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Publications and Preprints

My profile on Google Scholar.

46. Karin, J., Mintz, R., Raveh, B. and Nitzan, M., 2024. Interpreting single-cell and spatial omics data using deep networks training dynamics. bioRxiv, pp.2024-04.


45. Dubnov, S., Piran, Z., Soreq, H. and Nitzan, M., 2024. Identifying maximally informative signal-aware representations of single-cell data using the Information Bottleneck. bioRxiv, 2024-05.

44. Moriel, N.*, Memet, E.* and Nitzan, M., 2024. Optimal sequencing budget allocation for trajectory reconstruction of single cells. Bioinformatics, as part of ISMB 2024 Proceedings.

43. Piran, Z., Cohen, N., Hoshen, Y. and Nitzan, M. 2024. Disentanglement of single-cell data with biolord. Nature Biotechnology.

42. Moriel, N.*, Ricci, M.* and Nitzan M., 2024. Let's do the time-warp-attend: Learning topological invariants of dynamical systems. 12th International Conference on Learning Representations.

41. Piran, Z. and Nitzan, M. 2024. Uncovering hidden biological processes by probabilistic filtering of single-cell data, Nature Communications.

40. Lange, M.*, Piran, Z.*, Klein, M.*, Spanjaard, B.*, Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M. 2023. Mapping lineage-traced cells across time points with moslin. bioRxiv.

39. Klein, D. *, Palla, G. *, Lange, M. *, Klein, M. *, Piran, Z. *, Gander, M., Meng-Papaxanthos, L., Sterr, M., Bastidas-Ponce, A., Tarquis-Medina, M., Lickert, H., Bakhti, M., Nitzan, M., Cuturi, M. and Theis, F.J. 2023. Mapping cells through time and space with moscot. bioRxiv.

38. Avraham-Davidi, I.*, Mages, S.*, Klughammer, J.*, Moriel, N., Imada, S., Hofree, M., Murray, E., Chen, J., Pelka, K., Mehta, A., Boland, M., Delorey, T., Caplan, L., Dionne, D., Tirosh, I., Hacohen, N., Chen, F., Yilmaz, O., Roper, J., Rozenblatt-Rosen, O., Nitzan, M. and Regev, A., 2023. Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression. bioRxiv.

37. Sheng, Y., Barak, B. and Nitzan, M. 2023. Robust reconstruction of single cell RNA-seq data with iterative gene weight updates. Bioinformatics 39.

36. Karin, J., Bornfeld, Y. and Nitzan, M., 2023. scPrisma: inference, filtering and enhancement of periodic signals in single-cell data using spectral template matching. Nature Biotechnology. 

35. Mages, S.*, Moriel, N.*, Avraham-Davidi, I.*, Murray, E., Chen, F., Rozenblatt-Rosen, O., Klughammer, J., Regev, A. and Nitzan, M., 2023. TACCO: Unified annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nature Biotechnology.

34. Adler, M. *, Moriel, N. *, Goeva, A. *, Avraham-Davidi, I., Mages, S., Adams, T.S., Kaminski, N., Macosko, E.Z., Regev, A., Medzhitov, R. and Nitzan, M. 2023. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports 42, 5

33. Ricci, M., Moriel, N., Piran, Z. and Nitzan M., 2023. Phase2vec: Dynamical systems embedding with a physics-informed convolutional network. Eleventh International Conference on Learning Representations.

32. Vaknin, Y., Moriel, N. and Nitzan, M. 2022. Using co-localization priors and microenvironment statistics to reconstruct tissue organization from single-cell data. Learning Meaningful Representations of Life Workshop. In 36th Conference on Neural Information Processing Systems (NeurIPS2022). 

31. Moriel, N.*, Senel, E.*, Friedman, N., Rajewsky, N., Karaiskos, N., and Nitzan, M. 2021. NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport. Nature Protocols, pp. 1-24.

