Daniel Segrè

Affiliations

Bioinformatics Program, Boston University, Boston, MA, USA. dsegre@bu.edu.
Biological Design Center, Boston University, Boston, MA, USA. dsegre@bu.edu.
Department of Physics, Boston University, Boston, MA, USA. dsegre@bu.edu.
Department of Biomedical Engineering, Department of Biology, Boston University, Boston, MA, USA. dsegre@bu.edu.

ORCID: http://orcid.org/0000-0003-4859-1914

Publications (39)

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

Nature ecology & evolution

Avec: Joshua E Goldford , Hyman Hartman , Robert Marsland , Daniel Segrè

animalcules: interactive microbiome analytics and visualization in R.

Microbiome

Avec: Yue Zhao , Anthony Federico , Tyler Faits , Solaiappan Manimaran , Daniel Segrè , Stefano Monti , W Evan Johnson

A thermodynamic atlas of carbon redox chemical space.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Adrian Jinich , Benjamin Sanchez-Lengeling , Haniu Ren , Joshua E Goldford , Elad Noor , Jacob N Sanders , Daniel Segrè , Alán Aspuru-Guzik

Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors.

Environmental microbiology

Avec: Dalit Roth Rosenberg , Markus Haber , Joshua Goldford , Maya Lalzar , Dikla Aharonovich , Ashraf Al-Ashhab , Yoav Lehahn , Daniel Segrè , Laura Steindler , Daniel Sher

Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure.

Journal of molecular evolution

Avec: Devlin Moyer , Alan R Pacheco , David B Bernstein , Daniel Segrè

Microbial metabolites in the marine carbon cycle.

Nature microbiology

Avec: 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 , Assaf Vardi

Computational design and engineering of an

iScience

Avec: Ali R Zomorrodi , Colin Hemez , Pol Arranz-Gibert , Terrence Wu , Farren J Isaacs , Daniel Segrè

Toward FAIR Representations of Microbial Interactions.

mSystems

Avec: Alan R Pacheco , Charlie Pauvert , Dileep Kishore , Daniel Segrè

Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models.

bioRxiv : the preprint server for biology

Avec: Devlin C Moyer , Justin Reimertz , Daniel Segrè , Juan I Fuxman Bass

Designing Metabolic Division of Labor in Microbial Communities.

mSystems

Avec: Meghan Thommes , Taiyao Wang , Qi Zhao , Ioannis C Paschalidis , Daniel Segrè

A multidimensional perspective on microbial interactions.

FEMS microbiology letters

Avec: Alan R Pacheco , Daniel Segrè

Environmental microbiome engineering for the mitigation of climate change.

Global change biology

Avec: Michael R Silverstein , Daniel Segrè , Jennifer M Bhatnagar

Antagonistic epistasis of Hnf4α and FoxO1 metabolic networks through enhancer interactions in β-cell function.

Molecular metabolism

Avec: Taiyi Kuo , Wen Du , Yasutaka Miyachi , Prasanna K Dadi , David A Jacobson , Daniel Segrè , Domenico Accili

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of

Frontiers in genetics

Avec: Shany Ofaim , Snorre Sulheim , Eivind Almaas , Daniel Sher , Daniel Segrè

Non-additive microbial community responses to environmental complexity.

Nature communications

Avec: Alan R Pacheco , Melisa L Osborne , Daniel Segrè

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of

mSystems

Avec: Antonella Succurro , Daniel Segrè , Oliver Ebenhöh

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

Life (Basel, Switzerland)

Avec: Doron Lancet , Daniel Segrè , Amit Kahana

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS).

Nature protocols

Avec: Ilija Dukovski , Djordje Bajić , Jeremy M Chacón , Michael Quintin , Jean C C Vila , Snorre Sulheim , Alan R Pacheco , David B Bernstein , William J Riehl , Kirill S Korolev , Alvaro Sanchez , William R Harcombe , Daniel Segrè

Protein cost minimization promotes the emergence of coenzyme redundancy.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Joshua E Goldford , Ashish B George , Avi I Flamholz , Daniel Segrè

A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.

Communications biology

Avec: Luca Zoccarato , Daniel Sher , Takeshi Miki , Daniel Segrè , Hans-Peter Grossart

Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria.

Applied and environmental microbiology

Avec: Shira Givati , Elena Forchielli , Dikla Aharonovich , Noga Barak , Osnat Weissberg , Natalia Belkin , Eyal Rahav , Daniel Segrè , Daniel Sher

Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions.

mSystems

Avec: Charles Jo , David B Bernstein , Natalie Vaisman , Horacio M Frydman , Daniel Segrè

Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations.

