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Author Correction: A quantitative method for proteome reallocation using minimal regulatory interventions.

Gustavo Lastiri-Pancardo, Jonathan S Mercado-Hernández, Juhyun Kim, José I Jiménez, José Utrilla,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, 16(11):1277]

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The subcellular architecture of the xyl gene expression flow of the TOL catabolic plasmid of Pseudomonas putida mt-2

Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo,

ABSTRACT Despite intensive research on the biochemical and regulatory features of the archetypal catabolic TOL system borne by pWW0 of Pseudomonas putida mt-2, the physical arrangement and tridimensional logic of the xyl gene expression flow remains unknown. In this work, the spatial distribution of specific xyl mRNAs with respect to ... Read more >>

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A quantitative method for proteome reallocation using minimal regulatory interventions.

Gustavo Lastiri-Pancardo, Jonathan S Mercado-Hernández, Juhyun Kim, José I Jiménez, José Utrilla,

Engineering resource allocation in biological systems is an ongoing challenge. Organisms allocate resources for ensuring survival, reducing the productivity of synthetic biology functions. Here we present a new approach for engineering the resource allocation of Escherichia coli by rationally modifying its transcriptional regulatory network. Our method (ReProMin) identifies the minimal ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2020, 16(9):1026-1033]

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Crystal structure of human LDB1 in complex with SSBP2.

Hongyang Wang, Juhyun Kim, Zhizhi Wang, Xiao-Xue Yan, Ann Dean, Wenqing Xu,

The Lim domain binding proteins (LDB1 and LDB2 in human and Chip in Drosophila) play critical roles in cell fate decisions through partnership with multiple Lim-homeobox and Lim-only proteins in diverse developmental systems including cardiogenesis, neurogenesis, and hematopoiesis. In mammalian erythroid cells, LDB1 dimerization supports long-range connections between enhancers and ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2020, 117(2):1042-1048]

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DeepTetrad: high-throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana.

Eun-Cheon Lim, Jaeil Kim, Jihye Park, Eun-Jung Kim, Juhyun Kim, Yeong Mi Park, Hyun Seob Cho, Dohwan Byun, Ian R Henderson, Gregory P Copenhaver, Ildoo Hwang, Kyuha Choi,

Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. Here ... Read more >>

Plant J (The Plant journal : for cell and molecular biology)
[2020, 101(2):473-483]

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Trade-offs between gene expression, growth and phenotypic diversity in microbial populations.

Juhyun Kim, Alexander Darlington, Manuel Salvador, José Utrilla, José I Jiménez,

Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise ... Read more >>

Curr Opin Biotechnol (Current opinion in biotechnology)
[2020, 62:29-37]

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Device Optimization of Nano-Plate Transistors for 3.5 nm Technology Node.

Juhyun Kim, Myunggon Kang, Jongwook Jeon, Hyungcheol Shin,

In this paper, lateral gate-all-around nano-plate transistors (NP-FETs) for 3.5 nm technology node were optimized and compared with other nodes such as 7 nm and 5 nm node devices. The transistors' electrostatic was analyzed using a 3D TCAD simulation. We firstly optimized physical parameters such as channel radius and thickness. ... Read more >>

J Nanosci Nanotechnol (Journal of nanoscience and nanotechnology)
[2019, 19(10):6771-6775]

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A quantitative method for proteome reallocation using minimal regulatory interventions

Gustavo Lastiri-Pancardo, J.S Mercado-Hernandez, Juhyun Kim, José Jiménez, José Utrilla,

Abstract Engineering resource allocation in biological systems for synthetic biology applications is an ongoing challenge. Wild type organisms allocate abundant cellular resources for ensuring survival in changing environments, reducing the productivity of engineered functions. Here we present a novel approach for engineering the resource allocation of Escherichia coli by rationally ... Read more >>

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DeepTetrad: high-throughput analysis of meiotic tetrads by deep learning in plants

Eun-Cheon Lim, Jaeil Kim, Jihye Park, Eun-Jung Kim, Juhyun Kim, Hyun Seob Cho, Dohwan Byun, Ian Henderson, Gregory Copenhaver, Ildoo Hwang, Kyuha Choi,

