalowska I (2018) Bioinformatics. eLS, John Wiley & Sons, Ltd (Ed). doi:10.1002/9780470015902.a0005247.pub3
• Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA. (2018) Transcriptional interference by small transcripts in proximal promoter regions. Nucleic Acids Res. 2018 Feb 16;46(3):1069-1088.
• Shabardina V, Kischka T, Kmita H, Suzuki Y, Makalowski W. (2018) Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis. Int J Biol Sci 14(3):306-320. doi:10.7150/ijbs.23869
• Suzuki A, Suzuki M, Mizushima-Sugano J, Frith MC, Makalowski W, Kohl T, Sugano S, Tsichihara K, Suzuki Y (2017) Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. DNA Research. 24(6):585-596. DOI: 10.1093/dnares/dsx027.
• Farmanbar A, Firouzi S, Makalowski W, Iwanaga M, Uchimaru K, Utsunomiya A, Watanabe T, Nakai K (2017) Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization. Hum Genomics. 11(1):15. DOI: 10.1186/s40246-017-0112-8.
• Makalowski W, Kischka T, Makalowska I (2017) Contribution of Transposable Elements to Human Proteins. eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0020793.pub2