Elhanan Borenstein, Ph.D.


Associate Professor

Blavatnik School of Computer Science

and

Sackler Faculty of Medicine

Tel Aviv University

Affiliate Professor
Dept of Genome Sciences
University of Washington

External Professor
Santa Fe Institute
Publications
See also: Google Scholar, NCBI Bibliography
Journal Papers
»  Hillary S. Hayden*, Alexander Eng*, Christopher E.Pope, Mitchell J.Brittnacher, Anh T.Vo, Eli J. Weiss, Kyle R. Hager, Bryan D. Martin, Daniel H. Leung, Sonya L. Heltshe, Elhanan Borenstein¥, Samuel I. Miller¥, and Lucas R. Hoffman¥ (* equal contribution; ¥ co-corresponding authors)
Fecal Dysbiosis in Infants with Cystic Fibrosis is Associated with Early Linear Growth Failure
Nature Medicine, in press.
»  Cecilia Noecker,Hsuan-Chao Chiu, Colin P. McNally,and Elhanan Borenstein
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
mSystems, 4:e00579-19, 2019. (pdf)
»  Benjamin D. Ross*, Adrian J. Verster*, Matthew C. Radey, Danica T. Schmidtke, Christopher E. Pope, Lucas R. Hoffman, Adeline M. Hajjar, S. Brook Peterson, Elhanan Borenstein¥, and Joseph D. Mougous¥ (* equal contribution; ¥ co-corresponding authors)
Human gut bacteria contain acquired interbacterial defence systems
Nature, 575, 224-228, 2019. (pdf)
  §  Featured in UW Medicine Newsroom
§  Featured in Genetic Engineering & Biotechnology News
§  Featured in Science Daily
§  Featured in HHMI News
§  Featured in TAU Safra News
»  Gil Sharon, Nikki Jamie Cruz, Dae-Wook Kang, Michael J. Ganda, Bo Wang, Young-Mo Kim, Erika M. Zink, Cameron P. Casey, Bryn C. Taylor, Christianne J. Lane, Lisa M. Bramer, Nancy G. Isern, David W. Hoyt, Cecilia Noecker, Michael J. Sweredoski, Annie Moradian, Elhanan Borenstein, Janet K. Jansson, Rob Knight, Thomas O. Metz, Carlos Lois, Daniel H. Geschwind, Rosa Krajmalnik-Brown, and Sarkis K. Mazmanian
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice
Cell, 177:6, 1600-1618, 2019. (pdf)
  §  Featured in The Guardian
§  Featured in The Economist
§  Featured in Science Magazine
§  Featured in Caltech News
§  Featured in Neuroscience News
§  Featured in Genetic Engineering News
§  Featured in Tech Times, Medical News Today, Medical Xpress, Gizmag
»  Alexander Eng and Elhanan Borenstein
Microbial Community Design: Methods, Applications, and Opportunities
Current Opinion in Biotechnology, 58:117-128, 2019. (pdf)
»  Maria T. Nelson, Christopher E. Pope, Robyn L. Marsh, Daniel J. Wolter, Eli J. Weiss, Kyle R. Hager, Anh T. Vo, Mitchell J. Brittnacher, Matthew C. Radey, Hillary S. Hayden, Alexander Eng, Samuel I. Miller, Elhanan Borenstein, and Lucas R. Hoffman
Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Provides Optimized Viable Microbiome Profiles
Cell Reports, 26:8, 2019. (pdf)
»  Marie Lindefeldt, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, and Stefanie Prast-Nielsen
The Ketogenic Diet Influences Taxonomic and Functional Composition of the Gut Microbiota in Children with Severe Epilepsy
npj Biofilms and Microbiomes, 5:5, 2019.(pdf)
»  Adrian J. Verster and Elhanan Borenstein
Competitive Lottery-Based Assembly of Selected Clades in the Human Gut Microbiome
Microbiome, 6:186, 2018. (pdf)
»  Colin P. McNally and Elhanan Borenstein
Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding via Extensive Gene Loss
BMC Systems Biology, 12:69, 2018. (pdf, Supp Info)
»  Eria A. Rebollar, Ana Gutierrez-Preciado, Cecilia Noecker, Alexander Eng, Myra Hughey, Daniel Medina, Jenifer B. Walke, Elhanan Borenstein, Roderick V. Jensen, Lisa K. Belden, and Reid Harris
The skin microbiome of the Neotropical frog Craugastor fitzingeri: Inferring potential bacterial-host-pathogen interactions from metagenomic data
Frontiers in Microbiology, 9:466, 2018. (pdf)
»  Alexander Eng and Elhanan Borenstein
Taxa-function robustness in microbial communities
Microbiome, 6:45, 2018. (pdf)
»  Colin P. McNally, Alexander Eng, Cecilia Noecker, William C. Gagne-Maynard, and Elhanan Borenstein
BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data
Frontiers in Microbiology, 9:365, 2018. (pdf, software)
»  Susana Matamouros, Hillary S. Hayden, Kyle R. Hager, Mitchell J. Brittnacher, Kristina Lachance, Eli J. Weiss, Christopher E. Pope, Anne-Flore Imhaus, Colin P. McNally, Elhanan Borenstein, Lucas R. Hoffman, and Samuel I. Miller
Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis
PNAS (Proc. Natl. Acad. Sci. USA), 115(7), 1605-1610, 2018. (pdf)
»  Adrian J. Verster, Benjamin D. Ross, Matthew C. Radey, Yiqiao Bao, Andrew L. Goodman, Joseph D. Mougous, and Elhanan Borenstein
The landscape of type VI secretion across human gut microbiomes reveals its role in community composition
Cell Host and Microbe, 22, 411-419, 2017. (pdf, extended pdf with supp info)
  §  Featured in This Week in Microbiology (ASM Podcast): Covert pathogenesis
§  Featured in UW Medicine Newsroom
»  John C. Whitney, S. Brook Peterson, Jungyun Kim, Manuel Pazos, Adrian J. Verster, Matthew C. Radey, Hemantha D. Kulasekara, Mary Q. Ching, Nathan P. Bullen, Diane Bryant, Young Ah Goo, Michael G. Surette, Elhanan Borenstein, Waldemar Vollmer, and Joseph D. Mougous
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria
eLife, 6:e26938, 2017. (pdf)
»  Ohad Manor and Elhanan Borenstein
Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome
Microbiome, 5:19, 2017. (pdf)
»  Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Cecilia Noecker, Ohad Manor, Sarah Hilton, Thumbi Mwangi, Clayton Onyango, Gemina Garland-Lewis, Doug Call, Kariuki Njenga, Judith Wasserheit, Jennifer Zambriski, Judd Walson, Guy Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter Rabinowitz
Microbiome sharing between children, livestock and household surfaces in western Kenya
PLOS ONE, 12(2), 2017.
»  Ohad Manor and Elhanan Borenstein
Systematic characterization and analysis of the taxonomic drivers of functional shifts in the human microbiome
Cell Host and Microbe, 21, 254-267, 2017. (pdf, extended pdf with supp info)
  §  Featured in Science (Mining microbes: Creating genomic tools to fight disease)
§  Featured in UW NewsBeat
§  Featured in UW The Daily
§  Featured in FierceBiotech
§  Featured in TechCrunch
§  Featured in UW Accelerate
§  Recommended by Faculty of 1000

