[64] Jianing Fu, Thomas Hsiao, Elizabeth Waffarn, Wenzhao Meng, Katherine D. Long, Kristjana Frangaj, Rebecca Jones, Alaka Gorur, Areen Shtewe, Muyang Li, Constanza Bay Muntnich, Kortney Rogers, Wenyu Jiao, Monica Velasco, Rei Matsumoto, Masaru Kubota, Steven Wells, Nichole Danzl, Shilpa Ravella, Alina Iuga, Elena-Rodica Vasilescu, Adam Griesemer, Joshua Weiner, Donna L. Farber, Eline T. Luning Prak, Mercedes Martinez, Tomoaki Kato, Uri Hershberg and Megan Sykes. Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation in a pediatric-dominated cohort. Frontiers in Immunology (2024). PDF

[63] Martina Milighetti1,2, Yuta Nagano, James Henderson, Uri Hershberg5, Andreas
Tiffeau-Mayer, Anne-Florence Bitbol, and Benny Chain. Intra- and inter-chain contacts determine TCR specificity: applying protein co-evolution methods to TCRαβ pairing.  bioRxiv 2024. PDF

[62] Rei Matsumoto, Joshua Gray , Ksenia Rybkina , Hanna Oppenheimer,Lior Levy, Lilach M. Friedman , Muhammad Khamaisi, Wenzhao Meng ,Aaron M. Rosenfeld , Rebecca S. Guyer, Marissa C. Bradley, David Chen ,Mark A. Atkinson, Todd M. Brusko , Maigan Brusko, Thomas J. Connors ,Eline T. Luning Prak , Uri Hershberg, Peter A. Sims, Tomer Hertz &Donna L. Farber (2023) Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity. Nature Immunology, 1–12 (2023). PDF

[61] Jessica Mallaby, William Mwangi, Joseph Ng, Alexander Stewart, Daniel Dorey-Robinson, David Kipling, Uri Hershberg, Franca Fraternali, Venugopal Nair, Deborah Dunn-Walters (2023) Diversification of immunoglobulin genes by gene conversion in the domestic chicken (Gallus gallus domesticus). Discovery Immunology, Volume 2, Issue 1, 2023, kyad002. PDF

[60] Adam Craig, Mesut Yücel, Lev Muchnik, Uri Hershberg (2022) Impact of finite size effect on applicability of generalized fractal and spectral dimensions to biological networks. Chaos, Solitons & Fractals, 164:112707. PDF

[59] Jessica Mallaby, Joseph Ng, Alex Stewart, Emma Sinclair, Deborah Dunn-Walters, Uri Hershberg (2022) 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. Frontiers in Immunology, 13:837246. PDF

[58] 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. and Good-Jacobson, K.L.  (2022) Targeting BMI-1 in B cells restores effective humoral immune response and controls chronic viral infection. Nature Immunology, 23(1):86-98. PDF

[57] Alon, U., Mokryn, O. and Hershberg, U. (2021) 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. Frontiers in Immunology, 2021, 12, 804. PDF

[56] 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., and Freedman, B. D. (2020) BCR-Induced Ca2+ Signals Dynamically Tune Survival, Metabolic Reprogramming, and Proliferation of Naive B Cells. Cell Reports, 31, 107474. PDF

[55] Schwartz, G. W., Shauli, T., Linial, M., and Hershberg, U. (2019) Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Sci Rep, 9, 13109. PDF

[54] DeLaney, A. A., Berry, C. T., Christian, D. A., Hart, A., Bjanes, E., Wynosky-Dolfi, M. A., Li, X., Tummers, B., Udalova, I. A., Chen, Y. H., Hershberg, U., Freedman, B. D., Hunter, C. A., and Brodsky, I. E. (2019) Caspase-8 promotes c-Rel–dependent inflammatory cytokine expression and resistance against Toxoplasma gondii. Proceedings of the National Academy of Sciences, 116, 11926–11935. PDF

[53] 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., and Shlomchik, M. J. (2019) Liver Is a Generative Site for the B Cell Response to Ehrlichia muris. Immunity, 51, 1088–1101.e5. PDF

[52] Aaron M Rosenfeld, Wenzhao Meng, Dora Y Chen, Bochao Zhang, Tomer Granot, Donna L Farber, Uri Hershberg, Eline T Luning Prak (2018) Computational evaluation of B-cell clone sizes in bulk populations.  Frontiers in immunology, 9, 1472. PDF

[51] Yaari, G., Flajnik, M., and Hershberg, U (2018) Questions of Stochasticity and Control in Immune Repertoires. Trends in Immunology, 39(11):859-861. PDF

[50] 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., and Farber, D. L. (2018) Human Lymph Nodes Maintain TCF-1hi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. The Journal of Immunology, 201(7):2132-2140. PDF