Communications biology

Avec: Konrad Herbst , Taiyao Wang , Elena J Forchielli , Meghan Thommes , Ioannis Ch Paschalidis , Daniel Segrè

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

eLife

Avec: David B Bernstein , Floyd E Dewhirst , Daniel Segrè

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.

Genome biology

Avec: David B Bernstein , Snorre Sulheim , Eivind Almaas , Daniel Segrè

BowSaw: Inferring Higher-Order Trait Interactions Associated With Complex Biological Phenotypes.

Frontiers in molecular biosciences

Avec: Demetrius DiMucci , Mark Kon , Daniel Segrè

Growth instabilities shape morphology and genetic diversity of microbial colonies.

Physical biology

Avec: Alexander Golden , Ilija Dukovski , Daniel Segrè , Kirill S Korolev

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation.

mSystems

Avec: Dileep Kishore , Gabriel Birzu , Zhenjun Hu , Charles DeLisi , Kirill S Korolev , Daniel Segrè

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability.

Materials today. Bio

Avec: Charles Jo , Jing Zhang , Jenny M Tam , George M Church , Ahmad S Khalil , Daniel Segrè , Tzu-Chieh Tang

Quantitative principles of microbial metabolism shared across scales.

Nature microbiology

Avec: Daniel Sher , Daniel Segrè , Michael J Follows

Microbial carbon use efficiency predicted from genome-scale metabolic models.

Nature communications

Avec: Mustafa Saifuddin , Jennifer M Bhatnagar , Daniel Segrè , Adrien C Finzi

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

Nature communications

Avec: Alan R Pacheco , Mauricio Moel , Daniel Segrè

An evolutionary algorithm for designing microbial communities via environmental modification.

Journal of the Royal Society, Interface

Avec: Alan R Pacheco , Daniel Segrè

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges.

Biodesign research

Avec: 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 J Roberts , Daniel Segrè , Susan Solomon , Dominic Woolf , Stan D Wullschleger , Xiaohan Yang

Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies.

mSystems

Avec: Elena Forchielli , Daniel Sher , Daniel Segrè

Metabolic complexity drives divergence in microbial communities.

bioRxiv : the preprint server for biology

Avec: Michael Silverstein , Jennifer M Bhatnagar , Daniel Segrè

Metabolic complexity drives divergence in microbial communities.

Nature ecology & evolution

Avec: Michael R Silverstein , Jennifer M Bhatnagar , Daniel Segrè

Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study.

Gates open research

Avec: Rotem Lapidot , Tyler Faits , Arshad Ismail , Mushal Allam , Zamantungwak Khumalo , William MacLeod , Geoffrey Kwenda , Zachariah Mupila , Ruth Nakazwe , Daniel Segrè , William Evan Johnson , Donald M Thea , Lawrence Mwananyanda , Christopher J Gill

Metabolic Flux Modeling in Marine Ecosystems.

