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Journal Papers

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Multi-omic integration of microbiome data for identifying disease-associated modules

Eftat Muler, Itamar Shiryan, Elhanan Borenstein

Nature Communications, 15 (1), 2621, 2024


Positive effects of diet-induced microbiome modification on GDM in mice following human faecal transfer

Gut, Online, 2024


A manifold-based framework for studying the dynamics of the vaginal microbiome

Mor Tsamir-Rimon, Elhanan Borenstein

npj Biofilms and Microbiomes, 9 (1), 102, 2023


A data-driven approach for predicting the impact of drugs on the human microbiome

Yadid Algavi, Elhanan Borenstein

Nature Communications, 14 (1), 3614, 2023


Development and validation of a novel instrument to capture companion dog mortality data: the Dog Aging Project End of Life Survey

Kellyn E. McNulty, Kate E. Creevy, Annette Fitzpatrick, Vanessa Wilkins, Brian G. Barnett, Dog Aging Project Consortium, Audrey Ruple

Journal of the American Veterinary Medical Association, 261(9), 2023


Associations between physical activity and cognitive dysfunction in older companion dogs: Results from the Dog Aging Project

Emily E Bray, David A Raichlen, Kiersten K Forsyth, Daniel EL Promislow, Gene E Alexander, Evan L MacLean, Dog Aging Project Consortium

GeroScience, 45(2), 645-661, 2023


Banking on a new understanding: translational opportunities from veterinary biobanks

D LaLonde-Paul, L Mouttham, Dog Aging Project Consortium, DEL Promislow, MG Castelhano

GeroScience, 45, 1439–1450, 2023


A chemically controlled Cas9 switch enables temporal modulation of diverse effectors

Cindy T Wei, Nicholas A Popp, Omri Peleg, Rachel L Powell, Elhanan Borenstein, Dustin J Maly, Douglas M Fowler

Nature Chemical Biology, 19, 981–991, 2023


Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis

Yishay Pinto, Sigal Frishman, Sondra Turjeman, Adi Eshel, Meital Nuriel-Ohayon, Oshrit Shtossel, Oren Ziv, William Walters, Julie Parsonnet, Catherine Ley, Elizabeth L Johnson, Krithika Kumar, Ron Schweitzer, Soliman Khatib, Faiga Magzal, Efrat Muller, Snait Tamir, Kinneret Tenenbaum-Gavish, Samuli Rautava, Seppo Salminen, Erika Isolauri, Or Yariv, Yoav Peled, Eran Poran, Joseph Pardo, Rony Chen, Moshe Hod, Elhanan Borenstein, Ruth E Ley, Betty Schwartz, Yoram Louzoun, Eran Hadar, Omry Koren

Gut, 72:918-928, 2023


Lifetime prevalence of owner-reported medical conditions in the 25 most common dog breeds in the Dog Aging Project pack

Kiersten K. Forsyth, Brianah M. McCoy, Sarah M. Schmid, Daniel E. L. Promislow, Noah Snyder-Mackler,  The Dog Aging Project Consortium, Kate E. Creevy

Frontiers in Veterinary Science, 10, 2023


The microbiome’s fiber degradation profile and its relationship with the host diet

Yotam Cohen, Elhanan Borenstein

BMC biology, 20 (1), 1-14, 2022


The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis

Efrat Muller, Yadid M Algavi, Elhanan Borenstein


Integrating phylogenetic and functional data in microbiome studies

Gavin M Douglas, Molly G Hayes, Morgan GI Langille, Elhanan Borenstein

Bioinformatics, 38, 22, 5055–5063, 2022


Evaluation of cognitive function in the Dog Aging Project: associations with baseline canine characteristics

Scientific Reports, 12, 13316, 2022


Temporal Alignment of Longitudinal Microbiome Data

Ran Armoni, Elhanan Borenstein

Frontiers in Microbiology, 13, 2022


Lifetime prevalence of malignant and benign tumors in companion dogs: cross‐sectional analysis of Dog Aging Project (DAP) baseline survey

Stephen M Schwartz, Silvan R Urfer, Michelle White, Kate Megquier, Sandi Shrager, The Dog Aging Project Consortium, Audrey Ruple

Veterinary and Comparative Oncology, 20, 4, 797-804, 2022


Age and Physical Activity Levels in Companion Dogs: Results From the Dog Aging Project

