Selected scientific publications
see google scholar for a complete list

  1. Eimear E. Kenny, Itsik Pe'er, Amir Karban, Laurie Ozelius, Adele A. Mitchell, Sok Meng Ng, Monica Erazo, Harry Ostrer, Clara Abraham, Maria T. Abreu, Gil Atzmon, Nir Barzilai, Steven Brant, Edward R. Burns, Yehuda Chowers, Lorraine Clark, Ariel Darvasi, Dana Doheny, Richard H. Duerr, Rami Eliakim, Nir Giladi, Peter Gregersen, Hakon Hakonarson, Michelle R. Jones, Dermot P.B. McGovern, Jennifer Mulle, Avi Orr-Urtreger, Deborah D. Proctor, Ann Pulver, Jerome I. Rotter, Mark S. Silverberg, Thomas Ullman, Stephen T. Warren, Matti Waterman, Wei Zhang, Aviv Bergman, Lloyd Mayer, Seymour Katz, Robert J. Desnick, Judy H. Cho, and Inga Peter. 2012. A Genome-Wide Scan of Ashkenazi Jewish Crohn's Disease Suggests Novel Susceptibility Loci. PLoS Genetics 8:e1002559.
  2. Sandeep N. Wontakal*, Xingyi Guo*, Cameron Smith^, Thomas MacCarthy^, Emery H. Bresnick, Aviv Bergman, Michael Snyder, Deyou Zheng, Sherman Weissman, and Arthur I. Skoultchi. 2012. A core erythroid transcriptional network is repressed by a master regulator of myelolymphoid differentiation. Proceedings of the National Academy of Sciences USA. 109(10):3832-7.
  3. Pujato, M.*, MacCarthy, T.*, Fiser, A., Bergman, A., The evolution of robustness involves balancing of local sequence and network level mechanisms (In preparation). *equal contribution
  4. MacCarthy, T.*, Kalis, S.*, Fan M., Pham P., Bergman A., Scharff, M. D., Baughn, L. B., Insertion of overlapping AID hot spots alters the frequency and targeting of somatic hypermutation. (In preparation). *equal contribution
  5. MacCarthy, T.*, Adomako, A.*, Schlecht, N., Brandwein-Gensler, M., Smith, R.V., Prystowsky, M.B., Belbin, T., Bergman, A., Cancer as the disintegration of robustness: population-level variance in gene expression identifies key genes in head and neck cancer progression (In preparation). *equal contribution
  6. C. Hou and A. Bergman. 2011. Pulmonary diffusional screening may explain the mismatch in scaling laws of mammalian metabolic rates. (In preparation).
  7. C. Hou and A. Bergman. 2011. Metabolic basis of different patterns in cellular growth. (In preparation).
  8. C. Hou, K. Bolt and A. Bergman. 2011. A general life history theory for effects of caloric restriction on health maintenance. Submitted to BMC Systems Biology.
  9. C. Hou, K. Bolt, and A. Bergman. 2011. A general model for ontogenetic growth under food restriction. Proc. R. Soc. B. (In press).
  10. C. Hou, K. Bolt, and A. Bergman. 2011. Energetic basis of correlation between catch-up growth, health maintenance and aging. J. Gerontol. A Biol. Sci. (In Press).
  11. Huffman DM, Bergman A, Barzilai N, and Atzmon G. 2011. A Systems Approach to Longevity Genes Reveals MTP as a Model Buffered Age-Related Disease Gene. Aging Cell, (In revision).
  12. Fuller TF. Ophoff RA, Cai Chaochao, Langfelder P, Parish ST, Wexler EM, Geschwind DH, Atzmon G, Barzilai N, Bergman A, van den Berg LH, Coppola G, Effros RB, Horvath S. 2011. LRRN3 and LEF1 are causal driver genes of human aging. (Resubmission.)
  13. Barzilai N, Gabriely I, Atzmon G, Suh Y, Rothenberg D and Bergman A., 2010 Oct. Genetic studies reveal the role of the endocrine and metabolic systems in aging. J Clin Endocrinol Metab. 95(10):4493-500.PMID: 20926537. (In errata will be submitted.)
