Log in

Relevant bibliographies by topics / Transcriptome / Journal articles

To see the other types of publications on this topic, follow the link: Transcriptome.

Journal articles on the topic 'Transcriptome'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Transcriptome.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Tao, Feng, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P. Kowalski, and Edward M. Golenberg. "Optimization and application of non-native Phragmites australis transcriptome assemblies." PLOS ONE 18, no. 1 (2023): e0280354. http://dx.doi.org/10.1371/journal.pone.0280354.

Full text

Abstract:

Phragmites australis (common reed) has a cosmopolitan distribution and has been suggested as a model organism for the study of invasive plant species. In North America, the non-native subspecies (ssp. australis) is widely distributed across the contiguous 48 states in the United States and large parts of Canada. Even though millions of dollars are spent annually on Phragmites management, insufficient knowledge of P. australis impeded the efficiency of management. To solve this problem, transcriptomic information generated from multiple types of tissue could be a valuable resource for future st

APA, Harvard, Vancouver, ISO, and other styles

2

Kordonowy, Lauren L., and Matthew D. MacManes. "Characterization of a male reproductive transcriptome forPeromyscus eremicus(Cactus mouse)." PeerJ 4 (October 27, 2016): e2617. http://dx.doi.org/10.7717/peerj.2617.

Full text

Abstract:

Rodents of the genusPeromyscushave become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and va

APA, Harvard, Vancouver, ISO, and other styles

3

Ochsner, Scott A., Christopher M. Watkins, Apollo McOwiti, et al. "Transcriptomine, a web resource for nuclear receptor signaling transcriptomes." Physiological Genomics 44, no. 17 (2012): 853–63. http://dx.doi.org/10.1152/physiolgenomics.00033.2012.

Full text

Abstract:

The nuclear receptor (NR) superfamily of ligand-regulated transcription factors directs ligand- and tissue-specific transcriptomes in myriad developmental, metabolic, immunological, and reproductive processes. The NR signaling field has generated a wealth of genome-wide expression data points, but due to deficits in their accessibility, annotation, and integration, the full potential of these studies has not yet been realized. We searched public gene expression databases and MEDLINE for global transcriptomic datasets relevant to NRs, their ligands, and coregulators. We carried out extensive, d

APA, Harvard, Vancouver, ISO, and other styles

4

Duan, Hao, Qingchen Zhang, Feifei Cui, Quan Zou, and Zilong Zhang. "MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks." PLOS Computational Biology 20, no. 9 (2024): e1012409. http://dx.doi.org/10.1371/journal.pcbi.1012409.

Full text

Abstract:

Spatial transcriptome technology can parse transcriptomic data at the spatial level to detect high-throughput gene expression and preserve information regarding the spatial structure of tissues. Identifying spatial domains, that is identifying regions with similarities in gene expression and histology, is the most basic and critical aspect of spatial transcriptome data analysis. Most current methods identify spatial domains only through a single view, which may obscure certain important information and thus fail to make full use of the information embedded in spatial transcriptome data. Theref

APA, Harvard, Vancouver, ISO, and other styles

5

Macrander, Jason, Jyothirmayi Panda, Daniel Janies, Marymegan Daly, and Adam M. Reitzel. "Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data." PeerJ 6 (July 31, 2018): e5361. http://dx.doi.org/10.7717/peerj.5361.

Full text

Abstract:

The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of “venomics”: a rapidly growing field using combined transcriptomic and proteomic datasets to characterize toxin diversity in a variety of venomous taxa. Ultimately, the transcriptomic portion of these analyses follows very similar pathways after transcriptome assembly often including candidate toxin identification using BLAST, expression level screening, protein sequence alignmen

APA, Harvard, Vancouver, ISO, and other styles

6

MA, Hoi Tang, Chun Yin YU, and Lau Yan NG. "Abstract 7102: The central dogma of hepatocellular carcinoma: Genomic, transcriptomic, and proteomic changes." Cancer Research 84, no. 6_Supplement (2024): 7102. http://dx.doi.org/10.1158/1538-7445.am2024-7102.

