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1. Understanding tumor ecosystems by single-cell sequencing: promises and limitations

Author:
Ren, Xianwen; Kang, Boxi; Zhang, Zemin
Source:
Genome biology 2018 v.19 no.1 pp. 211
ISSN:
1474-760X
Subject:
transcriptome,   etc   ; animal tissues; genome; metastasis; neoplasms; therapeutics;     Show all 6 Subjects
Abstract:
... Cellular heterogeneity within and across tumors has been a major obstacle in understanding and treating cancer, and the complex heterogeneity is masked if bulk tumor tissues are used for analysis. The advent of rapidly developing single-cell sequencing technologies, which include methods related to single-cell genome, epigenome, transcriptome, and multi-omics sequencing, have been applied to cance ...
DOI:
10.1186/s13059-018-1593-z

2. Genome, Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells

Author:
Ranzau, Brodie L.; Komor, Alexis C.
Source:
Biochemistry 2018 v.58 no.5 pp. 330-335
ISSN:
1520-4995
Subject:
transcriptome,   etc   ; DNA; RNA; genome; methylation; nucleobases;     Show all 6 Subjects
Abstract:
... Base editors are tools that chemically modify the nucleobases of DNA and RNA in a programmable manner, allowing for genome, epigenome, and transcriptome editing in live cells. These tools can be used to introduce specific base transitions in DNA or RNA, manipulate methylation patterns in the epigenome, and create genetically encoded libraries in target genes. These various functions can be used to ...
DOI:
10.1021/acs.biochem.8b00958

3. Metabolomics 20 years on: what have we learned and what hurdles remain?

Author:
Alseekh, Saleh; Fernie, Alisdair R.
Source:
The plant journal 2018 v.94 no.6 pp. 933-942
ISSN:
0960-7412
Subject:
transcriptome,   etc   ; biochemical pathways; genome; metabolites; metabolome; metabolomics; proteome;     Show all 7 Subjects
Abstract:
... The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are c ...
DOI:
10.1111/tpj.13950

4. Squeakr: an exact and approximate k-mer counting system

Author:
Pandey, Prashant; Bender, Michael A; Johnson, Rob; Patro, Rob; Berger, Bonnie
Source:
Bioinformatics 2018 v.34 no.4 pp. 568-575
ISSN:
1460-2059
Subject:
transcriptome,   etc   ; algorithms; bioinformatics; genome; high-throughput nucleotide sequencing; messenger RNA;     Show all 6 Subjects
Abstract:
... k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data struc ...
DOI:
10.1093/bioinformatics/btx636

5. Meta-transcriptomics and the evolutionary biology of RNA viruses

Author:
Shi, Mang; Zhang, Yong-Zhen; Holmes, Edward C.
Source:
Virus research 2018 v.243 pp. 83-90
ISSN:
0168-1702
Subject:
transcriptome,   etc   ; RNA viruses; genome; invertebrate viruses; metagenomics; phylogeny; viruses;     Show all 7 Subjects
Abstract:
... Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insight ...
DOI:
10.1016/j.virusres.2017.10.016

6. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Author:
Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Mikenas, Jessica; Olivieri, Julia; Walker, Joseph F.; Smith, Stephen A.
Source:
Thenew phytologist 2018 v.217 no.2 pp. 855-870
ISSN:
0028-646X
Subject:
transcriptome,   etc   ; Caryophyllales; allopolyploidy; autopolyploidy; data collection; gene duplication; genome; phylogeny;     Show all 8 Subjects
Abstract:
... Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a data set of transcriptomes and genomes from 168 sp ...
DOI:
10.1111/nph.14812

7. Translational –omics: Future potential and current challenges in precision medicine

Author:
Wafi, Arsalan; Mirnezami, Reza
Source:
Methods 2018 v.151 pp. 3-11
ISSN:
1046-2023
Subject:
transcriptome,   etc   ; biotechnology; genome; health services; metabolome; pathogenesis; precision medicine; proteome; stakeholders;     Show all 9 Subjects
Abstract:
... Rapid advances in computational science and biotechnology are paving the way for precision medicine – a vision in next-generation healthcare that promises to provide a care package uniquely tailored to each individual’s molecular make-up. Until relatively recently, the focus has been firmly centred around the genome; however, over the past two decades there has been a surge in the study of molecul ...
DOI:
10.1016/j.ymeth.2018.05.009

8. De novo transcriptome assembly and functional annotation of the southern rock lobster (Jasus edwardsii)

Author:
Souza, Carla Anjos; Murphy, Nicholas; Strugnell, Jan M.
Source:
Marine genomics 2018 v.42 pp. 58-62
ISSN:
1874-7787
Subject:
transcriptome,   etc   ; Jasus edwardsii; animal tissues; ganglia; genome; genomics; hepatopancreas; lobsters; messenger RNA; sequence analysis;     Show all 10 Subjects
Abstract:
... Southern rock lobsters (Jasus edwardsii) are a valuable commodity and comprise important fishery resources in Australia and New Zealand. Population genomic methods (e.g. reduced representation sequencing) have been used to investigate patterns of dispersal and recruitment and the role of local adaptation within rock lobster species. However, application of these methods is constrained by the lack ...
DOI:
10.1016/j.margen.2018.05.005

