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

1.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85152429015&doi=10.1038%252fs41576-023-00586-w&partnerID=40&md5=e075d1923dc52c4783683a960d74051f

2.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85164233482&doi=10.1093%252fbioinformatics%252fbtad253&partnerID=40&md5=64ff41e008bdd19a5dba0be5a6d315b5

3.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85152629362&doi=10.1016%252fj.celrep.2023.112412&partnerID=40&md5=26adefad01d3abe5694320fa72d1973f

4.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148945488&doi=10.1038%252fs41587-023-01663-5&partnerID=40&md5=2026d946058edf37e220d322aff9944f

5.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148215857&doi=10.1038%252fs41587-023-01657-3&partnerID=40&md5=8f183adfcd35dfad9b81bc8f847a4835

6.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119933676&doi=10.1371%252fjournal.pcbi.1009576&partnerID=40&md5=92049e4fcc4391c89382a873b0c7ec6a

7.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85117965279&doi=10.1038%252fs41592-021-01264-7&partnerID=40&md5=206e0b3a914d50ddd7628241382be0c1

8.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111901166&doi=10.1038%252fs41596-021-00573-7&partnerID=40&md5=e760edf1f9575535a6ffc1feef117d84

9.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099542130&doi=10.1038%252fs41587-021-00831-9&partnerID=40&md5=d3bc380f34a9e192d8959bfdaec996a9

10.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099286111&doi=10.1038%252fs41587-020-00775-6&partnerID=40&md5=63eef9ded0c4af891c55b435bb62aa99

11.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102358490&doi=10.1073%252fpnas.1913931118&partnerID=40&md5=a825d85603c839f904d42b6a8a5ee7d5

12.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089975241&doi=10.1038%252fs41467-020-18108-1&partnerID=40&md5=8e46926c972ef6d23681e319fc84fa61

13.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087403881&doi=10.1084%252fJEM.20200483&partnerID=40&md5=63fafc8b9a71db6b59d4857fa6f222ba

14.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85084928186&partnerID=40&md5=dbce95c59e3dd9540b7832d12d7c724b

15.

Nitzan M, Karaiskos N, Friedman N, Rajewsky N. Gene expression cartography. Nature [Internet]. 2019;576(7785):132–7. Available from: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075376819&doi=10.1038%252fs41586-019-1773-3&partnerID=40&md5=4b8503c1de369b524d95ea87dc91a0fd

16.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032959829&doi=10.1007%252fs00355-017-1092-2&partnerID=40&md5=b2b1e1bcb22756868cb0a6c665a9ec70

17.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049526485&doi=10.3389%252ffncom.2018.00011&partnerID=40&md5=eedf76fa2e51d67e8927c8c59df18f57

18.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038627760&doi=10.1038%252fs41467-017-02288-4&partnerID=40&md5=44375d1c0e059c3cc8a634af7e657298

19.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019771051&doi=10.1146%252fannurev-biophys-070816-034058&partnerID=40&md5=6d4e258b9b93307ddfbe77ed405f254e

20.

Nitzan M, Casadiego J, Timme M. Revealing physical interaction networks from statistics of collective dynamics. Science Advances [Internet]. 2017;3(2). Available from: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031824236&doi=10.1126%252fsciadv.1600396&partnerID=40&md5=05559cda5db67edda8207e2c625345a3

21.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021987646&doi=10.1523%252fJNEUROSCI.3872-16.2017&partnerID=40&md5=f739397395b53ac9985b9a47aaa0b9de

22.

Nitzan M, Katzav E, Kühn R, Biham O. Distance distribution in configuration-model networks. Physical Review E [Internet]. 2016;93(6). Available from: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975290457&doi=10.1103%252fPhysRevE.93.062309&partnerID=40&md5=7019e9122f387dadae1893bb199f9cc7

23.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964320726&doi=10.1145%252f2835776.2835802&partnerID=40&md5=36b5913e6b00276a1fe612eab686cd96

24.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940179766&doi=10.1209%252f0295-5075%252f111%252f26006&partnerID=40&md5=4e235cdd9b29ddd3a5d21998b3034a4e

25.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930663043&doi=10.1103%252fPhysRevE.91.052706&partnerID=40&md5=402266c3c29f8a58ae0646cdf4c9899c

26.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929224575&doi=10.1038%252fncomms8075&partnerID=40&md5=5d9b7ee2bdc45796f0cfc6be3aff8463

27.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84962811934&doi=10.1080%252f15659801.2015.1042768&partnerID=40&md5=d2fca47b874e1cae9c15c06b35e921ae

28.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930631240&doi=10.1093%252fnar%252fgkv001&partnerID=40&md5=905a5f3d16acc8bc93b64ac4d4a7af60

29.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901273489&doi=10.1016%252fj.bpj.2014.03.040&partnerID=40&md5=446f7fdd800b040012d9eeaa62ceeb74

30.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901742837&doi=10.1016%252fj.bpj.2014.01.025&partnerID=40&md5=5e6e02a9d7a6d835d4971b0103b1b0f1

31.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84902240545&doi=10.1002%252fana.24137&partnerID=40&md5=006f9b4749bef4b8ba59c5ec46e03c6d

32.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883422155&doi=10.1128%252fmBio.00303-13&partnerID=40&md5=fca3ce4c938558e4214cd8711174f15e

33.

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: https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960289464&doi=10.1091%252fmbc.E11-01-0001&partnerID=40&md5=8a9e97a3c184ef1b43d6e007b2d068fc