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| Open AccessGenome-wide association analysis of plasma lipidome identifies 495 genetic associations
The human plasma lipidome captures risk for cardiometabolic diseases. Here, the authors perform univariate and multivariate genome-wide analyses of 179 lipid species in 7174 Finnish individuals, revealing genetic links between diseases and lipid species beyond the standard lipids HDL-Cholesterol, LDL-Cholesterol, Triglycerides, and total Cholesterol.
- Linda Ottensmann
- , Rubina Tabassum
- & Matti Pirinen
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Article
| Open AccesseQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk
Fetal development plays an important role in defining adult diabetes risk. Here, authors identified a genetic link between fetal pancreatic gene expression, obesity, and diabetes risk through eQTL mapping of iPSC-derived pancreatic progenitor cells.
- Jennifer P. Nguyen
- , Timothy D. Arthur
- & Kelly A. Frazer
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| Open AccessLeveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America
The Genomes-to-Fields (G2F) initiative has collected large amount of maize phenotype and genotype data. Here, the authors develop an automated workflow for curating the data, matching it with public weather and soil data, and generating environmental covariates for phenotypic data, which pave the way for several GxE investigations.
- Marco Lopez-Cruz
- , Fernando M. Aguate
- & Gustavo de los Campos
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Article
| Open AccessIsoform-resolved transcriptome of the human preimplantation embryo
Human embryo development involves extensive transcriptional remodeling. In this study, the authors apply long- and short-read RNA-Seq to profile the transcriptomes of 73 human preimplantation embryos spanning zygotic to blastocyst stages, identifying tens of thousands of additional isoforms transcribed from both known and unannotated gene loci.
- Denis Torre
- , Nancy J. Francoeur
- & Robert Sebra
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Article
| Open AccessFarnesoid X receptor activation by bile acids suppresses lipid peroxidation and ferroptosis
Ferroptosis is a regulated form of cell death occurring upon lipid peroxidation. Here, the authors discovered that activation of the Farnesoid X receptor by bile acids suppresses ferroptosis through upregulation of anti-ferroptotic genes.
- Juliane Tschuck
- , Lea Theilacker
- & Kamyar Hadian
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Article
| Open AccessRNA N6-methyladenosine modification-based biomarkers for absorbed ionizing radiation dose estimation
Radiation dosimetry are critical for the medical management of individuals exposed to ionizing radiation (IR). Here, authors show that the RNA m6A levels of Ncoa4, Ate1 and Fgf22 genes in peripheral blood cells could serve as dosimetry of IR exposure.
- Hongxia Chen
- , Xi Zhao
- & Gangqiao Zhou
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Article
| Open AccessThe chromatin network helps prevent cancer-associated mutagenesis at transcription-replication conflicts
Epigenetic alterations are frequent in human malignancies and have been shown to threaten genome integrity. Here the authors show that a chromatin network prevents R-loops and transcription-replication conflicts from genomic instability and mutagenic signatures frequently associated with cancer.
- Aleix Bayona-Feliu
- , Emilia Herrera-Moyano
- & Andrés Aguilera
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Article
| Open AccessXMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias
Fine-mapping prioritizes risk variants identified by genome-wide association studies to uncover biological mechanisms underlying complex traits. Here, the authors develop a reliable fine-mapping method (XMAP) by leveraging genetic diversity and accounting for confounding bias.
- Mingxuan Cai
- , Zhiwei Wang
- & Can Yang
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Article
| Open AccessSystematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation
Chameleolyser enables the accurate identification of genetic variants hidden within complex regions of the genome. Its application uncovers the disease-explanatory variant in 25 previously undiagnosed patients.
- Wouter Steyaert
- , Lonneke Haer-Wigman
- & Christian Gilissen
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Article
| Open AccessProlonging somatic cell proliferation through constitutive hox gene expression in C. elegans
Somatic cells in C. elegans stop dividing after completing their normal lineage at the end of development. Here, Heinze et al. show that constitutive expression of a hox gene prolongs proliferation beyond the restriction imposed by the cell lineage.
- Svenia D. Heinze
- , Simon Berger
- & Alex Hajnal
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Article
| Open AccessPH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes
How plant height is adaptive to high latitudes and high density planting is unclear. Here, the authors report a retrotransposon insertion in a WD40 protein encoding gene PH13 affects its interaction with GmCOP1s and increases the abundance of STF1/2, leading to reduced soybean height and increased shade resistance.
- Chao Qin
- , Ying-hui Li
- & Bin Liu
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Article
| Open AccessRNA-based translation activators for targeted gene upregulation
Many diseases are driven by the insufficient expression of critical genes, but few technologies are capable of rescuing these endogenous protein levels. Here, Cao et al. present an RNA-based technology that boosts protein production from endogenous mRNAs by upregulating their translation.
