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Journal articles on the topic 'Comparative transcriptomic'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Rossouw, Debra, Adri H. van den Dool, Dan Jacobson, and Florian F. Bauer. "Comparative Transcriptomic and Proteomic Profiling of Industrial Wine Yeast Strains." Applied and Environmental Microbiology 76, no. 12 (2010): 3911–23. http://dx.doi.org/10.1128/aem.00586-10.

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ABSTRACT The geno- and phenotypic diversity of commercial Saccharomyces cerevisiae wine yeast strains provides an opportunity to apply the system-wide approaches that are reasonably well established for laboratory strains to generate insight into the functioning of complex cellular networks in industrial environments. We have previously analyzed the transcriptomes of five industrial wine yeast strains at three time points during alcoholic fermentation. Here, we extend the comparative approach to include an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis of

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Udaondo, Zulema, Kanchana Sittikankaew, Tanaporn Uengwetwanit, et al. "Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon." Life 11, no. 8 (2021): 862. http://dx.doi.org/10.3390/life11080862.

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With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is undoubtedly crucial for the success of the research outcome, thus there is a need to compare these long-read sequencing platforms and evaluate them for specific research questions. This study aims to compare the performance of PacBio and ONT platforms for transcriptomic analysis by ut

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Miles, Lindsay S., Nadia A. Ayoub, Jessica E. Garb, Robert A. Haney, and Brian C. Verrelli. "Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider." Genes 11, no. 1 (2020): 87. http://dx.doi.org/10.3390/genes11010087.

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Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies in spiders despite their diversity within arthropods. Here, we generated a de novo ovarian transcriptome from 10 individuals of the western black widow spider (Latrodectus hesperus), a human health pest of high abundance in urban areas, to conduct comparative ovarian transcriptomic analyses. Biological

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Armstrong, Eric J., and Jonathon H. Stillman. "Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis." Integrative and Comparative Biology 56, no. 6 (2016): 1092–102. http://dx.doi.org/10.1093/icb/icw043.

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Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype–phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of fun

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Gross, Joshua B., Dennis A. Sun, Brian M. Carlson, Sivan Brodo-Abo, and Meredith E. Protas. "Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus." Genes 11, no. 1 (2019): 42. http://dx.doi.org/10.3390/genes11010042.

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Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave

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Tong, Xiangrong, Debin Wang, and Zichao Liu. "Comparative transcriptomic analysis between two leech species." Toxicon 158 (February 2019): S82—S83. http://dx.doi.org/10.1016/j.toxicon.2018.10.282.

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Mohamed, Amin R., Cheong Xin Chan, Mark A. Ragan, et al. "Comparative transcriptomic analyses of Chromera and Symbiodiniaceae." Environmental Microbiology Reports 12, no. 4 (2020): 435–43. http://dx.doi.org/10.1111/1758-2229.12859.

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8

Franck, Sooyoung, William L. Franck, Sean R. Birke, et al. "Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum." Symbiosis 63, no. 3 (2014): 123–35. http://dx.doi.org/10.1007/s13199-014-0294-y.

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Rahnama, Mostafa, Paul Maclean, Damien J. Fleetwood, and Richard D. Johnson. "VelA and LaeA are Key Regulators of Epichloë festucae Transcriptomic Response during Symbiosis with Perennial Ryegrass." Microorganisms 8, no. 1 (2019): 33. http://dx.doi.org/10.3390/microorganisms8010033.

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VelA (or VeA) is a key global regulator in fungal secondary metabolism and development which we previously showed is required during the symbiotic interaction of Epichloë festucae with perennial ryegrass. In this study, comparative transcriptomic analyses of ∆velA mutant compared to wild-type E. festucae, under three different conditions (in culture, infected seedlings, and infected mature plants), were performed to investigate the impact of VelA on E. festucae transcriptome. These comparative transcriptomic studies showed that VelA regulates the expression of genes encoding proteins involved

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Huang, Kuo-Yang, Po-Jung Huang, Fu-Man Ku, Rose Lin, John F. Alderete, and Petrus Tang. "Comparative Transcriptomic and Proteomic Analyses of Trichomonas vaginalis following Adherence to Fibronectin." Infection and Immunity 80, no. 11 (2012): 3900–3911. http://dx.doi.org/10.1128/iai.00611-12.

