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1. 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

2. The Magnifying GLASS: Longitudinal Analysis of Adult Diffuse Gliomas

Author:
Narayanan, Ashwin; Turcan, Sevin
Source:
Cell 2020 v.180 no.3 pp. 407-409
ISSN:
0092-8674
Subject:
sequence analysis,   etc   ; adults; glioma; longitudinal studies;     Show all 4 Subjects
Abstract:
... Diffuse gliomas inevitably progress, but our understanding of the molecular events associated with recurrence is limited. Recent work from the Glioma Longitudinal Analysis (GLASS) consortium (Barthel et al., 2019) reports temporal DNA sequencing on a large cohort of primary and recurrent glioma pairs, establishing the evolutionary molecular characteristics of adult diffuse gliomas. ...
DOI:
10.1016/j.cell.2020.01.016

3. Bezlotoxumab for prevention of Clostridium difficile infection recurrence: Distinguishing relapse from reinfection with whole genome sequencing

Author:
Zeng, Zhen; Zhao, Hailong; Dorr, Mary Beth; Shen, Judong; Wilcox, Mark H.; Poxton, Ian R.; Guris, Dalya; Li, Junhua; Shaw, Peter M.
Source:
Anaerobe 2020 v.61 pp. 102137
ISSN:
1075-9964
Subject:
sequence analysis,   etc   ; Clostridium difficile; relapse; ribotypes;     Show all 4 Subjects
Abstract:
... Bezlotoxumab has been shown to prevent Clostridium difficile infection recurrence (rCDI) in high-risk patients.We used whole genome sequencing to estimate the impact of bezlotoxumab on same-strain relapse or new-strain reinfection in MODIFY I/II trials. Reinfection with a new strain and relapse with the same strain were differentiated by the comparison of ribotype (RT) and pair-wise single-nucleot ...
DOI:
10.1016/j.anaerobe.2019.102137

4. Next-generation genome annotation: we still struggle to get it right

Author:
Salzberg, Steven L.
Source:
Genome biology 2019 v.20 no.1 pp. 92
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; automation; genome;     Show all 3 Subjects
Abstract:
... While the genome sequencing revolution has led to the sequencing and assembly of many thousands of new genomes, genome annotation still uses very nearly the same technology that we have used for the past two decades. The sheer number of genomes necessitates the use of fully automated procedures for annotation, but errors in annotation are just as prevalent as they were in the past, if not more so. ...
DOI:
10.1186/s13059-019-1715-2
PubMed:
31097009
PubMed Central:
PMC6521345

5. SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data

Author:
Peng, Tao; Zhu, Qin; Yin, Penghang; Tan, Kai
Source:
Genome biology 2019 v.20 no.1 pp. 88
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; algorithms; genes;     Show all 3 Subjects
Abstract:
... Single-cell RNA-seq data contain a large proportion of zeros for expressed genes. Such dropout events present a fundamental challenge for various types of data analyses. Here, we describe the SCRABBLE algorithm to address this problem. SCRABBLE leverages bulk data as a constraint and reduces unwanted bias towards expressed genes during imputation. Using both simulation and several types of experim ...
DOI:
10.1186/s13059-019-1681-8
PubMed:
31060596
PubMed Central:
PMC6501316

6. TransLiG: a de novo transcriptome assembler that uses line graph iteration

Author:
Liu, Juntao; Yu, Ting; Mu, Zengchao; Li, Guojun
Source:
Genome biology 2019 v.20 no.1 pp. 81
ISSN:
1474-760X
Subject:
sequence analysis,   etc   ; graphs; transcriptome;     Show all 3 Subjects
Abstract:
... We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to all the salient de novo assemblers in both accuracy and computing resources when tested on artificia ...
DOI:
10.1186/s13059-019-1690-7
PubMed:
31014374
PubMed Central:
PMC6480747

7. Whole-genome sequencing of prostate cancer reveals novel mutation-driven processes and molecular subgroups

Author:
Liang, Caixia; Niu, Lijuan; Xiao, Zejun; Zheng, Cuiling; Shen, Yinchen; Shi, Yuankai; Han, Xiaohong
Source:
Life sciences 2020 v.254 pp. 117218
ISSN:
0024-3205
Subject:
sequence analysis,   etc   ; genes; genomics; men; mutation; patients; prostatic neoplasms;     Show all 7 Subjects
Abstract:
... Prostate cancer (PCa) is the second most frequently diagnosed cancer in men. However, its genetic characteristics in the Chinese population have not been extensively profiled. Here we screened 27 Chinese patients and preformed whole-genome sequencing to dissect their genomic patterns. We found that 18.5% (5/27) tumors harbored non-protein coding mutations on FOXA1. Besides, novel focal amplificati ...
DOI:
10.1016/j.lfs.2019.117218

8. Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

Author:
Elfiky, Abdo A.
Source:
Life sciences 2020 v.248 pp. 117477
ISSN:
0024-3205
Subject:
sequence analysis,   etc   ; Coronavirinae; RNA-directed RNA polymerase; humans; models; China;     Show all 6 Subjects
Abstract:
... A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan, China (COVID-19). Until today >2700 deaths from the 80,000 confirmed cases reported mainly in China and 40 other countries. Human to human transmission is confirmed for COVID-19 by China a month ago. Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for >8000 cases with confirmed 774 deaths. ...
DOI:
10.1016/j.lfs.2020.117477
PubMed:
32119961
PubMed Central:
PMC7089605

9. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

Author:
Zhang, Yong-Zhen; Holmes, Edward C.
Source:
Cell 2020 v.181 no.2 pp. 223-227
ISSN:
0092-8674
Subject:
sequence analysis,   etc   ; animal viruses; genomics; pandemic; viruses; China;     Show all 6 Subjects
Abstract:
... The ongoing pandemic of a new human coronavirus, SARS-CoV-2, has generated enormous global concern. We and others in China were involved in the initial genome sequencing of the virus. Herein, we describe what genomic data reveal about the emergence SARS-CoV-2 and discuss the gaps in our understanding of its origins. ...
DOI:
10.1016/j.cell.2020.03.035
PubMed:
32220310
PubMed Central:
PMC7194821

10. Molecular confirmation and morphological reassessment of Udotea geppiorum (Bryopsidales, Chlorophyta) with ecological observations of mesophotic meadows in the Main Hawaiian Islands

Author:
Sauvage, Thomas; Ballantine, David L.; Peyton, Kimberly A.; Wade, Rachael M.; Sherwood, Alison R.; Keeley, Sterling; Smith, Celia
Source:
European journal of phycology 2020 v.55 no.2 pp. 186-196
ISSN:
1469-4433
Subject:
sequence analysis,   etc   ; Udotea; Udoteaceae; habitats; meadows; phylogeny; sediments; tongue; Maui;     Show all 9 Subjects
Abstract:
... Udotea geppiorum is reported to form meadows in deep-water, soft sediment habitats in the Main Hawaiian Islands. The identification of the species, initially published as U. argentea in the archipelago, is revised and confirmed based on morphological assessment and comparative DNA sequencing with western Pacific specimens. Udotea geppiorum is fully corticated and newly shown to display discrete co ...
DOI:
10.1080/09670262.2019.1668061

11. A computational system for identifying operons based on RNA-seq data

Author:
Tjaden, Brian
Source:
Methods 2020 v.176 pp. 62-70
ISSN:
1046-2023
Subject:
sequence analysis,   etc   ; biochemical pathways; databases; operon; probabilistic models; transcription (genetics);     Show all 6 Subjects
Abstract:
... An operon is a set of neighboring genes in a genome that is transcribed as a single polycistronic message. Genes that are part of the same operon often have related functional roles or participate in the same metabolic pathways. The majority of all bacterial genes are co-transcribed with one or more other genes as part of a multi-gene operon. Thus, accurate identification of operons is important i ...
DOI:
10.1016/j.ymeth.2019.03.026
PubMed:
30953757
PubMed Central:
PMC6776731

12. Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates

Author:
Gildea, Michael A.; Dwyer, Zachary W.; Pleiss, Jeffrey A.
Source:
Methods 2020 v.176 pp. 34-45
ISSN:
1046-2023
Subject:
sequence analysis,   etc   ; alternative splicing; introns; loci; messenger RNA; reverse transcription;     Show all 6 Subjects
Abstract:
... The study of pre-mRNA splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which enables the genome-wide detection of discrete splice isoforms. Quantification of these splice isoforms requires analysis of splicing informative sequencing reads, those that unambiguously map to a single splice isoform, including exon-intron spanning alignments corresponding to retained introns, ...
DOI:
10.1016/j.ymeth.2019.05.013
PubMed:
31121301
PubMed Central:
PMC6868320

13. Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Author:
Lou, Fangrui; Song, Na; Han, Zhiqiang; Gao, Tianxiang
Source:
International journal of biological macromolecules 2020 v.147 pp. 89-97
ISSN:
0141-8130
Subject:
sequence analysis,   etc   ; Tachypleus tridentatus; databases; genes; loci; secretion; transcriptome;     Show all 7 Subjects
Abstract:
... Tachypleus tridentatus is a keystone species in marine ecosystems. Its hemolymph also provides the limulus amebocyte lysate (LAL) for detection of bacterial endotoxin in human medical service. Here we combined SMRT sequencing and Illumina RNA-seq to characterize the novel isoforms, novel genetic loci, fusion isoforms formation and transcriptome structure and further to unveil the transcriptome com ...
DOI:
10.1016/j.ijbiomac.2020.01.029

14. The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing

Author:
de Freitas Martins, Ernane; Amorim, Rodrigo G.; Feliciano, Gustavo Troiano; Scheicher, Ralph Hendrik; Rocha, Alexandre Reily
Source:
Carbon 2020 v.158 pp. 314-319
ISSN:
0008-6223
Subject:
sequence analysis,   etc   ; DNA; electron transfer; graphene; mechanics; nucleotides; precision medicine;     Show all 7 Subjects
Abstract:
... Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a nitrogen-terminated nanogap on a graphene sheet with the aqueous environment fully taken into account. Our investigation is performed using a hybrid ...
DOI:
10.1016/j.carbon.2019.10.067

