Daniel Segrè, Ph.D. - Publications

Bioinformatics GRS Boston University, Boston, MA, United States 
Bioinformatics Biology, Ecology Biology, Microbiology Biology

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Goldford JE, Hartman H, Marsland R, Segrè D. Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. Nature Ecology & Evolution. PMID 31712697 DOI: 10.1038/S41559-019-1018-8  1
2019 Lancet D, Segrè D, Kahana A. Twenty Years of "Lipid World": A Fertile Partnership with David Deamer. Life (Basel, Switzerland). 9. PMID 31547028 DOI: 10.3390/Life9040077  1
2019 Saifuddin M, Bhatnagar JM, Segrè D, Finzi AC. Microbial carbon use efficiency predicted from genome-scale metabolic models. Nature Communications. 10: 3568. PMID 31395870 DOI: 10.1038/S41467-019-11488-Z  0.01
2019 Bernstein DB, Dewhirst FE, Segre D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. Elife. 8. PMID 31194675 DOI: 10.7554/Elife.39733  1
2019 Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. Fems Microbiology Letters. PMID 31187139 DOI: 10.1093/Femsle/Fnz125  1
2019 Pacheco AR, Moel M, Segrè D. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nature Communications. 10: 103. PMID 30626871 DOI: 10.1038/S41467-018-07946-9  1
2019 Bernstein DB, Dewhirst FE, Segrè D. Author response: Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome Elife. DOI: 10.7554/Elife.39733.031  1
2018 Maoz BM, Herland A, FitzGerald EA, Grevesse T, Vidoudez C, Pacheco AR, Sheehy SP, Park TE, Dauth S, Mannix R, Budnik N, Shores K, Cho A, Nawroth JC, Segrè D, et al. A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells. Nature Biotechnology. PMID 30125269 DOI: 10.1038/Nbt.4226  1
2018 Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, Segrè D, Mehta P, Sanchez A. Emergent simplicity in microbial community assembly. Science (New York, N.Y.). 361: 469-474. PMID 30072533 DOI: 10.1126/Science.Aat1168  1
2018 Hynes WF, Chacón J, Segrè D, Marx CJ, Cady NC, Harcombe WR. Bioprinting microbial communities to examine interspecies interactions in time and space Biomedical Physics & Engineering Express. 4: 055010. DOI: 10.1088/2057-1976/Aad544  0.01
2018 Goldford JE, Segrè D. Modern views of ancient metabolic networks Current Opinion in Systems Biology. 8: 117-124. DOI: 10.1016/J.Coisb.2018.01.004  1
2017 Zomorrodi AR, Segrè D. Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities. Nature Communications. 8: 1563. PMID 29146901 DOI: 10.1038/S41467-017-01407-5  1
2017 Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Reports. 20: 2666-2677. PMID 28903046 DOI: 10.1016/J.Celrep.2017.08.066  1
2017 Goldford JE, Hartman H, Smith TF, Segrè D. Remnants of an Ancient Metabolism without Phosphate. Cell. PMID 28262353 DOI: 10.1016/J.Cell.2017.02.001  1
2017 Jacobs C, Lambourne L, Xia Y, Segrè D. Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates. Plos One. 12: e0170164. PMID 28107392 DOI: 10.1371/Journal.Pone.0170164  1
2016 Zhao Q, Stettner AI, Reznik E, Paschalidis ICh, Segrè D. Mapping the landscape of metabolic goals of a cell. Genome Biology. 17: 109. PMID 27215445 DOI: 10.1186/S13059-016-0968-2  1
2016 Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. Plos Computational Biology. 12: e1004875. PMID 27081850 DOI: 10.1371/Journal.Pcbi.1004875  1
2016 Zomorrodi AR, Segrè D. Synthetic Ecology of Microbes: Mathematical Models and Applications. Journal of Molecular Biology. 428: 837-61. PMID 26522937 DOI: 10.1016/J.Jmb.2015.10.019  1
2015 Chubiz LM, Granger BR, Segrè D, Harcombe WR. Species interactions differ in their genetic robustness. Frontiers in Microbiology. 6: 271. PMID 25926820 DOI: 10.3389/Fmicb.2015.00271  1
2014 Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO. Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. Plos One. 9: e114608. PMID 25502413 DOI: 10.1371/Journal.Pone.0114608  1
2014 Brinsmade SR, Alexander EL, Livny J, Stettner AI, Segrè D, Rhee KY, Sonenshein AL. Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY. Proceedings of the National Academy of Sciences of the United States of America. 111: 8227-32. PMID 24843172 DOI: 10.1073/Pnas.1321308111  1
2014 Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Reports. 7: 1104-15. PMID 24794435 DOI: 10.1016/J.Celrep.2014.03.070  1