Full text

Abstract:

Abstract Cancer is a disease condition characterized by remarkable heterogeneity, wherein numerous molecular features display considerable disparities even with the same patient cohorts, leading to varied treatment outcomes. The primary factor contributing to the substantial differences observed across cancers stems from unique combinations of genetic mutations. Epigenetic alterations further contribute to differential gene expression and splicing, thereby enhancing transcriptomic diversity. The protein products originating from the cancer transcriptome constitute the specific intracellular an

APA, Harvard, Vancouver, ISO, and other styles

7

Chen, Wanze, Orane Guillaume-Gentil, Pernille Yde Rainer, et al. "Live-seq enables temporal transcriptomic recording of single cells." Nature 608, no. 7924 (2022): 733–40. http://dx.doi.org/10.1038/s41586-022-05046-9.

Full text

Abstract:

AbstractSingle-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell’s ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell tran

APA, Harvard, Vancouver, ISO, and other styles

8

Navarrete-López, Paula, Victoria Asselstine, María Maroto, Marta Lombó, Ángela Cánovas, and Alfonso Gutiérrez-Adán. "RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population." Current Issues in Molecular Biology 46, no. 9 (2024): 10430–43. http://dx.doi.org/10.3390/cimb46090620.

Full text

Abstract:

RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and

APA, Harvard, Vancouver, ISO, and other styles

9

Londin, Eric R., Eleftheria Hatzimichael, Phillipe Loher, et al. "Towards a Reference Human Platelet Transcriptome: Evaluation Of Inter-Individual Correlations and Its Relationship With a Platelet Proteome." Blood 122, no. 21 (2013): 2297. http://dx.doi.org/10.1182/blood.v122.21.2297.2297.

Full text

Abstract:

Abstract Next generation sequencing of RNA (RNA-seq) is an emerging technology that has so far been used successfully to profile the transcriptomes of several cell types and cell states. For the platelet transcriptome, RNA-seq descriptions exist for only a few subjects. Additionally, there have been no studies of the same individual’s transcriptome using two different technologies. As such, it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA platforms, and what the transcriptomes’ relationship is with the platelet proteome. We generated

APA, Harvard, Vancouver, ISO, and other styles

10

Ali, Abdullah Mahmood, and Azra Raza. "scRNAseq and High-Throughput Spatial Analysis of Tumor and Normal Microenvironment in Solid Tumors Reveal a Possible Origin of Circulating Tumor Hybrid Cells." Cancers 16, no. 7 (2024): 1444. http://dx.doi.org/10.3390/cancers16071444.

Full text

Abstract:

Metastatic cancer is a leading cause of death in cancer patients worldwide. While circulating hybrid cells (CHCs) are implicated in metastatic spread, studies documenting their tissue origin remain sparse, with limited candidate approaches using one–two markers. Utilizing high-throughput single-cell and spatial transcriptomics, we identified tumor hybrid cells (THCs) co-expressing epithelial and macrophage markers and expressing a distinct transcriptome. Rarely, normal tissue showed these cells (NHCs), but their transcriptome was easily distinguishable from THCs. THCs with unique transcriptome

APA, Harvard, Vancouver, ISO, and other styles

11

Chaudhuri, Roy R., Lu Yu, Alpa Kanji, et al. "Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome." Microbiology 157, no. 10 (2011): 2922–32. http://dx.doi.org/10.1099/mic.0.050278-0.

Full text

Abstract:

C ampylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In thi

APA, Harvard, Vancouver, ISO, and other styles

12

Lyu, Jun, and Chongyi Chen. "Transcriptome and Temporal Transcriptome Analyses in Single Cells." International Journal of Molecular Sciences 25, no. 23 (2024): 12845. http://dx.doi.org/10.3390/ijms252312845.

Full text

Abstract:

Transcriptome analysis in single cells, enabled by single-cell RNA sequencing, has become a prevalent approach in biomedical research, ranging from investigations of gene regulation to the characterization of tissue organization. Over the past decade, advances in single-cell RNA sequencing technology, including its underlying chemistry, have significantly enhanced its performance, marking notable improvements in methodology. A recent development in the field, which integrates RNA metabolic labeling with single-cell RNA sequencing, has enabled the profiling of temporal transcriptomes in individ

APA, Harvard, Vancouver, ISO, and other styles

13

Hofmann, Erich P., Rhett M. Rautsaw, Andrew J. Mason, Jason L. Strickland, and Christopher L. Parkinson. "Duvernoy’s Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes." Toxins 13, no. 5 (2021): 336. http://dx.doi.org/10.3390/toxins13050336.