Annual review of marine science

Avec: Helen Scott , Daniel Segrè

Réseau de co-auteurs

Alan R Pacheco 7 collaborations

Daniel Sher 6 collaborations

David B Bernstein 5 collaborations

Jennifer M Bhatnagar 4 collaborations

Joshua E Goldford 3 collaborations

Snorre Sulheim 3 collaborations

Kirill S Korolev 3 collaborations

Tyler Faits 2 collaborations

Dikla Aharonovich 2 collaborations

Dileep Kishore 2 collaborations

Meghan Thommes 2 collaborations

Taiyao Wang 2 collaborations

Michael R Silverstein 2 collaborations

Eivind Almaas 2 collaborations

Ilija Dukovski 2 collaborations

Elena Forchielli 2 collaborations

Charles Jo 2 collaborations

Charles DeLisi 2 collaborations

Hyman Hartman 1 collaboration

Robert Marsland 1 collaboration

Yue Zhao 1 collaboration

Anthony Federico 1 collaboration

Solaiappan Manimaran 1 collaboration

Stefano Monti 1 collaboration

W Evan Johnson 1 collaboration

Adrian Jinich 1 collaboration

Benjamin Sanchez-Lengeling 1 collaboration

Haniu Ren 1 collaboration

Elad Noor 1 collaboration

Jacob N Sanders 1 collaboration

Alán Aspuru-Guzik 1 collaboration

Dalit Roth Rosenberg 1 collaboration

Markus Haber 1 collaboration

Joshua Goldford 1 collaboration

Maya Lalzar 1 collaboration

Ashraf Al-Ashhab 1 collaboration

Yoav Lehahn 1 collaboration

Laura Steindler 1 collaboration

Devlin Moyer 1 collaboration

Mary Ann Moran 1 collaboration

Elizabeth B Kujawinski 1 collaboration

William F Schroer 1 collaboration

Shady A Amin 1 collaboration

Nicholas R Bates 1 collaboration

Erin M Bertrand 1 collaboration

Rogier Braakman 1 collaboration

C Titus Brown 1 collaboration

Markus W Covert 1 collaboration

Scott C Doney 1 collaboration

Sonya T Dyhrman 1 collaboration

Arthur S Edison 1 collaboration

A Murat Eren 1 collaboration

Naomi M Levine 1 collaboration

Liang Li 1 collaboration

Avena C Ross 1 collaboration

Mak A Saito 1 collaboration

Alyson E Santoro 1 collaboration

Ashley Shade 1 collaboration

Matthew B Sullivan 1 collaboration

Assaf Vardi 1 collaboration

Ali R Zomorrodi 1 collaboration

Colin Hemez 1 collaboration

Pol Arranz-Gibert 1 collaboration

Terrence Wu 1 collaboration

Farren J Isaacs 1 collaboration

Charlie Pauvert 1 collaboration

Devlin C Moyer 1 collaboration

Justin Reimertz 1 collaboration

Juan I Fuxman Bass 1 collaboration

Qi Zhao 1 collaboration

Ioannis C Paschalidis 1 collaboration

Taiyi Kuo 1 collaboration

Wen Du 1 collaboration

Yasutaka Miyachi 1 collaboration

Prasanna K Dadi 1 collaboration

David A Jacobson 1 collaboration

Domenico Accili 1 collaboration

Shany Ofaim 1 collaboration

Melisa L Osborne 1 collaboration

Antonella Succurro 1 collaboration

Oliver Ebenhöh 1 collaboration

Doron Lancet 1 collaboration

Amit Kahana 1 collaboration

Djordje Bajić 1 collaboration

Jeremy M Chacón 1 collaboration

Michael Quintin 1 collaboration

Jean C C Vila 1 collaboration

William J Riehl 1 collaboration

Alvaro Sanchez 1 collaboration

William R Harcombe 1 collaboration

Ashish B George 1 collaboration

Avi I Flamholz 1 collaboration

Luca Zoccarato 1 collaboration

Takeshi Miki 1 collaboration

Hans-Peter Grossart 1 collaboration

Shira Givati 1 collaboration

Noga Barak 1 collaboration

Osnat Weissberg 1 collaboration

Natalia Belkin 1 collaboration

Eyal Rahav 1 collaboration

Natalie Vaisman 1 collaboration

Horacio M Frydman 1 collaboration

Konrad Herbst 1 collaboration

Elena J Forchielli 1 collaboration

Ioannis Ch Paschalidis 1 collaboration

Floyd E Dewhirst 1 collaboration

Demetrius DiMucci 1 collaboration

Mark Kon 1 collaboration

Alexander Golden 1 collaboration

Gabriel Birzu 1 collaboration

Zhenjun Hu 1 collaboration

Jing Zhang 1 collaboration

Jenny M Tam 1 collaboration

George M Church 1 collaboration

Ahmad S Khalil 1 collaboration

Tzu-Chieh Tang 1 collaboration

Michael J Follows 1 collaboration

Mustafa Saifuddin 1 collaboration

Adrien C Finzi 1 collaboration

Mauricio Moel 1 collaboration

Aristides Patrinos 1 collaboration

Michael MacCracken 1 collaboration

Dan Drell 1 collaboration

George Annas 1 collaboration

Adam Arkin 1 collaboration

George Church 1 collaboration

Robert Cook-Deegan 1 collaboration

Henry Jacoby 1 collaboration

Mary Lidstrom 1 collaboration

Jerry Melillo 1 collaboration

Ron Milo 1 collaboration

Keith Paustian 1 collaboration

John Reilly 1 collaboration

Richard J Roberts 1 collaboration

Susan Solomon 1 collaboration

Dominic Woolf 1 collaboration

Stan D Wullschleger 1 collaboration

Xiaohan Yang 1 collaboration

Michael Silverstein 1 collaboration

Rotem Lapidot 1 collaboration

Arshad Ismail 1 collaboration

Mushal Allam 1 collaboration

Zamantungwak Khumalo 1 collaboration

William MacLeod 1 collaboration

Geoffrey Kwenda 1 collaboration

Zachariah Mupila 1 collaboration

Ruth Nakazwe 1 collaboration

William Evan Johnson 1 collaboration

Donald M Thea 1 collaboration

Lawrence Mwananyanda 1 collaboration

Christopher J Gill 1 collaboration

Helen Scott 1 collaboration