{"id":18,"date":"2012-06-18T20:43:32","date_gmt":"2012-06-19T00:43:32","guid":{"rendered":"https:\/\/www.bu.edu\/segrelab\/?page_id=18"},"modified":"2026-06-13T12:20:06","modified_gmt":"2026-06-13T16:20:06","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.bu.edu\/segrelab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

2026<\/h2>\n

Franziska Kratzl, Helen Scott, Simran Jayasinghe, Kendall Hughes, Melisa Osborne, Daniel Sher, Daniel Segr\u00e8:\u00a0 Organizing principles in the Nitrogen\u2013Carbon Landscape of Marine Heterotrophic Bacteria, BioRxiv<\/strong> (2026) https:\/\/doi.org\/10.64898\/2026.06.04.730220 [BioRxiv<\/a>]<\/p>\n

Arian Ferrero*, Franziska P. Kratzl*, Liam Kelley, Kirill Korolev, Davide Masoero, Daniel Segr\u00e8#<\/sup>, Ilija Dukovski#<\/sup>, Daniele de Martino#<\/sup>: Reconstructing heterogeneous metabolic trajectories of E. coli<\/em> diauxie via a dynamical Maximum Entropy Principle, BioRxiv<\/strong> (2026) https:\/\/doi.org\/10.64898\/2026.05.28.728366 [BioRxiv<\/a>]<\/p>\n

Alvin Lu,\u00a0 Liam Kelley, Ilija Dukovski, Daniel Segr\u00e8: Dynamic metabolic modeling of ATP allocation during viral infection, Journal of the Royal Society Interface<\/strong> (2026)\u00a023 (235): 20250254 [Interface<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Devlin C. Moyer, Justin Reimertz, Juan I. Fuxman Bass, Daniel Segr\u00e8: Flux sampling and context-specific genome-scale metabolic models for biotechnological applications, Trends in Biotechnology<\/strong> (2026), Vol. 44, No. 2, Pages 315-332 [Trends in Biotech]<\/a><\/p>\n

Ling-Dong Shi,\u00a0 Maria Florencia Ercoli, Jack Kim, Artur Teixeira de Araujo Jr., Subah Soni, Tracy Satomi Weitz, Alexandra M. Shigenaga,\u00a0 Ilija Dukovski,\u00a0 Rohan Sachdeva, Halbay Turumtay,\u00a0 Katherine B. Louie,\u00a0 Benjamin P. Bowen,\u00a0 Henrik V. Scheller, Daniel Segr\u00e8,\u00a0 Trent R. Northen,\u00a0 Pamela C. Ronald,\u00a0 Jillian F. Banfield: Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling, Nature Communications<\/strong> (2026) In press [Nature Comm<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Tanya T. Karagiannis, Ye Chen, Sarah Bald, Albert Tai,\u00a0 Sofiya Milman,\u00a0 Stacy L. Andersen, Thomas T. Perls, Daniel Segr\u00e8,\u00a0 Paola Sebastiani,\u00a0 Meghan I. Short: Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study, PLOS Computational Biology<\/strong> (2026) 22(1): e1013883. [PLOS CB<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Sarah Bald*<\/sup>, Jing Zhang*<\/sup>, Rowan Nelson*<\/sup>, Dillon C Scott, Ilija Dukovski, Markus de Raad, Trent Northen, Daniel Segr\u00e8: Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia, BioRxiv<\/strong> (2026) https:\/\/doi.org\/10.64898\/2026.01.11.698878 [BioRxiv<\/a>]<\/p>\n

2025<\/h2>\n

Ziwei Huang, Paola Sebastiani,\u00a0 Daniel Segr\u00e8,\u00a0 Stefano Monti: hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models, BioRxiv<\/strong> (2025) https:\/\/doi.org\/10.64898\/2025.12.08.692998 [BioRxiv<\/a>]<\/p>\n

Waseem Bashir Valiya Kalladi, Melisa Osborne, Helen Scott, Franziska Kratzl, Carolina Alejandra Martinez Gutierrez, Elena Jean Forchielli, Natasha Gurevich, Joseline Margarita Velasquez-Reyes, Krupa Sampat, Luca Zoccaratto, Konrad Herbst, Osnat Weissberg, Hans-Peter Grossart,\u00a0 Daniel Segr\u00e8, Daniel Jonathan Sher: Biological insights and methodological challenges learned from working with a diverse heterotrophic marine bacterial library, BioRxiv<\/strong> (2025) https:\/\/doi.org\/10.1101\/2025.11.25.689180 [BioRxiv<\/a>]<\/p>\n

Silvia Abb\u00e0, Liam D Adair, Francesca Barbero, Luca P Casacci, Iljia Dukovski, Francisca Font, Tom Hawtrey, Elizabeth J New, Jukkrit Nootem, Pramsak Patawanich, Lukas Patten, Marco Polin, Daniel Segr\u00e8, Nian Kee Tan, Irene Stefanini: Wasp intestinal cues drive yeast toward outbreeding strategies, ISME Journal <\/strong>(2025), Volume 19, Issue 1, wraf243, [<\/span>https:\/\/doi.org\/10.1093\/ismejo\/wraf243<\/a>]<\/p>\n

Ilija Dukovski, Lauren Golden, Jing Zhang, Melisa Osborne, Daniel Segr\u00e8, Kirill Korolev: Biophysical metabolic modeling of complex bacterial colony morphology, Cell Systems<\/strong> (2025) Vol. 16, Issue 8, 20 August 2025, 101352 [Cell Systems<\/a>][Hariri Institute article<\/a>][Previous version on BioRxiv<\/a>]<\/span><\/p>\n

Hui Shi, Ercole LiPuma, Haroon Qureshi, Phineas McMillan, Jing Zhang, Melisa Osborne, Ilija Dukovski, Daniel Segr\u00e8: Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: Pseudomonas simiae<\/em> as a case study, BioRxiv<\/strong> (2025) https:\/\/doi.org\/10.1101\/2025.08.05.668800 [BioRxiv<\/a>]<\/p>\n

Devlin C Moyer,\u00a0 Justin Reimertz,\u00a0 Daniel Segr\u00e8,\u00a0 Juan I Fuxman Bass: MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models, Genome Biology<\/strong> (2025) 26<\/b>, <\/span>79 [Genome Biology<\/a>]<\/span>\u00a0[Previous version on BioRxiv<\/a>]<\/p>\n

Zoey Werbin,\u00a0 Ilija Dukovski, Dylan Mankel,\u00a0 Daniel Segr\u00e8,\u00a0 Jennifer Bhatnagar,\u00a0 Winston Anthony,\u00a0 Marianna Felici: Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database, BioRxiv<\/strong> (2025)\u00a0https:\/\/doi.org\/10.1101\/2025.03.21.644662 [BioRxiv<\/a>]<\/p>\n

Hui Peng, Sergei Kotelnikov, Megan E. Egbert, Shany Ofaim, Grant C. Stevens, Sadhna Phanse, Tatiana Saccon, Mikhail Ignatov, Shubham Dutta, Zoe Istace, Mohamed Taha Moutaoufik, Hiroyuki Aoki, Neal Kewalramani, Jianxian Sun, Yufeng Gong, Dzmitry Padhorny, Gennady Poda, Andrey Alekseenko, Kathryn A. Porter, George Jones, Irina Rodionova, Hongbo Guo, Oxana Pogoutse, Suprama Datta, Milton Saier, Mark Crovella, Sandor Vajda, Gabriel Moreno-Hagelsieb, John Parkinson, Daniel Segr\u00e8, Mohan Babu, Dima Kozakov, Andrew Emili: Ligand interaction landscape of transcription factors and essential enzymes in E.\u00a0coli<\/em>, Cell<\/strong> (2025), Volume 188, Issue 5, 6 March 2025, Pages 1441-1455.e15. [Cell<\/a>]<\/p>\n

2024<\/h2>\n

Helen Scott, Daniel Segr\u00e8: Metabolic Flux Modeling in Marine Ecosystems, Annual Review of Marine Science <\/strong>(2024) Vol. 17:593-620 [Annual Reviews<\/a>]<\/p>\n

Daniel Sher, Daniel Segr\u00e8, Michael J. Follows: Quantitative principles of microbial metabolism shared across scales,\u00a0 Nature Microbiology<\/strong> (2024) Vol. 9, pages 1940\u20131953 [Nature Microbiology<\/a>]<\/p>\n

Michael R Silverstein, Jennifer M Bhatnagar, Daniel Segr\u00e8: Metabolic complexity drives divergence in microbial communities, Nature Ecology & Evolution<\/strong> (2024) 8, pages 1493\u20131504 [Nature Ecol & Evol<\/a>][Hariri Institute Article<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Shira Givati, Elena Forchielli, Dikla Aharonovich, Noga Barak, Osnat Weissberg, Natalia Belkin, Eyal Rahav, Daniel Segr\u00e8, Daniel Sher: Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria, Applied and Environmental Microbiology<\/strong> (2024) 0:e00256-24, https:\/\/doi.org\/10.1128\/aem.00256-24 [Applied Env. Microbiol.<\/a>] [Previous version on BioRxiv<\/a>]<\/span><\/p>\n

Konrad Herbst*, Elena Forchielli*, Taiyao Wang*, Meghan Thommes*, Ioannis Ch Paschalidis#<\/sup>, Daniel Segr\u00e8#<\/sup>: Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations, Communications Biology <\/strong>(2024) 7, Article number: 407\u00a0[CommBio<\/a>] [Previous version on BioRxiv<\/a>]<\/span><\/p>\n

2023<\/h2>\n

Dileep Kishore, Gabriel Birzu, Zhenjun Hu, Charles DeLisi, Kirill Korolev, Daniel Segr\u00e8: Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation, mSystems<\/strong> (2023) https:\/\/doi.org\/10.1128\/msystems.00961-22 [mSystems<\/a>][MiCoNE<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Daniel Segr\u00e8 in Voices<\/em> – What do you most want to understand about how collective features emerge in microbial communities?, Cell Systems <\/strong>(2023), 14, February 15, p. 91. [Cell Systems<\/a>]<\/p>\n

Charles Jo*, David B Bernstein*, Natalie Vaisman, Horacio M Frydman, Daniel Segr\u00e8: Construction and modeling of a co-culture microplate for real-time measurement of microbial interactions, mSystems<\/strong> (2023), e00017-21. <\/span>[mSystems<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Michael Silverstein, Daniel Segr\u00e8, Jennifer M. Bhatnagar: Environmental microbiome engineering for the mitigation of climate change, Global Change Biology<\/strong> (2023), 00:1\u201317. https:\/\/doi.org\/10.1111\/gcb.16609. [GCB<\/a>]<\/p>\n

Charles Jo*, Jing Zhang*, Jenny M. Tam, George M. Church, Ahmad S. Khalil, Daniel Segr\u00e8, Tzu-Chieh Tang: Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability, Materials Today Bio<\/strong> (2023), Volume 19, April 2023, 100560. [Materials Today Bio<\/a>]<\/p>\n

2022<\/h2>\n

Alan R. Pacheco*, Charlie Pauvert*, Dileep Kishore, Daniel Segr\u00e8: Toward FAIR Representations of Microbial Interactions, mSystems<\/strong> (2022) e00659-22 [mSystems<\/a>]<\/p>\n

Zhenjun Hu, Dileep Kishore, Yan Wang, Gabriel Birzu, Charles DeLisi, Kirill Korolev, Daniel Segr\u00e8: A resource for the comparison and integration of heterogeneous microbiome networks, BioRxiv<\/strong> (2022) https:\/\/doi.org\/10.1101\/2022.08.07.503059 [BioRxiv<\/a>]<\/p>\n

Alexander Golden, Ilija Dukovski, Daniel Segr\u00e8, Kirill S. Korolev: Growth instabilities shape morphology and genetic diversity of microbial colonies, Physical Biology<\/strong> (2022) 19 056005 [Phys. Biol.<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Ali R Zomorrodi, Colin Hemez, Pol Arranz-Gibert, Terrence Wu, Farren J Isaacs, Daniel Segr\u00e8: Computational design and engineering of an Escherichia coli<\/em> strain producing the nonstandard amino acid para-aminophenylalanine, iScience<\/strong> (2022) 25, 104562 [iScience<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Elena J. Forchielli, Daniel J. Sher, Daniel Segr\u00e8: Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies, mSystems<\/strong> (2022) e00070-22 [mSystems<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Mary Ann Moran, Elizabeth B. Kujawinski, William F. Schroer, Shady A. Amin, Nicholas R. Bates, Erin M. Bertrand, Rogier Braakman, C. Titus Brown, Markus W. Covert, Scott C. Doney, Sonya T. Dyhrman, Arthur S. Edison, A. Murat Eren, Naomi M. Levine, Liang Li, Avena C. Ross, Mak A. Saito, Alyson E. Santoro, Daniel Segr\u00e8, Ashley Shade, Matthew B. Sullivan and Assaf Vardi: Microbial metabolites in the marine carbon cycle, Nature Microbiology<\/strong> (2022) 7, 508\u2013523 [Nature Microbiology<\/a>]<\/p>\n

