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Welcome to the

TANNENBAUM RESE
ARCH GROUP
Theoretical Evolutionary Dynamics at Ben-Gurion University of the Negev

OVERVIEW           RESEARCH          PEOPLE          PUBLICATIONS

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OVERVIEW

We are a theoretical group studying various problems in evolutionary dynamics.  Evolutionary dynamics is a subfield of mathematical biology that deals with developing mathematical models describing various evolutionary processes.  These evolutionary processes can in principle be at length scales ranging from the molecular to the ecological, and at time scales corresponding to both micro-evolutionary and macro-evolutionary processes.

Because evolutionary processes are central to the formation and behavior of many biological systems, evolutionary dynamics is an important tool for understanding a wide range of biological phenomena.  Examples include the origin-of-life, viral replication dynamics, immune response to infection, the emergence of antibiotic drug resistance in bacteria, cancer, stem cells, aging, and the evolution and maintenance of sexual reproduction.

Furthermore, because many complex systems, such as the brain and networked societies, are formed by the self-organization of agents acting under various selection pressures, evolutionary dynamics has connections to fields such as game theory, mathematical economics, computational neuroscience, and information theory.  These complex systems exhibit common motifs such as cooperation, differentiation, and the division of labor, but also defection and parasitism.  Understanding the interplay between these various competing effects is crucial for understanding the proper function of a wide variety of complex systems.  As a result, in addition to modeling specific evolutionary processes, evolutionary dynamics is important for understanding "emergent" behaviors in complex systems.  

RESEARCH


Research in the Tannenbaum Group is in the following areas of evolutionary dynamics:  (1)  Quasispecies Theory.  (2)  DNA Damage, Mutation, and Repair.
(3)  Network Evolution and Systems Chemistry.  Below, we give a brief description of each research area.

QUASISPECIES THEORY

Quasispecies Theory deals with a certain class of evolutionary dynamics equations known as the quasispecies equations.  The quasispecies equations were originally developed by Manfred Eigen and Peter Schuster in the 1970s to model molecular evolutionary processes related to the origin of life.  Quasispecies theory has since been found to be a highly useful concept and tool for understanding the evolutionary dynamics of viruses.

Our work in this area has primarily focused on developing formulations of the quasispecies model that are appropriate for analyzing the evolutionary dynamics of cellular life. This necessitates accounting for a variety of biological features that were not considered in the original formulation of quasispecies theory.  Examples of biological details that we have incorporated into the quasispecies framework include the semiconservative nature of DNA replication, genetic repair and mutators, multi-gene genomes, and polysomic genomes.  Current group research in this area is focused on Horizontal Gene Transfer, an important source of genetic variation in prokaryotes.

DNA DAMAGE, MUTATION, AND REPAIR

This research category deals with problems related to DNA damage and repair, and modeling mutation-propagation in cellular populations.  Specific questions that we have dealt with or are dealing with include analyzing the role of asymmetric chromosome segregation on mutation-accumulation in stem cell populations, chromosomal instability and cancer, and the evolution and maintenance of sex as a way of repairing DNA damage and stopping mutation-accumulation in diploid genomes.

NETWORK EVOLUTION AND SYSTEMS CHEMISTRY

This area of research deals with modeling the dynamics associated with various cooperative behaviors, such as autocatalytic networks and hypercycles, and understanding the evolutionary basis for various differentiated labor strategies.  In some recent speculative papers, we have argued that these could provide a basis for understanding the emergence of a stem-cell-based tissue architecture in complex organisms, as well as the emergence of sleep and of REM and non-REM sleep states, which we argued is a manifestation of what we called a "temporally differentiated" labor strategy.

This research area also seeks to model biochemical implementations of various computational motifs, such as associative memory and learning, that may be relevant for understanding the structure of various biochemical networks in living cells.  The basis for this area of research is an emerging paradigm termed the "RNA Computer Hypothesis," which proposes that much of the basis for the existence of complex multicellular organisms arises from a vast RNA-based genetic regulatory network in the cells of higher eukaryotes.  If this framework is correct, then it will be necessary to determine the types of computational motifs that exist in living cells.