Full text

Abstract:

The venoms of small rear-fanged snakes (RFS) remain largely unexplored, despite increased recognition of their importance in understanding venom evolution more broadly. Sequencing the transcriptome of venom-producing glands has greatly increased the ability of researchers to examine and characterize the toxin repertoire of small taxa with low venom yields. Here, we use RNA-seq to characterize the Duvernoy’s gland transcriptome of the Plains Black-headed Snake, Tantilla nigriceps, a small, semi-fossorial colubrid that feeds on a variety of potentially dangerous arthropods including centipedes a

APA, Harvard, Vancouver, ISO, and other styles

14

Salazar, Juan Alfonso, Cristian Vergara-Pulgar, Claudia Jorquera, et al. "De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources." Agronomy 11, no. 5 (2021): 919. http://dx.doi.org/10.3390/agronomy11050919.

Full text

Abstract:

Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expr

APA, Harvard, Vancouver, ISO, and other styles

15

Wang, Xinjun, Zhe Sun, Yanfu Zhang, et al. "BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data." Nucleic Acids Research 48, no. 11 (2020): 5814–24. http://dx.doi.org/10.1093/nar/gkaa314.

Full text

Abstract:

Abstract Droplet-based single cell transcriptome sequencing (scRNA-seq) technology, largely represented by the 10× Genomics Chromium system, is able to measure the gene expression from tens of thousands of single cells simultaneously. More recently, coupled with the cutting-edge Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), the droplet-based system has allowed for immunophenotyping of single cells based on cell surface expression of specific proteins together with simultaneous transcriptome profiling in the same cell. Despite the rapid advances in technologies, nov

APA, Harvard, Vancouver, ISO, and other styles

16

Reznikov, Leah R., David K. Meyerholz, Mahmoud Abou Alaiwa, et al. "The vagal ganglia transcriptome identifies candidate therapeutics for airway hyperreactivity." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 2 (2018): L133—L148. http://dx.doi.org/10.1152/ajplung.00557.2017.

Full text

Abstract:

Mainstay therapeutics are ineffective in some people with asthma, suggesting a need for additional agents. In the current study, we used vagal ganglia transcriptome profiling and connectivity mapping to identify compounds beneficial for alleviating airway hyperreactivity (AHR). As a comparison, we also used previously published transcriptome data from sensitized mouse lungs and human asthmatic endobronchial biopsies. All transcriptomes revealed agents beneficial for mitigating AHR; however, only the vagal ganglia transcriptome identified agents used clinically to treat asthma (flunisolide, iso

APA, Harvard, Vancouver, ISO, and other styles

17

Apostolov, Apostol, Mladen Naydenov, Aive Kalinina, et al. "Endometrial Proliferative Phase-Centered View of Transcriptome Dynamics across the Menstrual Cycle." International Journal of Molecular Sciences 25, no. 10 (2024): 5320. http://dx.doi.org/10.3390/ijms25105320.

Full text

Abstract:

The endometrium, the inner mucosal lining of the uterus, undergoes complex molecular and cellular changes across the menstrual cycle in preparation for embryo implantation. Transcriptome-wide analyses have mainly been utilized to study endometrial receptivity, the prerequisite for successful implantation, with most studies, so far, comparing the endometrial transcriptomes between (i) secretory and proliferative endometrium or (ii) mid-secretory and early secretory endometrium. In the current study, we provide a complete transcriptome description of the endometrium across the entire menstrual c

APA, Harvard, Vancouver, ISO, and other styles

18

Cheng, Xuanjin, Junran Yan, Yongxing Liu, Jiahe Wang, and Stefan Taubert. "eVITTA: a web-based visualization and inference toolbox for transcriptome analysis." Nucleic Acids Research 49, W1 (2021): W207—W215. http://dx.doi.org/10.1093/nar/gkab366.

Full text

Abstract:

Abstract Transcriptome profiling is essential for gene regulation studies in development and disease. Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, inefficient in leveraging up-to-date and species-specific information, and limited in their visualization options. Additionally, there is no systematic way to explore data stored in the largest transcriptome repository, NCBI GEO. To fill these gaps, we have developed eVITTA (easy Visualization and Inference Toolbox for Transcriptome A

APA, Harvard, Vancouver, ISO, and other styles

19

Vonk, Freek J., Mátyás A. Bittenbinder, Harald M. I. Kerkkamp, et al. "A non-lethal method for studying scorpion venom gland transcriptomes, with a review of potentially suitable taxa to which it can be applied." PLOS ONE 16, no. 11 (2021): e0258712. http://dx.doi.org/10.1371/journal.pone.0258712.

