Genome Biology
Papers 6,629
1 page of 663 pages (6,629 results)
#1Xingguo Zhang (Henan Agricultural University)H-Index: 9
#2Manish K. Pandey (ICRISAT: International Crops Research Institute for the Semi-Arid Tropics)H-Index: 40
Last. Rajeev K. Varshney (Murdoch University)H-Index: 112
view all 11 authors...
Background null Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. null Results null Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gen...
#1Wei Hu (Chinese Academy of Tropical Agricultural Sciences)H-Index: 28
#2Changmian Ji (Chinese Academy of Tropical Agricultural Sciences)H-Index: 8
Last. Jinghao Yang (Chinese Academy of Tropical Agricultural Sciences)H-Index: 2
view all 34 authors...
Background null Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. null Results null We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a ge...
#1Hong Mei (ShanghaiTech University)H-Index: 2
#2Zhao Zha (ShanghaiTech University)H-Index: 3
Last. Jia LiuH-Index: 44
view all 10 authors...
#1Xianrong Wong (Johns Hopkins University)H-Index: 7
#2Victoria E. Hoskins (JHUSOM: Johns Hopkins University School of Medicine)H-Index: 4
Last. Karen L. Reddy (Johns Hopkins University)H-Index: 20
view all 6 authors...
BACKGROUND The dynamic 3D organization of the genome is central to gene regulation and development. The nuclear lamina influences genome organization through the tethering of lamina-associated domains (LADs) to the nuclear periphery. Evidence suggests that lamins A and C are the predominant lamins involved in the peripheral association of LADs, potentially serving different roles. RESULTS Here, we examine chromosome architecture in mouse cells in which lamin A or lamin C are downregulated. We fi...
#1Yu Chen (UAB: University of Alabama at Birmingham)
#2Yixin Zhang (UAB: University of Alabama at Birmingham)
Last. Zechen Chong (UAB: University of Alabama at Birmingham)H-Index: 23
view all 5 authors...
Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read ass...
#1Runze Wang (NAU: Nanjing Agricultural University)H-Index: 10
#2Xue Yongsong (NAU: Nanjing Agricultural University)H-Index: 2
Last. Jiaming Li (NAU: Nanjing Agricultural University)H-Index: 7
view all 19 authors...
Background null Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. null Results null We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lig...
#1Luyi Tian (WEHI: Walter and Eliza Hall Institute of Medical Research)H-Index: 12
#2Jafar S. Jabbari (WEHI: Walter and Eliza Hall Institute of Medical Research)H-Index: 5
Last. Changqing Wang (WEHI: Walter and Eliza Hall Institute of Medical Research)
view all 31 authors...
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. A...
#1Husam Babikir (UCSF: University of California, San Francisco)H-Index: 2
#2Lin Wang (UCSF: University of California, San Francisco)H-Index: 6
Last. Aaron Diaz (UCSF: University of California, San Francisco)H-Index: 19
view all 9 authors...
Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. To reconcile these findings, we profile 22 human IDH-mutant gliomas using scATAC-seq and scRNA-seq. We determine the cell-type-specific differences in transcription fact...
#1Tim R. Mercer (Garvan Institute of Medical Research)H-Index: 42
#2Joshua Xu (NCTR: National Center for Toxicological Research)H-Index: 18
Last. Weida Tong (NCTR: National Center for Toxicological Research)H-Index: 72
view all 4 authors...
#1Claudio Lorenzi (CNRS: Centre national de la recherche scientifique)H-Index: 4
#2Sylvain Barriere (CNRS: Centre national de la recherche scientifique)H-Index: 1
Last. William Ritchie (CNRS: Centre national de la recherche scientifique)H-Index: 28
view all 6 authors...
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available sampl...
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