Publications
Journal Papers
See also:
Diet-omics in the study of urban and rural crohn disease evolution (SOURCE) cohort
Tzipi Braun, Rui Feng, Amnon Amir, Nina Levhar, Hila Shacham, Ren Mao, Rotem Hadar, Itamar Toren, Yadid Algavi, Kathleen Abu-Saad, Shuoyu Zhuo, Gilat Efroni, Alona Malik, Orit Picard, Miri Yavzori, Bella Agranovich, Ta-Chiang Liu, Thaddeus S Stappenbeck, Lee Denson, Ofra Kalter-Leibovici, Eyal Gottlieb, Elhanan Borenstein, Eran Elinav, Minhu Chen, Shomron Ben-Horin, Yael Haberman
Nature Communications, 15:3764, 2024
Positive effects of diet-induced microbiome modification on GDM in mice following human faecal transfer
Sigal Frishman, Meital Nuriel-Ohayon, Sondra Turjeman, Yishay Pinto, Or Yariv, Kinneret Tenenbaum-Gavish, Yoav Peled, Eran Poran, Joseph Pardo, Rony Chen, Efrat Muller, Elhanan Borenstein, Moshe Hod, Yoram Louzoun, Betty Schwartz, Eran Hadar, Maria Carmen Collado, Omry Koren
Gut, Online, 2024
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
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 gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis
Efrat Muller, Yadid M Algavi, Elhanan Borenstein
npj Biofilms and Microbiomes, 8:79, 2022
Evaluation of cognitive function in the Dog Aging Project: associations with baseline canine characteristics
Scientific Reports, 12, 13316, 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
Once-daily feeding is associated with better health in companion dogs: results from the Dog Aging Project
Emily E. Bray, Zihan Zheng, M. Katherine Tolbert, Brianah M. McCoy, The Dog Aging Project Consortium, Matt Kaeberlein, Kathleen F. Kerr
GeroScience, 44, 1779–1790, 2022
An open science study of ageing in companion dogs
Kate E. Creevy, Joshua M. Akey, Matt Kaeberlein, Daniel E. L. Promislow, The Dog Aging Project Consortium
Nature, 602, 51–57, 2022
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
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
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
§ Featured in Genetic Engineering & Biotechnology News
§ Featured in Science Daily
§ Featured in HHMI News
§ Featured in TAU Safra News
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
§ 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
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
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
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
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
§ Featured in This Week in Microbiology (ASM Podcast): Covert pathogenesis
§ Featured in UW Medicine Newsroom
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
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)
§ 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
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
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
An algorithm for designing minimal microbial communities with desired metabolic capacities
Alexander Eng, Elhanan Borenstein
Bioinformatics, btw107, 2016
§ Featured in IEEE Pulse (Deciphering the Mysterious Microbiome)
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
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
§ Featured in Genetic Engineering & Biotechnology News (GEN)
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
§ 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
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
§ Featured in Science Daily
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
§ Featured in Genetic Engineering & Biotechnology News (GEN)
Emergent biosynthetic capacity in simple microbial communities
Hsuan-Chao Chiu, Roie Levy, Elhanan Borenstein
PLoS Computational Biology, 10 (7), e1003695, 2014
§ Featured in Featured in Santa Fe Institute News
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
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
§ Recommended by Faculty of 1000
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
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
§ Featured in UW Today
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
§ Featured in UW Today
§ Featured in Science Daily
§ Featured in The Seattle Times;
§ Highlighted in Nature Reviews Microbiology - see Metagenomics with guts
Computational systems biology and in silico modeling of the human microbiome
Elhanan Borenstein
Briefings in Bioinformatics, 13(6), 769-780, 2012
§ Recommended by Faculty of 1000
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
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