Maja Kuzman

Maja is a PhD student with a background in mathematics and a master degree in molecular biology. She is currently employed on a project that investigates genomics of basal metazoans.

As a junior researcher her work was focused on interaction between human microbiome and development of liver cirrhosis. She participated in three collaborations – first one with Dr. Sc. Marinom Lusic, Heidelberg University Hospital and German Center for Infection Research, Heidelberg, Germany, et al. Guillaume Filion, Center for Genomic Regulation (CRG), Barcelona, ​​Spain. She collaborated with these scientists to investigate the incorporation of HIV into the human genome.
She also worked with Ph.D. Petr Svoboda, Institute of Molecular Genetics, Prague, Czech Republic. The purpose of this collaboration was to analyse the impact of long terminal repeats on the evolution of genes in oocytes and zygotes in mammals. Finally, she has worked with leading global scientists in the field of cancer genomics: Gad Getz (Broad Institute of MIT and Harvard, USA), Paz Polak (Icahn School of Medicine at Mount Sinai, USA) and William Foulkes (McGill University, Canada). The results of the collaboration have been published on BioRxiv and the work is currently under review in the prestigious journal Nature.

She has experience in data analysis and application of statistical and machine learning methods in genomics, including data from metagenome sequencing, RNA seq, ChIP seq, DRIP seq, and Oxford Nanopore technologies.

Maja is a teaching assistant in graduate and undergraduate level courses, including Algorithms and Programming, Statistics and Machine Learning, Bioinformatics and Computational genomics.

Publications 

1. Kirsten KüblerRosa KarlićN.HaradhvalaKyungsik HaJaegil KimMaja KuzmanWei JiaoSitanshu GakkharKent W. MouwLior Z. BraunsteinOlivier ElementoAndrew V. BiankinIlse RoomanMendy MillerWouter R. KarthausChristopher D. NogiecEdouard JuvensonEdward CurryMari Mino-KenudsonLeif W. EllisenRobert BrownAlexander GusevCristian TomasettiMartijn P. LolkemaNeeltje SteeghsCarla van HerpenHong-Gee KimHwajin LeeKristian VlahovičekBradley E. BernsteinCharles L. SawyersKatherine A. HoadleyEdwin CuppenAmnon KorenPeter F. ArndtDavid N. LouisLincoln D. SteinWilliam D. FoulkesPaz PolakGad Getz Tumor mutational landscape is a record of the pre-malignant state. BioRxiv 517565 (2019)

2. Lucic, B.*, Chen, H.-C.*, Kuzman, M.*, Zorita, E*., Wegner, J., Minnerker, V., Weng, W., Fronza, R., Laufs, S., Schmidt, M., Stadhouders, R., V., Roukos, Vlahovicek, K.#, Filion, J. G.#, Lusic, M.# Spatially clustered loci with multiple enhancers are frequent targets of HIV-1. Nat Commun. 10.1038/s41467-019-12046-3 (2019)

3. Elek A, Kuzman M, Vlahovicek K (2018). coRdon: Codon Usage Analysis and Prediction of Gene Expressivity. 10.18129/B9.bioc.coRdon .

4. Franke, V., Ganesh, S., Karlic, R., Malik, R., Pasulka, J., Horvat, F., Kuzman, M., Fulka, H., Cernohorska, M., Urbanova, J., et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.- Genome Res. gr.216150.116. (2017)

5.  Fabijanić, M., and Vlahoviček, K. Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles.-  In Data Mining Techniques for the Life Sciences, O. Carugo, and F. Eisenhaber, eds. (Springer New York) (2016), pp. 509–531