2013 Gomes AL, Galagan JE, Segrè D. Resource competition may lead to effective treatment of antibiotic resistant infections. Plos One. 8: e80775. PMID 24349015 DOI: 10.1371/Journal.Pone.0080775  1
2013 Mazumdar V, Amar S, Segrè D. Metabolic proximity in the order of colonization of a microbial community. Plos One. 8: e77617. PMID 24204896 DOI: 10.1371/Journal.Pone.0077617  1
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/Journal.Pbio.1001638  1
2013 Reznik E, Mehta P, Segrè D. Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools. Plos Computational Biology. 9: e1003195. PMID 24009492 DOI: 10.1371/Journal.Pcbi.1003195  1
2013 Reznik E, Chaudhary O, Segrè D. The average enzyme principle. Febs Letters. 587: 2891-4. PMID 23892076 DOI: 10.1016/J.Febslet.2013.07.032  1
2013 Stettner AI, Segrè D. The cost of efficiency in energy metabolism. Proceedings of the National Academy of Sciences of the United States of America. 110: 9629-30. PMID 23729810 DOI: 10.1073/Pnas.1307485110  1
2013 Reznik E, Kaper TJ, Segrè D. The dynamics of hybrid metabolic-genetic oscillators. Chaos (Woodbury, N.Y.). 23: 013132. PMID 23556969 DOI: 10.1063/1.4793573  1
2013 Reznik E, Yohe S, Segrè D. Invariance and optimality in the regulation of an enzyme. Biology Direct. 8: 7. PMID 23522082 DOI: 10.1186/1745-6150-8-7  1
2012 Collins SB, Reznik E, Segrè D. Temporal expression-based analysis of metabolism. Plos Computational Biology. 8: e1002781. PMID 23209390 DOI: 10.1371/Journal.Pcbi.1002781  1
2012 Byrne D, Dumitriu A, Segrè D. Comparative multi-goal tradeoffs in systems engineering of microbial metabolism. Bmc Systems Biology. 6: 127. PMID 23009214 DOI: 10.1186/1752-0509-6-127  1
2012 Chiu HC, Marx CJ, Segrè D. Epistasis from functional dependence of fitness on underlying traits. Proceedings. Biological Sciences / the Royal Society. 279: 4156-64. PMID 22896647 DOI: 10.1098/Rspb.2012.1449  1
2012 Jacobs C, Segrè D. Organization principles in genetic interaction networks. Advances in Experimental Medicine and Biology. 751: 53-78. PMID 22821453 DOI: 10.1007/978-1-4614-3567-9_3  1
2012 Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease Plos One. 7. PMID 22675498 DOI: 10.1371/Journal.Pone.0037919  1
2012 Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT. Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor. Plos One. 7: e30827. PMID 22319591 DOI: 10.1371/Journal.Pone.0030827  1
2011 Zampieri M, Legname G, Segrè D, Altafini C. A system-level approach for deciphering the transcriptional response to prion infection. Bioinformatics (Oxford, England). 27: 3407-14. PMID 22016408 DOI: 10.1093/Bioinformatics/Btr580  0.04
2011 Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science (New York, N.Y.). 332: 1190-2. PMID 21636771 DOI: 10.1126/Science.1203799  1
2011 Klitgord N, Segrè D. Ecosystems biology of microbial metabolism. Current Opinion in Biotechnology. 22: 541-6. PMID 21592777 DOI: 10.1016/J.Copbio.2011.04.018  1
2011 Snitkin ES, Segrè D. Epistatic interaction maps relative to multiple metabolic phenotypes. Plos Genetics. 7: e1001294. PMID 21347328 DOI: 10.1371/Journal.Pgen.1001294  1
2011 Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research. 39: D11-4. PMID 21097892 DOI: 10.1093/Nar/Gkq1168  1
2011 Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT. Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor. Bioresource Technology. 102: 2623-8. PMID 21036604 DOI: 10.1016/J.Biortech.2010.10.033  1
2010 Schütte M, Skupin A, Segrè D, Ebenhöh O. Modeling the complex dynamics of enzyme-pathway coevolution. Chaos (Woodbury, N.Y.). 20: 045115. PMID 21198127 DOI: 10.1063/1.3530440  1
2010 Klitgord N, Segrè D. Environments that induce synthetic microbial ecosystems. Plos Computational Biology. 6: e1001002. PMID 21124952 DOI: 10.1371/Journal.Pcbi.1001002  1
2010 Reznik E, Segrè D. On the stability of metabolic cycles. Journal of Theoretical Biology. 266: 536-49. PMID 20673772 DOI: 10.1016/J.Jtbi.2010.07.023  1
2010 Segrè D, Marx CJ. Introduction to focus issue: genetic interactions. Chaos (Woodbury, N.Y.). 20: 026101. PMID 20590330 DOI: 10.1063/1.3456057  1