PEOPLE


PRINCIPAL INVESTIGATOR

Emmanuel David Tannenbaum *
Office:  30-204
Phone:  +972-8-642-8363
E-mail:  emanuelt@bgu.ac.il
[CV]
*On leave for the 2010-2011 academic year

CURRENT GROUP MEMBERS

Nathaniel Wagner (Staff Scientist)
Office:  30-206
Phone:  +972-8-642-8365  
E-mail:  nwagner@bgu.ac.il

Maya Kleiman (Ph.D. Student)
Office:  30-205
Phone:  +972-8-647-9470
E-mail:  km@bgu.ac.il

Eran Itan (Ph.D. Student)
Office:  30-206
Phone:  +972-8-642-8365
E-mail:  itan@bgu.ac.il

Yoav Raz (Master's Student)
Office:  30-206
Phone:  +972-8-642-8365
E-mail:  razyoav@bgu.ac.il

FORMER GROUP MEMBERS

Pavel Gorodetsky -- Master's Student (September, 2007 -- June, 2009)
[Master's Thesis]

Amit Kama -- Undergraduate Research Assistant (September, 2007 -- June, 2008)

PUBLICATIONS

1998 -- 2001 -- 2002 -- 2003 -- 2004 -- 2005 -- 2006 -- 2007 -- 2008 -- 2009
2010 

2010

36

E. Tannenbaum, T. Georgiou, and A. Tannenbaum
"Signals and Control Aspects of Optimal Mass Transport and the Boltzmann Entropy"
IEEE Conference on Decision and Control (2010)
(6 pages)

35

A. Kama and E. Tannenbaum
"Effect of the SOS Response on the Mean Fitness of Unicellular Populations:  A Quasispecies Approach"
PLoS ONE 5, e14113 (2010)
(9 pages)

34


E. Itan and E. Tannenbaum
"Semiconservative Quasispecies Equations for Polysomic Genomes:  The General Case"
Physical Review E
81, 061915 (2010)
(14 pages)

33

Y. Raz and E. Tannenbaum
"The Influence of Horizontal Gene Transfer on the Mean Fitness of Unicellular Populations in Static Environments"
Genetics 185, 327-337 (2010)
(11 pages)
       
32

N. Wagner, E. Tannenbaum, and G. Ashkenasy
"Second-Order Catalytic Quasispecies Yields Discontinuous Mean Fitness at Error Threshold"
Physical Review Letters 104, 188101 (2010)
(4 pages)

31

N. Wagner, A. Pross, and E. Tannenbaum
"Selection Advantage of Metabolic over Non-Metabolic Replicators:  A Kinetic Analysis"
Biosystems 99, 126-129 (2010)
(4 pages)

2009

30

M. Kleiman and E. Tannenbaum
"Diploidy and the Selective Advantage for Sexual Reproduction in Unicellular Organisms"
Theory in Biosciences 128, 249-285 (2009)
(37 pages)

29

E. Tannenbaum
"Selective Advantage for Sexual Reproduction with Random Haploid Fusion"
Theory in Biosciences 128, 85-96 (2009)
(12 pages)

28

E. Tannenbaum
"Speculations on the Emergence of Self-Awareness in Big-Brained Organisms:  The Roles of Associative Memory and Learning, Existential and Religious Questions, and the Emergence of Tautologies"
Consciousness and Cognition 18, 414-427 (2009)
(14 pages)

2008

27

E. Tannenbaum
"A Comparison of Sexual and Asexual Replication Strategies in a Simplified Model Based on the Yeast Life Cycle"
Theory in Biosciences 127, 323-333 (2008)
(11 pages)

26

P. Gorodetsky and E. Tannenbaum
"Effect of Mutators on Adaptability in Time-Varying Fitness Landscapes"
Physical Review E 77, 042901 (2008)
(4 pages)

25

E. Tannenbaum and J.F. Fontanari
"A Quasispecies Approach to the Evolution of Sexual Replication in Unicellular Organisms"
Theory in Biosciences 127, 53-65 (2008)
(13 pages)

24

E. Tannenbaum
"Temporal Differentiation and the Optimization of System Output"
Physical Review E 77, 011922 (2008)
(14 pages)

23

E. Tannenbaum
"Comparison of Three Replication Strategies in Complex Multicellular Organisms:  Asexual Replication, Sexual Replication with Identical Gametes, and Sexual Replication
with Distinct Sperm and Egg Gametes"
Physical Review E 77, 011915 (2008)
(16 pages)

2007

22

N. Gandhi, G. Ashkenasy, and E. Tannenbaum
"Associative Learning in Biochemical Networks"
Journal of Theoretical Biology 249, 58-66 (2007)
(9 pages)

21

B. Lee and E. Tannenbaum
"Asexual and Sexual Replication in Sporulating Organisms"
Physical Review E 76, 021909 (2007)
(9 pages)

20

E. Tannenbaum
"When Does Division of Labor Lead to Increased System Output?"
Journal of Theoretical Biology 247, 413-425 (2007)
(13 pages)