  14. Joseph J. Abrajano, Irfan A. Qureshi, Solen Gokhan, Aldrin E. Molero, Deyou Zheng, Aviv Bergman, and Mark F. Mehler, 2010. Corepressor for element-1-silencing transcription factor preferentially mediates gene networks underlying neural stem cell multilineage potential and fate restruction. Proceedings of the National Academy of Sciences USA
  15. Gil Atzmon, Miook Cho, Richard M. Cawthon, Temuri Budagov, Micol Katz, Xiaoman Yang, Glenn Siegel, Aviv Bergman, Derek M. Huffman, Clyde B. Schechter, Woodring E. Wright, Jerry W. Shay, Nir Barzilai, and Yousin Suh, 2010, Genetic variation in the human telomerase is associated with telomere length in Ashkenazi centenarians. Proceedings of the National Academy of Sciences USA, Jan 26: 107 Suppl 1:1710-7. Epub 2009 Nov 13. PubMed PMID: 19915151; PubMed Central PMCID: PMC2868292.
  16. Joseph J. Abrajano, Irfan A. Qureshi, Solen Gokhan, Deyou Zheng, Aviv Bergman, and Mark F. Mehler, 2009, Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturation. PLoS ONE 4(11): e7665.
  17. Joseph J. Abrajano, Irfan A. Qureshi, Solen Gokhan, Deyou Zheng, Aviv Bergman, and Mark F. Mehler, 2009, REST and CoREST modulate neuronal subtype specification, maturation and maintenance. PLoS ONE 4(12): e7936.
  18. Thomas MacCarthy*, Susan L. Kalis*, Sergio Roa, Phuong Pham, Myron F. Goodman, Matthew D. Scharff, Aviv Bergman, 2009, V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment. Proceedings of the National Academy of Sciences USA 106: 8629-8634. PMCID: PMC268254
  19. Thomas MacCarthy, Sergio Roa, Matthew D. Scharff, Aviv Bergman, 2009, SHMTool: a webserver for comparative analysis of somatic hypermutation datasets. DNA Repair 8:137-141. PMCID: PMC2659805.
  20. Paola Sebastiani, Monty Montano, Annibale Puca, Nadia Timofeev, Toshio Kojima, Meng C. Wang, Efthymia Melista, Micah Meltzer, Sylvia E. J. Fischer, Stacy Anderson, Stephen H. Hartley, Amanda Sedgewick, Yasumichi Arai, Aviv Bergman, Nir Barzilai, Dellara F. Terry, Alberto Riva, Chiara Viviani Anselmi, Alberto Malovini, Aya Kitamoto, Motoji Sawabe, Tomio Arai, Yasuyuki Gondo, Martin H. Steinberg, Nobuyoshi Hirose, Gil Atzmon, Gary Ruvkun, Clinton T. Baldwin, and Thomas T. Perls, 2009, RNA Editing Genes Associated With Extreme Old Age in Humans and With Lifespan in C. elegans. PLoS ONE. 4(12): e8210. Erratum in: PLoS One. 2009;4(12) doi: 10.1371/annotation/387f8074-5f80-4bdd-bb0b-b36d49a16ac0. PubMed PMID: 20011587; PubMed Central PMCID: PMC2788130.
  21. Geoffrey West and Aviv Bergman, 2009,Towards a Systems Biology Framework for Understanding Aging and Healthspan, Journals of Gerontology Series A: Biological Sciences and Medical Sciences 64(2): 8629-34.
  22. Thomas J. Belbin, Nicolas F. Schlecht, Richard V. Smith, Leslie R. Adrien, Nicole Kawachi, Margaret Brandwein-Gensler, Aviv Bergman, Quan Chen, Geoffrey Childs, Michael B. Prystowsky, 2008, Site-Specific Molecular Signatures Predict Aggressive Disease in HNSCC, Head and Neck Pathology 2(4):243-256.
  23. Sergio Roa, Elena Avdievich, Jonathan U. Peled, Thomas MacCarthy, Uwe Werling, Fei Li Kuang, Rui Kan, Chunfang Zhao, Aviv Bergman, Paula E. Cohen, Winfried Edelmann, Matthew D. Scharff,2008, Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression. Proceedings of the National Academy of Sciences USA 2008 Oct 21;105(42):16248-53. Epub 2008 Oct 14. PubMed PMID: 18854411; PubMed Central PMCID: PMC2571010.