Full text

Abstract:

Scorpion venoms are mixtures of proteins, peptides and small molecular compounds with high specificity for ion channels and are therefore considered to be promising candidates in the venoms-to-drugs pipeline. Transcriptomes are important tools for studying the composition and expression of scorpion venom. Unfortunately, studying the venom gland transcriptome traditionally requires sacrificing the animal and therefore is always a single snapshot in time. This paper describes a new way of generating a scorpion venom gland transcriptome without sacrificing the animal, thereby allowing the study o

APA, Harvard, Vancouver, ISO, and other styles

20

Darden, Dijoia B., Gabriela L. Ghita, Zhongkai Wang, et al. "Chronic Critical Illness Elicits a Unique Circulating Leukocyte Transcriptome in Sepsis Survivors." Journal of Clinical Medicine 10, no. 15 (2021): 3211. http://dx.doi.org/10.3390/jcm10153211.

Full text

Abstract:

Surgical sepsis has evolved into two major subpopulations: patients who rapidly recover, and those who develop chronic critical illness (CCI). Our primary aim was to determine whether CCI sepsis survivors manifest unique blood leukocyte transcriptomes in late sepsis that differ from transcriptomes among sepsis survivors with rapid recovery. In a prospective cohort study of surgical ICU patients, genome-wide expression analysis was conducted on total leukocytes in human whole blood collected on days 1 and 14 from sepsis survivors who rapidly recovered or developed CCI, defined as ICU length of

APA, Harvard, Vancouver, ISO, and other styles

21

Packer, Jonathan S., Qin Zhu, Chau Huynh, et al. "A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution." Science 365, no. 6459 (2019): eaax1971. http://dx.doi.org/10.1126/science.aax1971.

Full text

Abstract:

Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that (i) the correlation between a cell’s lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adop

APA, Harvard, Vancouver, ISO, and other styles

22

Chebbo, Mohamad, Said Assou, Veronique Pantesco, et al. "Platelets Purification Is a Crucial Step for Transcriptomic Analysis." International Journal of Molecular Sciences 23, no. 6 (2022): 3100. http://dx.doi.org/10.3390/ijms23063100.

Full text

Abstract:

Platelets are small anucleate cells derived from the fragmentation of megakaryocytes and are involved in different biological processes especially hemostasis, thrombosis, and immune response. Despite their lack of nucleus, platelets contain a reservoir of megakaryocyte-derived RNAs and all the machinery useful for mRNA translation. Interestingly, platelet transcriptome was analyzed in health and diseases and led to the identification of disease-specific molecular signatures. Platelet contamination by leukocytes and erythrocytes during platelet purification is a major problem in transcriptomic

APA, Harvard, Vancouver, ISO, and other styles

23

Sun, Mingwei, Yilian Zhao, Xiaobin Shao, et al. "EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)." Applied Bionics and Biomechanics 2022 (January 28, 2022): 1–9. http://dx.doi.org/10.1155/2022/7641048.

Full text

Abstract:

The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete tran

APA, Harvard, Vancouver, ISO, and other styles

24

Ghaffarinia, Ameneh, Szilárd Póliska, Ferhan Ayaydin, et al. "Unraveling Transcriptome Profile, Epigenetic Dynamics, and Morphological Changes in Psoriasis-like Keratinocytes: “Insights into Similarity with Psoriatic Lesional Epidermis”." Cells 12, no. 24 (2023): 2825. http://dx.doi.org/10.3390/cells12242825.

Full text

Abstract:

Keratinocytes are one of the primary cells affected by psoriasis inflammation. Our study aimed to delve deeper into their morphology, transcriptome, and epigenome changes in response to psoriasis-like inflammation. We created a novel cytokine mixture to mimic mild and severe psoriasis-like inflammatory conditions in cultured keratinocytes. Upon induction of inflammation, we observed that the keratinocytes exhibited a mesenchymal-like phenotype, further confirmed by increased VIM mRNA expression and results obtained from confocal microscopy. We performed RNA sequencing to achieve a more global

APA, Harvard, Vancouver, ISO, and other styles

25

Zhang, Wen. "Advancements of transcriptome imputation and related transcriptome-wide association studies." Current Research in Biochemistry and Molecular Biology 1, no. 1 (2019): 14–16. http://dx.doi.org/10.33702/crbmb.2019.1.1.4.

Full text

Abstract:

Despite the progresses of genome-wide association studies (GWASs) in revealing genetic mechanisms of human complex traits, the basis through which most identified risk variants function are highly unknown and need further investigations as well as discoveries. Recent advancements of transcriptome predictions put the transcriptome-wide association studies (TWASs) forward into a new era. TWAS through imputed transcriptomes could discover more gene-trait associations and relevant joint-tissue TWAS via eQTL analysis provide insights into furthering elucidations about gene-level association studies

APA, Harvard, Vancouver, ISO, and other styles

26

Gyoneva, Stefka, Raghavendra Hosur, David Gosselin, et al. "Cx3cr1-deficient microglia exhibit a premature aging transcriptome." Life Science Alliance 2, no. 6 (2019): e201900453. http://dx.doi.org/10.26508/lsa.201900453.

Full text

Abstract:

CX3CR1, one of the highest expressed genes in microglia in mice and humans, is implicated in numerous microglial functions. However, the molecular mechanisms underlying Cx3cr1 signaling are not well understood. Here, we analyzed transcriptomes of Cx3cr1-deficient microglia under varying conditions by RNA-sequencing (RNA-seq). In 2-mo-old mice, Cx3cr1 deletion resulted in the down-regulation of a subset of immune-related genes, without substantial epigenetic changes in markers of active chromatin. Surprisingly, Cx3cr1-deficient microglia from young mice exhibited a transcriptome consistent with

APA, Harvard, Vancouver, ISO, and other styles

27

Chen, Wan Guang, Yan Zhao Zhang, Yan Wei Cheng, and Hui Yuan Ya. "Analysis of Coexpression Genes in Oryza sativa L. Treated with Low-Energy Ion-Beam." Applied Mechanics and Materials 675-677 (October 2014): 1129–32. http://dx.doi.org/10.4028/www.scientific.net/amm.675-677.1129.

Full text

Abstract:

Xindao-18(Oryza sativa L. subsp. japonica Kato) were irratiated with a low-energy ion-beam, the growth form were observed and transcriptome of samples were sequenced by Illumina HiSeq2000 platform. The different expression genes were identified from transcriptomes control and treated samples. Finally, the coexpression of different gene expression were construce and seventy DEGs were annotated as transcription factor (TF). Among them, ten transcripts have the higher network density, and two genes, LOC_Os06g15330 and LOC_Os03g51970, had a still higher network density while elevate PCC paramater,

APA, Harvard, Vancouver, ISO, and other styles

28

Brenner, Eric, Gayatri R. Tiwari, Manav Kapoor, Yunlong Liu, Amy Brock, and R. Dayne Mayfield. "Single cell transcriptome profiling of the human alcohol-dependent brain." Human Molecular Genetics 29, no. 7 (2020): 1144–53. http://dx.doi.org/10.1093/hmg/ddaa038.

Full text

Abstract:

Abstract Alcoholism remains a prevalent health concern throughout the world. Previous studies have identified transcriptomic patterns in the brain associated with alcohol dependence in both humans and animal models. But none of these studies have systematically investigated expression within the unique cell types present in the brain. We utilized single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of over 16 000 nuclei isolated from the prefrontal cortex of alcoholic and control individuals. Each nucleus was assigned to one of seven major cell types by unsupervised clusteri

APA, Harvard, Vancouver, ISO, and other styles

29

Sheikh-Assadi, Morteza, Roohangiz Naderi, Seyed Alireza Salami, et al. "Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss." Plants 11, no. 18 (2022): 2365. http://dx.doi.org/10.3390/plants11182365.

Full text

Abstract:

A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed

APA, Harvard, Vancouver, ISO, and other styles

30

Herrera-Uribe, Juber, Kristen A. Byrne, Haibo Liu, Sage Becker, Crystal L. Loving, and Christopher K. Tuggle. "The transcriptional landscape of porcine peripheral blood immune cells." Journal of Immunology 204, no. 1_Supplement (2020): 92.18. http://dx.doi.org/10.4049/jimmunol.204.supp.92.18.

