Uri Hershberg - Publications

Affiliations: 
Biomedical Engineering (School of Biomedical Engineering, Science, and Health Systems) Drexel University, Philadelphia, PA, United States 
 Faculty of Science, Department of Human Biology University of Haifa, Haifa, Haifa District, Israel 
Area:
Biomedical Engineering, Systematic Biology, Immunology, Complex Systems, Cognition

52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Berry CT, Liu X, Myles A, Nandi S, Chen YH, Hershberg U, Brodsky IE, Cancro MP, Lengner CJ, May MJ, Freedman BD. BCR-Induced Ca Signals Dynamically Tune Survival, Metabolic Reprogramming, and Proliferation of Naive B Cells. Cell Reports. 31: 107474. PMID 32294437 DOI: 10.1016/J.Celrep.2020.03.038  1
2019 Schwartz GW, Shauli T, Linial M, Hershberg U. Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Scientific Reports. 9: 17238. PMID 31754132 DOI: 10.1038/S41598-019-53452-3  1
2019 Trivedi N, Weisel F, Smita S, Joachim S, Kader M, Radhakrishnan A, Clouser C, Rosenfeld AM, Chikina M, Vigneault F, Hershberg U, Ismail N, Shlomchik MJ. Liver Is a Generative Site for the B Cell Response to Ehrlichia muris. Immunity. PMID 31732168 DOI: 10.1016/J.Immuni.2019.10.004  1
2019 DeLaney AA, Berry CT, Christian DA, Hart A, Bjanes E, Wynosky-Dolfi MA, Li X, Tummers B, Udalova IA, Chen YH, Hershberg U, Freedman BD, Hunter CA, Brodsky IE. Caspase-8 promotes c-Rel-dependent inflammatory cytokine expression and resistance against . Proceedings of the National Academy of Sciences of the United States of America. PMID 31147458 DOI: 10.1073/Pnas.1820529116  1
2018 Vander Heiden JA, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen Iv FA, Ralph DK, Rosenfeld AM, Schramm CA, Christley S, Laserson U. AIRR Community Standardized Representations for Annotated Immune Repertoires. Frontiers in Immunology. 9: 2206. PMID 30323809 DOI: 10.3389/Fimmu.2018.02206  1
2018 Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U. ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data. Frontiers in Immunology. 9: 2107. PMID 30298069 DOI: 10.3389/Fimmu.2018.02107  1
2018 Yaari G, Flajnik M, Hershberg U. Questions of Stochasticity and Control in Immune Repertoires. Trends in Immunology. PMID 30243818 DOI: 10.1016/J.It.2018.09.001  1
2018 Miron M, Kumar BV, Meng W, Granot T, Carpenter DJ, Senda T, Chen D, M Rosenfeld A, Zhang B, Lerner H, Friedman AL, Hershberg U, Shen Y, Rahman A, Luning Prak ET, et al. Human Lymph Nodes Maintain TCF-1 Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. Journal of Immunology (Baltimore, Md. : 1950). PMID 30111633 DOI: 10.4049/Jimmunol.1800716  0.01
2018 Rosenfeld AM, Meng W, Chen DY, Zhang B, Granot T, Farber DL, Hershberg U, Luning Prak ET. Computational Evaluation of B-Cell Clone Sizes in Bulk Populations. Frontiers in Immunology. 9: 1472. PMID 30008715 DOI: 10.3389/Fimmu.2018.01472  1
2017 Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, et al. Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nature Immunology. 18: 1274-1278. PMID 29144493 DOI: 10.1038/Ni.3873  1
2017 Meng W, Zhang B, Schwartz GW, Rosenfeld AM, Ren D, Thome JJC, Carpenter DJ, Matsuoka N, Lerner H, Friedman AL, Granot T, Farber DL, Shlomchik MJ, Hershberg U, Luning Prak ET. An atlas of B-cell clonal distribution in the human body. Nature Biotechnology. PMID 28829438 DOI: 10.1038/Nbt.3942  1
2017 Valm AM, Cohen S, Legant WR, Melunis J, Hershberg U, Wait E, Cohen AR, Davidson MW, Betzig E, Lippincott-Schwartz J. Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature. PMID 28538724 DOI: 10.1038/Nature22369  1
2017 Bryan Wu Y, Rosenfeld AM, Upton N, Dhariwal J, Hershberg U, Kipling D, Johnston SL, Gould HJ. Insight into Rhinovirus-Induced Asthma Exacerbation Using High-Throughput Immunosequencing of B-Cell Repertoires Journal of Allergy and Clinical Immunology. 139: AB80. DOI: 10.1016/J.Jaci.2016.12.213  0.01
2017 Melunis J, Hershberg U. A spatially heterogeneous Gillespie algorithm modeling framework that enables individual molecule history and tracking Engineering Applications of Artificial Intelligence. 62: 304-311. DOI: 10.1016/J.Engappai.2016.09.010  0.01
2016 Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, et al. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. Bmc Bioinformatics. 17: 333. PMID 27766961 DOI: 10.1186/S12859-016-1214-3  1