Joshua E. Goldford, Ashish Bino George, Avi E. Flamholz, Daniel Segr\u00e8: Protein cost minimization promotes the emergence of coenzyme redundancy, Proc. Natl. Acad. Sci. USA<\/strong> (2022) 119 (14) e2110787119 [PNAS<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Luca Zoccarato, Daniel J Sher, Takeshi Miki, Daniel Segr\u00e8, Hans-Peter Grossart: A comparative whole-genome approach identifies bacterial traits for marine microbial interactions, Communications Biology<\/strong>, 5:276 (2022) [Comm.Biol.<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Rotem Lapidot, Tyler Faits, Arshad Ismail, Mushal Allam, Zamantungwak T.H Khumalo, William MacLeod, Geoffrey Kwenda, Zacharia Mupila, Ruth Nakazwe, Daniel Segr\u00e8, W. Evan Johnson, Donald M Thea, Lawrence Mwananyanda, Christopher J Gill: Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study, BioRxiv<\/strong> (2022) https:\/\/doi.org\/10.1101\/2021.10.13.21264939 [BioRxiv<\/a>].<\/p>\n

2021<\/h2>\n

Michael Quintin, Ilija Dukovski, Jennifer Bhatnagar, Daniel Segr\u00e8: Optimality of extracellular enzyme production and activity in dynamic flux balance modeling, BioRxiv<\/strong> (2021) https:\/\/doi.org\/10.1101\/2021.11.01.466736 [BioRxiv<\/a>]<\/p>\n

Ilija Dukovski, Djordje Baji\u0107, Jeremy M Chac\u00f3n, Michael Quintin, Jean CC Vila, Snorre Sulheim, Alan R Pacheco, David B Bernstein, William J Rieh, Kirill S Korolev, Alvaro Sanchez, William R Harcombe, Daniel Segr\u00e8: A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS), Nature Protocols<\/strong> (2021) 16<\/b>,\u00a0<\/span>5030\u20135082<\/span>\u00a0[Nature Protocols<\/a>][Read PDF<\/a>][COMETS<\/a>][Previous version on arXiv<\/a>].<\/p>\n

Devlin Moyer, Alan R. Pacheco, David B. Bernstein, Daniel Segr\u00e8: Stoichiometric modeling of artificial string chemistries reveals constraints on metabolic network structure, Journal of Molecular Evolution<\/strong> (2021) Volume 89, pages 472\u2013483 [J. Mol. Evol.<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Aaron Goldman, Greg Fournier, Johann Peter Gogarten, Anton S. Petrov, Lynn Rothschild, Daniel Segr\u00e8, Eric Smith, and Loren Williams: Understanding the early major transitions in evolutionary history Part 1: Stages in the emergence of complex life, Bulletin of the American Astronomical Society<\/strong>, 53(4). https:\/\/doi.org\/10.3847\/25c2cfeb.cb78fd8a [BAAS<\/a>]<\/p>\n

Aaron Goldman, Greg Fournier, Johann Peter Gogarten, Anton S. Petrov, Lynn Rothschild, Daniel Segr\u00e8, Eric Smith, and Loren Williams: Understanding the early major transitions in evolutionary history Part 2: Ancient evolution of biological systems and the biosphere, Bulletin of the American Astronomical Society<\/strong>, 53(4). https:\/\/doi.org\/10.3847\/25c2cfeb.2e749fbd [BAAS<\/a>]<\/p>\n

Alan Pacheco, Daniel Segr\u00e8: An evolutionary algorithm for designing microbial communities via environmental modification, Journal of the Royal Society Interface<\/b> (2021) 18: 20210348 [J.R.Soc.Interface<\/a>] [Previous version on BioRxiv<\/a>]<\/p>\n

Demetrius Dimucci, Mark Kon, Daniel Segr\u00e8:\u00a0BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes, Frontiers in Molecular Biosciences<\/strong>\u00a0(2021) 8:663532.doi: 10.3389\/fmolb.2021.663532 [Frontiers<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Dalit Roth Rosenberg, Markus Haber, Joshua Goldford, Maya Lalzar, Dikla Aharonovich, Ashraf Al-Ashhab, Yoav Lehahn, Michael D Krom, Daniel Segr\u00e8, Laura Steindler, Daniel J Sher: Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental and anthropogenic factors,\u00a0Environmental Microbiology <\/strong>(2021), 25 May 2021, https:\/\/doi.org\/10.1111\/1462-2920.15611 [Environ Microbiol<\/a>][Previous version on BioRxiv<\/a>]<\/p>\n

Taiyi Kuo, Wen Du, Yasutaka Miyachi, Prasanna K. Dadi, David A. Jacobson, Daniel Segr\u00e8, Domenico Accili: Antagonistic epistasis of Hnf4\u03b1 and FoxO1 metabolic networks through enhancer interactions in \u03b2-cell function, Molecular Metabolism<\/strong> (2021),\u00a0101256. [Molecular Metabolism<\/a>]<\/p>\n

Alan R Pacheco, Melisa Osborne & Daniel Segr\u00e8: Non-additive microbial community responses to environmental complexity, Nature Communications <\/strong>(2021) 12, 2365. [Nature Comm<\/a>] [The Brink news<\/a>](previously on BioRxiv<\/a>).<\/p>\n

Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segr\u00e8, Stefano Monti and
\nW. Evan Johnson: animalcules: interactive microbiome analytics and visualization in R, Microbiome <\/strong>(2021) 9, 76. [Microbiome<\/a>]<\/p>\n

David B. Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segr\u00e8: Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, Genome Biology<\/strong> (2021) 22, 64. [Genome Biology<\/a>]<\/p>\n