- Yang Cao
- , Huachun Liu
- & Bryan C. Dickinson
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Article
| Open AccessHidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants
The multiplex CRISPR system is the tool of choice for creating targeted tandemly arrayed genes (TAGs) deletions in plants. Here, the authors show that up to 80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion bi-alleles, an unwanted products of targeted TAG deletions.
- Jiuer Liu
- , Feng-Zhu Wang
- & Jian-Feng Li
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Article
| Open AccessA mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice
Cold stress hampers rice growth and yield. This paper demonstrates that mitochondrial superoxide plays a key role in cold responses, and identifies a pentatricopeptide repeat protein which modulates mitochondrial superoxide and rice cold tolerance.
- Xiaofeng Zu
- , Lilan Luo
- & Xiaofeng Cao
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Article
| Open AccessInvasive Californian death caps develop mushrooms unisexually and bisexually
The death cap mushroom Amanita phalloides is invading California but little is known about how it spreads through forests. Wang et al. discover that this fungus can develop mushrooms and sporulate without mating; the nuclei involved in unisexuality appear to have persisted in invaded habitats for decades.
- Yen-Wen Wang
- , Megan C. McKeon
- & Anne Pringle
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Article
| Open AccessA deep population reference panel of tandem repeat variation
Tandem repeats (TRs) comprise some of the most polymorphic regions of the human genome but are difficult to study. Here, the authors develop an ensemble-based genotyping method and characterize 1.7 million TRs across 3,550 humans from diverse populations.
- Helyaneh Ziaei Jam
- , Yang Li
- & Melissa Gymrek
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Article
| Open AccessGenome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease
Thyroid hormones play a critical role in regulation of multiple physiological functions. Here the authors via meta-analyses and detailed variant-to-gene mapping strategies implicate novel genes, pathways and associations for thyroid function and disease.
- Alexander T. Williams
- , Jing Chen
- & Catherine John
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Article
| Open AccessTelomouse—a mouse model with human-length telomeres generated by a single amino acid change in RTEL1
Telomeres are the protective caps of the chromosomes, which shorten with age. Smoom and colleagues developed a mouse strain with human-size telomeres. This mouse, termed Telomouse, is therefore an invaluable tool for studying human aging and cancer.
- Riham Smoom
- , Catherine Lee May
- & Yehuda Tzfati
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Article
| Open AccessDNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts
Epigenetic therapies are known to synergize with immunotherapies through the de-repression of endogenous retroviral element (ERV)-encoded promoters. Here the authors identify treatment-induced neoantigens and validate their ability to induce T cell response and anti-tumor effects in vitro and in patient samples.
- Ashish Goyal
- , Jens Bauer
- & Christoph Plass
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Article
| Open AccessMSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism
Interhomolog polymorphism, which is detected by MSH2-containing heterodimers, may affect crossover outcomes during meiosis. Here, the authors revealed antagonistic effects of MSH2 on interfering and non-interfering crossover pathways in Arabidopsis.
- Julia Dluzewska
- , Wojciech Dziegielewski
- & Piotr A. Ziolkowski
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Article
| Open Access3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription
In Drosophila, insulators may be involved in the organization of Topological Associated Domains, but the mechanism of action is a still a matter of investigation. Here the authors investigate the role of insulators in the 3D organization of the Drosophila genome by combining bioinformatics analysis and Hi-M, an imaging-based methods developed to detect the 3D positions of multiple genomic loci in single cells.
- Olivier Messina
- , Flavien Raynal
- & Marcelo Nollmann
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Article
| Open AccessCircular single-stranded DNA as switchable vector for gene expression in mammalian cells
Synthetic gene networks in mammalian cells are currently limited to either transcription factors or RNA regulators. Here, the authors develop a regulatory approach based on circular single-stranded DNA, which can be used as a conformationally switchable genetic vector in mammalian cells.
- Linlin Tang
- , Zhijin Tian
- & Jie Song
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Article
| Open AccessRobotized indoor phenotyping allows genomic prediction of adaptive traits in the field
Robotized indoor phenotyping allows measuring of plant physiological traits at high throughput, but is often considered as non-relevant for field conditions. Here, the authors show that maize traits measured indoor translate to the field and can be inferred via genomic prediction.
- Jugurta Bouidghaghen
- , Laurence Moreau
- & François Tardieu
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Article
| Open AccessLow mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.
- Ashley T. Sendell-Price
- , Frank J. Tulenko
- & Manfred Schartl
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Article
| Open AccessDeveloping mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library
Ddd-Aderived cytosine base editors (DdCBEs) are important for research of mitochondrial DNA mutation diseases. Here the authors report a strategy for screening and characterising dsDNA cytidine deaminases, and identify 7 DddA homologs which they optimise to minimise nuclear and mitochondrial off-target editing.