9. A high-resolution map of the human small non-coding transcriptome

Author:
Fehlmann, Tobias; Backes, Christina; Alles, Julia; Fischer, Ulrike; Hart, Martin; Kern, Fabian; Langseth, Hilde; Rounge, Trine; Umu, Sinan Ugur; Kahraman, Mustafa; Laufer, Thomas; Haas, Jan; Staehler, Cord; Ludwig, Nicole; Hübenthal, Matthias; Meder, Benjamin; Franke, Andre; Lenhof, Hans-Peter; Meese, Eckart; Keller, Andreas; Birol, Inanc
Source:
Bioinformatics 2018 v.34 no.10 pp. 1621-1628
ISSN:
1460-2059
Subject:
transcriptome,   etc   ; bioinformatics; data collection; genome; humans; lung neoplasms; microRNA; non-coding RNA; sequence analysis;     Show all 9 Subjects
Abstract:
... Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome. In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On ...
DOI:
10.1093/bioinformatics/btx814

10. Sensitive and specific detection of microRNAs based on two-stage amplification reaction using molecular beacons as turn-on probes

Author:
Zhang, Wancun; Hu, Fang; Zhang, Qi; Zhang, Jiaqi; Mao, Yibo; Wang, Peng; Gu, Yueqing
Source:
Talanta 2018 v.179 pp. 685-692
ISSN:
0039-9140
Subject:
transcriptome,   etc   ; computer simulation; detection limit; fluorescence; genome; humans; microRNA; monitoring; oligonucleotides; point-of-care systems;     Show all 10 Subjects
Abstract:
... In this study, a rapid, sensitive, and specific assay for detecting miRNAs was developed based on a two-stage amplification reaction (TSAR) using molecular beacons (MBs) as turn-on probes. In the TSAR, different miRNAs can be converted to the same reporter oligonucleotides (Y), which can hybridize with the same MB. Therefore, in combination with specific templates, this method can be applied to mu ...
DOI:
10.1016/j.talanta.2017.11.068

11. Applied Hologenomics: Feasibility and Potential in Aquaculture

Author:
Limborg, Morten T.; Alberdi, Antton; Kodama, Miyako; Roggenbuck, Michael; Kristiansen, Karsten; Gilbert, M. Thomas P.
Source:
Trends in biotechnology 2018 v.36 pp. 252-264
ISSN:
0167-7799
Subject:
transcriptome,   etc   ; aquaculture; fish; food production; genome; human population; intestinal microorganisms; livestock; metabolome; molecular biology; proteome;     Show all 11 Subjects
Abstract:
... Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular bio ...
DOI:
10.1016/j.tibtech.2017.12.006

12. The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

Author:
Hartono, Stella R.; Malapert, Amélie; Legros, Pénélope; Bernard, Pascal; Chédin, Frédéric; Vanoosthuyse, Vincent
Source:
Journal of molecular biology 2018 v.430 no.3 pp. 272-284
ISSN:
0022-2836
Subject:
transcriptome,   etc   ; DNA; Schizosaccharomyces pombe; antibodies; chromatin; double-stranded RNA; genome; messenger RNA; nucleic acid hybridization; ribonucleases;     Show all 10 Subjects
Abstract:
... R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, pre ...
DOI:
10.1016/j.jmb.2017.12.016

13. Functional Classification and Experimental Dissection of Long Noncoding RNAs

Author:
Kopp, Florian; Mendell, Joshua T.
Source:
Cell 2018 v.172 no.3 pp. 393-407
ISSN:
0092-8674
Subject:
transcriptome,   etc   ; DNA; gene expression; genome; loci; non-coding RNA; physiology; regulatory sequences; transcription (genetics);     Show all 9 Subjects
Abstract:
... Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding tra ...
DOI:
10.1016/j.cell.2018.01.011

14. Discovering novel hydrolases from hot environments

Author:
Wohlgemuth, Roland; Littlechild, Jennifer; Monti, Daniela; Schnorr, Kirk; van Rossum, Teunke; Siebers, Bettina; Menzel, Peter; Kublanov, Ilya V.; Rike, Anne Gunn; Skretas, Georgios; Szabo, Zalan; Peng, Xu; Young, Mark J.
Source:
Biotechnology advances 2018 v.36 no.8 pp. 2077-2100
ISSN:
0734-9750
Subject:
transcriptome,   etc   ; bioinformatics; cellulases; genome; high-throughput nucleotide sequencing; hot springs; marine environment; metagenomics; quorum sensing; screening; thermal stability; thermostable enzymes;     Show all 12 Subjects
Abstract:
... Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitu ...
DOI:
10.1016/j.biotechadv.2018.09.004

15. The roles of base excision repair enzyme OGG1 in gene expression

Author:
Wang, Ruoxi; Hao, Wenjing; Pan, Lang; Boldogh, Istvan; Ba, Xueqing
Source:
Cellular and molecular life sciences 2018 v.75 no.20 pp. 3741-3750
ISSN:
1420-682X
Subject:
transcriptome,   etc   ; DNA; DNA repair; chromatin; gene expression; genome; genomics; guanine; guanosinetriphosphatase; mutation; nitrogen; oxygen; signal transduction; transcription (genetics); transcription factors;     Show all 15 Subjects
Abstract:
... Modifications of DNA strands and nucleobases—both induced and accidental—are associated with unfavorable consequences including loss or gain in genetic information and mutations. Therefore, DNA repair proteins have essential roles in keeping genome fidelity. Recently, mounting evidence supports that 8-oxoguanine (8-oxoG), one of the most abundant genomic base modifications generated by reactive ox ...
DOI:
10.1007/s00018-018-2887-8

16. High-throughput sequencing for algal systematics

Author:
Oliveira, Mariana C.; Repetti, Sonja I.; Iha, Cintia; Jackson, Christopher J.; Díaz-Tapia, Pilar; Lubiana, Karoline Magalhães Ferreira; Cassano, Valéria; Costa, Joana F.; Cremen, Ma. Chiela M.; Marcelino, Vanessa R.; Verbruggen, Heroen
Source:
European journal of phycology 2018 v.53 no.3 pp. 256-272
ISSN:
1469-4433
Subject:
transcriptome,   etc   ; DNA barcoding; algae; bioinformatics; data collection; experimental design; genome; high-throughput nucleotide sequencing; paper; phylogeny; type collections;     Show all 11 Subjects
Abstract:
... In recent years, the use of molecular data in algal systematics has increased as high-throughput sequencing (HTS) has become more accessible, generating very large datasets at a reasonable cost. In this perspectives paper, our goal is to describe how HTS technologies can advance algal systematics. Following an introduction to some common HTS technologies, we discuss how metabarcoding can accelerat ...
DOI:
10.1080/09670262.2018.1441446

17. Avian transcriptomics: opportunities and challenges

Author:
Jax, Elinor; Wink, Michael; Kraus, Robert H. S.
Source:
Journal of ornithology 2018 v.159 no.3 pp. 599-629
ISSN:
2193-7192
Subject:
transcriptome,   etc   ; RNA; birds; genome; genomics; high-throughput nucleotide sequencing; interdisciplinary research; models; molecular biology; ornithology; phenotype; planning; researchers; technology; transcriptomics;     Show all 15 Subjects
Abstract:
... Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of a ...
DOI:
10.1007/s10336-018-1532-5

18. Bacterial RNA Biology on a Genome Scale

Author:
Hör, Jens; Gorski, Stanislaw A.; Vogel, Jörg
Source:
Molecular cell 2018 v.70 pp. 785-799
ISSN:
1097-2765
Subject:
transcriptome,   etc   ; RNA; RNA-binding proteins; bacteria; gene expression; genome; humans; microbial communities; sequence analysis; thermometers; translation (genetics);     Show all 11 Subjects
Abstract:
... Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, ...
DOI:
10.1016/j.molcel.2017.12.023

19. GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

Author:
Chen, Xiao; Wang, Yurui; Sheng, Yalan; Warren, Alan; Gao, Shan
Source:
Molecular ecology resources 2018 v.18 no.3 pp. 700-713
ISSN:
1755-098X
Subject:
transcriptome,   etc   ; Bayesian theory; Ciliophora; amino acid sequences; bioinformatics; databases; food webs; genome; phylogeny; statistical analysis; terrestrial ecosystems;     Show all 11 Subjects
Abstract:
... Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes is increasingly used to reconstruct the evolutionary history and classification of these microe ...
DOI:
10.1111/1755-0998.12750

20. A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production

Author:
Geisler, Christoph
Source:
BMC biotechnology 2018 v.18 no.1 pp. 8
ISSN:
1472-6750
Subject:
transcriptome,   etc   ; Errantivirus; Spodoptera frugiperda; bioinformatics; biosafety; cell lines; genetic databases; genome; high-throughput nucleotide sequencing; insect viruses; insects; open reading frames; proteins; transposons; viruses;     Show all 15 Subjects
Abstract:
... BACKGROUND: Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although ...
DOI:
10.1186/s12896-017-0412-z
PubMed:
29415704
PubMed Central:
PMC5803895