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Genome Biology
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Papers 6176
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Last. Lei Zhang (PKU: Peking University)H-Index: 2
view all 16 authors...
BACKGROUND: Tumor-reactive CD8+ tumor-infiltrating lymphocytes (TILs) represent a subtype of T cells that can recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. RESULTS: In this study, we segregate tumor-reactive and bystander CD8+ TILs, as well as naive and effector memory CD8+ T cell subtypes as controls from colorec...
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#1E. MadissoonH-Index: 2
#1E. Madissoon (EMBL-EBI: European Bioinformatics Institute)H-Index: 2
Last. Kerstin B. MeyerH-Index: 19
view all 22 authors...
Background The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design.
23 CitationsSource
#1Chao Li (CAS: Chinese Academy of Sciences)H-Index: 3
#2Yuan Zong (CAS: Chinese Academy of Sciences)H-Index: 7
Last. Caixia Gao (CAS: Chinese Academy of Sciences)H-Index: 27
view all 9 authors...
We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired sgRNAs, SWISS can produce insertions/deletions in addition to base editing. Rice mutants are generated using the SWISS system with efficiencies of cytosine conversion of 25.5%, aden...
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#1Yonghao Sun (HAU: Huazhong Agricultural University)
#2Liang Dong (HAU: Huazhong Agricultural University)
Last. David Jackson (HAU: Huazhong Agricultural University)H-Index: 46
view all 12 authors...
BACKGROUND Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown. RESULTS We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatori...
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#1Long Wang (NU: Nanjing University)H-Index: 7
#2Yingying Sun (NU: Nanjing University)
Last. Sihai Yang (NAU: Nanjing Agricultural University)H-Index: 23
view all 10 authors...
BACKGROUND Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown. RESULTS By parent-offspring whole genome sequencing, we estimate a mutation rate (3.38 × 10-6 per bp per generation) that is two orders of magnitude higher than reported for any non-viral organism, with 93-98% of mutations being RIP-associated. RIP mutations are, however, relatively rare...
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#1Lejon E M Kralemann (SLU: Swedish University of Agricultural Sciences)H-Index: 1
#2Shujing Liu (SLU: Swedish University of Agricultural Sciences)H-Index: 1
Last. Lars Hennig (SLU: Swedish University of Agricultural Sciences)H-Index: 49
view all 6 authors...
BACKGROUND Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive. RESULTS We show that UBP12 ...
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#1Craig H. Kerr (Stanford University)
#2Michael A. Skinnider (UBC: University of British Columbia)H-Index: 5
Last. Leonard J. Foster (UBC: University of British Columbia)H-Index: 51
view all 9 authors...
The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized. Here, we apply a combination of quantitative proteomic approaches to describe the effects of IFN signaling on the human...
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#1Fan Chen (UW: University of Wisconsin-Madison)H-Index: 1
#2Sunduz Keles (UW: University of Wisconsin-Madison)H-Index: 38
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data. We demonstrate SURF’s ability to accurately detect differential alternative transcriptional regulation events and associate them to local prot...
1 CitationsSource
#1Sharadha Sakthikumar (Science for Life Laboratory)
Last. Karin Forsberg-Nilsson (Science for Life Laboratory)H-Index: 19
view all 8 authors...
Whole Genome Sequencing of Glioblastoma Reveals Enrichment of Non-Coding Constraint Mutations in Known and Novel Genes
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#1Nicolai Karcher (University of Trento)H-Index: 3
#2Edoardo Pasolli (University of Naples Federico II)H-Index: 21
Last. Petra Louis (Aberd.: University of Aberdeen)H-Index: 44
view all 22 authors...
Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic...
1 CitationsSource
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