Full text

Abstract:

Abstract Blood consists of different immune cells with essential functions given by distinct molecular signatures including transcriptomic profiles. The porcine immune system shares many similarities with that in human; however, the porcine immune cell transcriptome has not been as comprehensively studied. To identify distinct transcriptomic profiles of major porcine peripheral blood immune cells, we employed magnetic separation and fluorescence activated cell sorting methods to isolate 9 different cell types from blood PBMCs from two healthy pigs, representing monocytes, neutrophils, NK cells

APA, Harvard, Vancouver, ISO, and other styles

31

Lu, Min R., Cheng-Kuo Lai, Ben-Yang Liao, and Isheng Jason Tsai. "Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages." Genome Biology and Evolution 12, no. 7 (2020): 1019–30. http://dx.doi.org/10.1093/gbe/evaa110.

Full text

Abstract:

Abstract Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolution and morphological divergences among nematodes, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were clustered broadly into embryo, larva, and adult stages, with the developmental plastic stages were sep

APA, Harvard, Vancouver, ISO, and other styles

32

Gonzalez-Ibeas, Daniel, Pedro J. Martinez-Garcia, Randi A. Famula, et al. "Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)." G3 Genes|Genomes|Genetics 6, no. 12 (2016): 3787–802. http://dx.doi.org/10.1534/g3.116.032805.

Full text

Abstract:

Abstract Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associat

APA, Harvard, Vancouver, ISO, and other styles

33

Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (December 28, 2017): 16. http://dx.doi.org/10.12688/gatesopenres.12783.1.

Full text

Abstract:

Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised the si

APA, Harvard, Vancouver, ISO, and other styles

34

Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (February 13, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.2.

Full text

Abstract:

Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a sing

APA, Harvard, Vancouver, ISO, and other styles

35

Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition." Gates Open Research 1 (March 8, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.3.

Full text

Abstract:

Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a sing

APA, Harvard, Vancouver, ISO, and other styles

36

Rychel, Kevin, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel, and Bernhard O. Palsson. "iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning." Nucleic Acids Research 49, no. D1 (2020): D112—D120. http://dx.doi.org/10.1093/nar/gkaa810.

Full text

Abstract:

Abstract Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their association to known genetic regulators. By grouping and analyzing genes based on observations from big data alone, iModulons can provide a novel perspective into how the composition of the transcriptome adapts to environmental conditions. Here, we present iModulonDB (imodulondb.org), a knowledgebase of prokaryotic transcriptional regulation

APA, Harvard, Vancouver, ISO, and other styles

37

Kakuk, Balázs, András Attila Kiss, Gábor Torma, et al. "Nanopore Assay Reveals Cell-Type-Dependent Gene Expression of Vesicular Stomatitis Indiana Virus and Differential Host Cell Response." Pathogens 10, no. 9 (2021): 1196. http://dx.doi.org/10.3390/pathogens10091196.

Full text

Abstract:

Vesicular stomatitis Indiana virus (VSIV) of genus Vesiculovirus, species IndianaVesiculovirus (formerly as Vesicular stomatitis virus, VSV) causes a disease in livestock that is very similar to the foot and mouth disease, thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches already reveal a hidden complexity of the transcriptomes in several viruses. This technique has been utilized for the sequencing of the VSIV genome, but our study is the first for the application of this technique for the profiling of the VSIV transcriptome. Since LRS is a

APA, Harvard, Vancouver, ISO, and other styles

38

Dong, Xiaomin, Yanan You, and Jia Qian Wu. "Building an RNA Sequencing Transcriptome of the Central Nervous System." Neuroscientist 22, no. 6 (2016): 579–92. http://dx.doi.org/10.1177/1073858415610541.

Full text

Abstract:

The composition and function of the central nervous system (CNS) is extremely complex. In addition to hundreds of subtypes of neurons, other cell types, including glia (astrocytes, oligodendrocytes, and microglia) and vascular cells (endothelial cells and pericytes) also play important roles in CNS function. Such heterogeneity makes the study of gene transcription in CNS challenging. Transcriptomic studies, namely the analyses of the expression levels and structures of all genes, are essential for interpreting the functional elements and understanding the molecular constituents of the CNS. Mic

APA, Harvard, Vancouver, ISO, and other styles

39

Rioux, Geneviève, Zainab Ridha, Mélissa Simard, Florence Turgeon, Sylvain L. Guérin, and Roxane Pouliot. "Transcriptome Profiling Analyses in Psoriasis: A Dynamic Contribution of Keratinocytes to the Pathogenesis." Genes 11, no. 10 (2020): 1155. http://dx.doi.org/10.3390/genes11101155.

