Zobrazeno 1 - 10
of 20
pro vyhledávání: '"Ilija Dukovski"'
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Autor:
Michael Quintin, Ilija Dukovski, Alvaro Sanchez, Kirill S. Korolev, Daniel Segrè, Alan R. Pacheco, Djordje Bajić, Snorre Sulheim, David B. Bernstein, Jean C. C. Vila, William R. Harcombe, Jeremy M. Chacón, William J. Riehl
Publikováno v:
Nature Protocols. 16:5030-5082
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing micro
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a3c6941fc7ccc669d8f63e7f9ca63682
https://doi.org/10.1038/s41596-021-00593-3
https://doi.org/10.1038/s41596-021-00593-3
Autor:
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, Daniel Segrè
Publikováno v:
Cell Reports, Vol 7, Iss 4, Pp 1104-1115 (2014)
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metabolic mo
Externí odkaz:
https://doaj.org/article/9e3b6f64f81a4eda9eb261e55bd39a3f
Cellular aggregates assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of an aggregate influen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::75d4ad0f9f50fbbc6c08416504cda2f3
https://doi.org/10.1101/2022.03.28.486080
https://doi.org/10.1101/2022.03.28.486080
Publikováno v:
Physical biology. 19(5)
Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::10240cb3246771a8864a9dabfad18c8e
https://pubmed.ncbi.nlm.nih.gov/35901792
https://pubmed.ncbi.nlm.nih.gov/35901792
In microbial communities, many vital metabolic functions, including the degradation of cellulose, proteins and other complex macromolecules, are carried out by costly, extracellularly secreted enzymes. While significant effort has been dedicated to a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::460dc6f2817099fcea0890842d556806
https://doi.org/10.1101/2021.11.01.466736
https://doi.org/10.1101/2021.11.01.466736
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Autor:
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
Publikováno v:
Nature protocols. 16(11)
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing micro
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::759f30853313deb5af827d9c6d51596c
https://pubmed.ncbi.nlm.nih.gov/34635859
https://pubmed.ncbi.nlm.nih.gov/34635859
Autor:
Todd Thorsen, David S. Kong, Johanna Bobrow, Alla Ostrinskaya, Daniel Segrè, Bea Yu, Ilija Dukovski
Understanding how production of specific metabolites by gut microbes is modulated by interactions with surrounding species and by environmental nutrient availability is an important open challenge in microbiome research. As part of this endeavor, thi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c97964fdfc9831ed20a774a084118211
https://doi.org/10.1101/444760
https://doi.org/10.1101/444760
Autor:
Ilija Dukovski, William R. Harcombe, Brian R. Granger, Daniel Segrè, Alex H. Lang, Pankaj Mehta, Gracia Bonilla, William J. Riehl, Nicholas Leiby, Christopher J. Marx, Alex Betts, Amrita Kar
Publikováno v:
Cell Reports, Vol 7, Iss 4, Pp 1104-1115 (2014)
SummaryThe interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f9a1d634449f840a99f7f7cbc971c95c
http://www.sciencedirect.com/science/article/pii/S2211124714002800
http://www.sciencedirect.com/science/article/pii/S2211124714002800
Autor:
Murugappan Muthukumar, Ilija Dukovski
Publikováno v:
The Journal of Chemical Physics. 118:6648-6655
We have investigated the molecular origins of shish-kebab morphology occurring in polymer crystallization under extensional flow. Emergence of shish-kebabs is intimately related to the discontinuous coil-stretch transition of isolated chains. Our com
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::24ac8a010a6b3057a90d3ea52e726681
https://doi.org/10.1063/1.1557473
https://doi.org/10.1063/1.1557473
Publikováno v:
The Journal of Chemical Physics. 113:3697-3703
We simulated benzene adsorption in Na–X and Na–Y zeolites on a lattice of binding sites using a two-replica cluster Monte Carlo algorithm. Evidence for a vapor–liquid phase transition is explored for a range of guest–guest and host–guest en
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3e1a88dd1baf8ec9786407ea72b01fe0
https://doi.org/10.1063/1.1287655
https://doi.org/10.1063/1.1287655