§  Featured on Cell Host and Microbe cover

   
»  Antoine M. Snijders, Sasha A. Langley, Young-Mo Kim, Colin J. Brislawn, Cecilia Noecker, Erika M. Zink, Sarah J. Fansler, Cameron P. Casey, Darla R. Miller, Yurong Huang, Gary H. Karpen, Susan E. Celniker, James B. Brown, Elhanan Borenstein, Janet K. Jansson, Thomas O. Metz, and Jian-Hua Mao
Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome
Nature Microbiology, 2, 16221, 2017. (pdf, Supp Info)
  §  Featured in Science Daily
§  Featured in PNNL News
»  Cecilia Noecker, Colin P. McNally, Alexander Eng, and Elhanan Borenstein
High-resolution characterization of the human microbiome
Translational Research, 179, 7-23, 2017. (pdf)
»  Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, and William Stafford Noble
An alignment-free metapeptide strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing
Journal of Proteome Research, 15(8), 2697-2705, 2016. (pdf)
»  Maximilian O. Press, Christine Queitsch, and Elhanan Borenstein
Evolutionary assembly patterns of prokaryotic genomes
Genome Research, 26:826-833, 2016. (pdf, Supp. Info)
»  Alexander Eng and Elhanan Borenstein
An algorithm for designing minimal microbial communities with desired metabolic capacities
Bioinformatics, 32(13), 2016. (pdf, Supp. Info, software)
  §  Featured in IEEE Pulse (Deciphering the Mysterious Microbiome)
»  Ohad Manor*, Roie Levy*, Christopher E. Pope, Hillary S. Hayden, Mitchell J. Brittnacher, Rogan Carr, Matthew C. Radey, Kyle R. Hager, Sonya L. Heltshe, Bonnie W. Ramsey, Samuel I. Miller, Lucas R. Hoffman¥, and Elhanan Borenstein¥ (* equal contribution; ¥ co-corresponding authors)
Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis
Scientific Reports, 6:22493, 2016. (pdf, Supp Info)
»  Cecilia Noecker, Alexander Eng, Sujatha Srinivasan, Casey M. Theriot, Vincent B. Young, Janet K. Jansson, David N. Fredricks, and Elhanan Borenstein
Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation
mSystems, 1:1, e00013-15, 2016. (pdf, Supp. Info, MIMOSA software)
  §  mSystems Editor's Pick
§  Featured in IEEE Pulse (Deciphering the Mysterious Microbiome)