30. Nitzan, M. and Brenner, M. 2021. Revealing lineage-related signals in single-cell gene expression using random matrix theory. Proceedings of the National Academy of Sciences (PNAS), 118(11).

29. Piran, Z., and Nitzan, M. 2021. Emphasizing cellular processes by filtering gene expression through projections. Learning Meaningful Representations of Life Workshop. In 35th Conference on Neural Information Processing Systems (NeurIPS2021).

28. Lange, M.*, Piran, Z.*, Klein, M., Theis, F.J., and Nitzan, M. 2021. Mapping lineage-traced single-cells across time-points. Learning Meaningful Representations of Life Workshop. In 35th Conference on Neural Information Processing Systems (NeurIPS2021).

27. Biancalani, T.,  Scalia, G.,  Buffoni, L., Avasthi, R., Lu, Z., Sanger, A., Tokcan, N.,  Vanderburg, C.R., Segerstolpe, A., Zhang, M., Avraham-Davidi, I., Vickovic, S., Nitzan, M., Ma, S., Subramanian, A., Lipinski, M., Buenrostro, J., Bear Brown, N., Fanelli, D., Zhuang, X., Macosko, E.Z., and Regev, A. 2021. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nature Methods, pp.1-11.

26. Sadeh, R., Sharkia, I., Fialkoff, G., Rahat, A., Gutin, J., Chappleboim, A., Nitzan, M., Fox-Fisher, I., Neiman, D., Meler, G., Kamari, Z., Yaish, D., Peretz, T., Hubert, A., Cohen, J., Salah, A., Temper, M., Grinshpun, A., Maoz, M., Abu-Gazala, S., Ben Ya'acov, A., Shteyer, E., Safadi, R., Kaplan, T., Shemer, R., Planer, D., Galun, E., Glaser, B., Zick, A., Dor, Y. and Friedman, N. 2021. ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nature biotechnology, pp.1-13.

25. Guo, Y., Nitzan, M. and Brenner, M.P., 2021. Programming cell growth into different cluster shapes using diffusible signals. PLOS Computational Biology, 17(11), e1009576

24. Barak, B.*, Nitzan, M.*, Tannenbaum, N.R.* and Yuval, J.*, 2020. Optimizing testing policies for detecting COVID-19 outbreaks. arXiv preprint arXiv:2007.04827.

23. Haralampiev, I.*, Prisner1, S.*, Nitzan, M., Schade, M., Jolmes, F., Schreiber, M., Loidolt-Krüger, M., Jongen, K., Chamiolo, J., Winter, F., Friedman, N., Seitz, O., Wolff, T. and Herrmann, A., 2020. Selective flexible packaging pathways of the segmented genome of influenza A virus. Nature Communications, 11(1), pp.1-13.

22. Holmes, A.B., Corinaldesi, C., Shen, Q., Kumar, R., Compagno, N., Wang, Z., Nitzan, M., Grunstein, E., Pasqualucci, L., Dalla-Favera, R. and Basso, K., 2020. Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome. Journal of Experimental Medicine, 217(10).

21. Nitzan, M.*, Karaiskos, N.*, Friedman, N. and Rajewsky, N. 2019. Gene expression cartography. Nature, 576(7785), pp.132-137.

20. Dauparas, J., Wang, H., Koo, P., Nitzan, M. and Ovchinnikov, O. 2019. Unified framework for modeling multivariate distributions in biological sequences. ICML19, Workshop on Computational Biology.

19. {Forrow, A., Hutter, J.C., Nitzan, M., Rigollet, P., Schiebinger, G. and Weed, J.}# 2018. Statistical optimal transport via factored couplings. arXiv 1806.07348. AISTATS19.

18. Schurr, R., Nitzan, M., Eliahou, R., Spinelli, L., Seeck, M., Blanke, O. and Arzy, S. 2018. Temporal dissociation of neocortical and hippocampal contributions to mental time travel using intracranial recordings in humans. Frontiers in Computational Neuroscience, 12, p. 11.

