Wang, Renying Zhang, Peijing Wang, Jingjing Ma, Lifeng E, Weigao Suo, Shengbao Jiang, Mengmeng Li, Jiaqi Chen, Haide Sun, Huiyu
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Published in
Nucleic acids research
How many cell types are there in nature? How do they change during the life cycle? These are two fundamental questions that researchers have been trying to understand in the area of biology. In this study, single-cell mRNA sequencing data were used to profile over 2.6 million individual cells from mice, zebrafish and Drosophila at different life st...
Scutenaire, Jérémy Plassard, Damien Matelot, Mélody Villa, Tommaso Zumsteg, Julie Libri, Domenico Séraphin, Bertrand
Published in
Nucleic acids research
mRNAs molecules carry information contained in genes to direct the formation of proteins. In specific circumstances, the cellular machinery modifies some mRNAs through the formation of m6A residues. To understand the function of these m6A marks, the authors used the yeast Saccharomyces cerevisiae in which their formation only occurs during meiosis ...
Akıncılar, Semih Can Chua, Joelle Yi Heng Ng, Qin Feng Chan, Claire Hian Tzer Eslami-S, Zahra Chen, Kaijing Low, Joo-Leng Arumugam, Surendar Aswad, Luay Chua, Clarinda
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Published in
Nucleic acids research
Healthy and cancer cells harbor the same DNA sequence, but reactivation of the Human Telomerase Reverse Transcriptase (hTERT) gene is observed only in cancer cells. How does that happen was not known for over three decades of research? This study identifies a specific DNA structure that forms only in cancer cells and brings the necessary molecular ...
Faulk, Christopher
Published in
Nucleic acids research
Creating reference animal genomes is typically a large, expensive process. Here I sequenced the genome of the black carpenter ant for only $1000 as a sole researcher in just one week. Along with the nuclear genome, I assembled the mitochondrial genome and two commensal bacteria species living within the ant. Nanopore technology also enabled epigene...
Miller, Henry E Montemayor, Daniel Li, Janet Levy, Simon A Pawar, Roshan Hartono, Stella Sharma, Kumar Frost, Bess Chedin, Frédéric Bishop, Alexander J R
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Published in
Nucleic acids research
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data...
Li, Zhichao Jiang, Xiaosen Fang, Mingyan Bai, Yong Liu, Siyang Huang, Shujia Jin, Xin
Published in
Nucleic acids research
A high-quality genome variation database derived from a large-scale population is one of the most important infrastructures for genomics, clinical and translational medicine research. Here, we developed the Chinese Millionome Database (CMDB), a database that contains 9.04 million single nucleotide variants (SNV) with allele frequency information de...
Lu, Jianguo Huang, Peilin Sun, Jialiang Liu, Jian
Published in
Nucleic acids research
Duplicated genes prevail in vertebrates and are important in the acquisition of new genes and novelties. Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates ...
Stam, Mark Lelièvre, Pernelle Hoebeke, Mark Corre, Erwan Barbeyron, Tristan Michel, Gurvan
Published in
Nucleic acids research
SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1-S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single...
Xin, Junyi Gu, Dongying Chen, Silu Ben, Shuai Li, Huiqin Zhang, Zhengdong Du, Mulong Wang, Meilin
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Nucleic acids research
Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains un...
Zhao, Hui Yang, Yuan Wang, Shuaiqi Yang, Xue Zhou, Kaicheng Xu, Caili Zhang, Xuyao Fan, Jiajun Hou, Dongyue Li, Xingxiu
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Published in
Nucleic acids research
Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values...