Yoram Louzoun

http://www.cs.biu.ac.il/~louzouy

 

    2012

  1. Benichou, J.; Ben–Hamo, R.; Louzoun, Y.; Efroni, S.; (2012) Rep-Seq: uncovering the immunological repertoire through next-generation sequencing, Immunology 135(3):183-191
  2. Magori-Cohen, R.; Louzoun, Y.; Herziger, Y.; Oron, E.; Arazi, A.; Tuppurainen, E.; Shpigel, N.Y.; Klement, E.; Sadilkova, L.; Nepereny, J.; (2012) Mathematical modelling and evaluation of the different routes of transmission of lumpy skin disease virus, Mathematical modelling 43:1
  3. Agranovich, A.; Louzoun, Y.; (2012) Predator-prey dynamics in a uniform medium lead to directed percolation and wave-train propagation, Physical Review E 85(3):31911
  4. Louzoun, Y.; Ganusov, V.V.; (2012) Evolution of viral life-cycle in response to cytotoxic T lymphocyte-mediated immunity, Journal of Theoretical Biology 310:3-13

    5. 2011

  5. Maman, Y.; Blancher, A.; Benichou, J.; Yablonka, A.; Efroni, S.; Louzoun, Y.; (2011) Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins, Journal of virology 85(9):4558-4566
  6. Kovjazin, R.; Volovitz, I.; Daon, Y.; Vider–Shalit, T.; Azran, R.; Tsaban, L.; Carmon, L.; Louzoun, Y.; (2011) Signal peptides and trans-membrane regions are broadly immunogenic and have high CD8+ T cell epitope densities: Implications for vaccine development, Molecular Immunology
  7. Toussaint, N.C.; Maman, Y.; Kohlbacher, O.; Louzoun, Y.; (2011) Universal peptide vaccines-Optimal peptide vaccine design based on viral sequence conservation, Vaccine
  8. Sekiguchi, D.R.; Smith, S.B.; Sutter, J.A.; Goodman, N.G.; Propert, K.; Louzoun, Y.; Rogers, W.; Luning Prak, E.T.; (2011) Circulating lymphocyte subsets in normal adults are variable and can be clustered into subgroups, Cytometry Part B: Clinical Cytometry
  9. Maman, Y.; Nir-Paz, R.; Louzoun, Y.; (2011) Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response, PLoS computational biology 7(10):e1002220
  10. Feldman, R.; Magori-Cohen, R.; Galili, G.; Singer, M.; Louzoun, Y.; (2011) Mother and infant coordinate heart rhythms through episodes of interaction synchrony, Infant Behavior and Development
  11. Liberman, G.; Louzoun, Y.; Colliot, O.; Ben Bashat, D.; (2011) T1 mapping, AIF and pharmacokinetic parameter extraction from dynamic contrast enhancement MRI data, Multimodal Brain Image Analysis 76-83
  12. Lavi, O.; Ginsberg, D.; Louzoun, Y.; (2011) Regulation of modular Cyclin and CDK feedback loops by an E2F transcription oscillator in the mammalian cell cycle, Mathematical Biosciences and Engineering (MBE) 8(2):445-461
  13. Agranovich, A.; Vider–Shalit, T.; Louzoun, Y.; (2011) Optimal viral immune surveillance evasion strategies, Theoretical Population Biology
  14. Weisman, O.; Magori-Cohen, R.; Louzoun, Y.; Eidelman, A.I.; Feldman, R.; (2011) Sleep-Wake Transitions in Premature Neonates Predict Early Development, Pediatrics 128(4):706-714
  15. Cohen, R.M.; Kleinstein, S.H.; Louzoun, Y.; (2011) Somatic hypermutation targeting is influenced by location within the immunoglobulin V region., Molecular immunology
  16. Lavi, O.; Klement, E.; Louzoun, Y.; (2011) Effect of Vaccination in Environmentally Induced Diseases, Bulletin of mathematical biology 73(5):1101-1117