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ABSTRACTThe morphological transformation ofTrichomonas vaginalisfrom an ellipsoid form in batch culture to an adherent amoeboid form results from the contact of parasites with vaginal epithelial cells and with immobilized fibronectin (FN), a basement membrane component. This suggests host signaling of the parasite. We applied integrated transcriptomic and proteomic approaches to investigate the molecular responses ofT. vaginalisupon binding to FN. A transcriptome analysis was performed by using large-scale expressed-sequence-tag (EST) sequencing. A total of 20,704 ESTs generated from batch cul

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Wu, Wenjing, Zhiqiang Li, Shijun Zhang, Yunling Ke, and Yahui Hou. "Transcriptome response to elevated atmospheric CO2concentration in the Formosan subterranean termite,Coptotermes formosanusShiraki (Isoptera: Rhinotermitidae)." PeerJ 4 (October 4, 2016): e2527. http://dx.doi.org/10.7717/peerj.2527.

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BackgroundCarbon dioxide (CO2) is a pervasive chemical stimulus that plays a critical role in insect life, eliciting behavioral and physiological responses across different species. High CO2concentration is a major feature of termite nests, which may be used as a cue for locating their nests. Termites also survive under an elevated CO2concentration. However, the mechanism by which elevated CO2concentration influences gene expression in termites is poorly understood.MethodsTo gain a better understanding of the molecular basis involved in the adaptation to CO2concentration, a transcriptome ofCop

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Hundley, Kelsey, Olena Vaske, Geoff Lyle, et al. "EPCO-23. COMPARATIVE TRANSCRIPTOMICS TO IDENTIFY TARGETED THERAPY CANDIDATES IN HIGH GRADE GLIOMA." Neuro-Oncology 22, Supplement_2 (2020): ii74. http://dx.doi.org/10.1093/neuonc/noaa215.302.

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Abstract Genomic characterization is often used for the identification of therapeutic targets in tumors. Recently, comparative transcriptomics has begun to be utilized for this purpose. In this pilot, we compare the transcriptome of a patient with recurrent high grade glioma (HGG) to our cohort to identify potential therapies. We reviewed transcriptomic profiles from patients who had resection of HGG at our institution over the past year as well as the UCSC cancer compendium. Briefly, tumor RNA was extracted from embedded tumor tissue sections with tumor cellularity higher than 20%. RNA librar

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Krüger, Manuela, Oushadee A. J. Abeyawardana, Claudia Krüger, Miloslav Juříček, and Helena Štorchová. "Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion." Cells 9, no. 12 (2020): 2700. http://dx.doi.org/10.3390/cells9122700.

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Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphr

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Liu, Xiaolei, Hongxing Yang, Yuan Wang, Zhaohai Zhu, Wei Zhang, and Jianming Li. "Comparative Transcriptomic Analysis to Identify Brassinosteroid Response Genes." Plant Physiology 184, no. 2 (2020): 1072–82. http://dx.doi.org/10.1104/pp.20.00386.

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Charlebois, Audrey, Mario Jacques, and Marie Archambault. "Comparative transcriptomic analysis ofClostridium perfringensbiofilms and planktonic cells." Avian Pathology 45, no. 5 (2016): 593–601. http://dx.doi.org/10.1080/03079457.2016.1189512.

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XU, Zhouheng, Yingli ZHU, Mengfei SUN, et al. "Comparative transcriptomic analysis of mouse striatum and retina." Journal of Shenzhen University Science and Engineering 37, no. 1 (2020): 17–24. http://dx.doi.org/10.3724/sp.j.1249.2020.01017.

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Liu, Tiancheng, Lin Yu, Lei Liu, Hong Li, and Yixue Li. "Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing." Computational and Mathematical Methods in Medicine 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/896176.