   
»  Cecilia Noecker and Elhanan Borenstein
Getting personal about nutrition
Trends in Molecular Medicine, 22(2), 83-85, 2016. (pdf)
»  Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich, and Elhanan Borenstein
NetCooperate: A network-based tool for inferring host-microbe and microbe-microbe cooperation
BMC Bioinformatics, 16:164, 2015. (pdf, software)
»  Ohad Manor and Elhanan Borenstein
MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
Genome Biology, 16:53, 2015. (pdf, Supp. Info, software)
  §  Featured in Genetic Engineering & Biotechnology News (GEN)
»  Sharon Greenblum, Rogan Carr, and Elhanan Borenstein
Extensive strain-level copy number variation across human gut microbiome species
Cell, 160, 583-594, 2015. (pdf, extended pdf with supp info)
  §  Featured in UW NewsBeat
§  Featured in Genomeweb
§  Featured in Medical News Today
§  Featured in Science Daily
§  Featured in Biomedical Computation Review (Computing the Gut)
§  Featured in IEEE Pulse (Deciphering the Mysterious Microbiome)

§  Featured on Cell cover

   
»  Fereydoun Hormozdiari, Osnat Penn, Elhanan Borenstein, and Evan E Eichler
The discovery of integrated gene networks for autism and related disorders
Genome Research, 25(1), 142-154, 2015.(pdf)
»  Matthew K Waldor, Gene Tyson, Elhanan Borenstein, Howard Ochman, Andrew Moeller, B. Brett Finlay, Heidi H. Kong, Jeffrey I. Gordon, Karen E. Nelson, Karim Dabbagh, and Hamilton Smith
Where next for microbiome research?
PLoS Biology, 13(1), 2015. (pdf)
  §  Featured in Genetic Engineering & Biotechnology News (GEN)
»  Jennifer Lachowiec, Tzitziki Lemus, Elhanan Borenstein¥, and Christine Queitsch¥ (¥ co-corresponding authors)
Hsp90 promotes kinase evolution
Molecular Biology and Evolution, 32(1), 91-99, 2015.(pdf)
»  Andrew B. Stergachis, Shane Neph, Richard Sandstrom, Eric Haugen, Alex P. Reynolds, Miaohua Zhang, Rachel Byron, Theresa Canfield, Sandra Stelhing-Sun, Kristen Lee, Robert E. Thurman, Shinny Vong, Daniel Bates, Fidencio Neri, Morgan Diegel, Erika Giste, Douglas Dunn, Jeff Vierstra, R. Scott Hansen, Audra K. Johnson, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Piper M. Treuting, Rajinder Kaul, Mark Groudine, M. A. Bender, Elhanan Borenstein, and John A. Stamatoyannopoulos
Conservation of trans-acting circuitry during mammalian regulatory evolution
Nature, 515, 365-370, 2014.(pdf)
  §  Featured in Nature News & Views
§  Featured in Science Daily
»  Rogan Carr and Elhanan Borenstein
Comparative analysis of functional metagenomic annotation and the mappability of short reads
PLoS ONE, 9(8), 2014. (pdf, software)
»  Ohad Manor, Roie Levy, and Elhanan Borenstein
Mapping the inner workings of the microbiome: Genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome
Cell Metabolism, 20(5), 742-752, 2014. (pdf)
  §  Featured in Genetic Engineering & Biotechnology News (GEN)
»  Hsuan-Chao Chiu, Roie Levy, and Elhanan Borenstein
Emergent biosynthetic capacity in simple microbial communities
PLoS Computational Biology, 10(7), 2014. (pdf)
  §  Featured in Featured in Santa Fe Institute News
»  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
§  Highlighted in Nature Medicine - see Microbiome models, on computers and in lab dishes, see progress
§  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