    17. 2010

  17. Itzhack, R.; Louzoun, Y.; (2010) Random distance dependent attachment as a model for neural network generation in the Caenorhabditis elegans, Bioinformatics 26(5):647-652
  18. Vider–Shalit, T.; Louzoun, Y.; (2010) MHC-I prediction using a combination of T cell epitopes and MHC-I binding peptides, Journal of immunological methods
  19. Itzhack, R.; Muchnik, L.; Erez, T.; Tsaban, L.; Goldenberg, J.; Solomon, S.; Louzoun, Y.; (2010) Empirical extraction of mechanisms underlying real world network generation, Physica A: Statistical Mechanics and its Applications 389(22):5308-5318
  20. Louzoun, Y.; Vider–Shalit, T.; (2010) PP-026-09 Viruses selectively mutate cd8+ T cell epitopes in proteins expressed in the early stages of the viral life cycle, International Immunology Meeting Abstracts 22(Suppl 1 Pt 2):ii49-ii56
  21. Atlan, H.; Louzoun, Y.; (2010) Emergence of Intentional Procedures in Self-Organizing Neural Networks, Causality Meaningful Complexity and Embodied Cognition, 46(1):47-56

    22. 2009

  22. Anderson, S.M.; Khalil, A.; Uduman, M.; Hershberg, U.; Louzoun, Y.; Haberman, A.M.; Kleinstein, S.H.; Shlomchik, M.J.; (2009) Taking advantage: high-affinity B cells in the germinal center have lower death rates, but similar rates of division compared to low-affinity cells The Journal of Immunology 183(11)7314-7325
  23. Merbl, Y.; Itzchak, R.; Vider–Shalit, T.; Louzoun, Y.; Quintana, F.J.; Vadai, E.; Eisenbach, L.; Cohen, I.R.; (2009) A systems immunology approach to the host-tumor interaction: large-scale patterns of natural autoantibodies distinguish healthy and tumor-bearing mice, PloS one 4(6):e6053
  24. Vider–Shalit, T.; Almani, M.; Sarid, R.; Louzoun, Y.; (2009) The HIV hide and seek game: an immunogenomic analysis of the HIV epitope repertoire, Aids 23(11):1311
  25. Vider–Shalit, T.; Sarid, R.; Maman, K.; Tsaban, L.; Levi, R.; Louzoun, Y.; (2009) Viruses selectively mutate their CD8+ T–Cell epitopes—a large-scale immunomic analysis, Bioinformatics 25(12):i39-i44
  26. Nudelman, G.; Weigert, M.; Louzoun, Y.; (2009) In-silico cell surface modeling reveals mechanism for initial steps of B-cell receptor signal transduction, Molecular immunology 46(15):3141-3150
  27. Almani, M.; Raffaeli, S.; Vider–Shalit, T.; Tsaban, L.; Fishbain, V.; Louzoun, Y.; (2009) Human self–protein CD8+ T–cell epitopes are both positively and negatively selected, European journal of immunology 39(4):1056-1065
  28. Lavi, O.; Louzoun, Y.; (2009) What cycles the cell?—Robust autonomous cell cycle models, Mathematical Medicine and Biology 26(4):337-359

    29. 2008

  29. Ginodi, I.; Vider–Shalit, T.; Tsaban, L.; Louzoun, Y.; (2008) Precise score for the prediction of peptides cleaved by the proteasome, Bioinformatics 24(4):477-483
  30. Lavi, O.; Louzoun, Y.; Klement, E.; (2008) Listeriosis: a model for the fine balance between immunity and morbidity, Epidemiology 19(4):581

    31. 2007

  31. Muchnik, L.; Itzhack, R.; Solomon, S.; Louzoun, Y.; (2007) Self-emergence of knowledge trees: Extraction of the Wikipedia hierarchies, Physical Review E 76(1):16106
  32. Louzoun, Y.; (2007) The evolution of mathematical immunology, Immunological reviews 216(1):9-20
  33. Vider–Shalit, T.; Raffaeli, S.; Louzoun, Y.; (2007) Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome, Molecular immunology 44(6):1253-1261
  34. Vider–Shalit, T.; Fishbain, V.; Raffaeli, S.; Louzoun, Y.; (2007) Phase-dependent immune evasion of herpesviruses, Journal of virology 81(17):9536-9545
  35. Louzoun, Y.; Atlan, H.; (2007) The emergence of goals in a self-organizing network: A non-mentalist model of intentional actions, Neural networks 20(2):156-171
  36. Itzhack, R.; Mogilevski, Y.; Louzoun, Y.; (2007) An optimal algorithm for counting network motifs, Physica A: Statistical Mechanics and its Applications 381:482-490
  37. Louzoun, Y.; Shnerb, N.M.; Solomon, S.; (2007) Microscopic noise, adaptation and survival in hostile environments" The European Physical Journal B-Condensed Matter and Complex Systems 56(2):141-148