Shany Ofaim, Snorre Sulheim, Eivind Almaas, Daniel Jonathan Sher, Daniel Segr\u00e8:\u00a0Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus,\u00a0Frontiers in Genetics <\/strong>(2021) 12:586293. doi: 10.3389\/fgene.2021.586293 [Frontiers<\/a>] (previous version: BioRxiv<\/a> 2020)<\/p>\n

2020<\/h2>\n

Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel\u00a0Segr\u00e8<\/span>, Alan Aspuru-Guzik: A thermodynamic atlas of carbon redox chemical space, Proc. Natl. Acad. Sci. USA<\/strong>\u00a0(2020), 117, 52, 32910\u201332918 | (previously appeared on BioRxiv (2018), https:\/\/doi.org\/10.1101\/245811) [PNAS<\/a>]<\/p>\n

Charles DeLisi, Aristides Patrinos, Michael MacCracken, Dan Drell, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Henry Jacoby, Mary Lidstrom, Jerry Melillo, Ron Milo, Keith Paustian, John Reilly, Richard Roberts, Daniel Segr\u00e8, Susan Solomon, Dominic Woolf, Stan D.Wullschleger, Xiaohan Yang: The role of synthetic biology in atmospheric greenhouse gas reduction: prospects and challenges, BioDesign<\/strong> Research (2020), Vol. 2020, Article ID 1016207. [BioDesign Research<\/a>]<\/p>\n

2019<\/h2>\n

Joshua E. Goldford, Hyman Hartman, Robert Marsland III,\u00a0Daniel Segr\u00e8:\u00a0Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism, Nature Ecology & Evolution<\/strong> (2019), doi:10.1038\/s41559-019-1018-8 [Nature Ecol. & Evol.<\/a>][SharedIt<\/a>](also\u00a0BioRxiv<\/a> 2018)<\/p>\n

Doron Lancet, Daniel Segr\u00e8, Amit Kahana:\u00a0Twenty Years of \u201cLipid World\u201d: A Fertile Partnership with David Deamer, Life<\/strong> (2019) 9(4), 77. [Life<\/a>]<\/p>\n

Mustafa Saifuddin, Jennifer M. Bhatnagar, Daniel Segr\u00e8 & Adrien C. Finzi:\u00a0Microbial carbon use efficiency predicted from genome-scale metabolic models, Nature Communications<\/strong>\u00a0(2019) 10,\u00a0 3568. [Nature Communications<\/a>]<\/p>\n

David Bernstein, Floyd Dewhirst, Daniel Segr\u00e8:\u00a0Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome, eLife<\/strong> 2019;8:e39733 DOI: 10.7554\/eLife.39733 [eLife<\/a>] (also\u00a0BioRxiv<\/a>,\u00a02018)<\/p>\n

Alan R Pacheco &\u00a0Daniel Segr\u00e8:\u00a0A multidimensional perspective on microbial interactions, FEMS Microbiology Letters<\/strong> (2019), Volume 366, Issue 11, June 2019, fnz125 [FEMS<\/a>]<\/span><\/span><\/p>\n

Meghan Thommes*, Taiyao Wang*, Qi Zhao, Ioannis Ch. Paschalidis, Daniel Segr\u00e8:\u00a0Designing metabolic division of labor in microbial communities, mSystems<\/strong>\u00a0(2019) 4:e00263-18. [mSystems<\/a>] (also\u00a0BioRxiv<\/a><\/span><\/span>, 2018).<\/span><\/span><\/p>\n

Antonella\u00a0<\/span>Succurro<\/span>,\u00a0<\/span>Daniel\u00a0<\/span>Segr\u00e8<\/span><\/span><\/span>,\u00a0<\/span>Oliver\u00a0<\/span>Ebenh\u00f6h:\u00a0Emergent sub-population behavior uncovered with a community dynamic metabolic model of Escherichia coli<\/em> diauxic growth, mSystems<\/strong> (2019) 4:e00230-18. [mSystems<\/a>] (also\u00a0BioRxiv<\/a>, 2018).<\/span><\/span><\/span><\/span><\/p>\n

Alan R Pacheco, Mauricio Moel, Daniel\u00a0Segr<\/span>\u00e8:\u00a0Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems, Nature Communications<\/strong> 10, 103 (2019) [Nature Communications<\/a>] (also BioRxiv,\u00a0<\/a>2018).<\/span><\/span><\/span><\/p>\n

2018<\/h2>\n

Bea Yu*, Ilija Dukovski*, David Kong, Johanna Bobrow, Alla Ostrinskaya, Daniel Segr\u00e8#, Todd Thorsen#: Experiments and simulations on short chain fatty acid production in a colonic bacterial community,\u00a0BioRxiv<\/strong> (2018), https:\/\/doi.org\/10.1101\/444760 [BioRxiv<\/a>]<\/p>\n

Ben M Maoz, Anna Herland, Edward A FitzGerald, Thomas Grevesse, Charles Vidoudez, Alan R Pacheco, Sean P Sheehy, Tae-Eun Park, Stephanie Dauth, Robert Mannix, Nikita Budnik, Kevin Shores, Alexander Cho, Janna C Nawroth, Daniel Segr\u00e8, Bogdan Budnik, Donald E Ingber & Kevin Kit Parker:\u00a0A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells, Nature Biotechnology<\/strong> (2018) 36, pages 865\u2013874 [Nature Biotechnology<\/a>][Harvard News<\/a>]<\/p>\n

William F Hynes, Jeremy Chac\u00f3n, Daniel Segr\u00e8, Christopher J Marx, Nathaniel C Cady and William R Harcombe:\u00a0Bioprinting microbial communities to examine interspecies interactions in time and space,\u00a0Biomedical Physics & Engineering Express<\/strong> (2018),\u00a0Biomed. Phys. Eng. Express 4 055010. [IOPscience<\/a>][PDF<\/a>]<\/p>\n

Joshua E. Goldford*, Nanxi Lu*, Djordje Bajic, Sylvie Estrela, Mikhail Tikhonov, Alicia Sanchez-Gorostiaga, Daniel\u00a0Segr\u00e8<\/span>, Pankaj Mehta, Alvaro Sanchez:\u00a0Emergent Simplicity in Microbial Community Assembly, Science<\/strong> (2018) Vol. 361, Issue 6401, pp. 469-474. [Science<\/a>]<\/span><\/span><\/p>\n