Hannah Lee, Devin Collins, Kate E Creevy, Daniel E L Promislow, The Dog Aging Project Consortium

The Journals of Gerontology: Series A, 77, 10, 1986–1993, 2022


Once-daily feeding is associated with better health in companion dogs: results from the Dog Aging Project

GeroScience, 44, 1779–1790, 2022


An open science study of ageing in companion dogs

Nature, 602, 51–57, 2022


Associations between Neighborhood Disadvantage and Dog Walking among Participants in the Dog Aging Project

Devin Collins, Hannah Lee, Matthew D. Dunbar, Kyle Crowder, The Dog Aging Project Consortium

International Journal of Environmental Research and Public Health, 19(18), 2022


Demographic factors associated with joint supplement use in dogs from the Dog Aging Project

Jessica M. Hoffman, M. Katherine Tolbert, Daniel E. L. Promislow, The Dog Aging Project Consortium

Frontiers in Veterinary Science, 9, 2022


MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data

Cecilia Noecker, Alexander Eng, Efrat Muller, Elhanan Borenstein

Bioinformatics, 38, 6, 1615–1623, 2022


A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations

Efar Muller, Yadid M Algavi, Elhanan Borenstein

Microbiome, 9 (1), 1-18, 2021


Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences

Alexander Eng, Hillary S Hayden, Christopher E Pope, Mitchell J Brittnacher, Anh T Vo, Eli J Weiss, Kyle R Hager, Daniel H Leung, Sonya L Heltshe, Daniel Raftery, Samuel I Miller, Lucas R Hoffman, Elhanan Borenstein

BMC microbiology, 21 (1), 1-17, 2021


Gastrointestinal Factors Associated With Hospitalization in Infants With Cystic Fibrosis: Results From the Baby Observational and Nutrition Study

Meghana Sathe, Rong Huang, Sonya Heltshe, Alexander Eng, Elhanan Borenstein, Samuel I Miller, Lucas Hoffman, Daniel Gelfond, Daniel H Leung, Drucy Borowitz, Bonnie Ramsey, A Jay Freeman

Journal of Pediatric Gastroenterology and Nutrition, 73 (3), 395-402, 2021


Microbial signature in IgE-mediated food allergies

Michael R Goldberg, Hadar Mor, Dafna Magid Neriya, Faiga Magzal, Efrat Muller, Michael Y Appel, Liat Nachshon, Elhanan Borenstein, Snait Tamir, Yoram Louzoun, Ilan Youngster, Arnon Elizur, Omry Koren

Genome medicine, 12 (1), 1-18, 2020


MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline

Alexander Eng, Adrian J Verster, Elhanan Borenstein

BMC bioinformatics, 21 (1), 1-9, 2020


The intestinal microbiome, weight, and metabolic changes in women treated by adjuvant chemotherapy for breast and gynecological malignancies

Atara Uzan-Yulzari, Maya Morr, Hala Tareef-Nabwani, Oren Ziv, Dafna Magid-Neriya, Ran Armoni, Efrat Muller, Anca Leibovici, Elhanan Borenstein, Yoram Louzoun, Ayelet Shai, Omry Koren

BMC Medicine, 18 (1), 1-10, 2020


Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation

Roni Shouval, Adi Eshel, Bar Dubovski, Amir A Kuperman, Ivetta Danylesko, Joshua A Fein, Shalev Fried, Mika Geva, Elizaveta Kouniavski, Hadar Neuman, Ayelet Armon-Omer, Radi Shahien, Efrat Muller, Cecilia Noecker, Elhanan Borenstein, Yoram Louzoun, Arnon Nagler, Omry Koren

Blood Advances, 4 (13), 2912-2917, 2020


Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome

Maria T Nelson, Daniel J Wolter, Alexander Eng, Eli J Weiss, Anh T Vo, Mitchell J Brittnacher, Hillary S Hayden, Sumedha Ravishankar, Gilbert Bautista, Anina Ratjen, Marcella Blackledge, Sharon McNamara, Laura Nay, Cheryl Majors, Samuel I Miller, Elhanan Borenstein, Richard H Simon, John J LiPuma, Luke R Hoffman

Thorax, 75:780-790, 2020


Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure

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)

Nature Medicine, 26, 215–221, 2020


Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies

Cecilia Noecker,Hsuan-Chao Chiu, Colin P. McNally,Elhanan Borenstein

mSystems, 4:e00579-19, 2019


Human gut bacteria contain acquired interbacterial defence systems

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)

Nature, 575, 224-228, 2019

§ Featured in UW Medicine Newsroom

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Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

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

Cell, 177:6, 1600-1618, 2019

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§  Featured in Tech Times, Medical News Today, Medical Xpress, Gizmag


Microbial community design: methods, applications, and opportunities

Alexander Eng, Elhanan Borenstein

Current Opinion in Biotechnology, 58:117-128, 2019


Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

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

Cell Reports, 26:8, 2019


2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century”

The 2017 NIH-wide microbiome workshop writing team

Microbiome, 7, 32, 2019


The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

Marie Lindefeldt, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, Stefanie Prast-Nielsen

npj Biofilms and Microbiomes, 5:5, 2019


Competitive lottery-based assembly of selected clades in the human gut microbiome

Adrian J Verster, Elhanan Borenstein

Microbiome, 6, 186, 2018


Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss

Colin P McNally, Elhanan Borenstein

BMC Systems Biology, 12 (1), 69, 2018


The skin microbiome of the Neotropical frog Craugastor fitzingeri: Inferring potential bacterial-host-pathogen interactions from metagenomic data

Eria Alaide Rebollar, Ana Gutiérrez-Preciado, Cecilia Noecker, Alexander Eng, Myra Hughey, Daniel Medina, Jenifer B Walke, Elhanan Borenstein, Roderick V Jensen, Lisa K Belden, Reid Harris

Frontiers in Microbiology, 9, 466, 2018


Taxa-function robustness in microbial communities

Alexander Eng, Elhanan Borenstein

Microbiome, 6 (45), 2018


BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data

Colin P McNally, Alexander Eng, Cecilia Noecker, William C Gagne-Maynard, Elhanan Borenstein

Frontiers in Microbiology, 9, 365, 2018


Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis

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, Samuel I Miller

Proceedings of the National Academy of Sciences, 115 (7), 1605-1610, 2018


The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition

Adrian Verster, Benjamin Ross, Matthew Radey, Yiqiao Bao, Andrew Goodman, Joseph Mougous, Elhanan Borenstein

Cell Host and Microbe, 22 (3), 411-419, 2017


A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

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, Joseph D Mougous

eLife, 6, e26938, 2017


Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome

Ohad Manor, Elhanan Borenstein

Microbiome, 5 (1), 19, 2017


Microbiome sharing between children, livestock and household surfaces in western Kenya

Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Cecilia Noecker, Ohad Manor, Sarah Hilton, Samuel M Thumbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R Call, M Kariuki Njenga, Judith N Wasserheit, Jennifer A Zambriski, Judd L Walson, Guy H Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M Rabinowitz

PLoS ONE, 12 (2), e0171017, 2017


Systematic characterization and analysis of the taxonomic drivers of functional shifts in the human microbiome

Ohad Manor, Elhanan Borenstein

Cell Host and Microbe, 21, 254-267, 2017

§ Featured in Science (Mining microbes: Creating genomic tools to fight disease)

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§ Featured on Cell Host and Microbe cover




Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

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, Jian-Hua Mao

Nature Microbiology, 2, 16221, 2017

§  Featured in Science Daily

§  Featured in PNNL News


High-Resolution Characterization of the Human Microbiome

Cecilia Noecker, Colin P McNally, Alexander Eng, Elhanan Borenstein

Translational Research, 179, 7-23, 2017


An alignment-free ‘metapeptide’strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing

Damon H May, Emma Timmins-Schiffman, Molly P Mikan, H Rodger Harvey, Elhanan Borenstein, Brook L Nunn, William Stafford Noble

Journal of Proteome Research, 15, 8, 2697–2705, 2016


Evolutionary assembly patterns of prokaryotic genomes

Maximilian O Press, Christine Queitsch, Elhanan Borenstein

Genome Research, 26 (6), 826-833, 2016


An algorithm for designing minimal microbial communities with desired metabolic capacities

Alexander Eng, Elhanan Borenstein

Bioinformatics, btw107, 2016


Getting Personal About Nutrition

Cecilia Noecker, Elhanan Borenstein

Trends in Molecular Medicine, 22 (2), 83–85, 2016


Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis

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)