[49] Heiden, J.A.V., Marquez, S., Marthandan, N., Bukhari, S.A.C., Busse, C.E., Corrie, B.D., Hershberg, U., Kleinstein, S.H., Matsen F.A. IV, Ralph, D.K., Rosenfeld, A.M., Schramm, C.A., The AIRR Community, Christley, S., and Laserson, U. (2018) AIRR Community Standardized Representations for Annotated Immune Repertoires. Frontiers in Immunology, 2018;9: 2206. PDF

[48] Rosenfeld, A.M., Meng, W., Luning Prak, E.T., Hershberg, U. (2018) ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data. Frontiers in Immunology, 2018;9: 2107. PDF | Website

[47] Rosenfeld, A. M., Chen, D. Y., Meng, W., Zhang, B., Granot, T., Farber, D. L., Hershberg, U., Luning Prak, E. T., and Tjetske, E. (2018) PROTOCOL: Computational evaluation of B-cell clone sizes in bulk populations. Frontiers in immunology, 2018;9:1472. PDF

[46] Rubelt, F., Busse, C.E., Bukhari, S., Burckert, J., Mariotti-Ferrandiz, E., Cowell, L.G., Watson, C.T., Marthandan, N., Faison, W.J., Hershberg, U., Laserson, U., Corrie, B.D., Davis, M.M., Peters, B., Lefranc, M., Scott, J.K., Breden, F., The AIRR Community, Luning Prak, E. T., and Kleinstein, S.H. (2017) Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nature Immunology, 18(12):1274-1278. PDF

[45] Melunis, J., and Hershberg, U. (2017) MiGHT, a multi-level Gillespie hybrid tracked modeling framework which allows for cellular and environmental adaptivity. Proceedings of the IEEE Symposium Series on Computational Intelligence (SSCI). PDF | at IEEE Xplore

[44] Meng, W.*, Zhang, B.*, (*authors contributed equally), 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.*, and Luning Prak, E. T.* (*co responding authors) (2017) An atlas of B-cell clonal distribution in the human body. Nature Biotechnology, 35(9):879-884. Epub August 21. PDF | Atlas

[43] Valm, A.M*., Cohen, S*.,(*authors contributed equally), Legant, W.R., Melunis, J., Hershberg, U., Wait, E., Cohen, A., Davidson, M.W., Betzig, E. and Lippincott-Schwartz, J. (2017) Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature, 546, 162. PDF | at Nature.com

[42] Melunis, J. and Hershberg, U. (2017) A spatially heterogeneous Gillespie algorithm modeling framework that enables individual molecule history and tracking. Engineering Applications of Artificial Intelligence, 62, 304. PDF

[41] Rosenfeld, A.M., Meng, W., Luning Prak, E.T. and Hershberg, U. (2017) ImmuneDB: A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. Bioinformatics, 33, 292. PDF | Website

[40] 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.M., Rounds, W., Rubelt, F., Scarborough, W., Scott, J.K., Uduman, M., Vander Heiden, J.A., Scheuermann, R.H., Monson, N., Kleinstein, S.H., Cowell, L.G. (2016) VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics, 17, 333. PDF

[39] Osmanlioglu, Y., Ontanon, S., Hershberg, U., Shokoufandeh, A. (2016) Efficient Approximation of Labeling Problems with Applications to Immune Repertoire Analysis. Proceedings of the International Conference on Pattern Recognition. (Best Scientific Paper Prize – Document Analysis, Biometrics and Pattern Recognition)PDF | at IEEE Xplore

[38] Antell, G. C., Dampier, W., Aiamkitsumrit, B., Nonnemacher, M. R., Jacobson, J. M., Pirrone, V., Zhong, W., Kercher, K., Passic, S., Williams, J. W., Schwartz, G., Hershberg, U., Krebs, F. C., and Wigdahl, B. (2016) Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures.. Retrovirology 13, 1–14. PDF | Link

[37] Yucel, M., Muchnik, L., and Hershberg, U. (2016) Detection of network communities with memory-biased random walk algorithms. Journal of Complex Networks, 5(1), 48-49. PDF

[36] Schwartz, G.W., Shokoufandeh, A., Ontanon, S., Hershberg, U. (2016) Using a novel clumpiness measure to unite data with metadata: finding common sequence patterns in immune receptor germline V genes Pattern Recognition Letters 74: 24-29 PDF

[35] Liu, X., Berry, C.T., Ruthel, G., Madara, J.J., MacGillivray, K., Gray, C.M., Madge, L.A., McCorkell, K.A., Beiting, D.P., Hershberg, U., May, M.J. and Freedman, B.D. (2016) T cell receptor-induced NF-κB signaling and transcriptional activation are regulated by STIM1- and Orai1-mediated calcium entry Journal of Biological Chemistry, 291(16), 8440-8452. PDF