Full text

Abstract:

Psoriasis is an immune-mediated inflammatory skin disease with a complex etiology involving environmental and genetic factors. A better insight into related genomic alteration helps design precise therapies leading to better treatment outcome. Gene expression in psoriasis can provide relevant information about the altered expression of mRNA transcripts, thus giving new insights into the disease onset. Techniques for transcriptome analyses, such as microarray and RNA sequencing (RNA-seq), are relevant tools for the discovery of new biomarkers as well as new therapeutic targets. This review summ

APA, Harvard, Vancouver, ISO, and other styles

40

Liu, Mingming, Zach N. Adelman, Kevin M. Myles, and Liqing Zhang. "A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs." Computational Biology Journal 2014 (May 28, 2014): 1–4. http://dx.doi.org/10.1155/2014/961823.

Full text

Abstract:

With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. As a consequence, de novo assembly strategies tend to generate a large number of redundant contigs due to sequence variations, which adversely affects downstream analysis and experiments. In this work we prop

APA, Harvard, Vancouver, ISO, and other styles

41

Liu, Bin, Bodo Rosenhahn, Thomas Illig, and David S. DeLuca. "A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data." PLOS Computational Biology 20, no. 7 (2024): e1011198. http://dx.doi.org/10.1371/journal.pcbi.1011198.

Full text

Abstract:

Interpreting transcriptome data is an important yet challenging aspect of bioinformatic analysis. While gene set enrichment analysis is a standard tool for interpreting regulatory changes, we utilize deep learning techniques, specifically autoencoder architectures, to learn latent variables that drive transcriptome signals. We investigate whether simple, variational autoencoder (VAE), and beta-weighted VAE are capable of learning reduced representations of transcriptomes that retain critical biological information. We propose a novel VAE that utilizes priors from biological data to direct the

APA, Harvard, Vancouver, ISO, and other styles

42

Birtolo, Maria Francesca, Roberta Armignacco, Nesrine Benanteur, et al. "Whole blood transcriptomic signature of Cushing's syndrome." European Journal of Endocrinology 191, no. 1 (2024): 55–63. http://dx.doi.org/10.1093/ejendo/lvae083.

Full text

Abstract:

Abstract Objective Cushing's syndrome is characterized by high morbidity and mortality with high interindividual variability. Easily measurable biomarkers, in addition to the hormone assays currently used for diagnosis, could reflect the individual biological impact of glucocorticoids. The aim of this study is to identify such biomarkers through the analysis of whole blood transcriptome. Design Whole blood transcriptome was evaluated in 57 samples from patients with overt Cushing's syndrome, mild Cushing's syndrome, eucortisolism, and adrenal insufficiency. Samples were randomly split into a t

APA, Harvard, Vancouver, ISO, and other styles

43

Gorbunova, Vera. "COMPARATIVE TRANSCRIPTOMIC OF LONGEVITY." Innovation in Aging 7, Supplement_1 (2023): 432. http://dx.doi.org/10.1093/geroni/igad104.1423.

Full text

Abstract:

Abstract Transcriptome analysis provides a nuanced view into the changes that occur in cells and tissues. Transcriptome changes rapidly and reproducibly in response to physiological influences and environmental insults. Recent years have seen an exponential increase in transcriptome data at bulk, single cell and spatial resolution that allows insights into the mechanisms and regulatory pathways of aging and longevity. In this session Drs. Gorbunova (University of Rochester) and Gladyshev (Harvard Medical School) will discuss comparative transcriptomics of longevity across species with diverse

APA, Harvard, Vancouver, ISO, and other styles

44

Chehimi, Samar N., Richard C. Crist, and Benjamin C. Reiner. "Unraveling Psychiatric Disorders through Neural Single-Cell Transcriptomics Approaches." Genes 14, no. 3 (2023): 771. http://dx.doi.org/10.3390/genes14030771.