- Haifeng Sun
- , Zhaojun Wang
- & Bin Shen
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Article
| Open AccessDe novo genome assembly depicts the immune genomic characteristics of cattle
The genomic organisation of the cattle genome has been assembled to a limited level of resolution. Here using long range nanopore sequencing the authors present a cattle genome assembly concentrating on characterising the immunogenomic loci, particularly T cell receptor (TR), immunoglobulin (IG) and MHC genes, from one animal.
- Ting-Ting Li
- , Tian Xia
- & Tao Li
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Article
| Open AccessA DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci
The mechanism of spatiotemporal gene regulation during animal development is a fundamental question in biology. Here the authors show that the DEAD-box helicase DDX-23 controls stem cell fate by driving the formation of NAB repressive transcriptional condensates.
- Akiko Doi
- , Gianmarco D. Suarez
- & H. Robert Horvitz
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Article
| Open AccessClinical utility of polygenic scores for cardiometabolic disease in Arabs
Arabs account for 5% of the world population and have a high burden of cardiometabolic disease. Here, the authors optimize polygenic scores for 10 cardiometabolic traits in 5399 Arabs, achieving a performance on par with that among European-ancestry individuals.
- Injeong Shim
- , Hiroyuki Kuwahara
- & Akl C. Fahed
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Article
| Open AccessSonogenetic control of multiplexed genome regulation and base editing
Exogenous control of genes in vivo is important. Here the authors report a system that can be inducibly activated through thermal energy produced by ultrasound absorption and use this to control induction of gene activation and base editing: they apply this in cell lines and in a mouse model.
- Pei Liu
- , Josquin Foiret
- & Lei S. Qi
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Article
| Open AccessReprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice
Skeletal muscle’s metabolic status has an impact on health and the prognosis of chronic diseases. Here the authors unveil an atlas of open chromatin regions in skeletal muscles using single-nucleus techniques on juvenile male mice, highlight regulatory dynamics between normal and denervated states, and pinpoint ELK4 as a pivotal factor in muscle atrophy.
- Hongchun Lin
- , Hui Peng
- & Zhaoyong Hu
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Article
| Open AccessPaternal DNA methylation is remodeled to maternal levels in rice zygote
Liu et al. show that zygotic remodelling of paternal DNA methylation is matched to maternal levels in hybrids and that parental-specific epigenomes are re-established during embryogenesis, highlighting genetic control of epigenetic inheritance.
- Qian Liu
- , Xuan Ma
- & Dao-Xiu Zhou
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Article
| Open AccessNeST: nested hierarchical structure identification in spatial transcriptomic data
A wide variety of tissues exhibit nested hierarchical organisation of cells in gene expression and activities. Here, authors present NeST, a method for spatial transcriptomics to identify such structures and uncover their functions via ligand-receptor communication, in both two and three dimensions.
- Benjamin L. Walker
- & Qing Nie
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Article
| Open AccessThe admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes
The brushtail possum is a treasured Australian marsupial, but also a harmful pest introduced into New Zealand. Here, using functional genomics and a new chromosome-level genome assembly of New Zealand possums, Bond et al. quantify their genome admixture and identify unique parent-specific and weaning associated gene expression.
- Donna M. Bond
- , Oscar Ortega-Recalde
- & Timothy A. Hore
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Article
| Open AccessFibrocystin/Polyductin releases a C-terminal fragment that translocates into mitochondria and suppresses cystogenesis
Fibrocystin/Polyductin (FPC) is a large ciliary membrane protein encoded by PKHD1 which, when mutated, causes ARPKD. Here, the authors show that FPC suppresses cyst development in the kidney of mouse models through the release and mitochondrial translocation of its C terminal product.
- Rebecca V Walker
- , Qin Yao
- & Feng Qian
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Article
| Open AccessMiniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
The filarial worm Brugia malayi has evolved a mutualistic association with the endosymbiotic bacteria Wolbachia. Here, Sounart et al describe a spatial transcriptomic technique that can spatially resolve these miniature specimens.
- Hailey Sounart
- , Denis Voronin
- & Stefania Giacomello
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Article
| Open AccessBenchmarking strategies for cross-species integration of single-cell RNA sequencing data
The growing number of available single-cell RNA-sequencing datasets from different species creates opportunities to explore evolutionary relationships between cell types across species. Here, the authors compare different strategies for cross-species integration of these data and offer guidelines for effective integration.
- Yuyao Song
- , Zhichao Miao
- & Irene Papatheodorou
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Article
| Open AccessMitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins
TDP43 proteinopathies are a devastating group of neurodegenerative disorders. Here the authors show that RNA-targeting CRISPR effector proteins can be used to mitigate TDP-43 pathology when targeting ataxin-2, a modifier of TDP-43-associated toxicity, and apply this to a mouse model.
- M. Alejandra Zeballos C.
