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The Faculty of Medicine - Biochemistry and Molecular Biology: Nitzan Mor


 Last updated September 2023 - Biochemistry and Molecular Biology 

List of Publications


Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, et al. Best practices for single-cell analysis across modalities. Nature Reviews Genetics [Internet]. 2023;24(8):550–72. Available from:


Sheng Y, Barak B, Nitzan M. Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates. Bioinformatics [Internet]. 2023;39:I423–30. Available from:


Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, et al. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports [Internet]. 2023;42(5). Available from:


Karin J, Bornfeld Y, Nitzan M. scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching. Nature Biotechnology [Internet]. 2023; Available from:


Mages S, Moriel N, Avraham-Davidi I, Murray E, Watter J, Chen F, et al. TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nature Biotechnology [Internet]. 2023; Available from:


Guo Y, Nitzan M, Brenner MP. Programming cell growth into different cluster shapes using diffusible signals. PLoS Computational Biology [Internet]. 2021;17(11). Available from:


Biancalani T, Scalia G, Buffoni L, Avasthi R, Lu Z, Sanger A, et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nature Methods [Internet]. 2021;18(11):1352–62. Available from:


Moriel N, Senel E, Friedman N, Rajewsky N, Karaiskos N, Nitzan M. NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport. Nature Protocols [Internet]. 2021;16(9):4177–200. Available from:


Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, et al. Author Correction: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin (Nature Biotechnology, (2021), 39, 5, (586-598), 10.1038/s41587-020-00775-6). Nature Biotechnology [Internet]. 2021;39(5):642. Available from:


Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, et al. ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nature Biotechnology [Internet]. 2021;39(5):586–98. Available from:


Nitzan M, Brenner MP. Revealing lineage-related signals in single-cell gene expression using random matrix theory. Proceedings of the National Academy of Sciences of the United States of America [Internet]. 2021;118(11). Available from:


Haralampiev I, Prisner S, Nitzan M, Schade M, Jolmes F, Schreiber M, et al. Selective flexible packaging pathways of the segmented genome of influenza A virus. Nature Communications [Internet]. 2020;11(1). Available from:


Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, et al. Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome. Journal of Experimental Medicine [Internet]. 2020;217(10). Available from:


Forrow A, Hütter JC, Nitzan M, Rigollet P, Schiebinger G, Weed J. Statistical optimal transport via factored couplings. In: AISTATS 2019 - 22nd International Conference on Artificial Intelligence and Statistics [Internet]. 2020. Available from:


Nitzan M, Karaiskos N, Friedman N, Rajewsky N. Gene expression cartography. Nature [Internet]. 2019;576(7785):132–7. Available from:


Nitzan M, Nitzan S, Segal-Halevi E. Flexible level-1 consensus ensuring stable social choice: analysis and algorithms. Social Choice and Welfare [Internet]. 2018;50(3):457–79. Available from:


Schurr R, Nitzan M, Eliahou R, Spinelli L, Seeck M, Blanke O, et al. Temporal dissociation of neocortical and hippocampal contributions to mental time travel using intracranial recordings in humans. Frontiers in Computational Neuroscience [Internet]. 2018;12. Available from:


Casadiego J, Nitzan M, Hallerberg S, Timme M. Model-free inference of direct network interactions from nonlinear collective dynamics. Nature Communications [Internet]. 2017;8(1). Available from:


Nitzan M, Rehani R, Margalit H. Integration of Bacterial Small RNAs in Regulatory Networks. Annual Review of Biophysics [Internet]. 2017;46:131–48. Available from:


Nitzan M, Casadiego J, Timme M. Revealing physical interaction networks from statistics of collective dynamics. Science Advances [Internet]. 2017;3(2). Available from:


Peer M, Nitzan M, Bick AS, Levin N, Arzy S. Evidence for functional networks within the human brain’s white matter. Journal of Neuroscience [Internet]. 2017;37(27):6394–407. Available from:


Nitzan M, Katzav E, Kühn R, Biham O. Distance distribution in configuration-model networks. Physical Review E [Internet]. 2016;93(6). Available from:


Rosenfeld N, Nitzan M, Globerson A. Discriminative learning of infection models. In: WSDM 2016 - Proceedings of the 9th ACM International Conference on Web Search and Data Mining [Internet]. 2016. p. 563–72. Available from:


Katzav E, Nitzan M, Ben-Avraham D, Krapivsky PL, Kühn R, Ross N, et al. Analytical results for the distribution of shortest path lengths in random networks. EPL [Internet]. 2015;111(2). Available from:


Nitzan M, Shimoni Y, Rosolio O, Margalit H, Biham O. Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics [Internet]. 2015;91(5). Available from:


Sajman J, Zenvirth D, Nitzan M, Margalit H, Simpson-Lavy KJ, Reiss Y, et al. Degradation of Ndd1 by APC/CCdh1 generates a feed forward loop that times mitotic protein accumulation. Nature Communications [Internet]. 2015;6. Available from:


Nitzan M, Mintzer S, Margalit H. Approaches and developments in studying the human microbiome network. Israel Journal of Ecology and Evolution [Internet]. 2015;61(2):90–4. Available from:


Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, et al. A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic Acids Research [Internet]. 2015;43(3):1357–69. Available from:


Nitzan M, Steiman-Shimony A, Altuvia Y, Biham O, Margalit H. Interactions between distant ceRNAs in regulatory networks. Biophysical Journal [Internet]. 2014;106(10):2254–66. Available from:


Nitzan M, Wassarman KM, Biham O, Margalit H. Global regulation of transcription by a small RNA: A quantitative view. Biophysical Journal [Internet]. 2014;106(5):1205–14. Available from:


Peer M, Nitzan M, Goldberg I, Katz J, Gomori JM, Ben-Hur T, et al. Reversible functional connectivity disturbances during transient global amnesia. Annals of Neurology [Internet]. 2014;75(5):634–43. Available from:


Mills E, Baruch K, Aviv G, Nitzan M, Rosenshine I. Dynamics of the type III secretion system activity of enteropathogenic Escherichia coli. mBio [Internet]. 2013;4(4). Available from:


Zahavi EE, Lieberman JA, Donnenberg MS, Nitzan M, Baruch K, Rosenshine I, et al. Bundle-forming pilus retraction enhances enteropathogenic Escherichia coli infectivity. Molecular Biology of the Cell [Internet]. 2011;22(14):2436–47. Available from: