Alan R. Pacheco*, Charlie Pauvert*, Dileep Kishore, Daniel Segrè: Toward FAIR Representations of Microbial Interactions, mSystems (2022) e00659-22 [mSystems]

Zhenjun Hu, Dileep Kishore, Yan Wang, Gabriel Birzu, Charles DeLisi, Kirill Korolev, Daniel Segrè: A resource for the comparison and integration of heterogeneous microbiome networks, BioRxiv (2022) [BioRxiv]

Elena Forchielli*, Taiyao Wang*, Meghan Thommes*, Ioannis Ch Paschalidis, Daniel Segrè: Prediction of representative phenotypes using multi-output subset selection, BioRxiv (2022) [BioRxiv]

Alexander Golden, Ilija Dukovski, Daniel Segrè, Kirill S. Korolev: Growth instabilities shape morphology and genetic diversity of microbial colonies, Physical Biology (2022) 19 056005 [Phys. Biol.] [Previous version on BioRxiv]

Ali R Zomorrodi, Colin Hemez, Pol Arranz-Gibert, Terrence Wu, Farren J Isaacs, Daniel Segrè: Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine, iScience (2022) 25, 104562 [iScience][Previous version on BioRxiv]

Elena J. Forchielli, Daniel J. Sher, Daniel Segrè: Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies, mSystems (2022) e00070-22 [mSystems][Previous version on BioRxiv]

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 Segrè, Ashley Shade, Matthew B. Sullivan and Assaf Vardi: Microbial metabolites in the marine carbon cycle, Nature Microbiology (2022) 7, 508–523 [Nature Microbiology]

Joshua E. Goldford, Ashish Bino George, Avi E. Flamholz, Daniel Segrè: Protein cost minimization promotes the emergence of coenzyme redundancy, Proc. Natl. Acad. Sci. USA (2022) 119 (14) e2110787119 [PNAS] [Previous version on BioRxiv]

Luca Zoccarato, Daniel J Sher, Takeshi Miki, Daniel Segrè, Hans-Peter Grossart: A comparative whole-genome approach identifies bacterial traits for marine microbial interactions, Communications Biology (2022), 5:276  [Comm.Biol.][Previous version on BioRxiv]

Rotem Lapidot, Tyler Faits, Arshad Ismail, Mushal Allam, Zamantungwak T.H Khumalo, William MacLeod, Geoffrey Kwenda, Zacharia Mupila, Ruth Nakazwe, Daniel Segrè, 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 (2022) [BioRxiv].


Michael Quintin, Ilija Dukovski, Jennifer Bhatnagar, Daniel Segrè: Optimality of extracellular enzyme production and activity in dynamic flux balance modeling, BioRxiv (2021) [BioRxiv]

Ilija Dukovski, Djordje Bajić, Jeremy M Chacón, 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 Segrè: A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS), Nature Protocols (2021) [Nature Protocols][Read PDF][COMETS][Previous version on arXiv].

Devlin Moyer, Alan R. Pacheco, David B. Bernstein, Daniel Segrè: Stoichiometric modeling of artificial string chemistries reveals constraints on metabolic network structure, Journal of Molecular Evolution (2021) [J. Mol. Evol.][Previous version on BioRxiv]

Aaron Goldman, Greg Fournier, Johann Peter Gogarten, Anton S. Petrov, Lynn Rothschild, Daniel Segrè, 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, 53(4). [BAAS]

Aaron Goldman, Greg Fournier, Johann Peter Gogarten, Anton S. Petrov, Lynn Rothschild, Daniel Segrè, 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, 53(4). [BAAS]

Alan Pacheco, Daniel Segrè: An evolutionary algorithm for designing microbial communities via environmental modification, Journal of the Royal Society Interface (2021) 18: 20210348 [J.R.Soc.Interface] [Previous version on BioRxiv]

Demetrius Dimucci, Mark Kon, Daniel Segrè: BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes, Frontiers in Molecular Biosciences (2021) 8:663532.doi: 10.3389/fmolb.2021.663532 [Frontiers][Previous version on BioRxiv]

Dalit Roth Rosenberg, Markus Haber, Joshua Goldford, Maya Lalzar, Dikla Aharonovich, Ashraf Al-Ashhab, Yoav Lehahn, Michael D Krom, Daniel Segrè, Laura Steindler, Daniel J Sher: Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental and anthropogenic factors, Environmental Microbiology (2021), 25 May 2021, [Environ Microbiol][Previous version on BioRxiv]

Taiyi Kuo, Wen Du, Yasutaka Miyachi, Prasanna K. Dadi, David A. Jacobson, Daniel Segrè, Domenico Accili: Antagonistic epistasis of Hnf4α and FoxO1 metabolic networks through enhancer interactions in β-cell function, Molecular Metabolism (2021), 101256. [Molecular Metabolism]

Alan R Pacheco, Melisa Osborne & Daniel Segrè: Non-additive microbial community responses to environmental complexity, Nature Communications (2021) 12, 2365. [Nature Comm] [The Brink news](previously on BioRxiv).

Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti and
W. Evan Johnson: animalcules: interactive microbiome analytics and visualization in R, Microbiome (2021) 9, 76. [Microbiome]

David B. Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè: Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, Genome Biology (2021) 22, 64. [Genome Biology]

Shany Ofaim, Snorre Sulheim, Eivind Almaas, Daniel Jonathan Sher, Daniel Segrè: Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus, Frontiers in Genetics (2021) 12:586293. doi: 10.3389/fgene.2021.586293 [Frontiers] (previous version: BioRxiv 2020)

Charles Jo*, David B Bernstein*, Natalie Vaisman, Horacio M Frydman, Daniel Segrè: A co-culture microplate for real-time measurement of microbial interactions, BioRxiv (2021), [BioRxiv]


Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segrè, Alan Aspuru-Guzik: A thermodynamic atlas of carbon redox chemical space, Proc. Natl. Acad. Sci. USA (2020), 117, 52, 32910–32918 | (previously appeared on BioRxiv (2018), [PNAS]

Dileep Kishore, Gabriel Birzu, Zhenjun Hu, Charles DeLisi, Kirill Korolev, Daniel Segrè: Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation, BioRxiv (2020), [BioRxiv]

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 Segrè, Susan Solomon, Dominic Woolf, Stan D.Wullschleger, Xiaohan Yang: The role of synthetic biology in atmospheric greenhouse gas reduction: prospects and challenges, BioDesign Research (2020), Vol. 2020, Article ID 1016207. [BioDesign Research]


Joshua E. Goldford, Hyman Hartman, Robert Marsland III, Daniel Segrè: Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism, Nature Ecology & Evolution (2019), doi:10.1038/s41559-019-1018-8 [Nature Ecol. & Evol.][SharedIt](also BioRxiv 2018)

Doron Lancet, Daniel Segrè, Amit Kahana: Twenty Years of “Lipid World”: A Fertile Partnership with David Deamer, Life (2019) 9(4), 77. [Life]

Mustafa Saifuddin, Jennifer M. Bhatnagar, Daniel Segrè & Adrien C. Finzi: Microbial carbon use efficiency predicted from genome-scale metabolic models, Nature Communications (2019) 10,  3568. [Nature Communications]

David Bernstein, Floyd Dewhirst, Daniel Segrè: Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome, eLife 2019;8:e39733 DOI: 10.7554/eLife.39733 [eLife] (also BioRxiv, 2018)

Alan R Pacheco & Daniel Segrè: A multidimensional perspective on microbial interactions, FEMS Microbiology Letters (2019), Volume 366, Issue 11, June 2019, fnz125 [FEMS]

Meghan Thommes*, Taiyao Wang*, Qi Zhao, Ioannis Ch. Paschalidis, Daniel Segrè: Designing metabolic division of labor in microbial communities, mSystems (2019) 4:e00263-18. [mSystems] (also BioRxiv, 2018).

Antonella SuccurroDaniel SegrèOliver Ebenhöh: Emergent sub-population behavior uncovered with a community dynamic metabolic model of Escherichia coli diauxic growth, mSystems (2019) 4:e00230-18. [mSystems] (also BioRxiv, 2018).

Alan R Pacheco, Mauricio Moel, Daniel Segrè: Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems, Nature Communications 10, 103 (2019) [Nature Communications] (also BioRxiv, 2018).


Bea Yu*, Ilija Dukovski*, David Kong, Johanna Bobrow, Alla Ostrinskaya, Daniel Segrè#, Todd Thorsen#: Experiments and simulations on short chain fatty acid production in a colonic bacterial community, BioRxiv (2018), [BioRxiv]

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 Segrè, Bogdan Budnik, Donald E Ingber & Kevin Kit Parker: A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells, Nature Biotechnology (2018) [Advance Online Publication][Harvard News]

William F Hynes, Jeremy Chacón, Daniel Segrè, Christopher J Marx, Nathaniel C Cady and William R Harcombe: Bioprinting microbial communities to examine interspecies interactions in time and space, Biomedical Physics & Engineering Express (2018), Biomed. Phys. Eng. Express 4 055010. [IOPscience][PDF]

Joshua E. Goldford*, Nanxi Lu*, Djordje Bajic, Sylvie Estrela, Mikhail Tikhonov, Alicia Sanchez-Gorostiaga, Daniel Segrè, Pankaj Mehta, Alvaro Sanchez: Emergent Simplicity in Microbial Community Assembly, Science (2018) Vol. 361, Issue 6401, pp. 469-474. [Science]

Demetrius DiMucci, Mark Kon, Daniel Segrè: Machine learning reveals missing edges and putative interaction mechanisms in microbial ecosystem networks, mSystems, 2018, 3:e00181-18. [mSystems]

Joshua E. Goldford, Daniel Segrè: Modern views of ancient metabolic networks, Current Opinions in Systems Biology, 2018, 8:117–124. [Curr Op Sys Bio]


Ali R. Zomorrodi and Daniel Segrè: Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities, Nature Communications (2017) 8: 1563 [Nature Communications]

Ed Reznik, Dimitris Christodoulou, Joshua Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, Elad Noor: Genome-scale analysis of small molecule regulatory networks reveals principles of metabolic regulation, Cell Reports (2017) 20, 2666–2677, September 12, 2017 [Cell Reports]

Joshua E. Goldford, Hyman Hartman, Temple F. Smith, Daniel Segrè: Remnants of an Ancient Metabolism without Phosphate, Cell (2017) 168, 1126–1134 [Cell][Press Release][Perspective][BU Research][Cover][Discover Magazine]

Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel SegrèUpon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates, PLOS ONE (2017) 12(1): e0170164. doi:10.1371/journal.pone.0170164 [PLOS ONE]


Lorenzo Castelli, Raffaele Pesenti and Daniel Segrè: The cell as a decision-making unit, IEEE Life Sciences Letters (2016), DOI: 10.1109/LLS.2016.2644648 [IEEE Xplore][University of Trieste News][Sky News][Il Piccolo]

Qi Zhao, Daniel Segrè and Ioannis Ch. Paschalidis: Optimal allocation of metabolic functions among organisms in a microbial ecosystem (2016), IEEE 55th Conference on Decision and Control (CDC), DOI: 10.1109/CDC.2016.7799357 [IEEE Xplore]

Qi Zhao*, Arion Stettner*, Ed Reznik, Ioannis Ch. Paschalidis, Daniel Segrè: Mapping the landscape of metabolic goals of a cell, Genome Biology (2016), 201617:109, DOI: 10.1186/s13059-016-0968-2. (*equal contributions) [Genome Biology] [Research Highlight]

Brian R. Granger*, Yi-Chien Chang*, Yan Wang, Charles DeLisi, Daniel Segrè, Zhenjun Hu: Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0, PLOS Computational Biology (2016) 12(4): e1004875. doi:10.1371/journal.pcbi.1004875. [PLOS CB]

Ali R. Zomorrodi and Daniel Segrè: Synthetic ecology of microbes: mathematical models and applications, Journal of Molecular Biology (2016) Vol. 428, Issue 5, Part B, Pages 837–861 [JMB (Open Access)]


Zhao Q, Stettner AI, Reznik E, Segrè D, Paschalidis IC. Learning cellular objectives from fluxes by inverse optimization, Proceedings of the 54th IEEE Annual Conference on Decision and Control, 2015:1271-1276 [IEEE Xplore]

Lon M. Chubiz, Brian Granger, Daniel Segrè and William Harcombe: Species interactions differ in their genetic robustness, Frontiers in Microbiology (2015) 6:271. doi: 10.3389/fmicb.2015.00271. [Frontiers]


Shaun R. Brinsmade, Elizabeth L. Alexander, Jonathan Livny, Arion I. Stettner, Daniel Segrè, Kyu Y. Rhee, Abraham L. Sonenshein: Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY, Proc. Natl. Acad. Sci. USA (2014) Vol. 111, no. 22, 8227–8232. [PNAS]

William R. Harcombe*, William J. Riehl*, Ilija Dukovski, Brian R. Granger, Alex Betts, Alex H. Lang, Gracia Bonilla, Amrita Kar, Nicholas Leiby, Pankaj Mehta, Christopher J. Marx, and Daniel Segrè: Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports (2014) 7, 1–12, May 22. [Cell Reports][COMETS]

Viswanadham Sridhara, Austin G. Meyer, Piyush Rai, Jeffrey E. Barrick, Pradeep Ravikumar, Daniel Segrè, Claus O Wilke: Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli, PLoS ONE, 2014, 9(12): e114608. [PLOS ONE]


Antonio L. C. Gomes, James E. Galagan and Daniel Segrè: Resource competition may lead to effective treatment of antibiotic resistant infections, PLOS ONE (2013), 8(12): e80775. [PLOS ONE][PDF]

Varun Mazumdar, Salomon Amar and Daniel Segre’: Metabolic proximity in the order of colonization of a microbial community, PLOS ONE (2013), 8(10): e77617. [PLOS ONE][PDF]

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

Brian P. Anton, Yi-Chien Chang et al: The COMBREX Project: Design, Methodology, and Initial Results, PLOS Biology (2013), 11(8): e1001638. [PLOS Biology]

Ed Reznik, Osman Chaudhary and Daniel Segre’: The Average Enzyme Principle, FEBS Letters (2013) 587, 2891–289. [FEBS Letters][Special Issue on 100 years of Michaelis-Menten]

Arion Stettner and Daniel Segre’: The cost of efficiency in energy metabolism, Proc. Natl. Acad. Sci. USA (2013) Vol. 110, no. 24, 9629-9630 [PNAS][PDF]

Ed Reznik, Alex Watson and Osman Chaudhary: The stubborn roots of metabolic cycles, J. R. Soc. Interface (2013), Vol. 10 No. 83, 20130087. [Interface]

Ed Reznik, Stefan Yohe and Daniel Segre’: Invariance and optimality in the regulation of an enzyme, Biology Direct (2013), 8:7. [Biology Direct]

Ed Reznik, Tasso J. Kaper and Daniel Segre’: The dynamics of hybrid metabolic-genetic oscillators, Chaos (2013), 23, 013132. [Chaos]


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

David Byrne, Alexandra Dumitriu, Daniel Segre’: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism, BMC Systems Biology (2012), 6:127. [BMC Sys Bio]

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 (2012), 279, 4156–4164. [ProcRoyalSocB]

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 Segrè#, Mihai Pop#, Salomon Amar#, Deep sequencing of the oral microbiome reveals signatures of periodontal disease, PLoS One (2012) 7(6): e37919. (*equal contributions; #corresponding authors) [PLoS One]

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

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 oneidensisNucleic Acids Research (2012) 40 (15):7132-7149. (*equal contributions) [NAR]

Miriam A. Rosenbaum, Haim Y. Bar, Qasim K. Beg, Daniel Segrè, James Booth, Michael Cotta, Largus T. Angenent: Transcriptional Analysis of Shewanella oneidensis MR-1 with an Electrode Compared to Fe(III)Citrate or Oxygen as Terminal Electron Acceptor. PLoS One (2012) 7(2):e30827. [PLoS One]


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

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

Ed Reznik, Daniel Segre’, William Erik Sherwood: The quasi-steady state assumption in an enzymatically open system (2011), preprint. [arXiv][PDF]

Niels Klitgord and Daniel Segre’: Ecosystems biology of microbial metabolism, Current Opinions in Biotechnology (2011), 22:1-6. [PDF]

Evan S. Snitkin and Daniel Segre’: Epistatic interaction maps relative to multiple metabolic phenotypes, PLoS Genetics (2011) 7(2): e1001294. [PLoS Genetics][Data]

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, Nucleic Acids Research (2011) 39, Database Issue, D11-D14. [PDF] [NAR] [COMBREX]

Miriam A. Rosenbaum, Haim Y. Bar, Qasim Beg, Daniel Segre’, James Booth, Michael A. Cotta, Largus T. Angenent: 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(2011) 102, 2623-2628. [PDF] [Cover] [PubMED]


Moritz Schuette, Alexander Skupin, Daniel Segre’ and Oliver Ebenhoeh: Modeling the complex dynamics of enzyme-pathway coevolution, Chaos (2010), 20, 045115.[PDF][Chaos]

Niels Klitgord and Daniel Segre’: Environments that induce synthetic microbial ecosystems, PLoS Computational Biology (2010), 6(11): e1001002.[PLoS Comp Bio] [F1000] [Supplementary Information]

Ed Reznik and Daniel Segre’: On the Stability of Metabolic Cycles, J. Theor. Biol. (2010), 266, pp. 536-549. [PDF] [PubMED]

Daniel Segre’ and Christopher Marx: Introduction to focus issue: genetic interactions, Chaos(2010), Jun; 20(2):026101. [PDF][Chaos Focus Issue]

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


Niels Klitgord and Daniel Segre’: The Importance of Compartmentalization in Metabolic Flux Models: Yeast as an Ecosystem of Organelles, Genome Informatics (2009) 22: 41-55.[PDF]

Moritz Schuette, Niels Klitgord, Daniel Segre’ and Oliver Ebenhoeh: Co-Evolution of Metabolism and Protein Sequences, Genome Informatics (2009) 22: 156-166.[PDF]

Varun Mazumdar, Evan Snitkin, Salomon Amar* and Daniel Segre’*: Metabolic network model of a human oral pathogen, Journal of Bacteriology (2009)  Jan; 191(1), 74-90. [PDF] [J. Bacteriology] [Cover] [P. gingivalis metabolic network] [OHMICS resources]


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, Genome Biology (2008) 9:R140. [Genome Biology] [Interactive Flux Visualization Tool]

Hsuan-Chao Chiu and Daniel Segre’: Comparative determination of biomass composition in differentially active metabolic states, Genome Informatics (2008) 20: 171-182. [PDF]

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

Evan S. Snitkin and Daniel Segre’: Optimality criteria for the prediction of metabolic fluxes in yeast mutants, Genome Informatics (2008) 20: 123-134 .[PDF]


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

Lan Hu, Daniel Segre’ and Temple F. Smith, Evolutionary changes in gene regulation from a comparative analysis of multiple drosophila species, Genome Informatics (2007), 18, 12-22. [PDF]


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


Daniel Segre’, Alexander DeLuna, George M. Church and Roy Kishony, Modular epistasis in yeast metabolism, Nature Genetics (2005), 37(1), 77-83. [PDF] [Nature Genetics] [F1000] [Data and Algorithms]

Daniel Segre’, Life as a cellular automaton, Journal of Biogeography (2005) 32, 1681. (Review of the The Principles of Life by Tibor Ganti). [PDF]

Daniel Segre’, Ventimila geni sotto i mari dei tropici, Darwin (2005) May-June, 56-61. (Review, in Italian). [PDF] [Links]


Daniel Segre’, The regulatory software of cellular metabolism, Trends in Biotechnology (2004), 22 (6), 261-265. (Commentary of Ihmels et al. Nat. Biotech. 2003) [PDF]

Daniel Segre’ and Doron Lancet, Theoretical and computational approaches to the study of the origins of life, in Origins: Genesis, Evolution and Diversity of Life (2004), COLE series, Vol.6, Kluwer, J. Seckbach (ed.) [Amazon]

Daniel Segre’, 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, Omics (2003), 7(3), 301-316. [PDF] [Biospice]

Daniel Segre’, Dennis Vitkup and George Church, Analysis of optimality in natural and perturbed metabolic networks, Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117. [PDF] [PNAS on line] [Supplementary Material]

Barak Shenhav, Daniel Segre’ and Doron Lancet, Mesobiotic emergence: molecular and ensemble complexity in early evolution, Advances in Complex Systems (2003), 6 (1), 15-35. [PDF]

Daniel Segre’, Barak Shenhav, Ron Kafri and Doron Lancet, The molecular roots of compositional inheritance, Journal of Theoretical Biology (2001), 213, 481-491. [PDF]

Daniel Segre’, Dafna Ben-Eli, David Deamer and Doron Lancet, The Lipid World, Origins Life Evol. Biosphere (2001) 31, 119-145. [PDF]

Yoav Gilad, Daniel Segre’, Karl Skorecki, Michael W. Nachman, Doron Lancet and Dror Sharon, Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes, Nature Genetics (2000) 26, 221-224. [PDF]

Daniel Segre’, Dafna Ben-Eli and Doron Lancet, Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies, Proc. Natl. Acad. Sci. USA (2000), 97(8), 4112-4117.[PDF] [PNAS on line] [Software & extras]

Daniel Segre’ and Doron Lancet, Composing Life, EMBO Reports (2000), 1(3), 217-222. [PDF] [cover]

Daniel Segre’ and Doron Lancet, A statistical chemistry approach to the origin of life, Chemtracts– Biochemistry and Molecular Biology (1999) 12 (6), 382-397. [preprint PDF]

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 Vol.213, Sheridan Books, Michigan, 2000, 373-378. [preprint PDF]

Daniel Segre’ , Doron Lancet, Ora Kedem and Yitzhak Pilpel, Graded Autocatalysis Replication Domain (GARD): kinetic analysis of self-replication in mutually catalytic sets, Origins Life Evol. Biosphere (1998) Vol.28, 501-514. [PDF] [Medline abstract]

Daniel Segre’, Yitzhak Pilpel and Doron Lancet, Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics, Physica A (1998) 249, 558-564.[PDF]

Daniel Segre’, 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, Vol.3755, 144-162 (1999). [PDF(5M)]

Daniel Segre’ 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, 123-131, Kluwer Academic Publishers, The Netherlands, 1998. [preprint PDF]

Daniel Segre’, 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, Editrice Compositori, Bologna, 1997, 469-476