2016 Rosenfeld AM, Meng W, Luning Prak ET, Hershberg U. ImmuneDB: A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. Bioinformatics (Oxford, England). PMID 27616708 DOI: 10.1093/Bioinformatics/Btw593  1
2016 Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, Schwartz G, Hershberg U, Krebs FC, Wigdahl B. Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures. Retrovirology. 13: 32. PMID 27143130 DOI: 10.1186/S12977-016-0266-9  1
2016 Liu X, Berry CT, Ruthel G, Madara JJ, MacGillivray K, Gray CM, Madge LA, McCorkell KA, Beiting DP, Hershberg U, May MJ, Freedman BD. T cell receptor-induced NF-κB signaling and transcriptional activation are regulated by STIM1- and Orai1-mediated calcium entry. The Journal of Biological Chemistry. PMID 26826124 DOI: 10.1074/Jbc.M115.713008  1
2016 Melunis J, Freedman B, Hershberg U. A molecular model of STIM1-Orai1 movement and binding and their influence on calcium dynamics in T cell receptor response International Workshop On Artificial Immune Systems, Ais 2015/Icsi3 2015 - Systems Immunology, Immunoinformatics and Immune-Computation: Immunology Without Borders, Proceedings. DOI: 10.1109/AISW.2015.7469234  1
2016 Yucel M, Muchnik L, Hershberg U. Detection of network communities with memory-biased random walk algorithms Journal of Complex Networks. 5: 48-69. DOI: 10.1093/Comnet/Cnw007  1
2016 Schwartz GW, Shokoufandeh A, Ontañón S, Hershberg U. 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. DOI: 10.1016/J.Patrec.2016.01.011  1
2015 Zhang B, Meng W, Luning Prak ET, Hershberg U. 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. PMID 26529062 DOI: 10.1016/J.Jim.2015.10.009  1
2015 Winter MR, Liu M, Monteleone D, Melunis J, Hershberg U, Goderie SK, Temple S, Cohen AR. Computational Image Analysis Reveals Intrinsic Multigenerational Differences between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells. Stem Cell Reports. PMID 26344906 DOI: 10.1016/J.Stemcr.2015.08.002  1
2015 Hershberg U, Luning Prak ET. The analysis of clonal expansions in normal and autoimmune B cell repertoires. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26194753 DOI: 10.1098/Rstb.2014.0239  1
2015 Reichenberger ER, Rosen G, Hershberg U, Hershberg R. Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biology and Evolution. 7: 1380-9. PMID 25861819 DOI: 10.1093/Gbe/Evv063  1
2015 Saini J, Hershberg U. B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions. Molecular Immunology. 65: 157-67. PMID 25660968 DOI: 10.1016/J.Molimm.2015.01.001  1
2015 Hamza N, Hershberg U, Kallenberg CG, Vissink A, Spijkervet FK, Bootsma H, Kroese FG, Bos NA. Ig gene analysis reveals altered selective pressures on Ig-producing cells in parotid glands of primary Sjögren's syndrome patients. Journal of Immunology (Baltimore, Md. : 1950). 194: 514-21. PMID 25488989 DOI: 10.4049/Jimmunol.1302644  1
2015 Maman Y, Hershberg U, Louzoun Y. Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies. Immunogenetics. 67: 15-24. PMID 25376343 DOI: 10.1007/S00251-014-0811-4  1
2014 Chernova I, Jones DD, Wilmore JR, Bortnick A, Yucel M, Hershberg U, Allman D. Lasting antibody responses are mediated by a combination of newly formed and established bone marrow plasma cells drawn from clonally distinct precursors. Journal of Immunology (Baltimore, Md. : 1950). 193: 4971-9. PMID 25326027 DOI: 10.4049/Jimmunol.1401264  1
2014 Meng W, Jayaraman S, Zhang B, Schwartz GW, Daber RD, Hershberg U, Garfall AL, Carlson CS, Luning Prak ET. Trials and Tribulations with VH Replacement. Frontiers in Immunology. 5: 10. PMID 24523721 DOI: 10.3389/Fimmu.2014.00010  1
2014 Hershberg U, Meng W, Zhang B, Haff N, St Clair EW, Cohen PL, McNair PD, Li L, Levesque MC, Luning Prak ET. Persistence and selection of an expanded B-cell clone in the setting of rituximab therapy for Sjögren's syndrome. Arthritis Research & Therapy. 16: R51. PMID 24517398 DOI: 10.1186/Ar4481  1
2014 Goenka R, Matthews AH, Zhang B, O'Neill PJ, Scholz JL, Migone TS, Leonard WJ, Stohl W, Hershberg U, Cancro MP. Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation. The Journal of Experimental Medicine. 211: 45-56. PMID 24367004 DOI: 10.1084/Jem.20130505  1
2014 Carlson CS, Garfall AL, Meng W, Daber R, Zhang B, Hershberg U, Cohen AD, Vogl DT, Brendan W, Carroll M, Stadtmauer EA, Prak EL. Detection of the Malignant B Cell Clone in Multiple Myeloma Via High Throughput Sequencing Is Robust to Significant Levels of Somatic Hypermutation Blood. 124: 3413-3413. DOI: 10.1182/Blood.V124.21.3413.3413  1
