אודות
Bioinformatics, immunology, neural computation, system biology, somatic selection, autoimmunity, genetic stability, germline diversity, dendritic cell, transcription elements, pathogens, computational and mathematical modeling, complex systems, cognition and inflammation
פרסומים
- Venezia the Living City, Hershberg, U. & Merelo Guervós, J. J., 2027, Artificial Life and Evolutionary Computation - 19th Italian Workshop, WIVACE 2025, Proceedings. Bianchini, M., Gori, M. & Maggini, M. (eds.). Springer Science and Business Media Deutschland GmbH, p. 3-16 14 p. (Communications in Computer and Information Science; vol. 3001 CCIS).
- Systematic analysis of CDR contacts and pairing constraints between T cell receptor αβ chains, Milighetti, M., Nagano, Y., Henderson, J., Hershberg, U., Tiffeau-Mayer, A., Bitbol, A. F. & Chain, B., 1 Aug 2026, In: Bioinformatics. 42, 8, btag551.
- Pediatric B cell repertoires are enriched for naive clonal phenotypes and are shaped by distinct selection dynamics, Hsiao, T., Shtewe, A. & Hershberg, U., 2025, In: Frontiers in Immunology. 16, 1618234.
- Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation in a pediatric-dominated cohort, Fu, J., Hsiao, T., Waffarn, E., Meng, W., Long, K. D., Frangaj, K., Jones, R., Gorur, A., Shtewe, A., Li, M., Muntnich, C. B., Rogers, K., Jiao, W., Velasco, M., Matsumoto, R., Kubota, M., Wells, S., Danzl, N., Ravella, S. & Iuga, A. & 9 others, , 2024, In: Frontiers in Immunology. 15, 1375486.
- Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity, Matsumoto, R., Gray, J., Rybkina, K., Oppenheimer, H., Levy, L., Friedman, L. M., Khamaisi, M., Meng, W., Rosenfeld, A. M., Guyer, R. S., Bradley, M. C., Chen, D., Atkinson, M. A., Brusko, T. M., Brusko, M., Connors, T. J., Luning Prak, E. T., Hershberg, U., Sims, P. A. & Hertz, T. & 1 others, , Aug 2023, In: Nature Immunology. 24, 8, p. 1370-1381 12 p.
- Diversification of immunoglobulin genes by gene conversion in the domestic chicken (Gallus gallus domesticus), Mallaby, J., Mwangi, W., Ng, J., Stewart, A., Dorey-Robinson, D., Kipling, D., Hershberg, U., Fraternali, F., Nair, V. & Dunn-Walters, D., 2023, In: Discovery Immunology. 2, 1, kyad002.
- Editorial: Quantification of immunological memory, Di Rosa, F., Castiglione, F., Hershberg, U. & Prisco, A., 2023, In: Frontiers in Immunology. 14, 1219067.
- Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire, Mallaby, J., Ng, J., Stewart, A., Sinclair, E., Dunn-Walters, D. & Hershberg, U., 8 Dec 2022, In: Frontiers in Immunology. 13, 837246.
- Impact of finite size effect on applicability of generalized fractal and spectral dimensions to biological networks, Craig, A., Yücel, M., Muchnik, L. & Hershberg, U., Nov 2022, In: Chaos, Solitons and Fractals. 164, 112707.
- Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection, Di Pietro, A., Polmear, J., Cooper, L., Damelang, T., Hussain, T., Hailes, L., O’Donnell, K., Udupa, V., Mi, T., Preston, S., Shtewe, A., Hershberg, U., Turner, S. J., La Gruta, N. L., Chung, A. W., Tarlinton, D. M., Scharer, C. D. & Good-Jacobson, K. L., Jan 2022, In: Nature Immunology. 23, 1, p. 86-98 13 p.
- Using Domain Based Latent Personal Analysis of B Cell Clone Diversity Patterns to Identify Novel Relationships Between the B Cell Clone Populations in Different Tissues, Alon, U., Mokryn, O. & Hershberg, U., 1 Apr 2021, In: Frontiers in Immunology. 12, 642673.
- BCR-Induced Ca2+ Signals Dynamically Tune Survival, Metabolic Reprogramming, and Proliferation of Naive B Cells, Berry, C. T., Liu, X., Myles, A., Nandi, S., Chen, Y. H., Hershberg, U., Brodsky, I. E., Cancro, M. P., Lengner, C. J., May, M. J. & Freedman, B. D., 14 Apr 2020, In: Cell Reports. 31, 2, 107474.
- Liver Is a Generative Site for the B Cell Response to Ehrlichia muris, Trivedi, N., Weisel, F., Smita, S., Joachim, S., Kader, M., Radhakrishnan, A., Clouser, C., Rosenfeld, A. M., Chikina, M., Vigneault, F., Hershberg, U., Ismail, N. & Shlomchik, M. J., 17 Dec 2019, In: Immunity. 51, 6, p. 1088-1101.e5
- Serine substitutions are linked to codon usage and differ for variable and conserved protein regions, Schwartz, G. W., Shauli, T., Linial, M. & Hershberg, U., 1 Dec 2019, In: Scientific Reports. 9, 1, 17238.
