PAPERS

MacCarthy T, Roa S, Scharff MD and Bergman A.2009, “SHMTool: a webserver for comparative analysis of somatic hypermutation datasets”. DNA Repair 8 137-141

Belbin TJ, Schlecht NF, Smith RV, Adrien LR, Kawachi N, Brandwein-Gensler M, Bergman A, Chen Q, Childs G, Prystowsky MB. 2008, “Site-Specific Molecular Signatures Predict Aggressive Disease in HNSCC”, Head and Neck Pathology (online first)

Roa S, Avdievich E, Peled JU, MacCarthy T,  Werling U, Kuang FL, Kan R, Zhao C, Bergman A, Cohen PE, Edelmann W and Scharff MD. 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 105(42):16248-53

MacCarthy T and Bergman A. 2008, “The Limits of Subfunctionalization”,BMC Evolutionary Biology 7:213.

MacCarthy T and Bergman A. 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.

Martin GM, Bergman A, Barzilai N. 2007, “Genetics of Human Aging”, PLoS Genetics Vol. 3 No. 7 e125.

Bergman A, Atzmon G, Ye K, MacCarthy T and Barzilai N. 2007, “Buffering Mechanisms in Aging: A systems approach towards uncovering the genetic component of aging”. PLoS Computational Biology Vol. 3 No. 8 e170.

Belbin TJ, Bergman A, Brandwein-Gensler M, Childs G, Hogue-Angeletti R, Negassa A, Prystowsky MB, Schlecht N, Smith RV. 2007, “Head and Neck Cancer: Reduce and Integrate for Optimal Outcome”, Cytogenetics and Genome Research 118:87–90.

Atzmon G, Rincon M, Schechter CB, Shuldiner AR, Lipton RB, Bergman A and Barzilai N. 2006, “Lipoprotein Genotype and the Pathway for Exceptional Longevity in Humans”, PLoS Biology 4:4

Siegal ML, Promislow D and Bergman A. 2006, “Functional and evolutionary inference in gene networks:  Does topology matter?” Genetica, 126(1) 83-103.

Siegal ML and Bergman A. 2006, “Canalization” in “Evolutionary Genetics: Concepts and Case Studies”, Charles Fox and Jason Wolf, Eds.

Mark L. Siegal, Daniel Promislow and Aviv Bergman, 2005,
Functional and evolutionary inference in gene networks: Does topology matter?
Genetica, special issue on "The microevolution of development: Patterns, processes, and mechanisms". (in press)

Mark L. Siegal and Aviv Bergman 2005,
Canalization.
in "Evolutionary Genetics: Concepts and Case Studies", Charles Fox and Jason Wolf, Eds.
Go to Amazon.

Aviv Bergman and Mark L. Siegal, 2003,
Evolutionary Capacitance as a General Feature of Complex Gene Networks.
Nature 424, 549-552. (PDF)
Commentary 1 (PDF)
Commentary 2 (PDF)

Joanna Masel and Aviv Bergman, 2003,
The Evolution of the Evolvability Properties of the Yeast Prion [PSI+].
Evolution 57(7) 1498-1512. (PDF)

Henrique Pereira, Aviv Bergman and Joan Roughgarden, 2003,
Socially Stable Territories: The Negotiation of Space by Interacting Foragers.
American Naturalist 161(1):143-152. (PDF)

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. (PDF)

Aviv Bergman and Moshe Tenennholtz, 2003,
Episodic Learning: Towards the Emergence of Partial Cooperation.
ComPlexUs, 1:112-116. (PDF)

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. (PDF)
Commentary 1 (PDF)
Commentary 2 (PDF)

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. (PDF)

Aviv Bergman and Moshe Tenennholtz, 2002,
On the Natural Selection of Market Choice.
Autonomous Agents and Multi-Agent Systems 5(4): 387-395. (PDF)

Maciej, F. Boni and A. Bergman, 2002,
Co-infectious micro-parasites in an invertebrate host population: A dynamics systems approach.
CCGBM Paper.

Aviv Bergman, Tom Wasow, Amy Perfors, Thorsten Brants and David Beaver, 2002,
Why Dose Ambiguity Exists?
Semfest 2002 Stanford University.

Samuel Karlin, Aviv Bergman and Andrew Gentles, 2001,
Annotation of the Drosophila genome.
Nature 411, 259-260. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

Dan Cohen and A. Bergman, 1998,
Evolutionary aspects of learning: the interface between fitness and action.
Proceedings of the 7th International Behavioral Ecology Congress.

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. (PDF)

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.

Lev A. Zhivotovsky, M. W. Feldman and A. Bergman, 1996,
On the evolution of phenotypic plasticity in spatially heterogeneous environment.
Evolution 50:547-558.

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.

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.

Aviv Bergman and M. W. Feldman, 1996,
Question marks about the period of punctuation.
Santa Fe Institute paper 96-02-006.

Aviv Bergman and M.W. Feldman, 1995,
On the evolution of learning: representation of a stochastic environment.
Theoretical Population Biology 48:251-276. (PDF)

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.

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.

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. (PDF)

Aviv Bergman, 1994,
An evolutionary approach to designing neural networks.
in: Computing with Biological Metaphors, Ray Paton Ed., pp 298-308: Oxford press.

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.

Aviv Bergman and M. W. Feldman, 1992,
Recombination dynamics and the fitness landscape.
Physica D 56:57-67.

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.

Aviv Bergman, 1992,
Predicting chaos.
in: Information Processing and Management of Uncertainty.

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.

Aviv Bergman and M. W. Feldman, 1990,
More on selection for and against recombination.
Theoretical Population Biology 38:68-92.

Eve Zoebisch and A. Bergman, 1990,
Designer network: An attack on the force-field parameter estimation problem.
American Chemical Society meeting San Francisco.

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.

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.

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.

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.

Aviv Bergman, 1988,
Variation and selection: An evolutionary model of learning in neural networks.
International Neural Network Society First Annual Meeting, Boston.

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.

Michel Kerszberg and A. Bergman, 1988,
The evolution of data processing abilities in competing automata.
in Computer Simulation in Brain Science, Ed. Rodney M.J.Cotterill, pp 249-259: Cambridge University Press.

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.

Aviv Bergman and M. Kerszberg, 1987,
Breeding intelligent automata.
IEEE First Annual Conference on Neural Networks, Vol II pp 63-70, San Diego.

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.

Aviv Bergman and P. G. Mulgaonkar, 1986,
Address block location: The SRI approach.
USPS Advanced Technology Conference, pp 161-178, Washington, D.C.

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.

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