Demetrius DiMucci, Mark Kon, Daniel Segr\u00e8: Machine learning reveals missing edges and putative interaction mechanisms in microbial ecosystem networks, mSystems<\/strong>, 2018,\u00a03:e00181-18. [mSystems<\/a>]<\/p>\n

Joshua E. Goldford, Daniel\u00a0<\/span>Segr\u00e8: Modern views of ancient metabolic networks, Current Opinions in Systems Biology<\/strong>, 2018, 8:117\u2013124. [Curr Op Sys Bio<\/a>]<\/span><\/p>\n

2017<\/h2>\n

Ali R. Zomorrodi and Daniel Segr\u00e8: Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities, Nature Communications <\/strong>(2017)\u00a08: 1563 [Nature Communications<\/a>]<\/p>\n

Ed Reznik, Dimitris Christodoulou, Joshua Goldford, Emma Briars, Uwe Sauer, Daniel Segr\u00e8, Elad Noor: Genome-scale analysis of small molecule regulatory networks reveals principles of metabolic regulation, Cell Reports\u00a0<\/strong>(2017)\u00a020, 2666\u20132677, September 12, 2017 [Cell Reports<\/a>]<\/p>\n

Joshua E. Goldford, Hyman Hartman, Temple F. Smith, Daniel Segr\u00e8:\u00a0Remnants of an Ancient Metabolism without Phosphate, Cell<\/strong> (2017) 168, 1126\u20131134 [Cell<\/a>][Press Release<\/a>][Perspective<\/a>][BU Research<\/a>][Cover<\/a>][Discover Magazine<\/a>]<\/p>\n

Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel\u00a0Segr\u00e8<\/span>:\u00a0Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates, PLOS ONE <\/strong>(2017)\u00a012(1): e0170164. doi:10.1371\/journal.pone.0170164 [PLOS ONE<\/a>]<\/span><\/p>\n

2016<\/h2>\n

Lorenzo Castelli, Raffaele Pesenti and Daniel\u00a0Segr\u00e8:\u00a0The cell as a decision-making unit,\u00a0IEEE Life Sciences Letters\u00a0<\/strong>(2016),\u00a0DOI: 10.1109\/LLS.2016.2644648 [IEEE Xplore<\/a>][University of Trieste News<\/a>][Sky News<\/a>][Il Piccolo<\/a>]<\/span><\/p>\n

Qi Zhao, Daniel Segr\u00e8 and Ioannis Ch. Paschalidis: Optimal allocation of metabolic functions among organisms in a microbial ecosystem (2016), IEEE 55th Conference on Decision and Control (CDC)<\/strong>,\u00a0DOI: 10.1109\/CDC.2016.7799357 [IEEE Xplore<\/a>]<\/p>\n

Qi Zhao*, Arion Stettner*, Ed Reznik, Ioannis Ch. Paschalidis, Daniel Segr\u00e8: Mapping the landscape of metabolic goals of a cell, Genome Biology<\/strong>\u00a0(2016), 201617:109,\u00a0DOI: 10.1186\/s13059-016-0968-2. (*equal contributions) [Genome Biology<\/a>] [Research Highlight<\/a>]<\/p>\n

Brian R. Granger*, Yi-Chien Chang*, Yan Wang, Charles DeLisi, Daniel Segr\u00e8, Zhenjun Hu:\u00a0Visualization of Metabolic Interaction\u00a0Networks in Microbial Communities Using\u00a0VisANT 5.0, PLOS Computational Biology<\/strong> (2016)\u00a012(4): e1004875. doi:10.1371\/journal.pcbi.1004875. [PLOS CB<\/a>]<\/p>\n

Ali R. Zomorrodi and\u00a0Daniel Segr\u00e8:\u00a0Synthetic ecology of microbes: mathematical models and applications, Journal of Molecular Biology\u00a0<\/strong>(2016) Vol. 428, Issue 5, Part B, Pages 837\u2013861\u00a0[JMB<\/a>]<\/span><\/p>\n

2015<\/h2>\n

Zhao Q, Stettner AI, Reznik E, Segr\u00e8 D, Paschalidis IC. Learning cellular objectives from fluxes by inverse optimization, Proceedings of the 54th IEEE Annual Conference on Decision and Control<\/strong>, 2015:1271-1276 [IEEE Xplore<\/a>]<\/p>\n

Lon M. Chubiz, Brian Granger, Daniel\u00a0Segr\u00e8<\/span>\u00a0and William Harcombe:\u00a0Species interactions differ in their genetic robustness,\u00a0Frontiers in Microbiology<\/strong> (2015) 6:271. doi: 10.3389\/fmicb.2015.00271. [Frontiers<\/a>]<\/p>\n

2014<\/h2>\n

Shaun R. Brinsmade, Elizabeth L. Alexander, Jonathan Livny, Arion I. Stettner, Daniel Segr\u00e8, Kyu Y. Rhee, Abraham L. Sonenshein: Hierarchical expression of genes controlled by the Bacillus subtilis<\/em> global regulatory protein CodY, Proc. Natl. Acad. Sci. USA<\/strong> (2014) Vol. 111, no. 22, 8227\u20138232.\u00a0[PNAS]<\/a><\/p>\n

William R. Harcombe*, William J. Riehl*, Ilija Dukovski, Brian R. Granger, Alex Betts, Alex H. Lang,\u00a0Gracia Bonilla, Amrita Kar, Nicholas Leiby, Pankaj Mehta, Christopher J. Marx,\u00a0and Daniel\u00a0Segr\u00e8<\/span>:\u00a0Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports<\/strong>\u00a0(2014)\u00a07, 1\u201312, May 22. [Cell Reports<\/a>][COMETS<\/a>]<\/p>\n

Viswanadham Sridhara, Austin G. Meyer, Piyush Rai, Jeffrey E. Barrick, Pradeep Ravikumar, Daniel Segr\u00e8, Claus O Wilke:\u00a0Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli,\u00a0PLoS ONE<\/strong>, 2014, 9(12): e114608. [PLOS ONE<\/a>]<\/p>\n

2013<\/h2>\n

Antonio L. C. Gomes, James E. Galagan and Daniel\u00a0Segr\u00e8<\/span>:\u00a0Resource competition may lead to effective treatment of antibiotic resistant infections, PLOS ONE <\/strong>(2013),\u00a08(12): e80775. [PLOS ONE]<\/a>[PDF]<\/a><\/p>\n