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High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO

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18

Pradeep, Chaithra, Dharam Nandan, Arya A. Das, and Dinesh Velayutham. "Comparative Transcriptome Profiling of Disruptive Technology, Single- Molecule Direct RNA Sequencing." Current Bioinformatics 15, no. 2 (2020): 165–72. http://dx.doi.org/10.2174/1574893614666191017154427.

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Background: The standard approach for transcriptomic profiling involves high throughput short-read sequencing technology, mainly dominated by Illumina. However, the short reads have limitations in transcriptome assembly and in obtaining full-length transcripts due to the complex nature of transcriptomes with variable length and multiple alternative spliced isoforms. Recent advances in long read sequencing by the Oxford Nanopore Technologies (ONT) offered both cDNA as well as direct RNA sequencing and has brought a paradigm change in the sequencing technology to greatly improve the assembly and

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19

Yan, Guoyong, Jin Sun, Zishuai Wang, Pei-Yuan Qian, and Lisheng He. "Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland." Marine Drugs 18, no. 4 (2020): 186. http://dx.doi.org/10.3390/md18040186.

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Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The saliv

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20

Traverso, Lucila, Ivana Sierra, Marcos Sterkel, Flavio Francini, and Sheila Ons. "Neuropeptidomics in Triatoma infestans . Comparative transcriptomic analysis among triatomines." Journal of Physiology-Paris 110, no. 3 (2016): 83–98. http://dx.doi.org/10.1016/j.jphysparis.2016.12.005.

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21

Stahl, Bethany A., and Joshua B. Gross. "A Comparative Transcriptomic Analysis of Development in TwoAstyanaxCavefish Populations." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 328, no. 6 (2017): 515–32. http://dx.doi.org/10.1002/jez.b.22749.

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22

Tan, Qiao Wen, and Marek Mutwil. "Malaria.tools—comparative genomic and transcriptomic database for Plasmodium species." Nucleic Acids Research 48, no. D1 (2019): D768—D775. http://dx.doi.org/10.1093/nar/gkz662.

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Abstract Malaria is a tropical parasitic disease caused by the Plasmodium genus, which resulted in an estimated 219 million cases of malaria and 435 000 malaria-related deaths in 2017. Despite the availability of the Plasmodium falciparum genome since 2002, 74% of the genes remain uncharacterized. To remedy this paucity of functional information, we used transcriptomic data to build gene co-expression networks for two Plasmodium species (P. falciparum and P. berghei), and included genomic data of four other Plasmodium species, P. yoelii, P. knowlesi, P. vivax and P. cynomolgi, as well as two n

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23

Li, Gang, Heying Qian, Xufang Luo, et al. "Transcriptomic Analysis of Resistant and SusceptibleBombyx moriStrains Following BmNPV Infection Provides Insights into the Antiviral Mechanisms." International Journal of Genomics 2016 (2016): 1–10. http://dx.doi.org/10.1155/2016/2086346.

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Purpose. To decipher transcriptomic changes and related genes with potential functions againstBombyx morinucleopolyhedrovirus infection and to increase the understanding of the enhanced virus resistance of silkworm on the transcriptomic level.Methods. We assembled and annotated transcriptomes of the Qiufeng (susceptible to infection) and QiufengN (resistant to infection) strains and performed comparative analysis in order to decipher transcriptomic changes and related genes with potential functions against BmNPV infection.Results. A total of 78,408 SNPs were identified in the Qiufeng strain of

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Jung, Jaejoon, and Woojun Park. "Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species." Applied and Environmental Microbiology 79, no. 20 (2013): 6351–61. http://dx.doi.org/10.1128/aem.02350-13.

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ABSTRACTAlishewanellaspecies are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history ofAlishewanellaspecies is reflected in their genomes, we performed comparative genomic and transcriptomic analyses ofA. jeotgali,A. aestuarii, andA. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred inA. jeotgaliandA. agribut not inA. aestuarii. Ha

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Wang, Shan, Rui Hou, Zhenmin Bao, et al. "Transcriptome Sequencing of Zhikong Scallop (Chlamys farreri) and Comparative Transcriptomic Analysis with Yesso Scallop (Patinopecten yessoensis)." PLoS ONE 8, no. 5 (2013): e63927. http://dx.doi.org/10.1371/journal.pone.0063927.