[34] Zhang, B., Meng, W., Luning Prak, E.T. and Hershberg U. (2015) 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 Journal of Immunological Methods 427: 105-116 PDF

[33] Winter, M.R., Liu, M., Monteleone, D., Melunis, J., Hershberg, U., Goderies, S.K., Temple, S. and Cohen, A.R. (2015) Computational Image Analysis Reveals Cell Intrinsic Multigenerational Differences among Neural Progenitors from Anterior and Posterior Cortex. Stem Cell Reports, Stem cell reports 5 (4), 609-620 PDF

[32] Hershberg U. and Luning Prak, E.T. (2015) The analysis of clonal expansions in normal and autoimmune B cell repertoires. Phil. Trans. R. Soc, Volume B 370. PDF

[31] Reichenberger, E.R., Rosen, G.L., Hershberg, U.*, Hershberg, R.* (*the authors contributed equally) (2015) Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biology and Evolution, Volume 7, Issue 5, pp 1380-1389. PDF | Link to map data

[30] Saini, J. and Hershberg, U. (2015) B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions (CDR). Molecular Immunology, Volume 65, pp 157-167. PDF

[29] Hamza, N., Hershberg, U., Kallenberg, C.G.M., Vissink, A., Spijkervet, F.K.L., Bootsma, H., Kroese, F.G.M., Bos, N.A. (2015) Ig Gene Analysis Reveals Altered Selective Pressures on Ig-Producing Cells in Parotid Glands of Primary Sjögre’s Syndrome Patients. The Journal of Immunology, Volume 194, Issue 2, pp 514-521. PDF

[28] Y. Maman, U. Hershberg, Y. Louzoun. (2015) Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies. Immunogenetics, Volume 67, Issue 1, pp 15-24. PDF

[27] Chernova, I., Jones, D. D., Wilmore, J. R., Bortnick, A., Yucel, M., Hershberg, U., and Allman, D. (2014) Lasting Antibody Responses Are Mediated by a Combination of Newly Formed and Established Bone Marrow Plasma Cells Drawn from Clonally Distinct Precursors. The Journal of Immunology, Volume 193, Issue 10, pp 4971-4979. PDF

[26] Hershberg, U., Meng, W., Zhang, B., Haff, N., St Clair, E. W., Cohen, P. L., McNair, P. D., Li, L., Levesque, M. C., and Luning Prak, E. T. (2014) Persistence and selection of an expanded B cell clone in the setting of rituximab therapy for Sjögren’s syndrome. Arthritis Research & Therapy 16, R51. PDF

[25] Yucel, M. and Hershberg, U. (2014) Memory as an organizer of dynamic modules in a network of potential interactions. Proceedings autonomous agents and multiagent systems (AAMAS 2014). PDF

[24] Meng, W., Jayaraman, S., Zhang, B., Schwartz, G. W., Daber, R., Hershberg, U., Garfall, A., Carlson, C. S., and Luning Prak, E. T. (2014) Trials and Tribulations with VH Replacement. Frontiers in Immunology 5. PDF

[23] Goenka, R., Matthews, A. H., Zhang, B., O’Neill, P. J., Scholz, J. L., Migone, T.-S., Leonard, W. J., Stohl, W., Hershberg, U., and Cancro, M. P. (2014) Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation. J Exp Med 211, 45-56. PDF

[22] Schwartz, G. W., and Hershberg, U. (2013) Germline amino acid diversity in B cell receptors is a good predictor of somatic selection pressures. Frontiers in Immunology 4. PDF

[21] Schwartz, G. W., and Hershberg, U. (2013) Conserved variation: identifying patterns of stability and variability in BCR and TCR V genes with different diversity and richness metrics. Phys Biol 10, 035005. PDF

[20] Zaslavsky, E., Nudelman, G., Marquez, S., Hershberg, U., Hartmann, B. M., Thakar, J., Sealfon, S. C., and Kleinstein, S. H. (2013) Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics 14, S1. PDF

[19] Reichenberger, E. R., Alexander, G. M., Perreault, M. J., Russell, J. A., Schwartzman, R. J., Hershberg, U.*, and Rosen, G.* (*the authors contributed equally) (2013) Establishing a relationship between bacteria in the human gut and Complex Regional Pain Syndrome. Brain, Behavior, and Immunity 29, 62-69. PDF

[18] Uduman, M., Yaari, G., Hershberg, U., Stern, J. A., Shlomchik, M. J., and Kleinstein, S. H. (2011) Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 39, W499-W504. PDF