2010 Riehl WJ, Krapivsky PL, Redner S, Segrè D. Signatures of arithmetic simplicity in metabolic network architecture. Plos Computational Biology. 6: e1000725. PMID 20369010 DOI: 10.1371/Journal.Pcbi.1000725  1
2010 Schuette M, Klitgord N, Segre D, Ebenhoeh O. Co-evolution of metabolism and protein sequences Genome Informatics. 22: 156-166. DOI: 10.1142/9781848165786_0013  1
2009 Mazumdar V, Snitkin ES, Amar S, Segrè D. Metabolic network model of a human oral pathogen. Journal of Bacteriology. 191: 74-90. PMID 18931137 DOI: 10.1128/Jb.01123-08  1
2008 Chiu HC, Segrè D. Comparative determination of biomass composition in differentially active metabolic States. Genome Informatics. International Conference On Genome Informatics. 20: 171-82. PMID 19425132 DOI: 10.1142/9781848163003_0015  1
2008 Riehl WJ, Segrè D. Optimal metabolic regulation using a constraint-based model. Genome Informatics. International Conference On Genome Informatics. 20: 159-70. PMID 19425131 DOI: 10.1142/9781848163003_0014  1
2008 Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segrè D. Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biology. 9: R140. PMID 18808699 DOI: 10.1186/Gb-2008-9-9-R140  1
2008 Snitkin ES, Segrè D. Optimality criteria for the prediction of metabolic fluxes in yeast mutants. Genome Informatics. 20: 123-134. DOI: 10.11234/Gi1990.20.123  1
2007 Wright MA, Kharchenko P, Church GM, Segrè D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proceedings of the National Academy of Sciences of the United States of America. 104: 10559-64. PMID 17563360 DOI: 10.1073/Pnas.0610776104  1
2007 Hu L, Segrè D, Smith TF. Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species. Genome Informatics. 18: 12-21. DOI: 10.11234/Gi1990.18.12  1
2006 Raymond J, Segrè D. The effect of oxygen on biochemical networks and the evolution of complex life. Science (New York, N.Y.). 311: 1764-7. PMID 16556842 DOI: 10.1126/Science.1118439  0.01
2005 Segrè D, Deluna A, Church GM, Kishony R. Modular epistasis in yeast metabolism. Nature Genetics. 37: 77-83. PMID 15592468 DOI: 10.1038/Ng1489  1
2005 Segrè D. Life as a chemical automaton Journal of Biogeography. 32: 1681-1681. DOI: 10.1111/J.1365-2699.2005.01297.X  0.01
2004 Segrè D. The regulatory software of cellular metabolism. Trends in Biotechnology. 22: 261-5. PMID 15158051 DOI: 10.1016/J.Tibtech.2004.04.013  0.01
2003 Segrè D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM. From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics : a Journal of Integrative Biology. 7: 301-16. PMID 14583118 DOI: 10.1089/153623103322452413  1
2002 Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proceedings of the National Academy of Sciences of the United States of America. 99: 15112-7. PMID 12415116 DOI: 10.1073/Pnas.232349399  1
2001 Segré D, Shenhav B, Kafri R, Lancet D. The molecular roots of compositional inheritance. Journal of Theoretical Biology. 213: 481-91. PMID 11735293 DOI: 10.1006/Jtbi.2001.2440  1
2001 Segré D, Ben-Eli D, Deamer DW, Lancet D. The lipid world. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 31: 119-45. PMID 11296516 DOI: 10.1023/A:1006746807104  1
2000 Gilad Y, Segré D, Skorecki K, Nachman MW, Lancet D, Sharon D. Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nature Genetics. 26: 221-4. PMID 11017082 DOI: 10.1038/79957  1
2000 Segré D, Ben-Eli D, Lancet D. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proceedings of the National Academy of Sciences of the United States of America. 97: 4112-7. PMID 10760281 DOI: 10.1073/Pnas.97.8.4112  1
1998 Segre D, Lancet D, Kedem O, Pilpel Y. Graded Autocatalysis Replication Domain (GARD): kinetic analysis of self-replication in mutually catalytic sets. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 28: 501-14. PMID 11536890 DOI: 10.1023/A:1006583712886  1
1998 Segré D, Pilpel Y, Lancet D. Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics Physica a: Statistical Mechanics and Its Applications. 249: 558-564. DOI: 10.1016/S0378-4371(97)00516-5  1
1996 Lancet D, Glusman G, Segré D, Kedem O, Pilpel Y. Self replication and chemical selection in primordial mutually catalytic sets Origins of Life and Evolution of the Biosphere. 26: 270-271. DOI: 10.1007/Bf02459752  0.04
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