Elhanan Borenstein, Ph.D.

Dept of Genome Sciences
University of Washington

3720 15th Ave NE
Foege Building, S103B
Box 355065
Seattle, WA 98195-5065

Phone: (206) 685-8165
Fax: (206) 685-7301



Publications
Journal Papers
»  Ohad Mahor, Roie Levy, and Elhanan Borenstein
Mapping the inner workings of the microbiome: Genomic- and metagenomic-based study of metabolism and of metabolic interactions in the human gut microbiome
Cell Metabolism, in press.
»  Hsuan-Chao Chiu, Roie Levy, and Elhanan Borenstein
Emergent biosynthetic capacity in simple microbial communities
PLoS Computational Biology, 10(7), 2014. (pdf)
»  Roie Levy and Elhanan Borenstein
Metagenomic systems biology and metabolic modeling of the human microbiome: From species composition to community assembly rules
Gut Microbes, 5(2), 2014. (pdf)
»  Lucas R. Hoffman, Christopher E. Pope, Hillary S. Hayden, Sonya Heltshe, Roie Levy, Sharon McNamara, Michael A. Jacobs, Laurence Rohmer, Matthew Radey, Bonnie W. Ramsey, Mitchell J. Brittnacher, Elhanan Borenstein, and Samuel I. Miller
Escherichia coli dysbiosis correlates with gastroiontestinal dysfunction in children with cystic fibrosis
Clinical Infectious Diseases, 58(3), 396-399, 2014. (pdf, Supp. Data.)
»  Rogan Carr, Shai S. Shen-Orr, and Elhanan Borenstein
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
PLoS Computational Biology, 9(10), 2013. (pdf)
  §  Recommended by Faculty of 1000
»  Roie Levy and Elhanan Borenstein
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
PNAS (Proc. Natl. Acad. Sci. USA), 110(31), 12804-12809, 2013. (pdf, Supp. Info.)
  §  Featured in UW Today
§  Recommended by Faculty of 1000
»  Maximilian O. Press*, Hui Li*, Nicole Creanza, Gunter Kramer, Christine Queitsch¥, Victor Sourjik¥, and Elhanan Borenstein¥ (* equal contribution; ¥ co-corresponding authors)
Genome-scale co-evolutionary inference identifies functions and clients of bacterial hsp90
PLoS Genetics, 9(7), 2013. (pdf)
»  Sharon Greenblum, Hsuan-Chao Chiu, Roie Levy, Rogan Carr, and Elhanan Borenstein
Towards a predictive systems-level model of the human microbiome: Progress, challenges, and opportunities
Current Opinion in Biotechnology, 24, 810-820, 2013. (pdf)
»  Brian J O’Roak, Laura Vives, Wenqing Fu, Jarrett D Egertson, Ian B Stanaway, Ian G Phelps, Gemma Carvill, Akash Kumar, Choli Lee, Katy Ankenman, Jeff Munson, Joseph B Hiatt, Emily H Turner, Roie Levy, Diana R O’Day, Niklas Krumm, Bradley P Coe, Beth K Martin, Elhanan Borenstein, Deborah A Nickerson, Heather C Mefford, Dan Doherty, Joshua M Akey, Raphael Bernier, Evan E Eichler, and Jay Shendure
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders
Science, 338, 1619-1622, 2012.
»  Shane Neph, Andrew B. Stergachis, Alex Reynolds, Richard Sandstrom, Elhanan Borenstein¥ and John A. Stamatoyannopoulos¥ (¥ co-corresponding authors)
Circuitry and dynamics of human transcription factor regulatory networks
Cell, 150(6), 1274-1286, 2012.(pdf, Supp. Info., browser)
  §  Featured in The Seattle Times
§  Featured in UW Today
»  Elhanan Borenstein
Computational systems biology and in silico modeling of the human microbiome
Briefings in Bioinformatics, 13(6), 769-780, 2012. (pdf)
  §  Recommended by Faculty of 1000
»  Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure, and Evan E. Eichler
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
Nature, 485, 246-250, 2012.
  §  Featured in The New York Times - see front page
§  Featured in Nature Reviews Genetics - see Fruits of exome sequencing for autism
§  Featured in UW Today
»  Roie Levy and Elhanan Borenstein
Reverse Ecology: From systems to environments and back
Advances in Experimental Medicine and Biology, 751, 329-345, 2012. (pdf)
»  Anat kreimer, Adi Doron, Elhanan Borenstein and Shiri Freilich
NetCmpt: A network-based tool for calculating the metabolic competition between bacterial species
Bioinformatics, 28 (16), 2195-2197, 2012. (pdf, software)
»  Sharon Greenblum, Peter J. Turnbaugh, and Elhanan Borenstein
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
PNAS (Proc. Natl. Acad. Sci. USA), 109(2), 594-599, 2012. (pdf, Supp. Info.)