  24. Thomas J. Belbin, Aviv Bergman, Margaret Brandwein-Gensler, Geoffrey Childs, Ruth Hogue-Angeletti, Abdissa Negassa, Michael B. Prystowsky, Nicolas F. Schlecht, Richard V. Smith, 2007, Head and Neck Cancer: Reduce and Integrate for Optimal Outcome.Cytogenetics and Genome Research 118:87–90.
  25. Aviv Bergman, Gil Atzmon, Kenny Ye, Thomas MacCarthy, and Nir Barzilai, 2007, Buffering Mechanisms in Aging: A systems approach towards uncovering the genetic component of aging. PLoS Computational Biology Vol. 3 No. 8 e170. Epub 2007 Jul 18. PubMed PMID: 17784782; PubMed Central PMCID: PMC1963511.
  26. Thomas MacCarthy and Aviv Bergman, 2007, Co-evolution of Robustness, Epistasis and Recombination Favors Asexual Reproduction.Proceedings of the National Academy of Sciences USA Vol. 104 No. 31 12801-12806. Epub 2007 Jul 23. PubMed PMID: 17646644; PubMed Central PMCID: PMC1931480.
  27. Thomas MacCarthy and Aviv Bergman, 2007, The Limits of SubfunctionalizationBMC Evolutionary Biology 7:213. PubMed PMID: 17988397; PubMed Central PMCID: PMC2213666.
  28. George M. Martin, Aviv Bergman, Nir Barzilai, 2007, Genetics of Human Aging, PLoS Genetics Vol. 3 No. 7 e125.
  29. Mark L. Siegal, Daniel Promislow and Aviv Bergman, 2007, Functional and evolutionary inference in gene networks: Does topology matter?Genetica 126(1) 83-103.
  30. Gil Atzmon, Marielisa Rincon, Clyde B. Schechter, Alan R. Shuldiner, Richard B. Lipton, Aviv Bergman and Nir Barzilai, 2006,Lipoprotein Genotype and Conserved Pathway for Exceptional Longevity in Humans, PLoS Biology 4:4 Epub 2006 Apr 4.PubMed PMID: 16602826; PubMed Central PMCID: PMC1413567.   
  31. Mark L. Siegal and Aviv Bergman 2006, Canalization. in: "Evolutionary Genetics: Concepts and Case Studies", Charles Fox and Jason Wolf, Eds., Oxford University Press.
  32. Aviv Bergman and Mark L. Siegal, 2003, Evolutionary Capacitance as a General Feature of Complex Gene Networks. Nature 424, 549-552.
  33. Joanna Masel and Aviv Bergman, 2003, The Evolution of the Evolvability Properties of the Yeast Prion [PSI+]. Evolution 57(7) 1498-1512.
  34. Henrique Pereira, Aviv Bergman and Joan Roughgarden, 2003, Socially Stable Territories: The Negotiation of Space by Interacting Foragers. American Naturalist 161(1):143-152.
  35. Aviv Bergman and M. W. Feldman, 2003, On the Population Genetics of Punctuation. in: "Evolutionary Dynamics-Exploring the Interplay of Selection, Accident, Neutrality, and Function" Jim Crutchfield, and Peter Schuster Eds. Pp 81-100: Oxford University Press.
  36. Aviv Bergman and Moshe Tenennholtz, 2003, Episodic Learning: Towards the Emergence of Partial Cooperation. ComPlexUs 1:112-116.
  37. Mark L. Siegal and Aviv Bergman, 2002, Waddington's Canalization Revisited: Developmental Stability and Evolution. Proceedings of the National Academy of Sciences USA Vol. 99 No. 16 10528-10532.
  38. Samuel Karlin, Luciano Brocchieri, Aviv Bergman, Jan Mrzek and Andrew J. Gentles, 2002, Amino Acid and Charge Runs in Complete Eukaryotic Genomes and Disease Associations. Proceedings of the National Academy of Sciences USA Vol. 99 No. 1 333-338.
