Zobrazeno 1 - 10
of 49
pro vyhledávání: '"Daniel C Zielinski"'
Autor:
Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R Lamoureux, Amir Akbari, Bernhard O Palsson, Daniel C Zielinski
Publikováno v:
PLoS Computational Biology, Vol 20, Iss 1, p e1011824 (2024)
The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Regulons are typically determined either from resource-intensive experimental measurement of functional binding sites,
Externí odkaz:
https://doaj.org/article/4b004a6fbf5042ac9478a0f1892886dc
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 1, p e1008208 (2021)
Mathematical models of metabolic networks utilize simulation to study system-level mechanisms and functions. Various approaches have been used to model the steady state behavior of metabolic networks using genome-scale reconstructions, but formulatin
Externí odkaz:
https://doaj.org/article/3846a1961c114a0ab1c5d9e49137eaf3
Publikováno v:
PLoS ONE, Vol 12, Iss 12, p e0189880 (2017)
Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful to
Externí odkaz:
https://doaj.org/article/71a238d681964bd7a612368d71130041
Autor:
Yujiro Hirose, Daniel C. Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L. Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O. Palsson, Victor Nizet
Publikováno v:
mSystems, Vol 9, Iss 9 (2024)
ABSTRACT Streptococcus pyogenes is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of S. pyogenes, serotype M1 strains hold the greatest clinical relevance due to thei
Externí odkaz:
https://doaj.org/article/370f8241006e4225bac7c0888054f2d2
Autor:
Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R Hyduke, Sangwoo Kim, Daniel C Zielinski, Bernhard O Palsson
Publikováno v:
PLoS Computational Biology, Vol 10, Iss 9, p e1003837 (2014)
Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succ
Externí odkaz:
https://doaj.org/article/04a38c5545694958a010207816f363fe
The transcriptional regulatory network (TRN) of E. coli consists of thousands of interactions between regulators and DNA sequences. Inherently the DNA sequence is the primary determinant of the TRN; however, it is well established that the presence o
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::321b17ba8a8e1db3cf00c496cfc8f56f
https://doi.org/10.1101/2022.02.20.481200
https://doi.org/10.1101/2022.02.20.481200
Autor:
Josefin Johnsen, Patrick V. Phaneuf, Bernhard O. Palsson, Lei Yang, Se Hyeuk Kim, Sebastian Schulz, Christopher Dalldorf, Emre Özdemir, James T. Yurkovich, Muyao Wu, Richard Szubin, Adam M. Feist, Daniel C. Zielinski
Microbes are being engineered for an increasingly large and diverse set of applications. However, the designing of microbial genomes remains challenging due to the general complexity of biological system. Adaptive Laboratory Evolution (ALE) leverages
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::798f0b7cfa614cb1fb7745259b2d853d
https://doi.org/10.1101/2021.07.19.452699
https://doi.org/10.1101/2021.07.19.452699
Publikováno v:
Nature communications, vol 12, iss 1
Nature Communications
Akbari, A, Yurkovich, J T, Zielinski, D C & Palsson, B O 2021, ' The quantitative metabolome is shaped by abiotic constraints ', Nature Communications, vol. 12, 3178 . https://doi.org/10.1038/s41467-021-23214-9
Nature Communications, Vol 12, Iss 1, Pp 1-19 (2021)
Nature Communications
Akbari, A, Yurkovich, J T, Zielinski, D C & Palsson, B O 2021, ' The quantitative metabolome is shaped by abiotic constraints ', Nature Communications, vol. 12, 3178 . https://doi.org/10.1038/s41467-021-23214-9
Nature Communications, Vol 12, Iss 1, Pp 1-19 (2021)
Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic con
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6fc8e175cf386ebbdcaed1ca78861d08
https://escholarship.org/uc/item/61b4k01z
https://escholarship.org/uc/item/61b4k01z
Autor:
Cameron R. Lamoureux, Katherine T. Decker, Anand V. Sastry, Kevin Rychel, Ye Gao, John Luke McConn, Daniel C. Zielinski, Bernhard O. Palsson
SummaryTranscriptomic data is accumulating rapidly; thus, development of scalable methods for extracting knowledge from this data is critical. We assembled a top-down transcriptional regulatory network forEscherichia colifrom a 1035-sample, single-pr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c3414416fab64e5a6fdf53459f3ddb90
https://doi.org/10.1101/2021.04.08.439047
https://doi.org/10.1101/2021.04.08.439047
Publikováno v:
Trends in Biochemical Sciences. 43:960-969
Reaction equilibrium constants (Keqs) are key parameters that impose thermodynamic constraints on the function of a metabolic network. An important approach for Keq estimation is the group contribution method, which utilizes chemical moiety-based est