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Chen, Shuangyan, Junting Jia, Liqin Cheng, et al. "Transcriptomic Analysis Reveals a Comprehensive Calcium- and Phytohormone-Dominated Signaling Response in Leymus chinensis Self-Incompatibility." International Journal of Molecular Sciences 20, no. 9 (2019): 2356. http://dx.doi.org/10.3390/ijms20092356.

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Sheepgrass (Leymus chinensis (Trin.) Tzvel.) is an economically and ecologically important forage in the grass family. Self-incompatibility (SI) limits its seed production due to the low seed-setting rate after self-pollination. However, investigations into the molecular mechanisms of sheepgrass SI are lacking. Therefore, microscopic observation of pollen germination and pollen tube growth, as well as transcriptomic analyses of pistils after self- and cross-pollination, were performed. The results indicated that pollen tube growth was rapidly inhibited from 10 to 30 min after self-pollination

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Sun, S., J. Li, D. Chen, et al. "Comparative transcriptomic analysis reveals a series of single nucleotide polymorphism between red- and white-fleshed loquats (Eriobotrya japonica)." Czech Journal of Genetics and Plant Breeding 53, No. 3 (2017): 97–106. http://dx.doi.org/10.17221/43/2016-cjgpb.

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Loquat (Eriobotrya japonica) is an economically important crop and red-fleshed cultivars have a much higher carotenoid content than white-fleshed cultivars. We used Illumina RNA-seq technology to gain a global overview of the loquat transcriptome from a mixture of fruit samples at different developmental stages for both red-fleshed and white-fleshed loquat. A total of 94.98 million paired-end short reads were obtained and 61 586 unigenes were generated from de novo assembly with an average length of 817 bp. Among these unigenes, 44 710 unigenes were annotated by blast against Nr, Swissprot, GO

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Butovich, Igor A., Nita Bhat, and Jadwiga C. Wojtowicz. "Comparative Transcriptomic and Lipidomic Analyses of Human Male and Female Meibomian Glands Reveal Common Signature Genes of Meibogenesis." International Journal of Molecular Sciences 20, no. 18 (2019): 4539. http://dx.doi.org/10.3390/ijms20184539.

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Meibum is a lipid secretion that is produced by holocrine Meibomian glands (MGs). MGs are a specialized type of sebaceous glands that are embedded in the human eyelids. Chemically, meibum and sebum are different. A detailed characterization of lipidome and transcriptome of MG is required to deconvolute a complex and poorly characterized array of biosynthetic reactions (termed meibogenesis) that lead to formation of meibum. Changes in the composition and quality of meibum have been linked to various ocular disorders, some of which are more prevalent in males, while others in females. To establi

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Gao, Shouguo, Zhijie Wu, Xingmin Feng, Jichun Chen, Sachiko Kajigaya, and Neal S. Young. "Comparative Single Cell Transcriptomic Analysis of the Hematopoietic System between Human and Mouse." Blood 134, Supplement_1 (2019): 3706. http://dx.doi.org/10.1182/blood-2019-123204.

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Single cell RNA-seq has been extensively applied to the hematopoiesis of human and mouse, but the cross-species comparison still has not been thoroughly studied. Here, using the 10X single cell platform and a canonical correlation analysis (CCA, https://satijalab.org/seurat/) computational strategy, we conducted comparative transcriptomic analysis of the hematopoietic hierarchy between human and mouse. We found that the hematopoietic stem and progenitor cell (HSPC) compartments in the two species were composed of subpopulations characterized by the same set of homologous genes, and the hematop

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Laurence, Flori, Mariani Valentina, Chardon Patrick, Lemonnier Gaétan, Lefevre François, and Rogel-Gaillard Claire. "Comparative transcriptomic analysis of PrV-host cell interactions in pig." Veterinary Immunology and Immunopathology 128, no. 1-3 (2009): 219–20. http://dx.doi.org/10.1016/j.vetimm.2008.10.024.