[17] Costa, K. D., Kleinstein, S. H., and Hershberg, U. (2011) Biomedical model fitting and error analysis. Science Signaling 4, tr9. PDF

[16] Zaslavsky, E.*, Hershberg, U*., (*the authors contributed equally) Seto, J., Pham, A. M., Marquez, S., Duke, J. L., Wetmur, J. G., Tenoever, B. R., Sealfon, S. C., and Kleinstein, S. H. (2010) Antiviral response dictated by choreographed cascade of transcription factors. The Journal of Immunology 184, 2908. PDF

[15] Anderson, S.M., Khalil, A., Uduman, M., Hershberg, U., Louzoun, Y., Haberman, A.M., Kleinstein, S.H., and Shlomchik M.J (2009) Taking advantage: Selection of high affinity B cells in the germinal center is controlled by death, not proliferation, Journal of Immunology Vol.183 issue 11 pp. 7314-25. PDF

[14] Herlands, R.A., Christensen, S. R., Sweet, R.A., Hershberg, U., and Shlomchik M,J. (2008) T Cell-Independent and Toll-like Receptor-Dependent Antigen-Driven Activation of Autoreactive B Cells, Immunity Vol. 29 Issue 2 pp. 249-60. PDF

[13] Hershberg, U., Uduman, M., Shlomchik, M.J. and Kleinstein S.H. (2008) Improved methods for detecting selection by mutation analysis of Ig V region sequences, International Immunology Vol 20 issue 5 pp. 683-694, (Cover article). PDF

[12] Herlands, R.A., William, J., Hershberg, U. and Shlomchik M,J. (2007) Anti-chromatin antibodies drive in vivo antigen-specific activation and somatic hypermutation of Rheumatoid factor B cells at extrafollicular sites, European Journal of Immunology. Vol. 37 pp. 3339-51. PDF

[11] Hershberg, U. and Shlomchik, M. J. (2006) Differences in potential for amino acid change following mutation reveals distinct strategies for kappa and lambda light chain variation. PNAS Vol.103 No.43 pp. 15963-8. PDF

[10] Shalit, A., Erez, T., Deters, A., Hershberg, U., Shir, E. and Solomon, S. (2005) Postext – A mind for society. Lecture Notes in Computer Science: Adaptive Agents and Multi-Agent Systems Vol. 3394 pp. 24-40. PDF

[9] Adam, R., Hershberg, U., Schul, Y. and Solomon, S. (2004) Testing the Turing Test – Do men pass it? International Journal of Modern Physics C Vol.15 No.8 pp. 1041-1047. PDF

[8] Cohen, I. R., Hershberg, U. and Solomon, S. (2004) Antigen-Receptor degeneracy and immunological paradigms, Molecular Immunology Vol. 40 issue 14/15 pp. 993-996. PDF

[7] Hershberg, U. and Ninio, A. (2004) Optimal exemplar learning in cognitive systems, Cognitive Systems (ESSCS). Vol. 6 issue 2/3 pp. 181-188, special issue on the Multidisciplinary Aspects of Learning. PDF

[6] Hershberg U. (2003) Useful Examples and a new model of the immune system, Revue d’Intelligence Artificielle Vol. 17 No. 5/6 pp. 763-773, special issue – Regards croises sur l’analogie (Duvignau, K., Gasquet, O., Gaume, B. Ed.) Hermes Lavoisier. PDF

[5] Hershberg, U., Solomon, S. and Cohen, I. R. (2003) What is the basis of the immune systems specificity?, Mathematical Modelling & Computing in Biology and Medicine, (V.Capasso Ed.), pp. 377-384, The MIRIAM Project Series, Progetto Leonardo, ESCULAPIO Pub. Co., Bologna, Italy. PDF

[4] Hershberg, U. (2002) Proposing a new focus for the study of natural and artificial cognitive systems, proceeding of the 2nd International Conference on Epigenetic Robotics pp.43-47. PDF

[3] Hershberg, U. and Ninio, A. (2002) Cognitive systems and the special order of their environment, Res-systemica : European Systems Science Journal, Vol. 2, Special Issue: Proceedings of the 5th European Systems Science Congress, October 02, Crete. (http://www.afscet.asso.fr/resSystemica/Crete02/Hersberg.pdf). PDF

[2] Hershberg, U., Louzoun, Y., Atlan, H. and Solomon, S. (2001) HIV time hierarchy: Winning the war while loosing all the battles, Physica A: Vol. 289 issue 1/2 pp.178-190, also placed on the net at xxx.lanl.gov (Nonlinear Sciences-Adaptation and Self Organizing Systems). PDF

[1] Hershberg, U. and Efroni, S. (2001) The immune system and other cognitive systems, Complexity, Vol. 6 issue 5 pp.14-21. PDF