| Year |
Citation |
Score |
| 2022 |
Noecker C, Eng A, Muller E, Borenstein E. MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. Bioinformatics (Oxford, England). PMID 34999748 DOI: 10.1093/bioinformatics/btac003 |
0.342 |
|
| 2020 |
Shouval R, Eshel A, Dubovski B, Kuperman AA, Danylesko I, Fein JA, Fried S, Geva M, Kouniavski E, Neuman H, Armon-Omer A, Shahien R, Muller E, Noecker C, Borenstein E, et al. Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation. Blood Advances. 4: 2912-2917. PMID 32598476 DOI: 10.1182/Bloodadvances.2020001827 |
0.339 |
|
| 2019 |
Noecker C, Chiu HC, McNally CP, Borenstein E. Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies. Msystems. 4. PMID 31848305 DOI: 10.1128/mSystems.00579-19 |
0.326 |
|
| 2019 |
Ross BD, Verster AJ, Radey MC, Schmidtke DT, Pope CE, Hoffman LR, Hajjar AM, Peterson SB, Borenstein E, Mougous JD. Human gut bacteria contain acquired interbacterial defence systems. Nature. PMID 31666699 DOI: 10.1038/S41586-019-1708-Z |
0.44 |
|
| 2019 |
Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, ... ... Borenstein E, et al. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell. 177: 1600-1618.e17. PMID 31150625 DOI: 10.1016/J.Cell.2019.05.004 |
0.322 |
|
| 2019 |
Eng A, Borenstein E. Microbial community design: methods, applications, and opportunities. Current Opinion in Biotechnology. 58: 117-128. PMID 30952088 DOI: 10.1016/J.Copbio.2019.03.002 |
0.326 |
|
| 2019 |
Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR. Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. Cell Reports. 26: 2227-2240.e5. PMID 30784601 DOI: 10.1016/J.Celrep.2019.01.091 |
0.307 |
|
| 2018 |
Verster AJ, Borenstein E. Competitive lottery-based assembly of selected clades in the human gut microbiome. Microbiome. 6: 186. PMID 30340536 DOI: 10.1186/S40168-018-0571-8 |
0.424 |
|
| 2018 |
McNally CP, Borenstein E. Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss. Bmc Systems Biology. 12: 69. PMID 29907104 DOI: 10.1186/S12918-018-0588-4 |
0.444 |
|
| 2018 |
Rebollar EA, Gutiérrez-Preciado A, Noecker C, Eng A, Hughey MC, Medina D, Walke JB, Borenstein E, Jensen RV, Belden LK, Harris RN. The Skin Microbiome of the Neotropical Frog: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data. Frontiers in Microbiology. 9: 466. PMID 29615997 DOI: 10.3389/Fmicb.2018.00466 |
0.419 |
|
| 2018 |
McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E. BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data. Frontiers in Microbiology. 9: 365. PMID 29545787 DOI: 10.3389/Fmicb.2018.00365 |
0.325 |
|
| 2018 |
Eng A, Borenstein E. Taxa-function robustness in microbial communities. Microbiome. 6: 45. PMID 29499759 DOI: 10.1186/S40168-018-0425-4 |
0.391 |
|
| 2018 |
Matamouros S, Hayden HS, Hager KR, Brittnacher MJ, Lachance K, Weiss EJ, Pope CE, Imhaus AF, McNally CP, Borenstein E, Hoffman LR, Miller SI. Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 29378945 DOI: 10.1073/Pnas.1714373115 |
0.3 |
|
| 2017 |
Verster AJ, Ross BD, Radey MC, Bao Y, Goodman AL, Mougous JD, Borenstein E. The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition. Cell Host & Microbe. 22: 411-419.e4. PMID 28910638 DOI: 10.1016/J.Chom.2017.08.010 |
0.345 |
|
| 2017 |
Whitney JC, Peterson SB, Kim J, Pazos M, Verster AJ, Radey MC, Kulasekara HD, Ching MQ, Bullen NP, Bryant D, Goo YA, Surette MG, Borenstein E, Vollmer W, Mougous JD. A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. Elife. 6. PMID 28696203 DOI: 10.7554/Elife.26938 |
0.399 |
|
| 2017 |
Manor O, Borenstein E. Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome. Microbiome. 5: 19. PMID 28179006 DOI: 10.1186/S40168-017-0231-4 |
0.446 |
|
| 2017 |
Mosites E, Sammons M, Otiang E, Eng A, Noecker C, Manor O, Hilton S, Thumbi SM, Onyango C, Garland-Lewis G, Call DR, Njenga MK, Wasserheit JN, Zambriski JA, Walson JL, ... ... Borenstein E, et al. Microbiome sharing between children, livestock and household surfaces in western Kenya. Plos One. 12: e0171017. PMID 28152044 DOI: 10.1371/Journal.Pone.0171017 |
0.311 |
|
| 2017 |
Manor O, Borenstein E. Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. Cell Host & Microbe. PMID 28111203 DOI: 10.1016/J.Chom.2016.12.014 |
0.367 |
|
| 2016 |
Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, et al. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nature Microbiology. 2: 16221. PMID 27892936 DOI: 10.1038/Nmicrobiol.2016.221 |
0.418 |
|
| 2016 |
Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Translational Research : the Journal of Laboratory and Clinical Medicine. PMID 27513210 DOI: 10.1016/J.Trsl.2016.07.012 |
0.429 |
|
| 2016 |
Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. Msystems. 1. PMID 27239563 DOI: 10.1128/mSystems.00013-15 |
0.369 |
|
| 2016 |
Press MO, Queitsch C, Borenstein E. Evolutionary assembly patterns of prokaryotic genomes. Genome Research. PMID 27197212 DOI: 10.1101/Gr.200097.115 |
0.39 |
|
| 2016 |
Eng A, Borenstein E. An algorithm for designing minimal microbial communities with desired metabolic capacities. Bioinformatics (Oxford, England). PMID 27153571 DOI: 10.1093/Bioinformatics/Btw107 |
0.35 |
|
| 2016 |
Mosites E, Mwangi T, Otiang E, Garland-Lewis G, Sammons M, Onyango C, Eng A, Noecker C, Manor O, Hilton S, Call D, Kariuki N, Zambriski J, Wasserheit J, Walson J, ... ... Borenstein E, et al. Characterising the taxonomic composition of children and livestock gut microbiomes and of environmental samples and the potential role for household-level microbiome sharing in western Kenya The Lancet Global Health. 4: S20. DOI: 10.1016/S2214-109X(16)30025-0 |
0.313 |
|
| 2015 |
Levy R, Carr R, Kreimer A, Freilich S, Borenstein E. NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. Bmc Bioinformatics. 16: 164. PMID 25980407 DOI: 10.1186/S12859-015-0588-Y |
0.464 |
|
| 2015 |
Manor O, Borenstein E. MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biology. 16: 53. PMID 25885687 DOI: 10.1186/S13059-015-0610-8 |
0.382 |
|
| 2015 |
Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell. 160: 583-94. PMID 25640238 DOI: 10.1016/J.Cell.2014.12.038 |
0.722 |
|
| 2015 |
Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H. Where next for microbiome research? Plos Biology. 13: e1002050. PMID 25602283 DOI: 10.1371/Journal.Pbio.1002050 |
0.353 |
|
| 2015 |
Hormozdiari F, Penn O, Borenstein E, Eichler EE. The discovery of integrated gene networks for autism and related disorders. Genome Research. 25: 142-54. PMID 25378250 DOI: 10.1101/Gr.178855.114 |
0.377 |
|
| 2014 |
Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, ... ... Borenstein E, et al. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature. 515: 365-70. PMID 25409825 DOI: 10.1038/Nature13972 |
0.384 |
|
| 2014 |
Manor O, Levy R, Borenstein E. Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome. Cell Metabolism. 20: 742-52. PMID 25176148 DOI: 10.1016/J.Cmet.2014.07.021 |
0.426 |
|
| 2014 |
Carr R, Borenstein E. Comparative analysis of functional metagenomic annotation and the mappability of short reads. Plos One. 9: e105776. PMID 25148512 DOI: 10.1371/Journal.Pone.0105776 |
0.352 |
|
| 2014 |
Chiu HC, Levy R, Borenstein E. Emergent biosynthetic capacity in simple microbial communities. Plos Computational Biology. 10: e1003695. PMID 24992662 DOI: 10.1371/Journal.Pcbi.1003695 |
0.457 |
|
| 2014 |
Levy R, Borenstein E. Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules. Gut Microbes. 5: 265-70. PMID 24637600 DOI: 10.4161/Gmic.28261 |
0.5 |
|
| 2013 |
Carr R, Shen-Orr SS, Borenstein E. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. Plos Computational Biology. 9: e1003292. PMID 24146609 DOI: 10.1371/Journal.Pcbi.1003292 |
0.408 |
|
| 2013 |
Press MO, Li H, Creanza N, Kramer G, Queitsch C, Sourjik V, Borenstein E. Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90. Plos Genetics. 9: e1003631. PMID 23874229 DOI: 10.1371/Journal.Pgen.1003631 |
0.319 |
|
| 2013 |
