Advances in technologies for 3D genomics research

2020 ◽  
Vol 63 (6) ◽  
pp. 811-824 ◽  
Author(s):  
Yan Zhang ◽  
Guoliang Li
Keyword(s):  
Genomics Research ◽  
3D Genomics

scholarly journals The Human Genome Organisation (HUGO) and the 2020 COVID-19 pandemic

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Benjamin Capps ◽  
◽  
Yann Joly ◽  
John Mulvihill ◽  
Won Bok Lee
Keyword(s):  
Human Genome ◽  
Law And Society ◽  
Genome Organisation ◽  
Global Response ◽  
Genomics Research ◽  
Human Genome Organisation ◽  
Ethics Law

AbstractThis letter is the Human Genome Organisation’s summary reaction to the 2020 COVID-19 pandemic. It identifies key areas for genomics research, and areas in which genomic scientists can contribute to a global response to the pandemic. The letter has been reviewed and endorsed by the HUGO Committee on Ethics, Law and Society (CELS) and the HUGO Council.

scholarly journals Advancing precision public health using human genomics: examples from the field and future research opportunities

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Megan C. Roberts ◽  
Alison E. Fohner ◽  
Latrice Landry ◽  
Dana Lee Olstad ◽  
Amelia K. Smit ◽  
...  
Keyword(s):  
Public Health ◽  
Precision Medicine ◽  
Behavioral Science ◽  
Public Health Research ◽  
Future Research ◽  
Human Genomics ◽  
Precision Public Health ◽  
Genomics Research ◽  
Health Initiatives ◽  
Public Health Initiatives

AbstractPrecision public health is a relatively new field that integrates components of precision medicine, such as human genomics research, with public health concepts to help improve population health. Despite interest in advancing precision public health initiatives using human genomics research, current and future opportunities in this emerging field remain largely undescribed. To that end, we provide examples of promising opportunities and current applications of genomics research within precision public health and outline future directions within five major domains of public health: biostatistics, environmental health, epidemiology, health policy and health services, and social and behavioral science. To further extend applications of genomics within precision public health research, three key cross-cutting challenges will need to be addressed: developing policies that implement precision public health initiatives at multiple levels, improving data integration and developing more rigorous methodologies, and incorporating initiatives that address health equity. Realizing the potential to better integrate human genomics within precision public health will require transdisciplinary efforts that leverage the strengths of both precision medicine and public health.

scholarly journals SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lidong Guo ◽  
Mengyang Xu ◽  
Wenchao Wang ◽  
Shengqiang Gu ◽  
Xia Zhao ◽  
...  
Keyword(s):  
High Efficiency ◽  
De Novo ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Draft Assembly ◽  
Screening Algorithm ◽  
Long Reads ◽  
Hybrid Genome ◽  
Genomics Research ◽  
Negative Effect

Abstract Background Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. Results In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder. Conclusions SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.

scholarly journals The state of the art in soybean transcriptomics resources and gene coexpression networks

2021 ◽  
Author(s):  
Fabricio Almeida-Silva ◽  
Kanhu C Moharana ◽  
Thiago M Venancio
Keyword(s):  
State Of The Art ◽  
The State ◽  
Gene Coexpression Network ◽  
Rna Seq ◽  
Transcriptomic Data ◽  
The Past ◽  
Gene Coexpression ◽  
Genomics Research ◽  
Public Repositories ◽  
Coexpression Networks

Abstract In the past decade, over 3000 samples of soybean transcriptomic data have accumulated in public repositories. Here, we review the state of the art in soybean transcriptomics, highlighting the major microarray and RNA-seq studies that investigated soybean transcriptional programs in different tissues and conditions. Further, we propose approaches for integrating such big data using gene coexpression network and outline important web resources that may facilitate soybean data acquisition and analysis, contributing to the acceleration of soybean breeding and functional genomics research.

Storage, visualization, and navigation of 3D genomics data

Methods ◽  
2018 ◽  
Vol 142 ◽  
pp. 74-80 ◽  
Author(s):  
Jérôme Waldispühl ◽  
Eric Zhang ◽  
Alexander Butyaev ◽  
Elena Nazarova ◽  
Yan Cyr
Keyword(s):  
3D Genomics
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