Varun Mazumdar, Salomon Amar and Daniel Segre’:\u00a0Metabolic proximity in the order of colonization of a microbial community, PLOS ONE <\/strong>(2013),\u00a08(10): e77617. [PLOS ONE]<\/a>[PDF]<\/a><\/p>\n

Ed Reznik, Pankaj Mehta and Daniel Segre’: Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools, PLOS Computational Biology<\/strong> (2013), 9(8): e1003195. [PLOS Comp Bio]<\/a><\/p>\n

Brian P. Anton, Yi-Chien Chang et al<\/em>:\u00a0The COMBREX Project: Design, Methodology, and Initial Results, PLOS Biology <\/strong>(2013), 11(8): e1001638. [PLOS Biology]<\/a><\/p>\n

Ed Reznik, Osman Chaudhary and Daniel Segre’: The Average Enzyme Principle,\u00a0FEBS Letters <\/strong>(2013) 587, 2891\u2013289.\u00a0[FEBS Letters]<\/a>[Special Issue on 100 years of Michaelis-Menten<\/a>]<\/p>\n

Arion Stettner and\u00a0Daniel Segre’: The cost of efficiency in energy metabolism,\u00a0Proc. Natl. Acad. Sci. USA<\/strong> (2013) Vol. 110, no. 24, 9629-9630\u00a0[PNAS]<\/a>[PDF]<\/a><\/p>\n

Ed Reznik, Alex Watson and Osman Chaudhary:\u00a0The stubborn roots of metabolic cycles,\u00a0J. R. Soc. Interface<\/strong> (2013), Vol. 10 No. 83, 20130087.\u00a0[Interface]<\/a><\/p>\n

Ed Reznik, Stefan Yohe and Daniel Segre’: Invariance and optimality in the regulation of an enzyme,\u00a0Biology Direct<\/strong> (2013), 8:7.\u00a0[Biology Direct]<\/a><\/p>\n

Ed Reznik, Tasso J. Kaper and Daniel Segre’: The dynamics of hybrid metabolic-genetic oscillators,\u00a0Chaos <\/strong>(2013), 23, 013132.\u00a0[Chaos]<\/a><\/p>\n

<\/h2>\n

2012<\/h2>\n

Sara B. Collins*, Ed Reznik*, Daniel Segre’: Temporal expression-based analysis of metabolism, PLoS Computational Biology<\/strong> (2012), 8(11): e1002781. (*equal contributions) [PLOS CB]<\/a><\/p>\n

David Byrne, Alexandra Dumitriu, Daniel Segre’: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism,\u00a0BMC Systems Biology<\/strong> (2012), 6:127. [BMC Sys Bio]<\/a><\/p>\n

Hsuan-Chao Chiu, Christopher J. Marx, Daniel Segre’: Epistasis from functional dependence of fitness on underlying traits, Proceedings of the Royal Society B: Biological Sciences<\/strong> (2012), 279, 4156\u20134164. [ProcRoyalSocB]<\/a><\/p>\n

Bo Liu*, Lina Faller*, Niels Klitgord*, Varun Mazumdar*, Mohammad Ghodsi, Dan D. Sommer, Theodore R. Gibbons, Todd J. Treangen, Yi-Chien Chang, Shan Li, O. Colin Stine, Hatice Hasturk, Simon Kasif, Daniel Segr\u00e8#, Mihai Pop#, Salomon Amar#, Deep sequencing of the oral microbiome reveals signatures of periodontal disease,\u00a0PLoS One<\/strong> (2012) 7(6): e37919. (*equal contributions; #corresponding authors) [PLoS One]<\/a><\/p>\n

Christopher Jacobs and Daniel Segre’: Organization principles in genetic interaction networks, Adv Exp Med Biol<\/strong> (2012) 751:53-78. (Special volume on Evolutionary Systems Biology, Orkun Soyer Ed.) <\/a>[Adv Exp Med Biol]<\/a>[PDF]<\/a><\/a><\/p>\n

Qasim K. Beg*, Mattia Zampieri*, Niels Klitgord, Sara B. Collins, Claudio Altafini, Margrethe H. Serres, Daniel Segre’: Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis<\/em>.\u00a0Nucleic Acids Research<\/strong> (2012)\u00a040\u00a0(15):7132-7149.\u00a0(*equal contributions) <\/a>[NAR<\/a>]<\/p>\n

Miriam A. Rosenbaum, Haim Y. Bar, Qasim K. Beg, Daniel Segr\u00e8, James Booth, Michael Cotta, Largus T. Angenent: Transcriptional Analysis of\u00a0Shewanella oneidensis\u00a0MR-1 with an Electrode Compared to Fe(III)Citrate or Oxygen as Terminal Electron Acceptor.\u00a0PLoS One<\/strong> (2012) 7(2):e30827. [PLoS One]<\/a><\/p>\n

<\/h2>\n

2011<\/h2>\n

Mattia Zampieri, Giuseppe Legname, Daniel Segre’, Claudio Altafini: A system-level approach for deciphering the transcriptional response to prion infection,\u00a0Bioinformatics<\/b> (2011) 27(24):3407-14. [PDF]<\/a> [Bioinformatics]<\/a><\/p>\n

Hsin-Hung Chou, Hsuan-Chao Chiu, Nigel F. Delaney, Daniel Segre’, Christopher J. Marx: Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation,\u00a0Science <\/b>(2011) 332, 1190. [PDF]<\/a> [Science]<\/a> [Perspective]<\/a><\/p>\n

Ed Reznik, Daniel Segre’, William Erik Sherwood: The quasi-steady state assumption in an enzymatically open system (2011), preprint.\u00a0[arXiv]<\/a>[PDF]<\/a><\/p>\n

Niels Klitgord and Daniel Segre’: Ecosystems biology of microbial metabolism,\u00a0Current Opinions in Biotechnology<\/b> (2011), 22:1-6. [PDF]<\/a><\/p>\n

Evan S. Snitkin and Daniel Segre’: Epistatic interaction maps relative to multiple metabolic phenotypes,\u00a0PLoS Genetics<\/b> (2011) 7(2): e1001294.\u00a0[PLoS Genetics]<\/a>[Data<\/a>]<\/p>\n

