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1. scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing

Author:
Wilson, Gavin W.; Derouet, Mathieu; Darling, Gail E.; Yeung, Jonathan C.
Source:
Genome biology 2021 v.22 no.1 pp. 144
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; genome;     Show all 3 Subjects
Abstract:
... Identifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to “collapse” ...
DOI:
10.1186/s13059-021-02364-5

2. A new era for plant science: spatial single-cell transcriptomics

Author:
Giacomello, Stefania
Source:
Current opinion in plant biology 2021 v.60 pp. 102041
ISSN:
1369-5266
Subject:
sequence analysis,   etc   ; transcription (genetics); transcriptomics;     Show all 3 Subjects
Abstract:
... To achieve a complete understanding of how organisms function, there is a need to study their fundamental unit, the cell, in its spatial context. In recent years, we have seen fast-paced technological progress to study the transcriptional content of single cells and their spatial relationships. This review highlights modern advancements in single-cell RNA-sequencing, provides an overview of the te ...
DOI:
10.1016/j.pbi.2021.102041

3. A benchmark for RNA-seq deconvolution analysis under dynamic testing environments

Author:
Jin, Haijing; Liu, Zhandong
Source:
Genome biology 2021 v.22 no.1 pp. 102
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; gene expression; genome; simulation models;     Show all 4 Subjects
Abstract:
... BACKGROUND: Deconvolution analyses have been widely used to track compositional alterations of cell types in gene expression data. Although a large number of novel methods have been developed, due to a lack of understanding of the effects of modeling assumptions and tuning parameters, it is challenging for researchers to select an optimal deconvolution method suitable for the targeted biological c ...
DOI:
10.1186/s13059-021-02290-6

4. Pseudofusicoccum sp. causing shoot canker in peach in Uruguay

Author:
Sessa, Lucía; Abreo, Eduardo; Lupo, Sandra
Source:
Australasian plant disease notes 2021 v.16 no.1 pp. 5
ISSN:
1833-928X
Subject:
sequence analysis,   etc   ; gummosis; pathogenicity; peaches; Uruguay;     Show all 5 Subjects
Abstract:
... We report the presence of a Pseudofusicoccum species associated with cankers showing gummosis in peach shoots for the first time. Identification was performed by sequence analysis of the concatenated ITS and EF1-α genes. The Pseudofusicoccum sp. was morphologically described and its pathogenicity was evaluated under laboratory conditions. ...
DOI:
10.1007/s13314-021-00416-0

5. Dichloroacetate attenuates the stemness of hepatocellular carcinoma cells via promoting nucleus‐cytoplasm translocation of YAP

Author:
Su, Duanyu; Lin, Zhian
Source:
Environmental toxicology 2021 v.36 no.5 pp. 975-983
ISSN:
1520-4081
Subject:
sequence analysis,   etc   ; cell viability; ecotoxicology; hepatoma;     Show all 4 Subjects
Abstract:
... The antitumor effects of dichloroacetate (DCA) have been widely explored, however, its roles in hepatocellular carcinoma (HCC) progression are still unclear. In the current work, we found that DCA had little effects on HCC cell viability, but could attenuate the stemness of HCC cells, which is evident by decreasing the tumor sphere‐formation ability, ALDH activity and the expression of stemness cr ...
DOI:
10.1002/tox.23098

6. Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues

Author:
Chen, Xianfeng; Sun, Zhifu
Source:
Genes 2021 v.12 no.5
ISSN:
2073-4425
Subject:
sequence analysis,   etc   ; gene expression; genes; humans;     Show all 4 Subjects
Abstract:
... Long non-coding RNAs (lncRNAs) are a large class of gene transcripts that do not code proteins; however, their functions are largely unknown and many new lncRNAs are yet to be discovered. Taking advantage of our previously developed, super-fast, novel lncRNA discovery pipeline, UClncR, and rich resources of GTEx RNA-seq data, we performed systematic novel lincRNA discovery for over 8000 samples ac ...
DOI:
10.3390/genes12050614

7. Identification of Circular RNAs in Hypothalamus of Gilts during the Onset of Puberty

Author:
Li, Qingnan; Pan, Xiangchun; Li, Nian; Gong, Wentao; Chen, Yaosheng; Yuan, Xiaolong
Source:
Genes 2021 v.12 no.1
ISSN:
2073-4425
Subject:
sequence analysis,   etc   ; hypothalamus; insulin; meiosis; oocytes; puberty;     Show all 6 Subjects
Abstract:
... The disorders of puberty have shown negative outcomes on health of mammals, and the hypothalamus is thought to be the main regulator of puberty by releasing GnRH. Many studies show that the circular RNAs (circRNAs) might be implicated in the timing of puberty in mammals. However, the circRNAs in the hypothalamus of gilts have not been explored. To profile the changes and biological functions of ci ...
DOI:
10.3390/genes12010084