15. Crowding-Induced DNA Translocation through a Protein Nanopore

Author:
Yao, Fujun; Peng, Xiao; Su, Zhuoqun; Tian, Lei; Guo, Yanli; Kang, Xiao-feng
Source:
Analytical chemistry 2020 v.92 no.5 pp. 3827-3833
ISSN:
1520-6882
Subject:
sequence analysis,   etc   ; DNA; Gibbs free energy; analytical methods; nanopores; solutes;     Show all 6 Subjects
Abstract:
... A crowded cellular environment is highly associated with many significant biological processes. However, the effect of molecular crowding on the translocation behavior of DNA through a pore has not been explored. Here, we use nanopore single-molecule analytical technique to quantify the thermodynamics and kinetics of DNA transport under heterogeneous cosolute PEGs. The results demonstrate that the ...
DOI:
10.1021/acs.analchem.9b05249

16. Rediscovering Halophila major (Zollinger) Miquel (1855) in Indonesia

Author:
Kurniawan, Fery; Imran, Zulhamsyah; Darus, Robba Fahrisy; Anggraeni, Fitriyah; Damar, Ario; Sunuddin, Adriani; Kamal, Mohammad Mukhlis; Murti Pratiwi, Niken Tunjung; Ayu, Inna Puspa; Iswantari, Aliati
Source:
Aquatic botany 2020 v.161 pp. 103171
ISSN:
0304-3770
Subject:
sequence analysis,   etc   ; DNA; Halophila; geographical distribution; nucleotide sequences; seagrasses; Indonesia;     Show all 7 Subjects
Abstract:
... Halophila major (Zollinger) Miquel (1855) has not been officially recorded as a species that exists in Indonesia until now. Evidence of this species for Indonesia was collected from four locations, including Sekotong Beach, Lombok, Tayando Island, Tual, Weduar Kei Besar Beach, Tual, and Malala Bay, Toli-toli, at a depth of 2–4 m. Morphological characteristics and DNA sequence analysis confirmed th ...
DOI:
10.1016/j.aquabot.2019.103171

17. Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics

Author:
Rich-Griffin, Charlotte; Stechemesser, Annika; Finch, Jessica; Lucas, Emma; Ott, Sascha; Schäfer, Patrick
Source:
Trends in plant science 2020 v.25 no.2 pp. 186-197
ISSN:
1360-1385
Subject:
sequence analysis,   etc   ; data collection; genomics; tissues; transcription (genetics); transcriptomics;     Show all 6 Subjects
Abstract:
... Plant function is the result of the concerted action of single cells in different tissues. Advances in RNA-seq technologies and tissue processing allow us now to capture transcriptional changes at single-cell resolution. The incredible potential of single-cell RNA-seq lies in the novel ability to study and exploit regulatory processes in complex tissues based on the behaviour of single cells. Impo ...
DOI:
10.1016/j.tplants.2019.10.008

18. Small genomes in most mites (but not ticks)

Author:
Gregory, T. Ryan; Young, Monica R.
Source:
International journal of acarology 2020 v.46 no.1 pp. 1-8
ISSN:
1945-3892
Subject:
sequence analysis,   etc   ; DNA; body size; genome; haploidy; mites; ticks;     Show all 7 Subjects
Abstract:
... Given their ecological and socioeconomic importance, it is not surprising that a number of mites (including ticks) have been the targets of recent genome sequencing projects. Less easily explained is why data on fundamental genetic parameters such as genome size (i.e. haploid DNA content) are greatly lacking for such a diverse and important group. Here, we compile the available genome size data fo ...
DOI:
10.1080/01647954.2019.1684561

19. Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

Author:
Jacobson, Elsie C.; Grand, Ralph S.; Perry, Jo K.; Vickers, Mark H.; Olins, Ada L.; Olins, Donald E.; O'Sullivan, Justin M.
Source:
Genomics 2020 v.112 no.1 pp. 151-162
ISSN:
0888-7543
Subject:
sequence analysis,   etc   ; cell lines; karyotyping; loci; myeloid leukemia; neoplasm cells;     Show all 6 Subjects
Abstract:
... Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used ...
DOI:
10.1016/j.ygeno.2019.05.009

20. Screen technical noise in single cell RNA sequencing data

Author:
Bai, Yu-Long; Baddoo, Melody; Flemington, Erik K.; Nakhoul, Hani N.; Liu, Yao-Zhong
Source:
Genomics 2020 v.112 no.1 pp. 346-355
ISSN:
0888-7543
Subject:
sequence analysis,   etc   ; computer software; data collection; genes; screening;     Show all 5 Subjects
Abstract:
... We proposed a data cleaning pipeline for single cell (SC) RNA-seq data, where we first screen genes (gene-wise screening) followed by screening cell libraries (library-wise screening). Gene-wise screening is based on the expectation that for a gene with a low technical noise, a gene's count in a library will tend to increase with the increase of library size, which was tested using negative binomi ...
DOI:
10.1016/j.ygeno.2019.02.014