Daniel Segrè

Daniel Segrè

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Daniel Segrè

Daniel Segrè

Publications by authors named "Daniel Segrè"

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Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism.

Nat Ecol Evol 2019 12 11;3(12):1715-1724. Epub 2019 Nov 11.

Bioinformatics Program, Boston University, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41559-019-1018-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881557PMC
December 2019

Twenty Years of "Lipid World": A Fertile Partnership with David Deamer.

Life (Basel) 2019 Sep 20;9(4). Epub 2019 Sep 20.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.

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http://dx.doi.org/10.3390/life9040077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6958426PMC
September 2019

A multidimensional perspective on microbial interactions.

FEMS Microbiol Lett 2019 Jun;366(11)

Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1093/femsle/fnz125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6610204PMC
June 2019

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.

Elife 2019 06 13;8. Epub 2019 Jun 13.

Department of Biomedical Engineering, Boston University, Boston, United States.

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http://dx.doi.org/10.7554/eLife.39733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609349PMC
June 2019

Designing Metabolic Division of Labor in Microbial Communities.

mSystems 2019 Mar-Apr;4(2). Epub 2019 Apr 9.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.

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http://msystems.asm.org/lookup/doi/10.1128/mSystems.00263-18
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http://dx.doi.org/10.1128/mSystems.00263-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456671PMC
April 2019

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.

Nat Commun 2019 01 9;10(1):103. Epub 2019 Jan 9.

Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1038/s41467-018-07946-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327061PMC
January 2019

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Diauxic Growth.

mSystems 2019 Jan-Feb;4(1). Epub 2019 Jan 15.

Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.

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http://dx.doi.org/10.1128/mSystems.00230-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446979PMC
January 2019

A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells.

Nat Biotechnol 2018 10 20;36(9):865-874. Epub 2018 Aug 20.

Disease Biophysics Group, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.4226DOI Listing
October 2018

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Oct 30.

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1128/mSystems.00181-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208640PMC
October 2018

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

Nat Commun 2017 11 16;8(1):1563. Epub 2017 Nov 16.

Bioinformatics Program, Boston University, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1038/s41467-017-01407-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691134PMC
November 2017

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

PLoS One 2017 20;12(1):e0170164. Epub 2017 Jan 20.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170164PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249160PMC
August 2017

Remnants of an Ancient Metabolism without Phosphate.

Cell 2017 03 2;168(6):1126-1134.e9. Epub 2017 Mar 2.

Bioinformatics Program, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston MA, 02215, USA; Department of Biology, Department of Physics, Boston University, Boston MA, 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674173013
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http://dx.doi.org/10.1016/j.cell.2017.02.001DOI Listing
March 2017

Mapping the landscape of metabolic goals of a cell.

Genome Biol 2016 05 23;17(1):109. Epub 2016 May 23.

Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-0968-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878026PMC
May 2016

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

PLoS Comput Biol 2016 Apr 15;12(4):e1004875. Epub 2016 Apr 15.

Center for Advanced Genomic Technology, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833320PMC
April 2016

Synthetic Ecology of Microbes: Mathematical Models and Applications.

J Mol Biol 2016 Feb 11;428(5 Pt B):837-61. Epub 2015 Nov 11.

Bioinformatics Program, Boston University, Boston, MA; Department of Biology, Boston University, Boston, MA; Department of Biomedical Engineering, Boston University, Boston, MA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.10.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798899PMC
February 2016

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli.

PLoS One 2014 12;9(12):e114608. Epub 2014 Dec 12.

Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America; Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114608PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264753PMC
October 2015

Species interactions differ in their genetic robustness.

Front Microbiol 2015 14;6:271. Epub 2015 Apr 14.

Department of Ecology, Evolution, and Behavior, University of Minnesota St. Paul, MN, USA ; BioTechnology Institute, University of Minnesota St. Paul, MN, USA.

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http://dx.doi.org/10.3389/fmicb.2015.00271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396422PMC
April 2015

Resource competition may lead to effective treatment of antibiotic resistant infections.

PLoS One 2013 13;8(12):e80775. Epub 2013 Dec 13.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America ; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America ; Department of Biology, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080775PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862480PMC
September 2014

Metabolic proximity in the order of colonization of a microbial community.

PLoS One 2013 30;8(10):e77617. Epub 2013 Oct 30.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077617PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813667PMC
August 2014

Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

Proc Natl Acad Sci U S A 2014 Jun 19;111(22):8227-32. Epub 2014 May 19.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111;

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http://dx.doi.org/10.1073/pnas.1321308111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050614PMC
June 2014

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.

Cell Rep 2014 May 1;7(4):1104-15. Epub 2014 May 1.

Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA; Department of Biology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.03.070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097880PMC
May 2014

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools.

PLoS Comput Biol 2013 29;9(8):e1003195. Epub 2013 Aug 29.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757068PMC
February 2014

The average enzyme principle.

FEBS Lett 2013 Sep 23;587(17):2891-4. Epub 2013 Jul 23.

Computational Biology Center, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.

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http://dx.doi.org/10.1016/j.febslet.2013.07.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983706PMC
September 2013

The cost of efficiency in energy metabolism.

Proc Natl Acad Sci U S A 2013 Jun 31;110(24):9629-30. Epub 2013 May 31.

Bioinformatics Program, Department of Biomedical Engineering, and Department of Biology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.1307485110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683743PMC
June 2013

Temporal expression-based analysis of metabolism.

PLoS Comput Biol 2012 29;8(11):e1002781. Epub 2012 Nov 29.

Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510039PMC
April 2013

Invariance and optimality in the regulation of an enzyme.

Biol Direct 2013 Mar 22;8. Epub 2013 Mar 22.

Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.

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http://dx.doi.org/10.1186/1745-6150-8-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665469PMC
March 2013

The dynamics of hybrid metabolic-genetic oscillators.

Chaos 2013 Mar;23(1):013132

Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.4793573DOI Listing
March 2013

Organization principles in genetic interaction networks.

Adv Exp Med Biol 2012 ;751:53-78

Boston University, Boston, MA 02215, USA.

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http://link.springer.com/10.1007/978-1-4614-3567-9_3
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http://dx.doi.org/10.1007/978-1-4614-3567-9_3DOI Listing
October 2012

Epistasis from functional dependence of fitness on underlying traits.

Proc Biol Sci 2012 Oct 15;279(1745):4156-64. Epub 2012 Aug 15.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1098/rspb.2012.1449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441082PMC
October 2012

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism.

BMC Syst Biol 2012 Sep 26;6:127. Epub 2012 Sep 26.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-6-127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484036PMC
September 2012

A system-level approach for deciphering the transcriptional response to prion infection.

Bioinformatics 2011 Dec 20;27(24):3407-14. Epub 2011 Oct 20.

Institute of Molecular Systems Biology, ETH, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btr580DOI Listing
December 2011

Ecosystems biology of microbial metabolism.

Curr Opin Biotechnol 2011 Aug 16;22(4):541-6. Epub 2011 May 16.

Bioinformatics Program, Department of Biology, Boston University, Boston, MA 02215, United States.

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http://dx.doi.org/10.1016/j.copbio.2011.04.018DOI Listing
August 2011

Diminishing returns epistasis among beneficial mutations decelerates adaptation.

Science 2011 Jun;332(6034):1190-2

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1126/science.1203799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244271PMC
June 2011

Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor.

Bioresour Technol 2011 Feb 12;102(3):2623-8. Epub 2010 Oct 12.

Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.biortech.2010.10.033DOI Listing
February 2011

Epistatic interaction maps relative to multiple metabolic phenotypes.

PLoS Genet 2011 Feb 10;7(2):e1001294. Epub 2011 Feb 10.

Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037399PMC
February 2011

Modeling the complex dynamics of enzyme-pathway coevolution.

Chaos 2010 Dec;20(4):045115

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.

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http://dx.doi.org/10.1063/1.3530440DOI Listing
December 2010

Environments that induce synthetic microbial ecosystems.

PLoS Comput Biol 2010 Nov 18;6(11):e1001002. Epub 2010 Nov 18.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987903PMC
November 2010

On the stability of metabolic cycles.

J Theor Biol 2010 Oct 29;266(4):536-49. Epub 2010 Jul 29.

Bioinformatics Program, 24 Cummington St, Boston, MA, United States. addresses:

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http://dx.doi.org/10.1016/j.jtbi.2010.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038548PMC
October 2010

Introduction to focus issue: genetic interactions.

Chaos 2010 Jun;20(2):026101

Department of Biology, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1063/1.3456057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909308PMC
June 2010

Signatures of arithmetic simplicity in metabolic network architecture.

PLoS Comput Biol 2010 Apr 1;6(4):e1000725. Epub 2010 Apr 1.

Program in Bioinformatics and Systems Biology, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848538PMC
April 2010

The importance of compartmentalization in metabolic flux models: yeast as an ecosystem of organelles.

Genome Inform 2010 Jan;22:41-55

Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

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http://prelude.bu.edu/publications/Klitgord_Segre_2009_submi
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January 2010

Co-evolution of metabolism and protein sequences.

Genome Inform 2010 Jan;22:156-66

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.

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January 2010

Optimality criteria for the prediction of metabolic fluxes in yeast mutants.

Genome Inform 2008 ;20:123-34

Graduate Program in Bioinformatics, Boston University, 44 Cummington St., Boston, Massachusetts 02215, USA.

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July 2009

Optimal metabolic regulation using a constraint-based model.

Genome Inform 2008 ;20:159-70

Graduate Program in Bioinformatics, Boston University, 44 Cummington St., Boston, Massachusetts 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245838PMC
http://dx.doi.org/10.1142/9781848163003_0014DOI Listing
July 2009

Comparative determination of biomass composition in differentially active metabolic States.

Genome Inform 2008 ;20:171-82

Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245841PMC
http://dx.doi.org/10.1142/9781848163003_0015DOI Listing
July 2009

Metabolic network model of a human oral pathogen.

J Bacteriol 2009 Jan 17;191(1):74-90. Epub 2008 Oct 17.

Boston University, Bioinformatics Program, Boston, MA 02215, USA.

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http://dx.doi.org/10.1128/JB.01123-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612419PMC
January 2009

Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species.

Genome Inform 2007 ;18:12-21

Boston University, Boston MA 02215, U.S.A.

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August 2008

Chromosomal periodicity of evolutionarily conserved gene pairs.

Proc Natl Acad Sci U S A 2007 Jun 11;104(25):10559-64. Epub 2007 Jun 11.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.0610776104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1890563PMC
June 2007

The effect of oxygen on biochemical networks and the evolution of complex life.

Science 2006 Mar;311(5768):1764-7

Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

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http://dx.doi.org/10.1126/science.1118439DOI Listing
March 2006

Modular epistasis in yeast metabolism.

Nat Genet 2005 Jan 12;37(1):77-83. Epub 2004 Dec 12.

Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ng1489DOI Listing
January 2005

The regulatory software of cellular metabolism.

Authors:
Daniel Segrè

Trends Biotechnol 2004 Jun;22(6):261-5

Department of Genetics, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01677799040011
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http://dx.doi.org/10.1016/j.tibtech.2004.04.013DOI Listing
June 2004

From annotated genomes to metabolic flux models and kinetic parameter fitting.

OMICS 2003 ;7(3):301-16

Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1089/153623103322452413DOI Listing
May 2004

Analysis of optimality in natural and perturbed metabolic networks.

Proc Natl Acad Sci U S A 2002 Nov 1;99(23):15112-7. Epub 2002 Nov 1.

Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.232349399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137552PMC
November 2002