Richard J. Roberts, Yi-Chien Chang, Zhenjun Hu, John N. Rachlin, Brian P. Anton, Revonda M. Pokrzywa, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, Mark G. McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin R. Tao, Stan Letovsky, Dennis Vitkup, Daniel Segre’, Steven L. Salzberg, Charles Delisi, Martin Steffen and Simon Kasif: COMBREX: a project to accelerate the functional annotation of prokaryotic genomes,\u00a0Nucleic Acids Research<\/b> (2011) 39, Database Issue, D11-D14. [PDF]<\/a> [NAR]<\/a> [COMBREX]<\/a><\/p>\n

Miriam A. Rosenbaum, Haim Y. Bar, Qasim Beg, Daniel Segr\u00e8, James Booth, Michael A. Cotta, Largus T. Angenent: Shewanella oneidensis<\/i> in a lactate-fed pure-culture and a glucose-fed co-culture with\u00a0Lactococcus lactis<\/i> with an electrode as electron acceptor,\u00a0Bioresource Technology<\/b>(2011) 102, 2623-2628. [PDF<\/a>]<\/a> [Cover]<\/a><\/p>\n

2010<\/h2>\n

Moritz Schuette, Alexander Skupin, Daniel Segr\u00e8 and Oliver Ebenhoeh: Modeling the complex dynamics of enzyme-pathway coevolution,\u00a0Chaos <\/b>(2010), 20, 045115.[<\/a>PDF]<\/a>[Chaos]<\/a><\/p>\n

Niels Klitgord and Daniel Segr\u00e8: Environments that induce synthetic microbial ecosystems, PLoS Computational Biology<\/b> (2010), 6(11): e1001002.[<\/a>PLoS Comp Bio]<\/a>[Synthetic Ecology]<\/a><\/p>\n

Ed Reznik and Daniel Segr\u00e8: On the Stability of Metabolic Cycles, J. Theor. Biol<\/b>. (2010), 266, pp. 536-549. [PDF<\/a>] [PubMED]<\/a><\/p>\n

Daniel Segr\u00e8 and Christopher Marx: Introduction to focus issue: genetic interactions, Chaos<\/b>(2010), Jun; 20(2):026101.\u00a0[PDF]<\/a>[Chaos Focus Issue]<\/a><\/p>\n

William J. Riehl, Paul Krapivsky, Sidney Redner and Daniel Segre’: Signatures of Arithmetic Simplicity in Metabolic Network Architecture,\u00a0PLoS Computational Biology<\/b> (2010), 6(4): e1000725. doi:10.1371\/journal.pcbi.1000725. [PLoS CB<\/a>][PDF<\/a>]<\/p>\n

2009<\/h2>\n

Niels Klitgord and Daniel Segre’: The Importance of Compartmentalization in Metabolic Flux Models: Yeast as an Ecosystem of Organelles,\u00a0Genome Informatics<\/b> (2009) 22: 41-55.[PDF<\/a>]<\/p>\n

Moritz Schuette, Niels Klitgord, Daniel Segre’ and Oliver Ebenhoeh: Co-Evolution of Metabolism and Protein Sequences,\u00a0Genome Informatics<\/b> (2009) 22: 156-166.[PDF<\/a>]<\/p>\n

Varun Mazumdar, Evan Snitkin, Salomon Amar*<\/sup> and Daniel Segre’*<\/sup>: Metabolic network model of a human oral pathogen,\u00a0Journal of Bacteriology <\/b>(2009)\u00a0 Jan; 191(1), 74-90. [PDF<\/a>] [J. Bacteriology<\/a>] [Cover]<\/a> [P. gingivalis<\/a><\/i> metabolic network<\/a>] [OHMICS<\/a> resources]<\/p>\n

2008<\/h2>\n

Evan S. Snitkin, Aimee M. Dudley, Daniel M. Janse, Kaisheen Wong, George M. Church, and Daniel Segre’: Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions,\u00a0Genome Biology<\/b> (2008) 9:R140. [Genome Biology<\/a>] [Interactive Flux Visualization Tool<\/a>]<\/p>\n

Hsuan-Chao Chiu and Daniel Segre’: Comparative determination of biomass composition in differentially active metabolic states,\u00a0Genome Informatics<\/b> (2008) 20: 171-182. [PDF<\/a>]<\/p>\n

William J. Riehl and <\/b>Daniel Segre’: Optimal metabolic regulation using a constraint-based model, Genome Informatics<\/b> (2008) 20: 159-170. [PDF<\/a>]<\/p>\n

Evan S. Snitkin and Daniel Segre’: Optimality criteria for the prediction of metabolic fluxes in yeast mutants,\u00a0Genome Informatics <\/b>(2008) 20: 123-134 .[PDF<\/a>]<\/p>\n

2007<\/h2>\n

Matthew A. Wright, Peter Kharchenko, George M. Church and Daniel Segre’, Chromosomal periodicity of evolutionarily conserved gene pairs,\u00a0Proc. Natl. Acad. Sci. USA<\/b> (2007), 104 (25), 10559-10564. [PDF]<\/a> [PNAS online]<\/a> [Supp. Info]<\/a> [MSB blog]<\/a><\/p>\n

Lan Hu, Daniel Segre’ and Temple F. Smith, Evolutionary changes in gene regulation from a comparative analysis of multiple drosophila species,\u00a0Genome Informatics<\/b> (2007), 18, 12-22. [PDF]<\/a><\/p>\n

2006<\/h2>\n

Jason Raymond and Daniel Segre’, The effect of oxygen on biochemical networks and the evolution of complex life,\u00a0Science<\/b> (2006), 311, 1764-1767. [PDF]<\/a> [Science]<\/a> [Perspective]<\/a> [Interactive Network]<\/a> [The Scientist]<\/a> [Seed]<\/a> [La Stampa]<\/a><\/p>\n

2005<\/h2>\n

Daniel Segre’, Alexander DeLuna, George M. Church and Roy Kishony, Modular epistasis in yeast metabolism,\u00a0Nature Genetics<\/b> (2005), 37(1), 77-83. [PDF]<\/a> [Nature Genetics]<\/a><\/p>\n

Daniel Segre’, Life as a cellular automaton,\u00a0Journal of Biogeography<\/b> (2005) 32, 1681. (Review of the\u00a0The Principles of Life<\/em> by Tibor Ganti). [PDF]<\/a><\/p>\n

Daniel Segre’, Ventimila geni sotto i mari dei tropici,\u00a0Darwin<\/b> (2005) May-June, 56-61. (Review, in Italian). [PDF] <\/a>[Links]<\/a><\/p>\n

