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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. 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

6. 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

7. Cis–trans controls and regulatory novelty accompanying allopolyploidization

Author:
Hu, Guanjing; Wendel, Jonathan F.
Source:
Thenew phytologist 2019 v.221 no.4 pp. 1691-1700
ISSN:
0028-646X
Subject:
transcriptomics,   etc   ; alleles; allopolyploidy; epigenetics; evolution; fractionation; gene duplication; gene expression; genomics; hybrids; models; phenotype;     Show all 12 Subjects
Abstract:
... Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression‐level dominance and revamping of co‐expression networks. Notwit ...
DOI:
10.1111/nph.15515

8. Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches

Author:
Leonavicius, Karolis; Nainys, Juozas; Kuciauskas, Dalius; Mazutis, Linas
Source:
Current opinion in biotechnology 2019 v.55 pp. 159-166
ISSN:
0958-1669
Subject:
transcriptomics,   etc   ; barcoding; data collection; diagnostic techniques; genomics; landscapes; nucleic acids; proteomics;     Show all 8 Subjects
Abstract:
... Biological samples are inherently heterogeneous and complex. Tackling this complexity requires innovative technological and analytical solutions. Recent advances in high-throughput single-cell isolation and nucleic acid barcoding methods are rapidly changing the technological landscape of biological sciences and now make it possible to measure the (epi)genomic, transcriptomic, or proteomic state o ...
DOI:
10.1016/j.copbio.2018.09.012

9. 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
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

10. Skin secretion transcriptome remains in chromatographic fractions suitable for molecular cloning

Author:
Proaño-Bolaños, Carolina; Zhou, Mei; Chen, Tianbao; Shaw, Chris
Source:
Analytical biochemistry 2019 v.564-565 pp. 13-15
ISSN:
0003-2697
Subject:
transcriptomics,   etc   ; Pelophylax; antimicrobial peptides; chromatography; frogs; messenger RNA; molecular cloning; secretion; skin (animal); transcriptome;     Show all 10 Subjects
Abstract:
... Traditional sources of mRNA for molecular cloning on amphibian skin secretion studies have been the frog's skin and skin secretions. Here, we demonstrate that mRNA isolated from chromatographic fractions of skin secretions is amenable for molecular cloning assays. We identified precursor sequences of the Arg0, Trp5, Leu8-bradykinin and six antimicrobial peptides of Pelophylax esculentus (Ranidae). ...
DOI:
10.1016/j.ab.2018.10.006

11. Multipartite genomes and the sRNome in response to temperature stress of an Arctic Pseudoalteromonas fuliginea BSW20308

Author:
Liao, Li; Liu, Chun; Zeng, Yinxin; Zhao, Bin; Zhang, Jin; Chen, Bo
Source:
Environmental microbiology 2019 v.21 no.1 pp. 272-285
ISSN:
1462-2912
Subject:
transcriptomics,   etc   ; Pseudoalteromonas; chromosomes; ecosystems; genome; global warming; heat stress; plasmids; sequence analysis; temperature; Arctic region;     Show all 11 Subjects
Abstract:
... Little is known about the survival and effect of rapid climate warming on Pseudoalteromonas in the Arctic, although it is abundant and important in this ecosystem. Here, we investigated a cold‐adapted Pseudoalteromonas fuliginea BSW20308 from the Arctic Ocean, from the genome to its transcriptomic responses towards temperature changes. It contained two circular chromosomes, with the second chromos ...
DOI:
10.1111/1462-2920.14455

12. Polycomb repressive complex 2 attenuates ABA‐induced senescence in Arabidopsis

Author:
Liu, Chunmei; Cheng, Jingfei; Zhuang, Yili; Ye, Luhuan; Li, Zijuan; Wang, Yuejun; Qi, Meifang; Xu, Lin; Zhang, Yijing
Source:
Theplant journal 2019 v.97 no.2 pp. 368-377
ISSN:
0960-7412
Subject:
transcriptomics,   etc   ; Arabidopsis thaliana; abscisic acid; crop yield; enzymes; epigenetics; genes; leaves; mutants; plant stress; stress tolerance;     Show all 11 Subjects
Abstract:
... The phytohormone abscisic acid (ABA)‐induced leaf senescence facilitates nutrient reuse and potentially contributes to enhancing plant stress tolerance. However, excessive senescence causes serious reductions in crop yield, and the mechanism by which senescence is finely tuned at different levels is still insufficiently understood. Here, we found that the double mutant of core enzymes of the polyc ...
DOI:
10.1111/tpj.14125

13. Transcriptomic and proteomic insight into the mechanism of cyclooctasulfur‐ versus thiosulfate‐oxidation by the chemolithoautotroph Sulfurimonas denitrificans

Author:
Götz, Florian; Pjevac, Petra; Markert, Stephanie; McNichol, Jesse; Becher, Dörte; Schweder, Thomas; Mussmann, Marc; Sievert, Stefan M.
Source:
Environmental microbiology 2019 v.21 no.1 pp. 244-258
ISSN:
1462-2912
Subject:
transcriptomics,   etc   ; bacteria; metabolism; models; multigene family; oxidation; proteins; proteome; proteomics; sulfur; thiosulfates; transcriptome;     Show all 12 Subjects
Abstract:
... Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero‐valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S₈). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, ...
DOI:
10.1111/1462-2920.14452

14. Exploiting transcriptomic data for metabolic engineering: toward a systematic strain design

Author:
Kim, Minsuk; Park, Beom Gi; Kim, Joonwon; Kim, Jin Young; Kim, Byung-Gee
Source:
Current opinion in biotechnology 2018 v.54 pp. 26-32
ISSN:
0958-1669
Subject:
transcriptomics,   etc   ; gene expression regulation; metabolic engineering;     Show all 3 Subjects
Abstract:
... Transcriptomics is now recognized as a primary tool for metabolic engineering as it can be used for identifying new strain designs by diagnosing current states of microbial cells. This review summarizes current application of transcriptomic data for strain design. Along with a few successful examples, limitations of conventionally used differentially expressed gene-based strain design approaches h ...
DOI:
10.1016/j.copbio.2018.01.020

15. SQUID: transcriptomic structural variation detection from RNA-seq

Author:
Ma, Cong; Shao, Mingfu; Kingsford, Carl
Source:
Genome biology 2018 v.19 no.1 pp. 52
ISSN:
1474-760X
Subject:
transcriptomics,   etc   ; algorithms; genes; models; neoplasms; sequence analysis;     Show all 6 Subjects
Abstract:
... Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a nove ...
DOI:
10.1186/s13059-018-1421-5

16. Retraction Note to: Cadmium permeates through calcium channels and activates transcriptomic complexity in wheat roots in response to cadmium stress

Author:
Yue, Jieyu; Zhang, Xin; Liu, Ning
Source:
Genes & genomics 2018 v.40 no.6 pp. 685
ISSN:
1976-9571
Subject:
transcriptomics,   etc   ; cadmium; calcium channels; permeates; roots; wheat;     Show all 6 Subjects
Abstract:
... The authors are retracting this article [1] because Figs. 1A, 1E and 1F have been taken without permission from the Master’s thesis of Qiaoling Wang. ...
DOI:
10.1007/s13258-018-0694-0

17. A senescence-delaying pre-culture medium for transcriptomics of Podospora anserina

Author:
Benocci, Tiziano; de Vries, Ronald P.; Daly, Paul
Source:
Journal of microbiological methods 2018 v.146 pp. 33-36
ISSN:
0167-7012
Subject:
transcriptomics,   etc   ; Podospora anserina; RNA; phytomass; recalcitrant species;     Show all 5 Subjects
Abstract:
... Podospora anserina is an efficient degrader of recalcitrant plant biomass but senesces quickly on most standard pre-culturing media. Among nine pre-culture media, sufficient growth without senescence was only observed on Luria-Bertani medium. The high quality RNA obtained from subsequent transfer cultures was suitable for transcriptomics. ...
DOI:
10.1016/j.mimet.2018.01.010

18. Nanomaterial toxicity for plants

Author:
Dev, Atul; Srivastava, AnupKumar; Karmakar, Surajit
Source:
Environmental chemistry letters 2018 v.16 no.1 pp. 85-100
ISSN:
1610-3653
Subject:
transcriptomics,   etc   ; ecosystems; humans; metabolomics; nanomaterials; proteomics; toxicity;     Show all 7 Subjects
Abstract:
... Nanomaterials occur widely in ecosystems as the result of both natural processes and human activities. Reports suggest that altered growth patterns in plants result from interactions of nanomaterials and plants. Plant physiological barriers provide some resistance against nanomaterial toxicity. Plants regulate its cell machinery to overcome nanomaterial-mediated stress. Engineered nanomaterials mo ...
DOI:
10.1007/s10311-017-0667-6

19. Analysis of the molecular basis of fruit cracking susceptibility in Litchi chinensis cv. Baitangying by transcriptome and quantitative proteome profiling

Author:
Wang, Jugang; Gao, Xiaomin; Ma, Zhiling; Chen, Jing; Liu, Yanan
Source:
Journal of plant physiology 2019 v.234-235 pp. 106-116
ISSN:
0176-1617
Subject:
transcriptomics,   etc   ; Litchi chinensis; cultivars; fruit cracking; genes; orchards; oxidation; pericarp; photosynthesis; proteins; proteome; proteomics; transcriptome; translation (genetics); unsaturated fatty acids;     Show all 15 Subjects
Abstract:
... Fruit cracking is a serious problem in Litchi chinensis cv. Baitangying orchards, but few advances have been made in understanding the molecular basis of cracking susceptibility in 'Baitangying'. In this work, we conducted transcriptome and quantitative proteome analyses of the pericarps of three kinds of litchi: noncracking 'Feizixiao' (cracking-resistant cultivar, F), noncracking 'Baitangying' ( ...
DOI:
10.1016/j.jplph.2019.01.014

20. A novel insect-infecting virga/nege-like virus group and its pervasive endogenization into insect genomes

Author:
Kondo, Hideki; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Suzuki, Nobuhiro
Source:
Virus research 2019 v.262 pp. 37-47
ISSN:
0168-1702
Subject:
transcriptomics,   etc   ; Bombus; Virgaviridae; bees; coat proteins; databases; fungi; genome; insect viruses; phylogeny; plant viruses; plants (botany); vertebrates; viruses;     Show all 14 Subjects
Abstract:
... Insects are the host and vector of diverse viruses including those that infect vertebrates, plants, and fungi. Recent wide-scale transcriptomic analyses have uncovered the existence of a number of novel insect viruses belonging to an alphavirus-like superfamily (virgavirus/negevirus-related lineage). In this study, through an in silico search using publicly available insect transcriptomic data, we ...
DOI:
10.1016/j.virusres.2017.11.020