"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.
"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.
Retroelement-driven structural mutations in cancer and healthy genomes
Publications
Rhie, A.; Nurk, S.; Cechova, M.; Hoyt, S. J.; Taylor, D. J.; Altemose, N.; Hook, P. W.; Koren, S.; Rautiainen, M.; Alexandrov, I. A.; Allen, J.; Asri, M.; Bzikadze, A. V.; Chen, N.-C.; Chin, C.-S.; Diekhans, M.; Flicek, P.; Formenti, G.; Fungtammasan, A.; Garcia Giron, C.; Garrison, E.; Gershman, A.; Gerton, J. L.; Grady, P. G. S.; Guarracino, A.; Haggerty, L.; Halabian, R.; Hansen, N. F.; Harris, R.; Hartley, G. A.; Harvey, W. T.; Haukness, M.; Heinz, J.; Hourlier, T.; Hubley, R. M.; Hunt, S. E.; Hwang, S.; Jain, M.; Kesharwani, R. K.; Lewis, A. P.; Li, H.; Logsdon, G. A.; Lucas, J. K.; Makalowski, W.; Markovic, C.; Martin, F. J.; Mc Cartney, A. M.; McCoy, R. C.; McDaniel, J.; McNulty, B. M.; Medvedev, P.; Mikheenko, A.; Munson, K. M.; Murphy, T. D.; Olsen, H. E.; Olson, N. D.; Paulin, L. F.; Porubsky, D.; Potapova, T.; Ryabov, F.; Salzberg, S. L.; Sauria, M. E. G.; Sedlazeck, F. J.; Shafin, K.; Shepelev, V. A.; Shumate, A.; Storer, J. M.; Surapaneni, L.; Taravella Oill, A. M.; Thibaud-Nissen, F.; Timp, W.; Tomaszkiewicz, M.; Vollger, M. R.; Walenz, B. P.; Watwood, A. C.; Weissensteiner, M. H.; Wenger, A. M.; Wilson, M. A.; Zarate, S.; Zhu, Y.; Zook, J. M.; Eichler, E. E.; O’Neill, R. J.; Schatz, M. C.; Miga, K. H.; Makova, K. D.; Phillippy, A. M., The complete sequence of a human Y chromosome. Nature 2023. doi: 10.1038/s41586-023-06457-y
Halabian R, Makałowski W. A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes. Biology. 2022; 11(7):1032.doi: 10.3390/biology11071032
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. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science. 2022 Apr;376(6588):eabk3112. doi: 10.1126/science.abk3112
Jonas Bohn, Reza Halabian, Lukas Schrader, Victoria Shabardina, Raphael Steffen, Yutaka Suzuki, Ulrich R Ernst, Jürgen Gadau, Wojciech Makalowski, Genome assembly and annotation of the California harvester ant Pogonomyrmex californicus, G3 Genes|Genomes|Genetics, Volume 11, Issue 1, January 2021, jkaa019,
doi: 10.1093/g3journal/jkaa019
Teachings
Winter semester of 2022, Bioinformatics 1 practicals course, Instructor, University of Münster, Germany
Winter semester of 2021, Bioinformatics 1 practicals course, Instructor, University of Münster, Germany
Winter semester of 2020, Bioinformatics 1 practicals course, Instructor, University of Münster, Germany
Winter semester of 2019, Bioinformatics 1 practicals course, Instructor, University of Münster, Germany
Winter semester of 2018, Bioinformatics 1 practicals course, Instructor, University of Münster, Germany
Conferences and workshops
July 3-6, 2023: Participation in the course of 14th Poznan summer school of bioinformatics with the topic of the analysis of single-cell data, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
November 3-5, 2021: Virtual Cold Spring Harbor Laboratory (CSHL) conference on genome informatics. Participant with a poster, Title: DNA transductions mediated by non-LTR retroelements in the complete human genome (T2T-CHM13), Reza Halabian et al.
October 6-9, 2020: Virtual Cold Spring Harbor Laboratory (CSHL) conference on transposable elements. Participant with a poster, Title: Frequent polymorphic DNA transductions in human populations, Reza Halabian and Wojciech Makalowski.
September 4-8, 2017: Participation in the course of 12th Poznan summer school of bioinformatics with the topic of NGS in medical research, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
2007, November: 5th national conference of biotechnology. Participant with an oral presentation, Title: Detection SNPs of Bovine Prolactin Gene, Tehran, Iran.
2006.09.12-24: Coursework training (2 weeks) in Bioinformatics for MD simulation, CinnaGen, Tehran, Iran.
2006.10.12-24: Coursework training (2 weeks) in PCR for Diagnosis: Design of Laboratory, Real Time PCR, Diagnosis for HIV. CinnaGene, Tehran, Iran.