Genome Biology
Papers 5960
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#2Ernesto Picardi (University of Bari)H-Index: 22
Last.Angela GalloH-Index: 20
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Background Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.
#1Zhongqu Duan (SJTU: Shanghai Jiao Tong University)
#2Yuyang Qiao (SJTU: Shanghai Jiao Tong University)
Last.Guichao Li (Fudan University)
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The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome. We applied it to 185 deep sequencing and 90 assembled Han Chinese genomes and detected 29.5 Mb novel genomic sequences and at least 188 novel protein-coding genes missing in the human reference genome (GRCh38). It can be an important resource for the...
#1Shan Li (NIH: National Institutes of Health)H-Index: 7
#2Evgeny Z. Kvon (LBNL: Lawrence Berkeley National Laboratory)
Last.Ivan Ovcharenko (NIH: National Institutes of Health)H-Index: 31
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Background Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations (deMs) in enhancer sequences. Here, we focus on elucidating the mechanism underlying the different densities of deMs in human enhancers.
#1Antonin Morillon (Curie Institute)H-Index: 12
#2Daniel Gautheret (Université Paris-Saclay)H-Index: 40
Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important p...
#2Kieran R. Campbell (UBC: University of British Columbia)H-Index: 2
Last.Esther KongH-Index: 7
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Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumor tissues and patient-derived mouse xenografts for scRNA-seq are not well understood. We use low temperature (6 °C) protease and collagenase (37 °C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNA-seq dataset ...
#1Adam Siepel (CSHL: Cold Spring Harbor Laboratory)H-Index: 49
The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences. However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the research community. I examine the roots of the incongruity between the importance of and the degree of investment in genomic software, and I suggest several potential remedies for curren...
#1Lipei Shao (Nanjing Medical University)H-Index: 3
#2Xianglin Zuo (Nanjing Medical University)
Last.Guangfu Jin (Nanjing Medical University)H-Index: 35
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Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechanisms of cancers. The tag-SNP rs753955 (A>G) in 13q12.12 is highly associated with lung cancer risk in the Chinese population. Here, we systematically investigate the biological significance and the underlying mechanism behind 13q12.12 risk locus in vitro and in vivo. We characterize a novel...
#1Bonnie Berger Leighton (MIT: Massachusetts Institute of Technology)H-Index: 52
#2Hyunghoon Cho (MIT: Massachusetts Institute of Technology)H-Index: 6
As the scale of genomic and health-related data explodes and our understanding of these data matures, the privacy of the individuals behind the data is increasingly at stake. Traditional approaches to protect privacy have fundamental limitations. Here we discuss emerging privacy-enhancing technologies that can enable broader data sharing and collaboration in genomics research.
#1Ardalan Naseri (UCF: University of Central Florida)H-Index: 4
#2Xiaoming Liu (USF: University of South Florida)
Last.Degui Zhi (University of Texas Health Science Center at Houston)H-Index: 22
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While genetic relatedness, usually manifested as segments identical by descent (IBD), is ubiquitous in modern large biobanks, current IBD detection methods are not efficient at such a scale. Here, we describe an efficient method, RaPID, for detecting IBD segments in a panel with phased haplotypes. RaPID achieves a time and space complexity linear to the input size and the number of reported IBDs. With simulation, we showed that RaPID is orders of magnitude faster than existing method while offer...
#1Fernando Meyer (BRICS)H-Index: 4
#2Andreas Bremges (BRICS)H-Index: 11
Last.David Koslicki (OSU: Oregon State University)H-Index: 9
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The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profi...