Publications

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2014

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 Early Edition]

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 Segre’: 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 bacterial growth conditions from bacterial physiology, BioRxiv (2014), doi: 10.1101/002287 [BioRxiv]

2013

Antonio L. C. Gomes, James E. Galagan and Daniel Segre’: 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]

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]

2012

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][PDF]

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]

2011

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]

2010

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]

2009

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]

2008

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. [PDF] [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]

2007

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]

2006

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]

2005

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]

1997-2004

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