- Questions of Stochasticity and Control in Immune Repertoires, Yaari, G., Flajnik, M. & Hershberg, U., Nov 2018, In: Trends in Immunology. 39, 11, p. 859-861 3 p.
- Human lymph nodes maintain TCF-1 hi memory T cells with high functional potential and clonal diversity throughout life, Miron, M., Kumar, B. V., Meng, W., Granot, T., Carpenter, D. J., Senda, T., Chen, D., Rosenfeld, A. M., Zhang, B., Lerner, H., Friedman, A. L., Hershberg, U., Shen, Y., Rahman, A., Luning Prak, E. T. & Farber, D. L., 1 Oct 2018, In: Journal of Immunology. 201, 7, p. 2132-2140 9 p.
- AIRR Community Standardized Representations for Annotated Immune Repertoires, The AIRR Community, 28 Sep 2018, In: Frontiers in Immunology. 9, 2206.
- Computational evaluation of B-cell clone sizes in bulk populations, Rosenfeld, A. M., Meng, W., Chen, D. Y., Zhang, B., Granot, T., Farber, D. L., Hershberg, U. & Prak, E. T. L., 29 Jun 2018, In: Frontiers in Immunology. 9, JUN, 1472.
- Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data, The AIRR Community, 16 Nov 2017, In: Nature Immunology. 18, 12, p. 1274-1278 5 p.
- An atlas of B-cell clonal distribution in the human body, Meng, W., Zhang, B., Schwartz, G. W., Rosenfeld, A. M., Ren, D., Thome, J. J. C., Carpenter, D. J., Matsuoka, N., Lerner, H., Friedman, A. L., Granot, T., Farber, D. L., Shlomchik, M. J., Hershberg, U. & Luning Prak, E. T., 1 Sep 2017, In: Nature Biotechnology. 35, 9, p. 879-886 8 p.
- MiGHT, a multi-level Gillespie hybrid tracked modeling framework which allows for cellular and environmental adaptivity, Melunis, J. & Hershberg, U., 1 Jul 2017, 2017 IEEE Symposium Series on Computational Intelligence, SSCI 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 1-8 8 p. (2017 IEEE Symposium Series on Computational Intelligence, SSCI 2017 - Proceedings; vol. 2018-January).
- A spatially heterogeneous Gillespie algorithm modeling framework that enables individual molecule history and tracking, Melunis, J. & Hershberg, U., Jun 2017, In: Engineering Applications of Artificial Intelligence. 62, p. 304-311 8 p.
- Applying systems-level spectral imaging and analysis to reveal the organelle interactome, Valm, A. M., Cohen, S., Legant, W. R., Melunis, J., Hershberg, U., Wait, E., Cohen, A. R., Davidson, M. W., Betzig, E. & Lippincott-Schwartz, J., 1 Jun 2017, In: Nature. 546, 7656, p. 162-167 6 p.
- Detection of network communities with memory-biased random walk algorithms, Yucel, M., Muchnik, L. & Hershberg, U., 1 Mar 2017, In: Journal of Complex Networks. 5, 1, p. 48-69 22 p., cnw007.
- ImmuneDB: A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data, Rosenfeld, A. M., Meng, W., Luning Prak, E. T. & Hershberg, U., 15 Jan 2017, In: Bioinformatics. 33, 2, p. 292-293 2 p.
- VDJML: A file format with tools for capturing the results of inferring immune receptor rearrangements, Toby, I. T., Levin, M. K., Salinas, E. A., Christley, S., Bhattacharya, S., Breden, F., Buntzman, A., Corrie, B., Fonner, J., Gupta, N. T., Hershberg, U., Marthandan, N., Rosenfeld, A., Rounds, W., Rubelt, F., Scarborough, W., Scott, J. K., Uduman, M., Vander Heiden, J. A. & Scheuermann, R. H. & 3 others, , 6 Oct 2016, In: BMC Bioinformatics. 17, 333.
- Efficient approximation of labeling problems with applications to immune repertoire analysis, Osmanlioglu, Y., Ontanon, S., Hershberg, U. & Shokoufandeh, A., 1 Jan 2016, 2016 23rd International Conference on Pattern Recognition, ICPR 2016. Institute of Electrical and Electronics Engineers Inc., p. 2410-2415 6 p. (Proceedings - International Conference on Pattern Recognition; vol. 0).
- Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment, Zhang, B., Meng, W., Luning Prak, E. T. & Hershberg, U., 1 Dec 2015, In: Journal of Immunological Methods. 427, p. 105-116 12 p.
- Computational image analysis reveals intrinsic multigenerational differences between anterior and posterior cerebral cortex neural progenitor cells, Winter, M. R., Liu, M., Monteleone, D., Melunis, J., Hershberg, U., Goderie, S. K., Temple, S. & Cohen, A. R., 13 Oct 2015, In: Stem Cell Reports. 5, 4, p. 609-620 12 p.
