Richard Szubin
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Explore the profile of Richard Szubin including associated specialties, affiliations and a list of published articles.
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66
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1383
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Recent Articles
1.
Dalldorf C, Hefner Y, Szubin R, Johnsen J, Mohamed E, Li G, et al.
Mol Biol Evol
. 2024 Nov;
41(11).
PMID: 39531644
The transcriptional regulatory network (TRN) in bacteria is thought to rapidly evolve in response to selection pressures, modulating transcription factor (TF) activities and interactions. In order to probe the limits...
2.
Rodionova I, Lim H, Gao Y, Rodionov D, Hutchison Y, Szubin R, et al.
Commun Biol
. 2024 Sep;
7(1):1160.
PMID: 39289465
Hydrogen sulfide (HS), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress and potentially increases antimicrobial resistance (AMR). CyuR is a Cys-dependent transcription regulator, responsible for the...
3.
Yuan Y, Al Bulushi T, Sastry A, Sancar C, Szubin R, Golden S, et al.
Proc Natl Acad Sci U S A
. 2024 Sep;
121(38):e2410492121.
PMID: 39269777
is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it...
4.
Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski D, et al.
mSystems
. 2024 Jun;
9(7):e0030524.
PMID: 38829048
Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth...
5.
Choe D, Olson C, Szubin R, Yang H, Sung J, Feist A, et al.
Nat Commun
. 2024 Mar;
15(1):2356.
PMID: 38490991
Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The...
6.
Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, et al.
mSystems
. 2024 Feb;
9(3):e0125723.
PMID: 38349131
Importance: We have studied , a beneficial probiotic microbe that plays a significant role in our health and production of sustainable foods, a type of foods that are nutritionally dense...
7.
Menon N, Poudel S, Sastry A, Rychel K, Szubin R, Dillon N, et al.
mSystems
. 2024 Jan;
9(2):e0060623.
PMID: 38189271
causes severe infections in humans, resists multiple antibiotics, and survives in stressful environmental conditions due to modulations of its complex transcriptional regulatory network (TRN). Unfortunately, our global understanding of the...
8.
Hyun J, Monk J, Szubin R, Hefner Y, Palsson B
Nat Commun
. 2023 Nov;
14(1):7690.
PMID: 38001096
Surveillance programs for managing antimicrobial resistance (AMR) have yielded thousands of genomes suited for data-driven mechanism discovery. We present a workflow integrating pangenomics, gene annotation, and machine learning to identify...
9.
Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, et al.
Cell Rep
. 2023 Sep;
42(9):113105.
PMID: 37713311
Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently...
10.
Sandberg T, Wise K, Dalldorf C, Szubin R, Feist A, Glass J, et al.
iScience
. 2023 Aug;
26(9):107500.
PMID: 37636038
The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the genome and chemically synthesized . Here, we report the...