  39. Aviv Bergman and Moshe Tenennholtz, 2002, On the Natural Selection of Market Choice. Autonomous Agents and Multi-Agent Systems 5(4): 387-395.
  40. Maciej, F. Boni and A. Bergman, 2002, Co-infectious micro-parasites in an invertebrate host population: A dynamics systems approach. CCGBM Paper.
  41. Aviv Bergman, Tom Wasow, Amy Perfors, Thorsten Brants and David Beaver, 2002, Why Dose Ambiguity Exists? Semfest 2002 Stanford University.
  42. Samuel Karlin, Aviv Bergman and Andrew Gentles, 2001, Annotation of the Drosophila genome. Nature 411, 259-260.
  43. David B. Goldstein, G. W. Roemer, D. A. Smith, A. Bergman and R. K. Wayne, 1999, The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151: 797-801.
  44. Benjamin Kerr, D. W. Schwilk, A. Bergman and M. W. Feldman, 1999, Rekindling an old flame: A haploid model for the evolution and impact of flammability in re-sprouting plants. Evolutionary Ecology Research 1: 807-833.
  45. David D. Pollock, A. Bergman and M. W. Feldman and D. B. Goldstein, 1998, Microsatellite behavior with range constraints: Parameter estimation and improved distance estimation. Theoretical Population Biology 53:256-271.
  46. Ilan Eshel, M. W. Feldman and A. Bergman, 1998, Long-term evolution, short-term evolution, and population genetics theory. J. Theor. Biol. 191:391-396.
  47. Freddy B. Christiansen, S. P. Otto, M. W. Feldman and A. Bergman, 1998, Waiting with and without recombination: The time to production of a double mutant. Theoretical Population Biology 53: 199-215.
  48. Dan Cohen and A. Bergman, 1998, Evolutionary aspects of learning: the interface between fitness and action. Proceedings of the 7th International Behavioral Ecology Congress.
  49. Aviv Bergman, 1997, Self-organization by simulated evolution. in: Pattern Formation in the Physical and Biological Science, H.F. Nijhout, Lynn Nadel and Danniel L. Stein Eds., pp 13-21: Addison Wesley Publishing Company.
  50. Marcus W. Feldman, A. Bergman, D.D. Pollock and D. B. Goldstein, 1997, Microsatellite genetic distances with range constraints: Analytic description and problems of estimation. Genetics 145: 207-216.
  51. Lev A. Zhivotovsky, M. W. Feldman and A. Bergman, 1996, Fitness patterns and phenotypic plasticity in a spatially heterogeneous environment. Genetical Research 68: 241-248.
  52. Lev A. Zhivotovsky, M. W. Feldman and A. Bergman, 1996, On the evolution of phenotypic plasticity in spatially heterogeneous environment. Evolution 50:547-558.
  53. Lev A. Zhivotovsky, A. Bergman and M. W. Feldman, 1996, A Model of Individual Adaptive Behavior in a Fluctuating Environment. in: Adaptive Individuals in Evolving Populations: Models and Algorithms, R. Belew and. M Mitchel Eds. Pp 131-153: Addison Wesley Publishing Company, Reading MA.
  54. Jonathan Roughgarden, A. Bergman, S. Shafir and C. Taylor, 1996, Adaptive Computation in Ecology and Evolution: A Guide to Future Research. in: Adaptive Individuals in Evolving Populations: Models and Algorithms Eds. Richard K. Belew and Melanie Mitchell. Proceedings Volume XXVI Santa Fe Institute.
  55. Aviv Bergman and M. W. Feldman, 1996, Question marks about the period of punctuation. Santa Fe Institute paper 96-02-006.
  56. Aviv Bergman and M.W. Feldman, 1995, On the evolution of learning: representation of a stochastic environment. Theoretical Population Biology 48:251-276.
  57. Aviv Bergman, S. P. Otto and M. W. Feldman, 1995, On the Evolution of recombination in haploids and diploids. II. Stochastic models. Complexity 2:49-57.
  58. Aviv Bergman, S. P. Otto and M. W. Feldman, 1995, On the Evolution of recombination in haploids and diploids. I. Deterministic models. Complexity 1:57-67.