2014 Garfall AL, Prak ETL, Meng W, Daber R, Zhang B, Hershberg U, Vogl DT, Weiss BM, Carroll M, Stadtmauer EA, Carlson C. High-Throughput Sequencing of Antibody Genes Successfully Identifies Clonal Ig Rearrangements in Multiple Myeloma Patients Biology of Blood and Marrow Transplantation. 20. DOI: 10.1016/J.Bbmt.2013.12.090  1
2013 Schwartz GW, Hershberg U. Germline Amino Acid Diversity in B Cell Receptors is a Good Predictor of Somatic Selection Pressures. Frontiers in Immunology. 4: 357. PMID 24265630 DOI: 10.3389/Fimmu.2013.00357  1
2013 Schwartz GW, Hershberg U. Conserved variation: identifying patterns of stability and variability in BCR and TCR V genes with different diversity and richness metrics. Physical Biology. 10: 035005. PMID 23735612 DOI: 10.1088/1478-3975/10/3/035005  1
2013 Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. Bmc Bioinformatics. 14: S1. PMID 23734902 DOI: 10.1186/1471-2105-14-S6-S1  1
2013 Reichenberger ER, Alexander GM, Perreault MJ, Russell JA, Schwartzman RJ, Hershberg U, Rosen G. Establishing a relationship between bacteria in the human gut and complex regional pain syndrome. Brain, Behavior, and Immunity. 29: 62-9. PMID 23261776 DOI: 10.1016/J.Bbi.2012.12.005  1
2011 Costa KD, Kleinstein SH, Hershberg U. Biomedical model fitting and error analysis. Science Signaling. 4: tr9. PMID 21954296 DOI: 10.1126/Scisignal.2001983  1
2011 Uduman M, Yaari G, Hershberg U, Stern JA, Shlomchik MJ, Kleinstein SH. Detecting selection in immunoglobulin sequences. Nucleic Acids Research. 39: W499-504. PMID 21665923 DOI: 10.1093/Nar/Gkr413  1
2010 Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC, Kleinstein SH. Antiviral response dictated by choreographed cascade of transcription factors. Journal of Immunology (Baltimore, Md. : 1950). 184: 2908-17. PMID 20164420 DOI: 10.4049/Jimmunol.0903453  1
2009 Anderson SM, Khalil A, Uduman M, Hershberg U, Louzoun Y, Haberman AM, Kleinstein SH, Shlomchik MJ. Taking advantage: high-affinity B cells in the germinal center have lower death rates, but similar rates of division, compared to low-affinity cells. Journal of Immunology (Baltimore, Md. : 1950). 183: 7314-25. PMID 19917681 DOI: 10.4049/Jimmunol.0902452  1
2008 Herlands RA, Christensen SR, Sweet RA, Hershberg U, Shlomchik MJ. T cell-independent and toll-like receptor-dependent antigen-driven activation of autoreactive B cells. Immunity. 29: 249-60. PMID 18691914 DOI: 10.1016/J.Immuni.2008.06.009  1
2008 Hershberg U, Uduman M, Shlomchik MJ, Kleinstein SH. Improved methods for detecting selection by mutation analysis of Ig V region sequences. International Immunology. 20: 683-94. PMID 18397909 DOI: 10.1093/Intimm/Dxn026  1
2007 Herlands RA, William J, Hershberg U, Shlomchik MJ. Anti-chromatin antibodies drive in vivo antigen-specific activation and somatic hypermutation of rheumatoid factor B cells at extrafollicular sites. European Journal of Immunology. 37: 3339-51. PMID 18034429 DOI: 10.1002/Eji.200737752  1
2006 Hershberg U, Shlomchik MJ. Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation. Proceedings of the National Academy of Sciences of the United States of America. 103: 15963-8. PMID 17038496 DOI: 10.1073/Pnas.0607581103  1
2005 Shalit A, Erez T, Deters A, Hershberg U, Shir E, Solomon S. Postext - A mind for society Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3394: 24-40. DOI: 10.1007/978-3-540-32274-0_2  1
2004 Cohen IR, Hershberg U, Solomon S. Antigen-receptor degeneracy and immunological paradigms. Molecular Immunology. 40: 993-6. PMID 15036901 DOI: 10.1016/J.Molimm.2003.11.020  1
2004 Adam R, Hershberg U, Schul Y, Solomon S. Testing the turing test - Do men pass it? International Journal of Modern Physics C. 15: 1041-1047. DOI: 10.1142/S0129183104006522  1
2003 Hershberg U. Useful examples and a new model of the immune system Revue D'Intelligence Artificielle. 17: 763-773.  1
2001 Hershberg U, Louzoun Y, Atlan H, Solomon S. HIV time hierarchy: Winning the war while, loosing all the battles Physica a: Statistical Mechanics and Its Applications. 289: 178-190. DOI: 10.1016/S0378-4371(00)00466-0  1
2001 Hershberg U, Efroni S. The immune system and other cognitive systems Complexity. 6: 14-21. DOI: 10.1002/Cplx.1046  0.01
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