19

E. Tannenbaum
"Extracting Viability Landscapes from Mutagen-Response Experiments"
Journal of Theoretical Biology 245, 37-43 (2007)
(7 pages)

2006

18

E. Tannenbaum, J.L. Sherley, and E.I. Shakhnovich
"Semiconservative Quasispecies Equations for Polysomic Genomes:  The Haploid Case"
Journal of Theoretical Biology 241, 791-805 (2006)
(15 pages)

17

E. Tannenbaum
"Selective Advantage for Sexual Reproduction"
Physical Review E 73, 061925 (2006)
(9 pages)

16

E. Tannenbaum
"An RNA-Centered View of Eukaryotic Cells"
Biosystems 84, 217-224 (2006)
(8 pages)

15

E. Tannenbaum
"Selective Advantage for Multicellular Replicative Strategies:  A Two-Cell Example"
Physical Review E 73, 010904 (2006)
(4 pages)

2005

14

E. Tannenbaum and E.I. Shakhnovich
"Semiconservative Replication, Genetic Repair, and Many-Gened Genomes:  Extending the Quasispecies Paradigm to Living Systems"
Physics of Life Reviews 2, 290-317 (2005)
(28 pages)

13

E. Tannenbaum, J.L. Sherley, and E.I. Shakhnovich
"Evolutionary Dynamics of Adult Stem Cells:  Comparison of Random and Immortal Strand Segregation Mechanisms"
Physical Review E 71, 041914 (2005)
(9 pages)

2004

12

E. Tannenbaum, J.L. Sherley, and E.I. Shakhnovich
"Imperfect DNA Lesion Repair in the Semiconservative Quasispecies Model:  Derivation of the Hamming Class Equations and Solution of the
Single-Fitness-Peak Landscape"
Physical Review E 70, 061915 (2004)
(15 pages)

11

S. Kallush, E. Tannenbaum, and B. Segev
"Local Group Velocity and Path-Delay:  Semiclassical Propagators for the Time Evolution of Wigner Functions in Deep Tunneling and in Dispersive Media"
Chemical Physics Letters 396, 261-267 (2004)
(7 pages)

10

E. Tannenbaum and E.I. Shakhnovich
"Solution of the Quasispecies Model for an Arbitrary Gene Network"
Physical Review E 70, 021903 (2004)
(15 pages)

9

E. Tannenbaum, E.J. Deeds, and E.I. Shakhnovich
"Semiconservative Replication in the Quasispecies Model"
Physical Review E 69, 061916 (2004)
(14 pages)

8

E. Tannenbaum and E.I. Shakhnovich
"Error and Repair Catastrophes:  A Two-Dimensional Phase Diagram in the Quasispecies Model"
Physical Review E 69, 011902 (2004)
(11 pages)

2003

7

E. Hershkovitz, E. Tannenbaum, S.B. Howerton, A. Sheth, A. Tannenbaum, and L.D. Williams
"Automated Identification of RNA Conformational Motifs:  Theory and Application to the HM LSU 23S rRNA"
Nucleic Acids Research 31, 6249-6257 (2003)
(9 pages)

6

E. Tannenbaum, E.J. Deeds, and E.I. Shakhnovich
"Equilibrium Distribution of Mutators in the Single Fitness Peak Model"
Physical Review Letters 91, 138105 (2003)
(4 pages)

2002

5

E. Tannenbaum and E.J. Heller
"Determination of Bound-Free Dissocative Couplings Via Classical Fourier Coefficients"
Journal of Chemical Physics 117, 9574-9579 (2002)
(6 pages)

4

E. Tannenbaum, K.J. Higgins, W. Klemperer, B. Segev, and E.J. Heller
"A Perturbative Approach to Vibrational Predissociation Rates:  Application to ArHF"
Journal of Physical Chemistry B 106, 8100-8107 (2002)
(8 pages)

3

E. Tannenbaum
"Partial-Differential-Equation-Based Approach to Classical Phase-Space Deformations"
Physical Review E 65, 066613 (2002)
(10 pages)

2001

2

E. Tannenbaum and E.J. Heller
"Semiclassical Quantization Using Invariant Tori:  A Gradient-Descent Approach"
Journal of Physical Chemistry A 105, 2803-2813 (2001)
(11 pages)

1998

1

Y. Kannai and E. Tannenbaum
"Paths Leading to the Nash Set for Non-Smooth Games"
International Journal of Game Theory 27, 393-405 (1998)
(13 pages)