  59. Aviv Bergman, D. B. Goldstein, M. W. Feldman and K. E. Holsinger, 1995, Population structure, fitness surfaces, and linkage in the shifting balance process. Genetical Research 66:85-92.
  60. Aviv Bergman, 1994, An evolutionary approach to designing neural networks. in: Computing with Biological Metaphors, Ray Paton Ed., pp 298-308: Oxford press.
  61. David B. Goldstein, A. Bergman and M. W. Feldman, 1993, The evolution of interference: Reduction of recombination among three loci. Theoretical Population Biology 44:246-259.
  62. Aviv Bergman and M. W. Feldman, 1992, Recombination dynamics and the fitness landscape. Physica D 56:57-67.
  63. Aviv Bergman, P. Grassberger and T. P. Meyer, 1992, Forecasting probabilities with neural networks. in: Nonlinear Modeling and Forecasting, SFI Studies in the Sciences of Complexity, Proc. Vol. XII, M. Casdagli and S. Eubank Eds. Pp 305-315: Addison-Wesley.
  64. Aviv Bergman, 1992, Predicting chaos. in: Information Processing and Management of Uncertainty.
  65. Steve Barnard and A. Bergman, 1991, Adaptation in signal spaces. in: Parallel Problem Solving from Nature, H. P. Schwefel and R. Manner Eds. pp 395-404: Springer-Verlag.
  66. Aviv Bergman and M. W. Feldman, 1990, More on selection for and against recombination. Theoretical Population Biology 38:68-92.
  67. Eve Zoebisch and A. Bergman, 1990, Designer network: An attack on the force-field parameter estimation problem. American Chemical Society meeting San Francisco.
  68. Cregg. K. Cowan, A. Bergman and D. Nitzan, 1990, Automatic placement of vision sensors. Proc. of 16th NSF Grantees Conference on Production Research and Technology, Arizona State University.
  69. Aviv Bergman, 1990, Self-organization by simulated evolution. in: Lectures in the Sciences of Complexity, Erica Jen Ed., pp 455-463: Addison Wesley Publishing Company.
  70. Aviv Bergman and C. K. Cowan, 1989, Determining the camera and light source location for a visual task. International Conference on Robotics and Automation, IEEE.
  71. Cregg. K. Cowan, A. Bergman and D. Nitzan, 1989, Automatic placement of vision sensors. Proc. of 15th NSF Grantees Conference on Production Research and Technology, University of California, Berkeley.
  72. Aviv Bergman, 1988, Variation and selection: An evolutionary model of learning in neural networks. International Neural Network Society First Annual Meeting, Boston.
  73. Aviv Bergman, E. Bracha, P. G. Mulgaonkar and T. Shaham, 1988, Advanced research in address block location. Proc. of USPS Third Advanced Technology Conference, pp 218-232, Washington, D.C.
  74. Michel Kerszberg and A. Bergman, 1988, The evolution of data processing abilities in competing automata. in: Computer Simulation in Brain Science, Rodney M.J.Cotterill, Ed., pp 249-259: Cambridge University Press.
  75. Aviv Bergman and P. G. Mulgaonkar, 1988, Neural networks for address-block ranking: A comparison with classical techniques. Proc. of USPS Third Advanced Technology Conference, pp 736-750, Washington, D.C.
  76. Aviv Bergman and M. Kerszberg, 1987, Breeding intelligent automata. IEEE First Annual Conference on Neural Networks, Vol II pp 63-70, San Diego.
  77. Michel Kerszberg and A. Bergman, 1986, The evolution of computational capabilities in population of competing automata. STATPHYS-16 the 16th International Conference of Thermodynamics and Statistical Mechanics, Boston.
  78. Aviv Bergman and P. G. Mulgaonkar, 1986, Address block location: The SRI approach. USPS Advanced Technology Conference, pp 161-178, Washington, D.C.
  79. Cregg. K. Cowan and A. Bergman, 1986, Noise-tolerant range analysis for autonomous navigation. AAAI-86 Fifth National Conference on AI, pp 1122-1126, Philadelphia.