Scientific Reports, 6, 22493, 2016


Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

Cecilia Noecker, Alexander Eng, Sujatha Srinivasan, Casey M Theriot, Vincent B Young, Janet K Jansson, David N Fredricks, Elhanan Borenstein

mSystems, 1 (1), e00013-15, 2016

§ mSystems Editor's Pick

§  Featured in IEEE Pulse (Deciphering the Mysterious Microbiome)


NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich, Elhanan Borenstein

BMC bioinformatics, 16 (1), 164, 2015


MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

Ohad Manor, Elhanan Borenstein

Genome Biology, 16 (53), 2015


Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

Sharon Greenblum, Rogan Carr, Elhanan Borenstein

Cell, 160 (4), 583-594, 2015

§ Featured in UW NewsBeat

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Where next for microbiome research?

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, Hamilton Smith

PLoS biology, 13 (1), e1002050, 2015


The discovery of integrated gene networks for autism and related disorders

Fereydoun Hormozdiari, Osnat Penn, Elhanan Borenstein, Evan Eichler

Genome Research, 25 (1), 142-154, 2015


Hsp90 promotes kinase evolution

Jennifer Lachowiec, Tzitziki Lemus, Elhanan Borenstein¥, and Christine Queitsch¥ (¥ co-corresponding authors)

Molecular Biology and Evolution, 32 (1), 91-99, 2015


Conservation of trans-acting circuitry during mammalian regulatory evolution

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, MA Bender, Elhanan Borenstein, John A Stamatoyannopoulos

Nature, 515 (7527), 365-370, 2014

§ Featured in Nature News & Views

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Mapping the Inner Workings of the Microbiome: Genomic-and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

Ohad Manor, Roie Levy, Elhanan Borenstein

Cell Metabolism, 20 (5), 742-752, 2014


Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

Rogan Carr, Elhanan Borenstein

PLoS ONE, 9 (8), e105776, 2014


Emergent biosynthetic capacity in simple microbial communities

Hsuan-Chao Chiu, Roie Levy, Elhanan Borenstein

PLoS Computational Biology, 10 (7), e1003695, 2014


Metagenomic systems biology and metabolic modeling of the human microbiome: From species composition to community assembly rules

Roie Levy, Elhanan Borenstein

Gut Microbes, 5 (2), 23-22, 2014


Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis

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, Samuel I Miller

Clinical Infectious Diseases, 58 (3), 396-399, 2014


Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

Rogan Carr, Shai S Shen-Orr, Elhanan Borenstein

PLoS Computational Biology, 9 (10), e1003292, 2013

§  Recommended by Faculty of 1000


Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

Sharon Greenblum, Hsuan-Chao Chiu, Roie Levy, Rogan Carr, Elhanan Borenstein

Current Opinion in Biotechnology, 24 (4), 810-820, 2013


Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

Roie Levy, Elhanan Borenstein

Proceedings of the National Academy of Sciences, 110 (31), 12804-12809, 2013

§  Featured in UW Today

§  Highlighted in Nature Medicine - see Microbiome models, on computers and in lab dishes, see progress

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Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90

Maximilian O. Press*, Hui Li*, Nicole Creanza, Gunter Kramer, Christine Queitsch¥, Victor Sourjik¥, Elhanan Borenstein¥ (* equal contribution; ¥ co-corresponding authors)

PLoS genetics, 9 (7), e1003631, 2013


Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

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, Jay Shendure

Science, 338, 1619-1622, 2012


Circuitry and dynamics of human transcription factor regulatory networks

Shane Neph, Andrew B. Stergachis, Alex Reynolds, Richard Sandstrom, Elhanan Borenstein¥ and John A. Stamatoyannopoulos¥ (¥ co-corresponding authors)

Cell, 150(6), 1274-1286, 2012

§  Featured in The Seattle Times

§  Featured in UW Today


NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species

Anat Kreimer, Adi Doron-Faigenboim, Elhanan Borenstein, Shiri Freilich

Bioinformatics, 28 (16), 2195-2197, 2012


Most Networks in Wagner's Model Are Cycling

Ricardo Pinho, Elhanan Borenstein, Marcus W Feldman

PLoS ONE, 7(4), e34285, 2012


Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

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, Evan E Eichler

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

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NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

