Z. Jeffrey Chen
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View article: Discrete differential geometry for simulating nonlinear behaviors of flexible systems: A survey
Discrete differential geometry for simulating nonlinear behaviors of flexible systems: A survey Open
View article: Experimental Study on the Tribological Performance of Shark Denticle-Inspired Texture for Roller Cone Bit Bearings
Experimental Study on the Tribological Performance of Shark Denticle-Inspired Texture for Roller Cone Bit Bearings Open
During drilling in complex formations, the sliding bearings of roller cone bits are continuously subjected to low-speed, heavy-load, and boundary lubrication conditions, under which adhesive failure readily occurs, severely limiting drilli…
View article: Discrete Differential Geometry for Simulating Nonlinear Behaviors of Flexible Systems: A Survey
Discrete Differential Geometry for Simulating Nonlinear Behaviors of Flexible Systems: A Survey Open
Flexible slender structures such as rods, ribbons, plates, and shells exhibit extreme nonlinear responses bending, twisting, buckling, wrinkling, and self contact, that defy conventional simulation frameworks. Discrete Differential Geometr…
View article: AutoCode: LLMs as Problem Setters for Competitive Programming
AutoCode: LLMs as Problem Setters for Competitive Programming Open
Writing competitive programming problems is exacting. Authors must: set constraints, input distributions, and edge cases that rule out shortcuts; target specific algorithms (e.g., max-flow, dynamic programming, data structures); and calibr…
View article: <scp>SCL15</scp> Regulates the Release of Seed Dormancy in <scp> <i>Arabidopsis thaliana</i> </scp> by Integrating the Circadian Clock, Hormonal Signals and Cell Wall Remodelling
<span>SCL15</span> Regulates the Release of Seed Dormancy in <span> <i>Arabidopsis thaliana</i> </span> by Integrating the Circadian Clock, Hormonal Signals and Cell Wall Remodelling Open
Dormancy release and germination of the seed are two separate, but continuous phases controlled by both external (e.g., light and temperature) and internal (e.g., circadian clock and hormones) cues. In eudicot seeds, the endosperm tissues …
View article: Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance
Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance Open
Advancements in genomic and epigenetic research in both plants and animals have transformed breeding methods and biotechnological strategies for crop improvement, particularly in the face of extreme weather challenges. These breakthroughs …
View article: Collision-Free Motion Planning for Reconfigurable Cable-Driven Parallel Mechanisms Using Lie Algebra Space Interpolation
Collision-Free Motion Planning for Reconfigurable Cable-Driven Parallel Mechanisms Using Lie Algebra Space Interpolation Open
View article: Developmental variations of the reproductive organs of ganders from different goose breeds and the underlying mechanisms
Developmental variations of the reproductive organs of ganders from different goose breeds and the underlying mechanisms Open
View article: Genome resources for three modern cotton lines guide future breeding efforts
Genome resources for three modern cotton lines guide future breeding efforts Open
View article: Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants
Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants Open
As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic res…
View article: Cytoplasmic genome contributions to domestication and improvement of modern maize
Cytoplasmic genome contributions to domestication and improvement of modern maize Open
Background Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have …
View article: Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids
Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids Open
The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To dis…
View article: Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in<i>Arabidopsis</i>hybrids
Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in<i>Arabidopsis</i>hybrids Open
The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cyto…
View article: Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids
Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids Open
Hybrid vigor or heterosis has been widely applied in agriculture and extensively studied using genetic and gene expression approaches. However, the biochemical mechanism underlying heterosis remains elusive. One theory suggests that a decr…
View article: Asymmetric variation in DNA methylation during domestication and de-domestication of rice
Asymmetric variation in DNA methylation during domestication and de-domestication of rice Open
Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop…
View article: Protein nonadditive expression and solubility in<i>Arabidopsis</i>hybrids and allotetraploids
Protein nonadditive expression and solubility in<i>Arabidopsis</i>hybrids and allotetraploids Open
Interspecific hybridization in plants often leads to allopolyploids including most important crops such as wheat, cotton, and canola, while many other crops such as corn and sorghum are grown as hybrid. Both allopolyploids and hybrids show…
View article: Endosperm and Maternal-specific expression of<i>EIN2</i>in the endosperm affects endosperm cellularization and seed size in<i>Arabidopsis</i>
Endosperm and Maternal-specific expression of<i>EIN2</i>in the endosperm affects endosperm cellularization and seed size in<i>Arabidopsis</i> Open
Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) enco…
View article: Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
View article: Additional file 2 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 2 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 2: Table S1. Nine BM6S3 and six MB6S3 lines were genotyped using MaizeSNP6K.
View article: Additional file 10 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 10 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 10: Dataset S5. Transgenerational methylation loci correlate with gene expression levels.
View article: Additional file 9 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 9 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 9: Dataset S4. Transgenerational DNA methylation in backcross lines derived from modern maize W22 and teosinte.
View article: Additional file 3 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 3 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 3: Table S2. Summary of high-throughput data for backcrossing lineages.
View article: Additional file 8 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 8 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 8: Dataset S3. Initiation and transmission of transgenerational TCM and TCdM loci dependent on siRNAs.
View article: Additional file 6 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 6 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 6: Dataset S1. Hybrid-induced DNA methylation changes are transgenerational in multiple generations of backcrossing and selfing.
View article: Additional file 5 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 5 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 5: Table S4. Primer pairs used in this study.
View article: Additional file 7 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 7 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 7: Dataset S2. Transgenerational DNA methylation states resemble the nonrecurrent parent.
View article: Additional file 4 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
Additional file 4 of Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize Open
Additional file 4: Table S3. Transgenerational hybrid-induced DMRs for backcross lines.
View article: An epigenetic basis of inbreeding depression in maize
An epigenetic basis of inbreeding depression in maize Open
Inbreeding depression is linked to persistent epigenetic and gene expression changes, which are reversible by random mating.
View article: Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids
Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids Open
During evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying process remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidops…
View article: LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation
LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation Open
Background Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic…