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1. Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

Author:
Mahmoud, Medhat; Zywicki, Marek; Twardowski, Tomasz; Karlowski, Wojciech M.
Source:
Genomics 2019 v.111 no.1 pp. 43-49
ISSN:
0888-7543
Subject:
transcriptomics,   etc   ; cost effectiveness; genomics;     Show all 3 Subjects
Abstract:
... Long sequencing reads offer unprecedented opportunities in analysis and reconstruction of complex genomic regions. However, the gain in sequence length is often traded for quality. Therefore, recently several approaches have been proposed (e.g. higher sequencing coverage, hybrid assembly or sequence correction) to enhance the quality of long sequencing reads. A simple and cost-effective approach i ...
DOI:
10.1016/j.ygeno.2017.12.011

2. Transcriptomic Resources for Parasitic Nematodes of Veterinary Importance

Author:
Jex, Aaron R.; Gasser, Robin B.; Schwarz, Erich M.
Source:
Trends in parasitology 2019 v.35 no.1 pp. 72-84
ISSN:
1471-4922
Subject:
transcriptomics,   etc   ; Nematoda; animal pathogens; genomics; parasitism; transcriptome;     Show all 6 Subjects
Abstract:
... Parasitic nematodes are important pathogens of animals, causing diseases that impact on agricultural production worldwide. Research on these worms has been constrained by a lack of genetic and genomic tools. Nonetheless, over the past decade this field has made substantial advances, many of which have been led by transcriptomic sequencing. The present review summarises major transcriptomic studies ...
DOI:
10.1016/j.pt.2018.09.010

3. A panoramic view of RNA modifications: exploring new frontiers

Author:
Zhang, Zijun; Park, Eddie; Lin, Lan; Xing, Yi
Source:
Genome biology 2018 v.19 no.1 pp. 11
ISSN:
1474-760X
Subject:
transcriptomics,   etc   ; RNA; epigenetics; China;     Show all 4 Subjects
Abstract:
... Meeting report on the Cold Spring Harbor Asia conference on RNA Modifications and Epitranscriptomics, held in Suzhou, China, 13–17 November, 2017. ...
DOI:
10.1186/s13059-018-1394-4

4. Solving Mendelian Mysteries: The Non-coding Genome May Hold the Key

Author:
Valente, Enza Maria; Bhatia, Kailash P.
Source:
Cell 2018 v.172 pp. 889-891
ISSN:
0092-8674
Subject:
transcriptomics,   etc   ; genes; genomics; mutation;     Show all 4 Subjects
Abstract:
... Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism. ...
DOI:
10.1016/j.cell.2018.02.022

5. Beyond bulk: a review of single cell transcriptomics methodologies and applications

Author:
Kulkarni, Ashwinikumar; Anderson, Ashley G.; Merullo, Devin P.; Konopka, Genevieve
Source:
Current opinion in biotechnology 2019 v.58 pp. 129-136
ISSN:
0958-1669
Subject:
transcriptomics,   etc   ; bioinformatics; brain; gene expression; neurophysiology; sequence analysis; transcriptome;     Show all 7 Subjects
Abstract:
... Single-cell RNA sequencing (scRNA-seq) is a promising approach to study the transcriptomes of individual cells in the brain and the central nervous system (CNS). This technology acts as a bridge between neuroscience, computational biology, and systems biology, enabling an unbiased and novel understanding of the cellular composition of the brain and CNS. Gene expression at the single cell resolutio ...
DOI:
10.1016/j.copbio.2019.03.001

6. Biofilms in Chronic Wounds: Pathogenesis and Diagnosis

Author:
Wu, Yuan-Kun; Cheng, Nai-Chen; Cheng, Chao-Min
Source:
Trends in biotechnology 2019 v.37 no.5 pp. 505-517
ISSN:
0167-7799
Subject:
transcriptomics,   etc   ; biofilm; microbiology; pathogenesis; point-of-care systems;     Show all 5 Subjects
Abstract:
... Chronic non-healing wounds have become a major worldwide healthcare burden. The impact of biofilms on chronic wound infection is well established. Despite increasing understanding of the underlying mechanism of biofilm formation in chronic wounds, current strategies for biofilm diagnosis in chronic wounds are still far from ideal. In this review, we briefly summarize the mechanism of biofilm forma ...
DOI:
10.1016/j.tibtech.2018.10.011

7. Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain

Author:
Kalamakis, Georgios; Brüne, Daniel; Ravichandran, Srikanth; Bolz, Jan; Fan, Wenqiang; Ziebell, Frederik; Stiehl, Thomas; Catalá-Martinez, Francisco; Kupke, Janina; Zhao, Sheng; Llorens-Bobadilla, Enric; Bauer, Katharina; Limpert, Stefanie; Berger, Birgit; Christen, Urs; Schmezer, Peter; Mallm, Jan Philipp; Berninger, Benedikt; Anders, Simon; del Sol, Antonio; Marciniak-Czochra, Anna; Martin-Villalba, Ana
Source:
Cell 2019 v.176 no.6 pp. 1407-1419.e14
ISSN:
0092-8674
Subject:
transcriptomics,   etc   ; antagonists; brain; homeostasis; mice; neural stem cells; neutralization;     Show all 7 Subjects
Abstract:
... The function of somatic stem cells declines with age. Understanding the molecular underpinnings of this decline is key to counteract age-related disease. Here, we report a dramatic drop in the neural stem cells (NSCs) number in the aging murine brain. We find that this smaller stem cell reservoir is protected from full depletion by an increase in quiescence that makes old NSCs more resistant to re ...
DOI:
10.1016/j.cell.2019.01.040

8. Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

Author:
Bossert, Silas; Murray, Elizabeth A.; Almeida, Eduardo A.B.; Brady, Seán G.; Blaimer, Bonnie B.; Danforth, Bryan N.
Source:
Molecular phylogenetics and evolution 2019 v.130 pp. 121-131
ISSN:
1055-7903
Subject:
transcriptomics,   etc   ; Ctenoplectra; bees; data collection; exons; genomics; monophyly; transcriptome;     Show all 8 Subjects
Abstract:
... Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineages is now a standard method, it is still not clear ...
DOI:
10.1016/j.ympev.2018.10.012

9. Phylogenomics supports the monophyly of the Cercozoa

Author:
Irwin, Nicholas A.T.; Tikhonenkov, Denis V.; Hehenberger, Elisabeth; Mylnikov, Alexander P.; Burki, Fabien; Keeling, Patrick J.
Source:
Molecular phylogenetics and evolution 2019 v.130 pp. 416-423
ISSN:
1055-7903
Subject:
transcriptomics,   etc   ; Cercozoa; data collection; genome; monophyly; paraphyly; protists; topology; transcriptome;     Show all 9 Subjects
Abstract:
... The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and rai ...
DOI:
10.1016/j.ympev.2018.09.004

10. Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research

Author:
Boldogkői, Zsolt; Moldován, Norbert; Balázs, Zsolt; Snyder, Michael; Tombácz, Dóra
Source:
Trends in microbiology 2019
ISSN:
0966-842X
Subject:
transcriptomics,   etc   ; DNA; genome; messenger RNA; nanopores; transcription (genetics); transcriptome; viruses;     Show all 8 Subjects
Abstract:
... Long-read sequencing (LRS) has become increasingly popular due to its strengths in de novo assembly and in resolving complex DNA regions as well as in determining full-length RNA molecules. Two important LRS technologies have been developed during the past few years, including single-molecule, real-time sequencing by Pacific Biosciences, and nanopore sequencing by Oxford Nanopore Technologies. Alt ...
DOI:
10.1016/j.tim.2019.01.010

11. Coordination of cardiac rhythmic output and circadian metabolic regulation in the heart

Author:
Hsieh, PaishiunNelson; Zhang, Lilei; Jain, MukeshKumar
Source:
Cellular and molecular life sciences 2018 v.75 no.3 pp. 403-416
ISSN:
1420-682X
Subject:
transcriptomics,   etc   ; energy; heart; metabolism; sleep;     Show all 5 Subjects
Abstract:
... Over the course of a 24-h day, demand on the heart rises and falls with the sleep/wake cycles of the organism. Cardiac metabolism oscillates appropriately, with the relative contributions of major energy sources changing in a circadian fashion. The cardiac peripheral clock is hypothesized to drive many of these changes, yet the precise mechanisms linking the cardiac clock to metabolism remain a so ...
DOI:
10.1007/s00018-017-2606-x
PubMed:
28825119
PubMed Central:
PMC5765194

12. Correction to: Transcriptome profiling of fully open flowers in a frost‑tolerant almond genotype in response to freezing stress

Author:
Hosseinpour, Batool; Sepahvand, Sadegh; Aliabad, KazemKamali; Bakhtiarizadeh, MohammadReza; Imani, Ali; Assareh, Reza; Salami, SeyedAlireza
Source:
Molecular genetics and genomics 2018 v.293 no.1 pp. 165
ISSN:
1617-4615
Subject:
transcriptomics,   etc   ; almonds; cold stress; genotype;     Show all 4 Subjects
Abstract:
... In the original publication of the article, the affiliation of the third author has been incorrectly published as University of Yazd. However, the correct affiliation is Yazd University. ...
DOI:
10.1007/s00438-017-1380-7

13. Use of omics analytical methods in the study of genetically modified maize varieties tested in 90 days feeding trials

Author:
Corujo, Maria; Pla, Maria; van Dijk, Jeroen; Voorhuijzen, Marleen; Staats, Martijn; Slot, Martijn; Lommen, Arjen; Barros, Eugenia; Nadal, Anna; Puigdomènech, Pere; Paz, José Luís La; van der Voet, Hilko; Kok, Esther
Source:
Food chemistry 2019 v.292 pp. 359-371
ISSN:
0308-8146
Subject:
transcriptomics,   etc   ; analytical methods; corn; cultivars; foods; metabolomics; proteomics; risk assessment; transgenic plants; Europe;     Show all 10 Subjects
Abstract:
... Genetically modified (GM) maize and their non-modified counterparts were compared using MON810 varieties, the only GMO event cultivated in Europe. The differences in grain samples were analysed by omics profiles, including transcriptomics, proteomics and metabolomics. Other cultivated maize varieties were analysed as a reference for the variability that will exist between cultivated varieties. The ...
DOI:
10.1016/j.foodchem.2018.05.109

14. miR-126 regulates glycogen trophoblast proliferation and DNA methylation in the murine placenta

Author:
Sharma, Abhijeet; Lacko, Lauretta A.; Argueta, Lissenya B.; Glendinning, Michael D.; Stuhlmann, Heidi
Source:
Developmental biology 2019 v.449 no.1 pp. 21-34
ISSN:
0012-1606
Subject:
transcriptomics,   etc   ; DNA methylation; animal models; energy; genes; glycogen; humans; hyperplasia; mice; microRNA; pregnancy; trophoblast;     Show all 12 Subjects
Abstract:
... A functional placenta develops through a delicate interplay of its vascular and trophoblast compartments. We have identified a previously unknown expression domain for the endothelial-specific microRNA miR-126 in trophoblasts of murine and human placentas. Here, we determine the role of miR-126 in placental development using a mouse model with a targeted deletion of miR-126. In addition to vascula ...
DOI:
10.1016/j.ydbio.2019.01.019

15. Comparative transcriptome analysis reveals key genes in the regulation of squalene and β-sitosterol biosynthesis in Torreya grandis

Author:
Suo, Jinwei; Tong, Ke; Wu, Jiasheng; Ding, Mingzhu; Chen, Wenchao; Yang, Yi; Lou, Heqiang; Hu, Yuanyuan; Yu, Weiwu; Song, Lili
Source:
Industrial crops and products 2019 v.131 pp. 182-193
ISSN:
0926-6690
Subject:
transcriptomics,   etc   ; Torreya grandis; beta-sitosterol; bioactive compounds; biosynthesis; cultivars; phosphates; seeds; squalene; transcriptome; unigenes;     Show all 11 Subjects
Abstract:
... Torreya grandis (T. grandis, Taxaceae) is both economically and medicinally valuable species being rich in various bioactive compounds (e.g., squalene and β-sitosterol). However, the contents of these compounds are various and cultivar specific, and the complicated regulatory mechanisms of their biosynthesis in T. grandis are still unknown. To uncover the underlying molecular mechanisms that contr ...
DOI:
10.1016/j.indcrop.2019.01.035

16. Metatranscriptomics reveals microbial adaptation and resistance to extreme environment coupling with bioleaching performance