  §  Featured in This Week in PNAS
§  Featured in UW Today
§  Featured in Science Daily
§  Featured in The Seattle Times;
§  Highlighted in Nature Reviews Microbiology - see Metagenomics with guts)
»  Ricardo Pinho, Elhanan Borenstein, and Marcus W. Feldman
Most networks in Wagner's model are cycling
PLoS ONE, 7(4), e34285, 2012. (pdf, Supp. Info.)
»  Rogan Carr and Elhanan Borenstein
NetSeed: A network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment
Bioinformatics, 28(5), 734-735, 2012. (pdf, software)
»  James J. Cai, Elhanan Borenstein and Dmitri A. Petrov
Broker genes in human disease
Genome Biology and Evolution, 2, 815-825, 2010. (pdf, Supp. Info.)
»  Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan and Eytan Ruppin
Decoupling environment-dependent and independent genetic robustness across bacterial species
PLoS Computational Biology, 6(2), 2010. (pdf, Supp. Info.)
»  Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna and Eytan Ruppin
Metabolic-network driven analysis of bacterial ecological strategies
Genome Biology, 10(6):R61, 2009. (pdf, Supp. Info.)
»  James J. Cai, Elhanan Borenstein, Rong Chen and Dmitri A. Petrov
Similarly strong purifying selection acts on human disease genes of all evolutionary ages
Genome Biology and Evolution, 1(1), 131-144, 2009. (pdf, Supp. Info.)
»  Elhanan Borenstein and Marcus W. Feldman
Topological signatures of species interactions in metabolic networks
Journal of Computational Biology, 16(2), 191-200, 2009. (pdf)
  §  Featured in Stanford Report, Feb 25, 2009 - see Reversing ecology reveals ancient environments
§  Featured in Frontiers in Ecology & the Environment - see Reverse ecology uses genes to predict environment
»  Elhanan Borenstein and David C. Krakauer
An end to endless forms: Epistasis, phenotype distribution bias, and non-uniform evolution
PLoS Computational Biology, 4(10), 2008. (pdf)
  §  Featured in Nature Reviews Genetics - see Modelling the evolutionarily possible
»  Elhanan Borenstein, Martin Kupiec, Marcus W. Feldman and Eytan Ruppin
Large-scale reconstruction and phylogenetic analysis of metabolic environments
PNAS (Proc. Natl. Acad. Sci. USA), 105(38), 14482-14487, 2008. (pdf, Supp. Info.)
  §  Featured in Genome Biology, 9:239, 2008 - see Network-based approaches for linking
metabolism with environment
  §  Recommended by Faculty of 1000
»  Laurent Lehmann, Kevin R. Foster, Elhanan Borenstein and Marcus W. Feldman
Social and individual learning of helping in humans and other species
Trends in Ecology and Evolution, 23(12), 664-671, 2008. (pdf)
»  Kreimer Anat*, Elhanan Borenstein*, Uri Gophna and Eytan Ruppin (*equal contribution)
The evolution of modularity in bacterial metabolic networks
PNAS (Proc. Natl. Acad. Sci. USA), 105(19), 6976-6981, 2008. (pdf, Supp. Info., Dataset 1)
»  Elhanan Borenstein, Marcus W. Feldman and Kenichi Aoki
Evolution of learning in fluctuating environments: When selection favors both individual and social learning
Evolution, 62(3), 586-602, 2008. (pdf)
»  Elhanan Borenstein*, Tomer Shlomi*, Eytan Ruppin and Roded Sharan (*equal contribution)
Gene loss rate: A probabilistic measure for the conservation of Eukaryotic genes
Nucleic Acids Research, 35(1), e7, 2007. (pdf, Supp. Info.)
»  Elhanan Borenstein and Eytan Ruppin
Direct evolution of genetic robustness in microRNA
PNAS (Proc. Natl. Acad. Sci. USA), 103(17), 6593-6598, 2006. (pdf, Supp. Info.)
»  Elhanan Borenstein, Isaac Meilijson and Eytan Ruppin
The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes
Journal of Evolutionary Biology, 19(5), 1555-1570, 2006. (pdf, Supp. Info.)
