Publications and Preprints
My profile on Google Scholar.
60. Friedman, R., Moriel, N., Ricci, M., Pelc, G., Weiss, Y. and Nitzan, M. Characterizing Nonlinear Dynamics via Smooth Prototype Equivalences. arXiv: 2503.10336.
59. Lisek, K.*, Theurillat, I.*, Pentimalli, T.M.*, Beier, S., León-Periñán, D., Antonatou, A., Dubnov, S., Müller, M., Hubl, F., Xhuri, A., Romanowicz, H., Smolarz, B., Montaudon, E., Raimundo, S., Margineanu, A., Schott, M. , Kunz, S. , Marangoni, E. , Karaiskos, N., Nitzan, M., Birchmeier, W., Rajewsky, N. Spatiotemporal dynamics of tumor microenvironment remodeling. bioRxiv 2025-07.
58. Pelc, G.*, McKeithan, W.L.*, Guo, Y., Brenner, M.P., Lim, W.A. and Nitzan, M. Coupling differential adhesion to cell signaling avoids kinetic traps to yield robust multicellular self-organization. bioRxiv 2025-10.
57. Karin, J., Friedman, R., Nitzan, M. Decoding Condition-Specific Cellular Crosstalk in Spatial Omics via Bilinear Edge Classification. bioRxiv 2026-05.
56. Dubnov, S., Laski, L., Zchut, I., Avidan, O., Bennet, E.R., Greenberg, D.S., Tujerman, A., Nitzan, M., Paldor, I. and Soreq, H. A cell-type-resolved microRNA atlas of adult human brain reveals aging-associated signatures. bioRxiv 2026-01.
55. Heyman, Y.*, Erez, M.*, Burnham, P., Nitzan, M. and Raj, A. Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation. bioRxiv 2025-11.
54. Dubnov, S., Piran, Z., Alper, A., Yefroimsky, A., Soreq, H. and Nitzan, M., 2026. Identifying maximally informative signal-aware representations of single-cell data using the Information Bottleneck. Cell Systems.
53. Rappeport, H. and Nitzan, M., 2026. Fitness and Overfitness: Implicit Regularization in Evolutionary Dynamics. PRX Life.
52. Erez, M.*, Friedman, R.* and Nitzan, M. 2026. Neighborhood-Informed Positional Information for Precise Cell Identity Specification. Molecular Systems Biology.
51. Chen, S., Ricci, M., Tabatabai, A.P., Shankar, S., Nitzan, M. and Murrell, M.P. 2026. Topological control of spontaneous failure in active nematic solids. Nature Materials.
50. Karin, J., Piran, Z. and Nitzan, M. 2025. Enhancing swarms' durability to threats via a GNN-based generative modeling. Physical Review E.
49. Viñas Torné, R., Wiatrak, M., Piran, Z., Fan, S., Jiang, L., Teichmann, S.A., Nitzan, M. and Brbić, M. 2025. Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation. Nature Biotechnology.
48. Ricci, M., Pelc, G., Piran, Z., Moriel, N. and Nitzan, M. 2025. TRENDy: Temporal regression of effective nonlinear dynamics. 13th International Conference on Learning Representations.
47. 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. 2025. Mapping cells through time and space with moscot. Nature, 1-11.
46. 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., Strasser, R., Lalakova, J., Niesnerova, A., Xu, H., Rouault, M., Tirosh, I., Hacohen, N., Chen, F., Yilmaz, O., Roper, J., Rozenblatt-Rosen, O., Nitzan, M. and Regev, A., 2025. Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics. eLife, 14.
45. Karin, J.*, Mintz, R.*, Raveh, B. and Nitzan, M., 2024. Interpreting single-cell and spatial omics data using deep neural network training dynamics. Nature Computational Science, 1-14.
44. Lange, M.*, Piran, Z.*, Klein, M.*, Spanjaard, B.*, Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M. 2024. Mapping lineage-traced cells across time points with moslin. Genome Biology, 25(1), 277.
43. Bonev, B., Castelo-Branco, G., Chen, F., Codeluppi, S., Corces, R., Fan, J., Haiman, M., Harris, K., Inoue, F., Kellis, M., Levine, A., Lotfollahi, M., Luo, C., Maynard, K.R., Nitzan, M., Ramani, V., Regev, A., Satijia, R., Schirmer, L., Shen, Y., Sun, N., Theis, F., Wang, X., Welch, J., Bayraktar, O., Gokce, O., Habib, N., Konopka, G., Liddelow, S., Macosko, E., Nowakowski, T.J. 2024. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nature Neuroscience, 27(12), 2292-2309.
42. Piran, Z., Cohen, N., Hoshen, Y. and Nitzan, M. 2024. Disentanglement of single-cell data with biolord. Nature Biotechnology, 1-6.
41. 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.
40. Piran, Z. and Nitzan, M. 2024. Uncovering hidden biological processes by probabilistic filtering of single-cell data, Nature Communications, 15(1), 760.
39. Moriel, N.*, Memet, E.* and Nitzan, M., 2024. Optimal sequencing budget allocation for trajectory reconstruction of single cells. Bioinformatics, 40 (i446-52), as part of ISMB 2024 Proceedings.
38. Klughammer, J., Abravanel, D.L., Segerstolpe, Å., Blosser, T.R., Goltsev, Y., Cui, Y., Goodwin, D.R., Sinha, A., Ashenberg, O., Slyper, M. and Vigneau, S.,.. , Mages, S., Moriel, N., Murray, E., Napolitano, S., Nguyen, K., Nitzan, M., ..., Regev, A. and Wagle, N. 2024. A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features. Nature Medicine, pp.1-14.
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. 11th 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. 2018. Flexible 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