8. Reprogramming of m⁶A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia

Author:
Wang, Yan-Jie; Yang, Bing; Lai, Qiao; Shi, Jun-Fang; Peng, Jiang-Yun; Zhang, Yin; Hu, Kai-Shun; Li, Ya-Qing; Peng, Jing-Wen; Yang, Zhi-Zhi; Li, Yao-Ting; Pan, Yue; Koeffler, H. Phillip; Liao, Jian-You; Yin, Dong
Source:
RNA biology 2021 v.18 no.1 pp. 131-143
ISSN:
1555-8584
Subject:
sequence analysis,   etc   ; energy; hypoxia; proteome; transcriptome; transcriptomics;     Show all 6 Subjects
Abstract:
... Hypoxia causes a series of responses supporting cells to survive in harsh environments. Substantial post-transcriptional and translational regulation during hypoxia has been observed. However, detailed regulatory mechanism in response to hypoxia is still far from complete. RNA m⁶A modification has been proven to govern the life cycle of RNAs. Here, we reported that total m⁶A level of mRNAs was dec ...
DOI:
10.1080/15476286.2020.1804697

9. Screening, isolation and identification of distillery spent wash decolourizing bacteriafrom soil

Author:
Shinde, A.B.; Nakade, D.B.
Source:
BIOINFOLET 2021 v.18 no.1a pp. 90-94
ISSN:
0976-4755
Subject:
sequence analysis,   etc   ; decolorization; nucleotide sequences; soil; wastewater;     Show all 5 Subjects
Abstract:
... Distilleries produce a large amount of waste water, commonly known as spent wash. Present study was undertaken to isolate and screen distillery spent wash decolorizing bacteria from soil samples. Total 45 bacterial isolates, capable of decolourizing distillery spent wash, were obtained from soil samples. Out of these, 6 isolates showing maximum decolorization were characterized by morphological an ...

10. Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Author:
Yang, Shiyi; Corbett, Sean E.; Koga, Yusuke; Wang, Zhe; Johnson, W Evan; Yajima, Masanao; Campbell, Joshua D.
Source:
Genome biology 2020 v.21 no.1 pp. 57
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; decontamination;     Show all 3 Subjects
Abstract:
... Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a novel Bayesian method to estimate and remove contamination in individual cells. De ...
DOI:
10.1186/s13059-020-1950-6
PubMed:
32138770
PubMed Central:
PMC7059395

11. The current revolution in transposable element biology enabled by long reads

Author:
Shahid, Saima; Slotkin, R Keith
Source:
Current opinion in plant biology 2020 v.54 pp. 49-56
ISSN:
1369-5266
Subject:
sequence analysis,   etc   ; genes; transposons;     Show all 3 Subjects
Abstract:
... Technological advancement in DNA sequencing read-length has drastically changed the quality and completeness of decoded genomes. The aim of this article is not to describe the different technologies of long-read sequencing, or the widely appreciated power of this technology in genome sequencing, assembly, and gene annotation. Instead, in this article, we provide our opinion that with the exception ...
DOI:
10.1016/j.pbi.2019.12.012

12. Best practices on the differential expression analysis of multi-species RNA-seq

Author:
Chung, Matthew; Bruno, Vincent M.; Rasko, David A.; Cuomo, Christina A.; Muñoz, José F.; Livny, Jonathan; Shetty, Amol C.; Mahurkar, Anup; Dunning Hotopp, Julie C.
Source:
Genome biology 2021 v.22 no.1 pp. 121
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; data collection; gene expression regulation; transcriptome; transcriptomics;     Show all 6 Subjects
Abstract:
... Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of ...
DOI:
10.1186/s13059-021-02337-8

13. Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

Author:
Fremin, Brayon J.; Bhatt, Ami S.
Source:
Genome biology 2021 v.22 no.1 pp. 100
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; automation; genome; humans; metagenomics; microbiome; ribosomes;     Show all 8 Subjects
Abstract:
... BACKGROUND: Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RN ...
DOI:
10.1186/s13059-021-02319-w

14. MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks

Author:
Yu, Hengshi; Welch, Joshua D.
Source:
Genome biology 2021 v.22 no.1 pp. 158
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; data collection; drug therapy; gene expression; genome; Michigan;     Show all 6 Subjects
Abstract:
... Deep generative models such as variational autoencoders (VAEs) and generative adversarial networks (GANs) generate and manipulate high-dimensional images. We systematically assess the complementary strengths and weaknesses of these models on single-cell gene expression data. We also develop MichiGAN, a novel neural network that combines the strengths of VAEs and GANs to sample from disentangled re ...
DOI:
10.1186/s13059-021-02373-4