Author:
Ma, Liyuan; Wang, Hongmei; Wu, Jiangjun; Wang, Yuguang; Zhang, Du; Liu, Xueduan
Source:
Bioresource technology 2019 v.280 pp. 9-17
ISSN:
0960-8524
Subject:
transcriptomics,   etc   ; bioleaching; cell proliferation; functional properties; gene expression regulation; genes; microorganisms; sequence analysis; signal transduction;     Show all 9 Subjects
Abstract:
... Chalcopyrite bioleaching by 2, 4 and 6 acidophilic strains with the same inoculation density were studied, respectively. The results indicated that the 6-strain community firstly adapted to bioleaching environment, dissolved the chalcopyrite rapidly and maintained an efficient work until late stage. Transcriptome profiles of the 6-strain community at 6th and 30th day during bioleaching process wer ...
DOI:
10.1016/j.biortech.2019.01.117

17. Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics

Author:
Starke, Robert; Jehmlich, Nico; Bastida, Felipe
Source:
Journal of proteomics 2019 v.198 pp. 50-58
ISSN:
1874-3919
Subject:
transcriptomics,   etc   ; ecosystem services; metagenomics; microbial communities; microorganisms; proteins; soil; soil ecosystems;     Show all 8 Subjects
Abstract:
... Metaproteomics was established to analyse both the structure and the function of microbial communities and, particularly in soils, their contribution to ecosystem services. In this review, we provide an overview on how the study of the soil metaproteome can provide fundamental information on the role of microbial communities in soil ecosystem services. We further discuss the strengths and weakness ...
DOI:
10.1016/j.jprot.2018.11.011

18. Initial characterization of Wnt-Tcf functions during Ciona heart development

Author:
Kaplan, Nicole A.; Wang, Wei; Christiaen, Lionel
Source:
Developmental biology 2019 v.448 no.2 pp. 199-209
ISSN:
0012-1606
Subject:
transcriptomics,   etc   ; Ciona; cardiomyocytes; gene expression regulation; head; mesoderm; muscle development; muscles; organogenesis; pharynx; signal transduction; vertebrates;     Show all 12 Subjects
Abstract:
... In vertebrate embryos, the cardiopharyngeal mesoderm gives rise to both cardiac and branchiomeric head muscles. The canonical Wnt signaling pathway regulates many aspects of cardiomyocyte specification, and modulates a balance between skeletal and cardiac myogenesis during vertebrate head muscle development. However, the role of Wnt signaling during ascidian cardiopharyngeal development remains el ...
DOI:
10.1016/j.ydbio.2018.12.018

19. Systematic identification of a neutral site on chromosome of Synechococcus sp. PCC7002, a promising photosynthetic chassis strain

Author:
Wang, Min; Luan, Guodong; Lu, Xuefeng
Source:
Journal of biotechnology 2019 v.295 pp. 37-40
ISSN:
0168-1656
Subject:
transcriptomics,   etc   ; Synechococcus sp. PCC 7002; biofuels; databases; ethanol; genes; genetic engineering; genomics; loci; photosynthesis;     Show all 10 Subjects
Abstract:
... Cyanobacteria based photosynthetic biomanufacturing is supposed to be one of the alternative routes for sustainable production of biofuels and biochemicals. Synechococcus sp. PCC 7002 is a promising cyanobacterial chassis strain possessing desired properties for scaled cultivation in future. Development of cyanobacterial cell factories requires modifications of PCC7002 chromosome to expand the pho ...
DOI:
10.1016/j.jbiotec.2019.02.007

20. An optimized method to obtain high-quality RNA from cassava storage root

Author:
Guan, Lulu; Ma, Xiaowen; Zhou, Xiaoxia; Tan, Bowen; Wang, Zhen-Yu
Source:
3 Biotech 2019 v.9 no.4 pp. 118
ISSN:
2190-572X
Subject:
transcriptomics,   etc   ; Manihot esculenta; RNA; cassava; genes; molecular biology; polyphenols; polysaccharides; quantitative polymerase chain reaction; roots;     Show all 10 Subjects
Abstract:
... Extracting RNA with high quality and integrity is crucial for molecular biology studies in eukaryotes. However, RNA isolation from cassava storage root raises a great concern because it contains large amounts of polysaccharides and polyphenol compounds. In the current study, four RNA extraction methods were evaluated for extracting RNA from cassava storage root. We found that the modified TM metho ...
DOI:
10.1007/s13205-019-1608-9