Abstract Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. ... Read more >>

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Afterglow dielectric-barrier discharge air plasma (ADDAP) for the inactivation of Escherichia coli O157:H7

Juhyun Kim, Chulkyoon Mok, Pradeep Puligundla, Taehoon Lee,

The afterglow of an atmospheric pressure plasma can conveniently be used for large scale decontamination operations. In the present study, an afterglow dielectric-barrier discharge air plasma (ADDAP) was used to inactivate Escherichia coli O157:H7, which was used as a model microorganism for studying the inactivation effect of the plasma. ADDAP ... Read more >>

(Lebensmittel-Wissenschaft + [i.e. und] Technologie. Food science + technology. Science + technologie alimentaire)
[2019, 105:177-181]

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Microbial Genes for a Circular and Sustainable Bio-PET Economy.

Manuel Salvador, Umar Abdulmutalib, Jaime Gonzalez, Juhyun Kim, Alex A Smith, Jean-Loup Faulon, Ren Wei, Wolfgang Zimmermann, Jose I Jimenez,

Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for ... Read more >>

Genes (Basel) (Genes)
[2019, 10(5):]

Cited: 4 times

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Genes for a Circular and Sustainable Bio-PET Economy

Manuel Salvador, Umar Abdulmutalib, Jaime Gonzalez, Juhyun Kim, Alex Smith, Jean-Loup Faulon, Wolfgang Zimmermann, Jose Jimenez,

Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for ... Read more >>

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OPENMENDEL: a cooperative programming project for statistical genetics.

Hua Zhou, Janet S Sinsheimer, Douglas M Bates, Benjamin B Chu, Christopher A German, Sarah S Ji, Kevin L Keys, Juhyun Kim, Seyoon Ko, Gordon D Mosher, Jeanette C Papp, Eric M Sobel, Jing Zhai, Jin J Zhou, Kenneth Lange,

Statistical methods for genome-wide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software. In our view, a collaborative effort of statistical geneticists is required to develop open source software targeted ... Read more >>

Hum. Genet. (Human genetics)
[2020, 139(1):61-71]

Cited: 1 time

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Spatial organization of the gene expression hardware in Pseudomonas putida.

Juhyun Kim, Angel Goñi-Moreno, Belén Calles, Víctor de Lorenzo,

The localization of ribosomes, RNA polymerase (RNAP) and the nucleoid of Pseudomonas putida cells has been inspected with genetic, microscopical and physiological approaches. To this end, strains of P. putida were constructed with fluorescent tags to either ribosomal proteins or the RNAP or both. Their relative positions in respect to ... Read more >>

Environ. Microbiol. (Environmental microbiology)
[2019, 21(5):1645-1658]

Cited: 1 time

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Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes.

Heïdi Serra, Kyuha Choi, Xiaohui Zhao, Alexander R Blackwell, Juhyun Kim, Ian R Henderson,

During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying ... Read more >>

PLoS Genet (PLoS genetics)
[2018, 14(12):e1007843]

Cited: 2 times

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Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations.

Alexander P S Darlington, Juhyun Kim, José I Jiménez, Declan G Bates,

The use of orthogonal ribosomes in combination with dynamic resource allocation controllers is a promising approach for relieving the negative effects of cellular resource limitations on the modularity of synthetic gene circuits. Here, we develop a detailed mechanistic model of gene expression and resource allocation, which when simplified to a ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2018, 7(11):2485-2496]

Cited: 1 time

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The interplay of EIIANtr with C-source regulation of the Pu promoter of Pseudomonas putida mt-2.

Danilo Pérez-Pantoja, Juhyun Kim, Raúl Platero, Víctor de Lorenzo,

The presence of some sugars (e.g. glucose) downregulates the activity of the Pu promoter of plasmid pWW0 of Pseudomonas putida mt-2, which drives the upper TOL operon for biodegradation of m-xylene. Genetic evidence produced 20 years ago documented an effect of the EIIANtr (PtsN) protein of the nitrogen-related phosphoenolpyruvate-dependent phosphotransferase ... Read more >>

Environ. Microbiol. (Environmental microbiology)
[2018, 20(12):4555-4566]

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Algorithms for Fitting the Constrained Lasso.