- , Hayden J. Moore
- & Thomas Gaj
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Article
| Open AccessRewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication
The integration of transcriptomics and epigenomics data helps to better understand the regulatory and topological changes in glioblastoma subtypes. Here, the authors map the promoter-enhancer interactome and regulatory landscape and show changes in promoter-enhancer interactions, chromatin accessibility, and redistribution of histone marks across four glioblastoma subtypes.
- Chaitali Chakraborty
- , Itzel Nissen
- & Silvia Remeseiro
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Article
| Open AccessLipid nanoparticles with PEG-variant surface modifications mediate genome editing in the mouse retina
There is a need for development of efficient delivery vehicles for the treatment of inherited retinal degeneration with gene therapy. Here, Gautam et al., show that surface modifications of lipid nanoparticles with PEG variants alters their cellular tropism allowing gene editing in diverse retinal cell types in mice.
- Milan Gautam
- , Antony Jozic
- & Gaurav Sahay
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Article
| Open AccessCharacterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis
Horse chestnut (Aesculus chinensis) is a tree species that can produce medicinal compounds such as aescin and aesculin. Here, the authors assemble its genome, identify key genes involved in the biosynthesis of these two group of compounds, and achieve the de novo synthesis of aesculin in E. coli.
- Wei Sun
- , Qinggang Yin
- & Shilin Chen
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Article
| Open AccessNext-generation CRISPR gene-drive systems using Cas12a nuclease
One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives, which manipulate insect populations due to their ability to rapidly propagate desired genetic traits into a target population. Here the authors describe a Cas12a gene drive system whose activity can be finetuned in a temperature-dependent manner.
- Sara Sanz Juste
- , Emily M. Okamoto
- & Víctor López Del Amo
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Article
| Open AccessSimulation of undiagnosed patients with novel genetic conditions
Rare Mendelian disorders pose a major diagnostic challenge, but evaluation of automated tools that aim to uncover causal genes tools is limited. Here, the authors present a computational pipeline that simulates realistic clinical datasets to address this deficit.
- Emily Alsentzer
- , Samuel G. Finlayson
- & Isaac S. Kohane
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Article
| Open AccessOncogenic context shapes the fitness landscape of tumor suppression
Alterations in oncogenes and tumor suppressor genes are a hallmark of cancer, yet how they interact remains poorly understood. Here, the authors describe a quantitative functional cancer genomics platform in genetically engineered mice, and uncover complex interactions between tumor suppressors and KRAS, BRAF, and EGFR oncogenes across more than 100 different lung tumor genotypes.
- Lily M. Blair
- , Joseph M. Juan
- & Ian P. Winters
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Article
| Open AccessSARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
SARS-CoV-2 wastewater surveillance could provide an important means of monitoring population trends as clinical testing decreases. Here, the authors demonstrate the use of wastewater to track variants of concern through a sentinel wastewater surveillance system in South Africa.
- Mukhlid Yousif
- , Said Rachida
- & Kerrigan McCarthy
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Article
| Open AccessSingle-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects
Here the authors develop DAESC, a statistical method for differential allele-specific expression analysis using single-cell RNA-seq data. Application of DAESC identifies dynamic regulatory effects along endoderm differentiation and differential effects between type 2 diabetes and healthy controls.
- Guanghao Qi
- , Benjamin J. Strober
- & Alexis Battle
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Article
| Open AccessRegulation of CTCF loop formation during pancreatic cell differentiation
Here the authors show that differentiation of hESCs into pancreatic cells involves changes in CTCF loops by alteration of pioneer factor recruitment, histone modifications, and DNA methylation, leading to changes in enhancer-promoter interactions and gene expression.
- Xiaowen Lyu
- , M. Jordan Rowley
- & Victor G. Corces
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Article
| Open AccessMitogenomic evolutionary rates in bilateria are influenced by parasitic lifestyle and locomotory capacity
The diversity of mitogenomic evolutionary rates among animal lineages remains poorly explained. Here, an analysis of mitogenomes of almost 11,000 bilaterian species provides evidence that parasitism and locomotory capacity are major variables explaining elevation of mitogenomic evolutionary rates.
- Ivan Jakovlić
- , Hong Zou
- & Dong Zhang
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Article
| Open AccessImmunosuppression causes dynamic changes in expression QTLs in psoriatic skin
Psoriasis is a chronic, systemic inflammatory condition primarily affecting skin. Here, the authors investigate the genetic basis of gene expression in skin biopsies from psoriasis patients and interactions with inflammation to better understand mechanisms of the disease.
- Qian Xiao
- , Joseph Mears
- & Soumya Raychaudhuri
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Article
| Open AccessThe pan-genome and local adaptation of Arabidopsis thaliana
Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.
- Minghui Kang
- , Haolin Wu
- & Jianquan Liu
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