    38. 2006

  38. Louzoun, Y.; Vider, T.; Weigert, M.; (2006) T–Cell epitope repertoire as predicted from human and viral genomes, Molecular immunology 43(6):559-569
  39. Louzoun, Y.; Muchnik, L.; Solomon, S.; (2006) Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW, Bioinformatics 22(5):581-588
  40. Nudelman, G.; Louzoun, Y.; (2006) Cell surface dynamics: the balance between diffusion, aggregation and endocytosis, IEE Proceedings-Systems Biology 153(1):34-42
  41. Muchnik, L.; Louzoun, Y.; Solomon, S.; (2006) Agent Based Simulation Design Principles—Applications to Stock Market, Practical Fruits of Econophysics :183-188
  42. Agranovich, A.; Louzoun, Y.; Shnerb, N.; Moalem, S.; (2006) Catalyst-induced growth with limited catalyst lifespan and competition, Journal of theoretical biology 241(2):307-320
  43. Magori-Cohen, R.; Louzoun, Y.; Kleinstein, S.H.; (2006) Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees, Bioinformatics 22(14):e332-e340
  44. Louzoun, Y.; Muchnick&, L.; Solomon, S.; (2006) Copying nodes vs. Editing links: the source of the difference between genetic networks and the WWW, Bioinformatics 22(5):581-588

    45. 2005

  45. Louzoun, Y.; Friedman, T.; Luning Prak, E.; Litwin, S.; Weigert, M.; (2005) Analysis of B cell receptor production and rearrangement, Seminars in Immunology 14(3):169-190

    46. 2004

  46. Li, Y.; Louzoun, Y.; Weigert, M.; (2004) Editing anti-DNA B cells by Vλx, The Journal of experimental medicine 199(3):337
  47. Louzoun, Y.; Vider, T.; (2004) Score for proteasomal peptide production probability, Immunology 1:45-50
  48. Goldenberg, J.; Libai, B.; Louzoun, Y.; Mazursky, D.; Solomon, S.; (2004) Inevitably reborn: the reawakening of extinct innovations, Technological Forecasting and Social Change 71(9):881-896
  49. Nudelman, G.; Louzoun, Y.; (2004) The role of lipid rafts in cell surface BCR antigen binding dynamics, Engineering in Medicine and Biology Society, 2004. IEMBS '04. 26th Annual International Conference of the IEEE (1):667-670
  50. Gilboa, A.; Shalev, A.Y.; Laor, L.; Lester, H.; Louzoun, Y.; Chisin, R.; Bonne, O.; (2004) Functional connectivity of the prefrontal cortex and the amygdala in posttraumatic stress disorder, Biological psychiatry 55(3):263-272
  51. Louzoun, Y.; Solomon, S.; Goldenberg, J.; Mazursky, D.; The Risk at Being Unfair

    52. 2003

  52. Bhanot, G.; Louzoun, Y.; Zhu, J.; DeLisi, C.; (2003) The importance of thermodynamic equilibrium for high throughput gene expression arrays, Biophysical journal 84(1):124-135
  53. Kleinstein, S.H.; Louzoun, Y.; Shlomchik, M.J.; (2003) Estimating hypermutation rates from clonal tree data, The Journal of Immunology 171(9):4639
  54. Louzoun, Y.; Solomon, S.; Atlan, H.; Cohen, I.R.; (2003) Proliferation and competition in discrete biological systems, Bulletin of mathematical biology 65(3):375-396
  55. Louzoun, Y.; Weigert, M.; Bhanot, G.; (2003) Dynamical analysis of a degenerate primary and secondary humoral immune response, Bulletin of mathematical biology 65(3):535-545
  56. Bonne, O.; Gilboa, A.; Louzoun, Y.; Brandes, D.; Yona, I.; Lester, H.; Barkai, G.; Freedman, N.; Chisin, R.; Shalev, A.Y.; (2003) Resting regional cerebral perfusion in recent posttraumatic stress disorder, Biological Psychiatry 54(10):1077-1086
  57. Bonne, O.; Gilboa, A.; Louzoun, Y.; Kempf-Sherf, O.; Katz, M.; Fishman, Y.; Ben-Nahum, Z.; Krausz, Y.; Bocher, M.; Lester, H.; (2003) Cerebral blood flow in chronic symptomatic mild traumatic brain injury, Psychiatry Research: Neuroimaging 124(3):141-152
  58. Bonne, O.; Louzoun, Y.; Aharon, I.; Krausz, Y.; Karger, H.; Lerer, B.; Bocher, M.; Freedman, N.; Chisin, R.; (2003) Cerebral blood flow in depressed patients: a methodological comparison of statistical parametric mapping and region of interest analyses, Psychiatry Research: Neuroimaging 122(1):49-57

    59. 2002

  59. Louzoun, Y.; Friedman, T.; Luning Prak, E.; Litwin, S.; Weigert, M.; (2002) Analysis of B cell receptor production and rearrangement* 1:: Part I. Light chain rearrangement, Seminars in Immunology 14(3):169-190
  60. Louzoun, Y.; Luning Prak, E.; Friedman, T.; Litwin, S.; Weigert, M.; (2002) Comment on Langman and Cohn, Seminars in Immunology 14(3):231-232
  61. Louzoun, Y.; Luning, P.E.; Litwin, S.; Weigert, M.; (2002) D is for different-differences between H and L chain rearrangement., Seminars in immunology 14(3):239
  62. Louzoun, Y.; Solomon, S.; (2002) Power Law Volatility Auto-Correlations in Stochastic Logistic Systems, Computing in Economics and Finance

    63. 2001

  63. Louzoun, Y.; Solomon, S.; Atlan, H.; Cohen, I.R.; (2001) Modeling complexity in biology, Physica A: Statistical Mechanics and its Applications 297(1):242-252
  64. Shnerb, NM; Bettelheim, E.; Louzoun, Y.; Agam, O.; Solomon, S.; (2001) Adaptation of autocatalytic fluctuations to diffusive noise, Physical Review E 63(2):21103
  65. Louzoun, Y.; Solomon, S.; (2001) Volatility driven market in a generalized Lotka-Voltera formalism, Physica A: Statistical Mechanics and its Applications 302(1):220-233
  66. Louzoun, Y.; Atlan, H.; Cohen, I.R.; (2001) Modeling the Influence of TH1-and TH2-type Cells in Autoimmune Diseases, Journal of autoimmunity 17(4):311-321

    67. 2000

  67. Shnerb, N.M.; Louzoun, Y.; Bettelheim, E.; Solomon, S.; (2000) The importance of being discrete: Life always wins on the surface, Proceedings of the National Academy of Sciences 97(19):10322
  68. Louzoun, Y.; Solomon, S.; Atlan, H.; Cohen, I.R.; (2000) The emergence of spatial complexity in the immune system, Arxiv preprint cond-mat/0008133
  69. Louzoun, Y.; Cohen, I.; Atlan, H.; (2000) Destruction of CD4 T lymphocytes alone cannot account for their long-term decrease in AIDS, Arxiv preprint math/0008052
  70. Louzoun, Y.; Solomon, S.; Atlan, H.; Cohen, I.; (2000) Microscopic Discrete Proliferating Components Cause the Self-Organized Emergence of Macroscopic Adaptive Features in Biological Systems, Arxiv preprint nlin/0006043
  71. Hershberg, U.; Louzoun, Y.; Atlan, H.; Solomon, S.; (2000) HIV time hierarchy: winning the war while, loosing all the battles Physica A: Statistical Mechanics and its Applications 289(1):178-190