»  Elhanan Borenstein, Jeremy Kendal and Marcus W. Feldman
Cultural niche construction in a metapopulation
Theoretical Population Biology, 70(1), 92-104, 2006 (pdf)
»  Elhanan Borenstein and Eytan Ruppin
The evolution of imitation and mirror neurons in adaptive agents
Cognitive Systems Research (special issue on Epigenetic Robotics), 6(3), 229-242, 2005. (pdf)
»  Elhanan Borenstein and Eytan Ruppin
The evolutionary link between mirror neurons and imitation: An evolutionary adaptive agents model
Behavioral and Brain Sciences, 28:2, 127-128, 2005. (html,pdf)
»  Elhanan Borenstein and Eytan Ruppin
Enhancing autonomous agents evolution with learning by imitation (extended version)
Journal of Artificial Intelligence and the Simulation of Behaviour (AISBJ), 1(4), 335-347, 2003. (pdf)
Peer Reviewed Conference Papers
»  Elhanan Borenstein, and Marcus Feldman
Topological Signatures of Species Interactions in Metabolic Networks
4th Annual RECOMB Satellite on Systems Biology, Boston, 2008 (also published in JCB)
»  Elhanan Borenstein, Martin Kupiec, Marcus Feldman and Eytan Ruppin
Large-scale phylogenetic analysis of inferred metabolic growth environments and the evolution of metabolic networks
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2008), 2008
»  Elhanan Borenstein, Martin Kupiec, Marcus Feldman and Eytan Ruppin
Large-scale reconstruction and analysis of growth environments
Proceedings of the Eighth International Conference on Systems Biology (ICSB 2007), 2007. Plenary talk
»  Elhanan Borenstein and Eytan Ruppin
Evolving imitating agents and the emergence of a neural mirror system
Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9), 2004, MIT Press. (pdf)
»  Elhanan Borenstein and Eytan Ruppin
Enhancing autonomous agents evolution with learning by imitation
Proceedings of the AISB 2003 Convention: Cognition in Machines and Animals, Aberystwyth, Wales, April 2003. (pdf)
Conference Abstracts, Posters and Presentations
»  Elhanan Borenstein and Marcus Feldman
Super-Metabolism and Functional Capacity in Microbial Communities
5th Annual RECOMB Satellite on Systems Biology, Boston, December 2009.
»  Elhanan Borenstein, David Relman and Marcus Feldman
Computational Analysis of Metabolic Interactions in the Human Microbiome
Bio-X/Agilent Technical Summit, Stanford University, August 2009.
»  Elhanan Borenstein, Martin Kupiec, Marcus Feldman and Eytan Ruppin
Large-scale reconstruction and phylogenetic analysis of metabolic growth environments
Biomedical Computation at Stanford (BCATS), October 2007.
»  Elhanan Borenstein, Martin Kupiec, Marcus Feldman and Eytan Ruppin
The evolution of growth environments as inferred from large-scale metabolic networks data
CSHL/WT Meeting on Functional Genomics and Systems Biology, October 2007.
»  Elhanan Borenstein, Eytan Ruppin and Marcus Feldman
Using an information theory based approach to detect the phyletic ancestor in noisy data
Life Sciences Society Computational Systems Bioinformatics Conference (CSB2007), August 2007.
»  Elhanan Borenstein, Jeremy Kendal and Marcus Feldman
Explaining the variance in the onset of demographic transitions: The metapopulation cultural niche construction model
The Center for Complexity Science Meeting, April 2005, Tel-Aviv University.
»  Elhanan Borenstein and Eytan Ruppin
The evolution of genetic robustness: A case study
The Center for Complexity Science Meeting, April 2005, Tel-Aviv University.
»  Elhanan Borenstein, Isaac Meilijson and Eytan Ruppin
Learning decreases drawdowns in the fitness landscape and accelerates evolution
The Winter School in Theoretical Physics on Biological Networks and Evolution, The Institute for Advanced Studies, Hebrew University, January 2005.
»  Elhanan Borenstein and Erin Cline
Cellular automata model of cystogenesis and tubulogenesis
Proceedings of the Santa-Fe Institute Complex Systems Summer School, June 2004. (pdf)
»  Elhanan Borenstein, Isaac Meilijson and Eytan Ruppin
Evolution, learning and imitation
The Third Complexity International Conference, Jerusalem, December 2003.
PhD Dissertations
»  Elhanan Borenstein
Evolutionary Dynamics of Adaptive Populations: The Effect of Phenotypic Plasticity, Imitation and Culture on Evolution