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Jiao, Xiaoming, Xiaochun Zhao, Xue-Rong Zhou, et al. "Comparative Transcriptomic Analysis of Developing Cotton Cotyledons and Embryo Axis." PLoS ONE 8, no. 8 (2013): e71756. http://dx.doi.org/10.1371/journal.pone.0071756.

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Manganaris, G. A., A. Jajo, P. Holford, et al. "COMPARATIVE TRANSCRIPTOMIC ANALYSIS OF PLUM FRUIT TREATED WITH 1-MCP." Acta Horticulturae, no. 877 (November 2010): 1105–9. http://dx.doi.org/10.17660/actahortic.2010.877.150.

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Pan, Ye, Peng Lü, Qinyun Wang, et al. "Comparative transcriptomic analysis ofBombyx morifat body tissue following dietary restriction." Archives of Insect Biochemistry and Physiology 95, no. 1 (2017): e21388. http://dx.doi.org/10.1002/arch.21388.

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Fumagalli, Maria Rita, Francesc Font-Clos, Simone Milan, Stefano Zapperi, and Caterina A. M. La Porta. "Comparative analysis of metabolic and transcriptomic features of Nothobranchius furzeri." Journal of The Royal Society Interface 17, no. 168 (2020): 20200217. http://dx.doi.org/10.1098/rsif.2020.0217.

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Some species have a longer lifespan than others, but usually lifespan is correlated with typical body weight. Here, we study the lifetime evolution of the metabolic behaviour of Nothobranchius furzeri , a killifish with an extremely short lifespan with respect to other fishes, even when taking into account rescaling by body weight. Comparison of the gene expression patterns of N. furzeri with those of zebrafish Danio rerio and mouse ( Mus musculus ) shows that a broad set of metabolic genes and pathways are affected in N. furzeri during ageing in a way that is consistent with a global deregula

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Park, Hee, Soon Myung, and Wonyong Kim. "Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci." BMC Microbiology 12, no. 1 (2012): 77. http://dx.doi.org/10.1186/1471-2180-12-77.

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Lo, Alvin W., Christine A. Seers, John D. Boyce, et al. "Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells." BMC Microbiology 9, no. 1 (2009): 18. http://dx.doi.org/10.1186/1471-2180-9-18.

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Zhang, Wen-Qian, Miao Zhao, Ming-Yu Huang, and Ji-Long Liu. "Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats." Cellular Physiology and Biochemistry 50, no. 2 (2018): 668–78. http://dx.doi.org/10.1159/000494187.

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Background/Aims: Embryo implantation is an essential process for eutherian pregnancy, but this process varies across eutherians. The genomic mechanisms that led to the emergence and diversification of embryo implantation are largely unknown. Methods: In this study, we analyzed transcriptomic changes during embryo implantation in mice and rats by using RNA-seq. Bioinformatics and evolutionary analyses were performed to characterize implantation-associated genes in these two species. Results: We identified a total of 518 differentially expressed genes in mouse uterus during implantation, of whic

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Mehta, Abijeet Singh, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, and Amit Singh. "Comparative transcriptomic analysis and structure prediction of novel Newt proteins." PLOS ONE 14, no. 8 (2019): e0220416. http://dx.doi.org/10.1371/journal.pone.0220416.

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Lim, Jolyn Jia Jia, Jace Koh, Jia Rong Moo, et al. "Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom." Computational and Structural Biotechnology Journal 18 (2020): 3788–95. http://dx.doi.org/10.1016/j.csbj.2020.11.019.

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Boher, Pau, Marçal Soler, Anna Sánchez, et al. "A comparative transcriptomic approach to understanding the formation of cork." Plant Molecular Biology 96, no. 1-2 (2017): 103–18. http://dx.doi.org/10.1007/s11103-017-0682-9.

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Liu, Dong, Jiahui Xu, Yanyan Wang, et al. "Comparative transcriptomic analysis of Clostridium acetobutylicum biofilm and planktonic cells." Journal of Biotechnology 218 (January 2016): 1–12. http://dx.doi.org/10.1016/j.jbiotec.2015.11.017.