- The analysis of clonal expansions in normal and autoimmune B cell repertoires, Hershberg, U. & Luning Prak, E. T., 5 Sep 2015, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 370, 1676
- B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions, Saini, J. & Hershberg, U., 1 May 2015, In: Molecular Immunology. 65, 1, p. 157-167 11 p.
- Prokaryotic nucleotide composition is shaped by both phylogeny and the environment, Reichenberger, E. R., Rosen, G., Hershberg, U. & Hershberg, R., May 2015, In: Genome Biology and Evolution. 7, 5, p. 1380-1389 10 p.
- Lasting antibody responses are mediated by a combination of newly formed and established bone marrow plasma cells drawn from clonally distinct precursors, Chernova, I., Jones, D. D., Wilmore, J. R., Bortnick, A., Yucel, M., Hershberg, U. & Allman, D., 15 Nov 2014, In: Journal of Immunology. 193, 10, p. 4971-4979 9 p.
- Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren's syndrome, Hershberg, U., Meng, W., Zhang, B., Haff, N., St Clair, E. W., Cohen, P. L., McNair, P. D., Li, L., Levesque, M. C. & Luning Prak, E. T., 11 Feb 2014, In: Arthritis Research and Therapy. 16, 1, R51.
- Memory as an organizer of dynamic modules in a network of potential interactions, Yucel, M. & Hershberg, U., 2014, Proceedings of the 2014 Spatial computing workshop, 13th Autonomous Agents and Multiagent Systems. 6 p.
- Conserved variation: Identifying patterns of stability and variability in BCR and TCR v genes with different diversity and richness metrics, Schwartz, G. W. & Hershberg, U., Jun 2013, In: Physical Biology. 10, 3, 035005.
- Establishing a relationship between bacteria in the human gut and Complex Regional Pain Syndrome, Reichenberger, E. R., Alexander, G. M., Perreault, M. J., Russell, J. A., Schwartzman, R. J., Hershberg, U. & Rosen, G., Mar 2013, In: Brain, Behavior, and Immunity. 29, p. 62-69 8 p.
- Germline amino acid diversity in B cell receptors is a good predictor of somatic selection pressures, Schwartz, G. W. & Hershberg, U., 2013, In: Frontiers in Immunology. 4, NOV, Article 357.
- Biomedical model fitting and error analysis, Costa, K. D., Kleinstein, S. H. & Hershberg, U., 27 Sep 2011, In: Science Signaling. 4, 192, tr9.
- Układ odpornościowy a inne systemy poznawcze, Hershberg, U. & Efroni, S., 2011, In: Avant. 2, p. 129-145
- Taking advantage: High-affinity B cells in the germinal center have lower death rates, but similar rates of division, compared to low-affinity cells, Anderson, S. M., Khalil, A., Uduman, M., Hershberg, U., Louzoun, Y., Haberman, A. M., Kleinstein, S. H. & Shlomchik, M. J., 1 Dec 2009, In: Journal of Immunology. 183, 11, p. 7314-7325 12 p.
- T Cell-Independent and Toll-like Receptor-Dependent Antigen-Driven Activation of Autoreactive B Cells, Herlands, R. A., Christensen, S. R., Sweet, R. A., Hershberg, U. & Shlomchik, M. J., 15 Aug 2008, In: Immunity. 29, 2, p. 249-260 12 p.
- Improved methods for detecting selection by mutation analysis of Ig V region sequences, Hershberg, U., Uduman, M., Shlomchik, M. J. & Kleinstein, S. H., May 2008, In: International Immunology. 20, 5, p. 683-694 12 p.
- Anti-chromatin antibodies drive in vivo antigen-specific activation and somatic hypermutation of rheumatoid factor B cells at extrafollicular sites, Herlands, R. A., William, J., Hershberg, U. & Shlomchik, M. J., Dec 2007, In: European Journal of Immunology. 37, 12, p. 3339-3351 13 p.
- Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation, Hershberg, U. & Shlomchik, M. J., 24 Oct 2006, In: Proceedings of the National Academy of Sciences of the United States of America. 103, 43, p. 15963-15968 6 p.
- Postext - A mind for society, Shalit, A., Erez, T., Deters, A., Hershberg, U., Shir, E. & Solomon, S., 2005, Adaptive Agents and Multi-Agent Systems II - Adaptation and Multi-Agent Learning. Springer Verlag, p. 24-40 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3394 LNAI).
- Antigen-receptor degeneracy and immunological paradigms, Cohen, I. R., Hershberg, U. & Solomon, S., Feb 2004, In: Molecular Immunology. 40, 14-15, p. 993-996 4 p.
- Useful examples and a new model of the immune system, Hershberg, U., 2003, In: Revue d'Intelligence Artificielle. 17, 5-6, p. 763-773 11 p.
- HIV time hierarchy: Winning the war while, loosing all the battles, Hershberg, U., Louzoun, Y., Atlan, H. & Solomon, S., 2001, In: Physica A: Statistical Mechanics and its Applications. 289, 1-2, p. 178-190 13 p.
- The immune system and other cognitive systems, Hershberg, U. & Efroni, S., 2001, In: Complexity. 6, 5, p. 14-21 8 p.