1997-2004<\/h2>\n

Daniel Segr\u00e8, The regulatory software of cellular metabolism,\u00a0Trends in Biotechnology<\/b> (2004), 22 (6), 261-265. (Commentary of Ihmels et al. Nat. Biotech. 2003) <\/a>[PDF]<\/a><\/p>\n

Daniel Segr\u00e8 and Doron Lancet, Theoretical and computational approaches to the study of the origins of life, in\u00a0Origins: Genesis, Evolution and Diversity of Life<\/b> (2004), COLE series, Vol.6, Kluwer, J. Seckbach (ed.) [Amazon]<\/a><\/p>\n

Daniel Segr\u00e8, Jeremy Zucker, Jeremy Katz, Xiaoxia Lin, Patrik D’haeseleer, Wayne P. Rindone, Peter Kharchenko, Dat Nguyen, Matthew A. Wright and George M. Church, From annotated genomes to metabolic flux models and kinetic parameter fitting,\u00a0Omics<\/b> (2003), 7(3), 301-316. [PDF]<\/a> [Biospice]<\/a><\/p>\n

Daniel Segr\u00e8, Dennis Vitkup and George Church, Analysis of optimality in natural and perturbed metabolic networks,\u00a0Proc. Natl. Acad. Sci. USA <\/b>(2002), 99(23), 15112-15117. [PDF]<\/a> [PNAS]<\/a> [MOMA Supplementary Material (not maintained)]<\/a><\/p>\n

Barak Shenhav, Daniel Segre’ and Doron Lancet, Mesobiotic emergence: molecular and ensemble complexity in early evolution,\u00a0Advances in Complex Systems<\/b> (2003), 6 (1), 15-35. [PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Barak Shenhav, Ron Kafri and Doron Lancet, The molecular roots of compositional inheritance,\u00a0Journal of Theoretical Biology<\/b> (2001), 213, 481-491. [PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Dafna Ben-Eli, David Deamer and Doron Lancet, The Lipid World,\u00a0Origins Life Evol. Biosphere<\/b> (2001) 31, 119-145. [PDF]<\/a>[OLEB<\/a>]<\/p>\n

Yoav Gilad, Daniel Segr\u00e8, Karl Skorecki, Michael W. Nachman, Doron Lancet and Dror Sharon, Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes, Nature Genetics<\/b> (2000) 26, 221-224. [PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Dafna Ben-Eli and Doron Lancet, Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies, Proc. Natl. Acad. Sci. USA<\/b> (2000), 97(8), 4112-4117. [PDF]<\/a> [PNAS]<\/a><\/p>\n

Daniel Segr\u00e8 and Doron Lancet, Composing Life, EMBO Reports<\/b> (2000), 1(3), 217-222. [PDF]<\/a> [cover]<\/a><\/p>\n

Daniel Segre’ and Doron Lancet, A statistical chemistry approach to the origin of life,\u00a0Chemtracts<\/b>– Biochemistry and Molecular Biology (1999) 12 (6), 382-397. [PDF]<\/a><\/p>\n

Daniel Segre’, Dafna Ben-Eli and Doron Lancet, Prebiotic evolution of amphiphilic assemblies far from equilibrium: from compositional information to sequence-based biopolymers, Astronomical Society of the Pacific Conference Series<\/b> Vol.213, Sheridan Books, Michigan, 2000, 373-378. [PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Doron Lancet, Ora Kedem and Yitzhak Pilpel, Graded Autocatalysis Replication Domain (GARD): kinetic analysis of self-replication in mutually catalytic sets,\u00a0Origins Life Evol. Biosphere<\/b> (1998) Vol.28, 501-514. [OLEB<\/a>] [PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Yitzhak Pilpel and Doron Lancet, Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics,\u00a0Physica A<\/b> (1998) 249, 558-564.[PDF] <\/a><\/p>\n

Daniel Segr\u00e8, Dafna Ben-Eli, Yitzhak Pilpel, Ora Kedem and Doron Lancet, GARDobes: Primordial cell nano-precursors with organic catalysis, compositional genome and capacity to evolve, In Instruments, Methods, and Missions for Astrobiology II, Richard B. Hoover, Ed., Proceedings of SPIE<\/b>, Vol.3755, 144-162 (1999). [PDF]<\/a><\/p>\n

Daniel Segr\u00e8 and Doron Lancet, Mutually catalytic amphiphiles: simulated chemical evolution and implications to exobiology, J.Chela-Flores and F.Raulin (eds), Exobiology: Matter, Energy and Information in the Origin and Evolution of Life in the Universe<\/b>, 123-131, Kluwer Academic Publishers, The Netherlands, 1998. [preprint PDF]<\/a><\/p>\n

Daniel Segr\u00e8, Yitzhak Pilpel, Gustavo Glusman and Doron Lancet, Self-replication and evolution in primordial mutually catalytic set, in C. B. Cosmovici, S. Bowyer, D. Werthimer, Astronomical and Biochemical Origins and the Search for Life in the Universe<\/b>, Editrice Compositori, Bologna, 1997, 469-476 [PDF<\/a>]<\/p>\n","protected":false},"excerpt":{"rendered":"

2026 Franziska Kratzl, Helen Scott, Simran Jayasinghe, Kendall Hughes, Melisa Osborne, Daniel Sher, Daniel Segr\u00e8:\u00a0 Organizing principles in the Nitrogen\u2013Carbon Landscape of Marine Heterotrophic Bacteria, BioRxiv (2026) https:\/\/doi.org\/10.64898\/2026.06.04.730220 [BioRxiv] Arian Ferrero*, Franziska P. Kratzl*, Liam Kelley, Kirill Korolev, Davide Masoero, Daniel Segr\u00e8#, Ilija Dukovski#, Daniele de Martino#: Reconstructing heterogeneous metabolic trajectories of E. coli diauxie […]<\/p>\n","protected":false},"author":6218,"featured_media":0,"parent":0,"menu_order":20,"comment_status":"closed","ping_status":"closed","template":"page-templates\/no-sidebars.php","meta":[],"_links":{"self":[{"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/pages\/18"}],"collection":[{"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/users\/6218"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":50,"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":2977,"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/pages\/18\/revisions\/2977"}],"wp:attachment":[{"href":"https:\/\/www.bu.edu\/segrelab\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}