15. Molecular characterization of a 'Candidatus Phytoplasma asteris'-related strain (16SrI-B / cpn60UT I-IB) affecting daisies (Argyranthemum spp.) in Mexico

Author:
García-Barrera, Laura J.; Flores, Alejandra Chamorro; Zamora, Stefani Aletse Meza; Ortíz-Gamino, Diana; Dumonceaux, Tim J.; Pérez-López, Edel
Source:
Australasian plant disease notes 2021 v.16 no.1 pp. 2
ISSN:
1833-928X
Subject:
sequence analysis,   etc   ; Argyranthemum; chaperonins; computer software; flowers; loci; phyllody; Mexico;     Show all 8 Subjects
Abstract:
... From 2018 to 2019 symptoms consistent with infection by plant pathogenic phytoplasma bacteria were observed in commercial flower greenhouses located in Atlixco, Puebla, Mexico. Two varieties of Argyranthemum spp. plants exhibited symptoms of phyllody, causing serious concerns among farmers. To determine if phytoplasmas were associated with the symptomatic plants, the 16S rRNA-encoding locus (F2nR2 ...
DOI:
10.1007/s13314-020-00415-7

16. PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data

Author:
Song, Dongyuan; Li, Jingyi Jessica
Source:
Genome biology 2021 v.22 no.1 pp. 124
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; RNA; gene expression regulation; genes; uncertainty;     Show all 5 Subjects
Abstract:
... To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posed p-values or restrictive models. Here we propose PseudotimeDE, a DE gene identificatio ...
DOI:
10.1186/s13059-021-02341-y

17. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

Author:
Huang, Ruizhu; Soneson, Charlotte; Germain, Pierre-Luc; Schmidt, Thomas S.B.; Mering, Christian Von; Robinson, Mark D.
Source:
Genome biology 2021 v.22 no.1 pp. 157
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; data collection; genome; genomics; microRNA; microbiome; phylogeny;     Show all 7 Subjects
Abstract:
... treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or leaves that contain features of interest, in a data-driven way. It outperforms currently available methods on synthetic data, and we highlight the approach on various applications, including ...
DOI:
10.1186/s13059-021-02368-1

18. Nkx2-2 expressing taste cells in endoderm-derived taste papillae are committed to the type III lineage

Author:
Qin, Yumei; Sukumaran, Sunil K.; Margolskee, Robert F.
Source:
Developmental biology 2021 v.477 pp. 232-240
ISSN:
0012-1606
Subject:
sequence analysis,   etc   ; adults; hybridization; mice; taste; tongue; transcription factors;     Show all 7 Subjects
Abstract:
... In mammals, multiple cell-signaling pathways and transcription factors regulate development of the embryonic taste system and turnover of taste cells in the adult stage. Using single-cell RNA-Seq of mouse taste cells, we found that the homeobox-containing transcription factor Nkx2-2, a target of the Sonic Hedgehog pathway and a key regulator of the development and regeneration of multiple cell typ ...
DOI:
10.1016/j.ydbio.2021.05.020

19. Two new rare species of Candolleomyces with pale spores from China

Author:
Bau, Tolgor; Yan, Jun-Qing
Source:
MycoKeys 2021 v.80 pp. 149-161
ISSN:
1314-4049
Subject:
sequence analysis,   etc   ; color; new combination; phylogeny; rare species; China;     Show all 6 Subjects
Abstract:
... Most species of Candolleomyces have brown or dark brown spores. Although pale-spored members are rare in the genus we frequently collected two such species from many Provinces during our investigations in subtropical China from 2016–2020. As revealed by morphological characterisation and multigene phylogenetic analyses (ITS LSU β-tub and tef-1α) these species which we have named C. subcacao and C. ...
DOI:
10.3897/mycokeys.80.67166

20. All food processes have a residual risk, some are small, some very small and some are extremely small: zero risk does not exist

Author:
Zwietering, Marcel H; Garre, Alberto; Wiedmann, Martin; Buchanan, Robert L
Source:
Current opinion in food science 2021 v.39 pp. 83-92
ISSN:
2214-7993
Subject:
sequence analysis,   etc   ; food production; food safety; monitoring; risk; zero tolerance;     Show all 6 Subjects
Abstract:
... As risk-based approaches are increasingly recognized and used to manage food safety hazards, their implementation requires a recognition and appreciation of residual risk. We define residual risk as the one that remains even after a fully compliant food safety system has been implemented. As true ‘zero risk’ is essentially unattainable, understanding and assessing the residual risks for different ...
DOI:
10.1016/j.cofs.2020.12.017