Levy R, Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proceedings of the National Academy of Sciences of the United States of America. 110: 12804-9. PMID 23858463 DOI: 10.1073/Pnas.1300926110 |
0.504 |
|
| 2013 |
Greenblum S, Chiu HC, Levy R, Carr R, Borenstein E. Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. Current Opinion in Biotechnology. 24: 810-20. PMID 23623295 DOI: 10.1016/J.Copbio.2013.04.001 |
0.723 |
|
| 2012 |
O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, ... ... Borenstein E, et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science (New York, N.Y.). 338: 1619-22. PMID 23160955 DOI: 10.1126/Science.1227764 |
0.328 |
|
| 2012 |
Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell. 150: 1274-86. PMID 22959076 DOI: 10.1016/J.Cell.2012.04.040 |
0.33 |
|
| 2012 |
Levy R, Borenstein E. Reverse Ecology: from systems to environments and back. Advances in Experimental Medicine and Biology. 751: 329-45. PMID 22821465 DOI: 10.1007/978-1-4614-3567-9_15 |
0.43 |
|
| 2012 |
Kreimer A, Doron-Faigenboim A, Borenstein E, Freilich S. NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species. Bioinformatics (Oxford, England). 28: 2195-7. PMID 22668793 DOI: 10.1093/Bioinformatics/Bts323 |
0.396 |
|
| 2012 |
Borenstein E. Computational systems biology and in silico modeling of the human microbiome. Briefings in Bioinformatics. 13: 769-80. PMID 22589385 DOI: 10.1093/Bib/Bbs022 |
0.481 |
|
| 2012 |
Pinho R, Borenstein E, Feldman MW. Most networks in Wagner's model are cycling. Plos One. 7: e34285. PMID 22511935 DOI: 10.1371/Journal.Pone.0034285 |
0.339 |
|
| 2012 |
Carr R, Borenstein E. NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. Bioinformatics (Oxford, England). 28: 734-5. PMID 22219204 DOI: 10.1093/Bioinformatics/Btr721 |
0.329 |
|
| 2012 |
Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proceedings of the National Academy of Sciences of the United States of America. 109: 594-9. PMID 22184244 DOI: 10.1073/Pnas.1116053109 |
0.734 |
|
| 2010 |
Cai JJ, Borenstein E, Petrov DA. Broker genes in human disease. Genome Biology and Evolution. 2: 815-25. PMID 20937604 DOI: 10.1093/Gbe/Evq064 |
0.555 |
|
| 2010 |
Freilich S, Kreimer A, Borenstein E, Gophna U, Sharan R, Ruppin E. Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. Plos Computational Biology. 6: e1000690. PMID 20195496 DOI: 10.1371/Journal.Pcbi.1000690 |
0.458 |
|
| 2009 |
Cai JJ, Borenstein E, Chen R, Petrov DA. Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution. 1: 131-44. PMID 20333184 DOI: 10.1093/Gbe/Evp013 |
0.528 |
|
| 2009 |
Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, Ruppin E. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biology. 10: R61. PMID 19500338 DOI: 10.1186/Gb-2009-10-6-R61 |
0.426 |
|
| 2009 |
Borenstein E, Feldman MW. Topological signatures of species interactions in metabolic networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 191-200. PMID 19178139 DOI: 10.1089/Cmb.2008.06Tt |
0.46 |
|
| 2008 |
Borenstein E, Krakauer DC. An end to endless forms: epistasis, phenotype distribution bias, and nonuniform evolution. Plos Computational Biology. 4: e1000202. PMID 18949026 DOI: 10.1371/Journal.Pcbi.1000202 |
0.418 |
|
| 2008 |
Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proceedings of the National Academy of Sciences of the United States of America. 105: 14482-7. PMID 18787117 DOI: 10.1073/Pnas.0806162105 |
0.396 |
|
| 2008 |
Kreimer A, Borenstein E, Gophna U, Ruppin E. The evolution of modularity in bacterial metabolic networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 6976-81. PMID 18460604 DOI: 10.1073/Pnas.0712149105 |
0.415 |
|
| 2007 |
Borenstein E, Shlomi T, Ruppin E, Sharan R. Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. Nucleic Acids Research. 35: e7. PMID 17158152 DOI: 10.1093/Nar/Gkl792 |
0.402 |
|
| 2006 |
Borenstein E, Meilijson I, Ruppin E. The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes. Journal of Evolutionary Biology. 19: 1555-70. PMID 16910985 DOI: 10.1111/J.1420-9101.2006.01125.X |
0.322 |
|
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