Rogan Carr, Elhanan Borenstein

Bioinformatics, 28(5), 734-735, 2012


Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

Sharon Greenblum, Peter J Turnbaugh, Elhanan Borenstein

PNAS (Proc. Natl. Acad. Sci. USA), 109(2), 594-599, 2012

§  Featured in This Week in PNAS

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§  Highlighted in Nature Reviews Microbiology - see Metagenomics with guts


Reverse ecology: from systems to environments and back

Roie Levy, Elhanan Borenstein

Advances in Experimental Medicine and Biology, 751, 329-345, 2012


Computational systems biology and in silico modeling of the human microbiome

Elhanan Borenstein

Briefings in Bioinformatics, 13(6), 769-780, 2012

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Decoupling environment-dependent and independent genetic robustness across bacterial species

Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin

PLoS Computational Biology, 6(2), 2010


Broker genes in human disease

James J. Cai, Elhanan Borenstein, Dmitri A. Petrov

Genome Biology and Evolution, 2, 815-825, 2010


Metabolic-network-driven analysis of bacterial ecological strategies

Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin

Genome Biology, 10(6):R61, 2009


Topological signatures of species interactions in metabolic networks

Elhanan Borenstein, Marcus W Feldman

Journal of Computational Biology, 16(2), 191-200, 2009

§ 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


Similarly strong purifying selection acts on human disease genes of all evolutionary ages

James J Cai, Elhanan Borenstein, Rong Chen, Dmitri A Petrov

Genome Biology and Evolution, 1(1), 131-144, 2009


Social and individual learning of helping in humans and other species

Laurent Lehmann, Kevin R Foster, Elhanan Borenstein, Marcus W Feldman

Trends in Ecology and Evolution, 23(12), 664-671, 2008


An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution

Elhanan Borenstein, David C Krakauer

PLoS Computational Biology, 4(10), 2008

§  Featured in Nature Reviews Genetics - see Modelling the evolutionarily possible


Large-scale reconstruction and phylogenetic analysis of metabolic environments

Elhanan Borenstein, Martin Kupiec, Marcus W Feldman, Eytan Ruppin

PNAS (Proc. Natl. Acad. Sci. USA), 105(38), 14482-14487, 2008

§ Featured in Genome Biology, 9:239, 2008 - see Network-based approaches for linking metabolism with environment

§ Recommended by Faculty of 1000


The evolution of modularity in bacterial metabolic networks

Anat Kreimer, Elhanan Borenstein, Uri Gophna, Eytan Ruppin

PNAS (Proc. Natl. Acad. Sci. USA), 105(19), 6976-6981, 2008


Evolution of learning in fluctuating environments: when selection favors both social and exploratory individual learning

Elhanan Borenstein, Marcus W Feldman, Kenichi Aoki

Evolution, 62(3), 586-602, 2008


Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Elhanan Borenstein, Tomer Shlomi, Eytan Ruppin, Roded Sharan

Nucleic Acids Research, 35(1), e7, 2007


Cultural niche construction in a metapopulation

Elhanan Borenstein, Jeremy Kendal, Marcus Feldman

Theoretical Population Biology, 70(1), 92-104, 2006


The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes

Elhanan Borenstein, Isaac Meilijson, Eytan Ruppin

Journal of Evolutionary Biology, 19(5), 1555-1570, 2006


Direct evolution of genetic robustness in microRNA

Elhanan Borenstein, Eytan Ruppin

PNAS (Proc. Natl. Acad. Sci. USA), 103(17), 6593-6598, 2006


The evolution of imitation and mirror neurons in adaptive agents

Elhanan Borenstein, Eytan Ruppin

Cognitive Systems Research (special issue on Epigenetic Robotics), 6(3), 229-242, 2005


The evolutionary link between mirror neurons and imitation: An evolutionary adaptive agents model

Elhanan Borenstein, Eytan Ruppin

Behavioral and Brain Sciences, 28:2, 127-128, 2005


Cellular automata Model of cystogenesis and tubulogenesis

Elhanan Borenstein, Erin Cline

Proceedings of the Santa-Fe Institute Complex Systems Summer School, 2004


Evolving imitating agents and the emergence of a neural mirror system

Elhanan Borenstein, Eytan Ruppin

Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9), 2004


Enhancing autonomous agents evolution with learning by imitation

Elhanan Borenstein, Eytan Ruppin

Journal of Artificial Intelligence and the Simulation of Behaviour (AISBJ), 1(4), 335-347, 2003

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