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Minagawa, Hirotaka, Masao Honda, Kenji Miyazaki, et al. "Comparative proteomic and transcriptomic profiling of the human hepatocellular carcinoma." Biochemical and Biophysical Research Communications 366, no. 1 (2008): 186–92. http://dx.doi.org/10.1016/j.bbrc.2007.11.101.

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Zhou, Rong-Qiong, Guang-Xu Ma, Pasi K. Korhonen, et al. "Comparative transcriptomic analyses of male and female adult Toxocara canis." Gene 600 (February 2017): 85–89. http://dx.doi.org/10.1016/j.gene.2016.11.024.

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Liu, Zichao, Feng Zhao, Xiangrong Tong, et al. "Comparative transcriptomic analysis reveals the mechanism of leech environmental adaptation." Gene 664 (July 2018): 70–77. http://dx.doi.org/10.1016/j.gene.2018.04.063.

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Li, X., M. H. Patel, C. M. Brumfiel, et al. "104 Comparative transcriptomic profiles of cutaneous sarcoidosis and granuloma annulare." Journal of Investigative Dermatology 141, no. 5 (2021): S18. http://dx.doi.org/10.1016/j.jid.2021.02.122.

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46

Zubcevic, Jasenka, Ashley Baker, and Christopher J. Martyniuk. "Transcriptional networks in rodent models support a role for gut-brain communication in neurogenic hypertension: a review of the evidence." Physiological Genomics 49, no. 7 (2017): 327–38. http://dx.doi.org/10.1152/physiolgenomics.00010.2017.

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Hypertension (HTN) is the most prevalent condition observed in primary health care. Hypertension shows complex etiology, and neuroinflammation, overactive sympathetic drive, and the microbiome are each associated with the disease. To obtain mechanistic perspective into neurogenic HTN, we first constructed a framework for transcriptional regulators of the disease using the Comparative Toxicogenomics Database. This approach yielded a core group of 178 transcripts that are prevalent in studies of HTN, including leptin and neuropeptide Y. We then conducted a meta-analysis for transcriptome data ge

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Li, Xin, Chenying Duan, Ruyi Li, and Dong Wang. "Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies." Animals 11, no. 1 (2021): 80. http://dx.doi.org/10.3390/ani11010080.

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To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next,

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Zhang. "Comparative Transcriptomic Analysis of the Larval and Adult Stages of Taenia pisiformis." Genes 10, no. 7 (2019): 507. http://dx.doi.org/10.3390/genes10070507.

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Taenia pisiformis is a tapeworm causing economic losses in the rabbit breeding industry worldwide. Due to the absence of genomic data, our knowledge on the developmental process of T. pisiformis is still inadequate. In this study, to better characterize differential and specific genes and pathways associated with the parasite developments, a comparative transcriptomic analysis of the larval stage (TpM) and the adult stage (TpA) of T. pisiformis was performed by Illumina RNA sequencing (RNA-seq) technology and de novo analysis. In total, 68,588 unigenes were assembled with an average length of

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Chetal, Kashish, and Sarath Chandra Janga. "OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/318217.

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Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets.Description. We present operomeDB, a database whic

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Peery, Rhiannon M., Chandra H. McAllister, Catherine I. Cullingham, Elizabeth L. Mahon, Adriana Arango-Velez, and Janice E. K. Cooke. "Comparative genomics of the chitinase gene family in lodgepole and jack pines: contrasting responses to biotic threats and landscape level investigation of genetic differentiation." Botany 99, no. 6 (2021): 355–78. http://dx.doi.org/10.1139/cjb-2020-0125.

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The sister species, lodgepole pine (Pinus contorta var. latifolia Engelm.) and jack pine (Pinus banksiana Lamb), face pressures from a multitude of biotic agents, including mountain pine beetle (Dendroctonus ponderosae Hopkins, 1902) and their pathogenic fungal associates (e.g., Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf.), mistletoe (Arceuthobium americanum Nutt. ex A.Gray), and the pathogen causing western gall rust (Cronartium harknessii E. Meinecke). Here, we report new stem tissue transcriptome resources developed for lodgepole and jack pi

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