Full text

Abstract:

The development of single-cell and single-nucleus transcriptome technologies is enabling the unraveling of the molecular and cellular heterogeneity of psychiatric disorders. The complexity of the brain and the relationships between different brain regions can be better understood through the classification of individual cell populations based on their molecular markers and transcriptomic features. Analysis of these unique cell types can explain their involvement in the pathology of psychiatric disorders. Recent studies in both human and animal models have emphasized the importance of transcrip

APA, Harvard, Vancouver, ISO, and other styles

45

Ibeh, Neke, Charles Y. Feigin, Stephen R. Frankenberg, Davis J. McCarthy, Andrew J. Pask, and Irene Gallego Romero. "De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata)." Gigabyte 2024 (May 2, 2024): 1–16. http://dx.doi.org/10.46471/gigabyte.118.

Full text

Abstract:

Marsupials exhibit distinctive modes of reproduction and early development that set them apart from their eutherian counterparts and render them invaluable for comparative studies. However, marsupial genomic resources still lag far behind those of eutherian mammals. We present a series of novel genomic resources for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that, due to its ease of husbandry and ex-utero development, is emerging as a laboratory model. We constructed a highly representative multi-tissue de novo transcriptome assembly of dunnart RNA-seq reads spa

APA, Harvard, Vancouver, ISO, and other styles

46

Cheon, Seongmin, Sung-Gwon Lee, Hyun-Hee Hong, Hyun-Gwan Lee, Kwang Young Kim, and Chungoo Park. "A guide to phylotranscriptomic analysis for phycologists." Algae 36, no. 4 (2021): 333–40. http://dx.doi.org/10.4490/algae.2021.36.12.7.

Full text

Abstract:

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analys

APA, Harvard, Vancouver, ISO, and other styles

47

Ilgisonis, Ekaterina V., Elena A. Ponomarenko, Svetlana N. Tarbeeva, et al. "Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq." Frontiers in Molecular Biosciences 9 (December 5, 2022). http://dx.doi.org/10.3389/fmolb.2022.944639.

Full text

Abstract:

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM &gt; 0 and TPM &gt; 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for v

APA, Harvard, Vancouver, ISO, and other styles

48

Sudhakaran, Meenakshi, Tatiana García Navarrete, Katherine Mejía-Guerra, et al. "Transcriptome reprogramming through alternative splicing triggered by apigenin drives cell death in triple-negative breast cancer." Cell Death & Disease 14, no. 12 (2023). http://dx.doi.org/10.1038/s41419-023-06342-6.

Full text

Abstract:

AbstractTriple-negative breast cancer (TNBC) is characterized by its aggressiveness and resistance to cancer-specific transcriptome alterations. Alternative splicing (AS) is a major contributor to the diversification of cancer-specific transcriptomes. The TNBC transcriptome landscape is characterized by aberrantly spliced isoforms that promote tumor growth and resistance, underscoring the need to identify approaches that reprogram AS circuitry towards transcriptomes, favoring a delay in tumorigenesis or responsiveness to therapy. We have previously shown that flavonoid apigenin is associated w

APA, Harvard, Vancouver, ISO, and other styles

49

Ma, Fuqiang, and Chaogu Zheng. "Transcriptome age of individual cell types in Caenorhabditis elegans." Proceedings of the National Academy of Sciences 120, no. 9 (2023). http://dx.doi.org/10.1073/pnas.2216351120.

Full text

Abstract:

The phylotranscriptomic analysis of development in several species revealed the expression of older and more conserved genes in midembryonic stages and younger and more divergent genes in early and late embryonic stages, which supported the hourglass mode of development. However, previous work only studied the transcriptome age of whole embryos or embryonic sublineages, leaving the cellular basis of the hourglass pattern and the variation of transcriptome ages among cell types unexplored. By analyzing both bulk and single-cell transcriptomic data, we studied the transcriptome age of the nemato

APA, Harvard, Vancouver, ISO, and other styles

50

Abebe, Jonathan S., Yasmine Alwie, Erik Fuhrmann, et al. "Nanopore guided annotation of transcriptome architectures." mSystems, July 2, 2024. http://dx.doi.org/10.1128/msystems.00505-24.

Full text

Abstract:

ABSTRACT Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails, on individual RNA molecules. The success of these analyses is highly dependent on the provision of high-resolution transcriptome annotations in combination with workflows that minimize misalignments and other analysis artifacts. Existing software solutions for generating high-resolution transcr

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!