17. Nitzan, M., Nitzan, S. and Segal-Halevi, E. 2018Flexible level-1 consensus ensuring stable social choice: analysis and algorithms. Social Choice and Welfare 50(3), pp.457-79.

16. Nitzan, M., Casadiego, J. and Timme, M. 2017. Revealing physical interactions from statistics of collective dynamics. Science Advances, 3(2), p.e1600396. 

15. Casadiego, J., Nitzan, M., Hallerberg, S. and Timme, M. 2017. Model-free inference of direct network interactions from nonlinear collective dynamics. Nature Communications, 8.

14. Nitzan, M., Rehani, R. and Margalit, H. 2017. Integration of bacterial small RNAs in regulatory networks. Annual Review of Biophysics, 46(1). 

13. Peer, M., Nitzan, M., Bick, A.S., Levin, N. and Arzy, S. 2017. Evidence for functional networks within the human brain's white matter. Journal of Neuroscience, pp.3872-16.

12. Rosenfeld, N., Nitzan, M. and Globerson, A., 2016, February. Discriminative Learning of Infection Models. In Proceedings of the Ninth ACM International Conference on Web Search and Data Mining (pp. 563-572). ACM.

11. Nitzan, M., Katzav, E., Kuehn, R. and Biham, O., 2016. Distance distribution in configuration-model networks. Physical Review E, 93(6), p.062309.

10. Katzav, E., Nitzan, M., ben-Avraham, D., Krapivsky, P.L., Kühn, R., Ross, N. and Biham, O., 2015. Analytical results for the distribution of shortest path lengths in random networks. Europhysics Letters, 111(2), p.26006.

9. Nitzan, M., Fechter, P., Peer, A., Altuvia, Y., Bronesky, D., Vandenesch, F., Romby, P., Biham, O. and Margalit, H., 2015. A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic acids research, 43(3), pp.1357-1369.      


8. Nitzan, M., Shimoni, Y., Rosolio, O., Margalit, H. and Biham, O., 2015. Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations. Physical Review E, 91(5), p.052706.

7. Nitzan, M., Mintzer, S. and Margalit, H., 2015. Approaches and developments in studying the human microbiome network. Israel Journal of Ecology & Evolution, 61(2), pp.90-94. 

6. Sajman, J., Zenvirth, D., Nitzan, M., Margalit, H., Simpson-Lavy, K.J., Reiss, Y., Cohen, I., Ravid, T. and Brandeis, M., 2015. Degradation of Ndd1 by APC/CCdh1 generates a feed forward loop that times mitotic protein accumulation. Nature communications, 6.

5. Nitzan, M., Steiman-Shimony, A., Altuvia, Y., Biham, O. and Margalit, H., 2014. Interactions between distant ceRNAs in regulatory networks. Biophysical journal, 106(10), pp.2254-2266.

4. Nitzan, M., Wassarman, K.M., Biham, O. and Margalit, H., 2014. Global regulation of transcription by a small RNA: a quantitative view. Biophysical journal, 106(5), pp.1205-1214.


3. Peer, M., Nitzan, M., Goldberg, I., Katz, J., Gomori, J.M., Ben‐Hur, T. and Arzy, S., 2014. Reversible functional connectivity disturbances during transient global amnesia. Annals of neurology, 75(5), pp.634-643.

2. Mills, E., Baruch, K., Aviv, G., Nitzan, M. and Rosenshine, I., 2013. Dynamics of the type III secretion system activity of enteropathogenic Escherichia coli. MBio, 4(4), pp.e00303-13.

1. Zahavi, E.E., Lieberman, J.A., Donnenberg, M.S., Nitzan, M., Baruch, K., Rosenshine, I., Turner, J.R., Melamed-Book, N., Feinstein, N., Zlotkin-Rivkin, E. and Aroeti, B., 2011. Bundle-forming pilus retraction enhances enteropathogenic Escherichia coli infectivity. Molecular biology of the cell, 22(14), pp.2436-2447. 

# Alphabetical order

* Equal contribution 

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