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Published in Genome Biology14.03
Daniel E. Martin-Herranz1
Estimated H-index: 1
(EMBL-EBI: European Bioinformatics Institute),
Erfan Aref-Eshghi5
Estimated H-index: 5
(UWO: University of Western Ontario)
+ -3 AuthorsJanet M. Thornton117
Estimated H-index: 117
(EMBL-EBI: European Bioinformatics Institute)
Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harboring mutations in proteins of the epigenetic machinery. Using the Horvath epigenetic ...
Published on Feb 13, 2019in Genome Biology14.03
Domenico Alessandro Silvestris1
Estimated H-index: 1
,
Ernesto Picardi22
Estimated H-index: 22
(University of Bari)
+ 7 AuthorsAngela Gallo20
Estimated H-index: 20
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.
Published on Dec 1, 2019in Genome Biology14.03
Bonnie Berger Leighton52
Estimated H-index: 52
(MIT: Massachusetts Institute of Technology),
Hyunghoon Cho6
Estimated H-index: 6
(MIT: Massachusetts Institute of Technology)
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.
Published on Dec 1, 2019in Genome Biology14.03
Lipei Shao3
Estimated H-index: 3
(Nanjing Medical University),
Xianglin Zuo (Nanjing Medical University)+ 17 AuthorsGuangfu Jin35
Estimated H-index: 35
(Nanjing Medical University)
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...
Published on Dec 1, 2019in Genome Biology14.03
Antonin Morillon12
Estimated H-index: 12
(Curie Institute),
Daniel Gautheret40
Estimated H-index: 40
(Université Paris-Saclay)
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...
Published in Genome Biology14.03
Zhongqu Duan (SJTU: Shanghai Jiao Tong University), Yuyang Qiao (SJTU: Shanghai Jiao Tong University)+ -3 AuthorsGuichao Li (Fudan University)
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...
Published on Dec 1, 2019in Genome Biology14.03
Shan Li7
Estimated H-index: 7
(NIH: National Institutes of Health),
Evgeny Z. Kvon (LBNL: Lawrence Berkeley National Laboratory)+ 2 AuthorsIvan Ovcharenko31
Estimated H-index: 31
(NIH: National Institutes of Health)
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.
Published on Jan 25, 2019in Genome Biology14.03
Jean-Philippe Fortin9
Estimated H-index: 9
(Genentech),
Jenille Tan5
Estimated H-index: 5
(Genentech)
+ 4 AuthorsScott E. Martin4
Estimated H-index: 4
(Genentech)
Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed. In this work, we analyze CRISPR essentiality screen data from 391 cancer cell lines to characterize biases induced by multi-target sgRNAs. We investi...
Published in Genome Biology14.03
Adam Siepel49
Estimated H-index: 49
(CSHL: Cold Spring Harbor Laboratory)
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...
Published in Genome Biology14.03
Fernando Meyer3
Estimated H-index: 3
(BRICS),
Andreas Bremges11
Estimated H-index: 11
(BRICS)
+ -3 AuthorsDavid Koslicki9
Estimated H-index: 9
(OSU: Oregon State University)
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...
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