Brian R Gaines, Juhyun Kim, Hua Zhou,

We compare alternative computing strategies for solving the constrained lasso problem. As its name suggests, the constrained lasso extends the widely-used lasso to handle linear constraints, which allow the user to incorporate prior information into the model. In addition to quadratic programming, we employ the alternating direction method of multipliers ... Read more >>

J Comput Graph Stat (Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America)
[2018, 27(4):861-871]

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MGLM: An R Package for Multivariate Categorical Data Analysis.

Juhyun Kim, Yiwen Zhang, Joshua Day, Hua Zhou,

Data with multiple responses is ubiquitous in modern applications. However, few tools are available for regression analysis of multivariate counts. The most popular multinomial-logit model has a very restrictive mean-variance structure, limiting its applicability to many data sets. This article introduces an R package MGLM, short for multivariate response generalized ... Read more >>

(The R journal)
[2018, 10(1):73-90]

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Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences.

Arielle Baker, Brian Kalmbach, Mieko Morishima, Juhyun Kim, Ashley Juavinett, Nuo Li, Nikolai Dembrow,

Neocortical pyramidal neurons with somata in layers 5 and 6 are among the most visually striking and enigmatic neurons in the brain. These deep-layer pyramidal neurons (DLPNs) integrate a plethora of cortical and extracortical synaptic inputs along their impressive dendritic arbors. The pattern of cortical output to both local and ... Read more >>

J. Neurosci. (The Journal of neuroscience : the official journal of the Society for Neuroscience)
[2018, 38(24):5441-5455]

Cited: 6 times

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2-Methylacrylamide as a bioisoster of thiourea group for 1,3-dibenzylthioureido TRPV1 receptor antagonists.

Seol Rin Park, Juhyun Kim, Sun Young Lee, Young-Ho Park, Hee-Doo Kim,

In order to replace thiourea group with the more drug-like moiety for 1,3-dibenzylthioureas having TRPV1 antagonist activity, we introduced a set of functional groups between the two aromatic rings based on bioisosteric replacement. The synthesized bioisosteres of 1,3-dibenzylthioureas were tested for their antagonist activities on TRPV1 by 45Ca2+-influx assay using ... Read more >>

Bioorg. Med. Chem. Lett. (Bioorganic & medicinal chemistry letters)
[2018, 28(11):2080-2083]

Cited: 0 times

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Variance Component Selection With Applications to Microbiome Taxonomic Data.

Jing Zhai, Juhyun Kim, Kenneth S Knox, Homer L Twigg, Hua Zhou, Jin J Zhou,

High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a ... Read more >>

(Frontiers in microbiology)
[2018, 9:509]

Cited: 2 times

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Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes.

Alexander P S Darlington, Juhyun Kim, José I Jiménez, Declan G Bates,

Introduction of synthetic circuits into microbes creates competition between circuit and host genes for shared cellular resources, such as ribosomes. This can lead to the emergence of unwanted coupling between the expression of different circuit genes, complicating the design process and potentially leading to circuit failure. By expressing a synthetic ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):695]

Cited: 3 times

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Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions.

Kyuha Choi, Xiaohui Zhao, Andrew J Tock, Christophe Lambing, Charles J Underwood, Thomas J Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A Ziolkowski, Nataliya E Yelina, Ildoo Hwang, Robert A Martienssen, Ian R Henderson,

Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, ... Read more >>

Genome Res (Genome research)
[2018, 28(4):532-546]

Cited: 32 times

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A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus.

Juhyun Kim, Youngsung Joo, Jinseul Kyung, Myeongjune Jeon, Jong Yoon Park, Ho Gyun Lee, Doo Soo Chung, Eunju Lee, Ilha Lee,

Ranunculus trichophyllus is an amphibious plant that produces thin and cylindrical leaves if grown under water but thick and broad leaves if grown on land. We found that such heterophylly is widely controlled by two plant hormones, abscisic acid (ABA) and ethylene, which control terrestrial and aquatic leaf development respectively. ... Read more >>

PLoS Genet. (PLoS genetics)
[2018, 14(2):e1007208]

Cited: 4 times

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