Comparison of software packages for detecting differential expression in RNA-seq studies

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Items 101–200 of 424

1. Differential Expression Analysis for RNA-Seq: An Overview of Statistical Methods and Computational Software
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2. A pupal transcriptomic screen identifies Ral as a target of store-operated calcium entry in Drosophila neurons
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4. Small RNA in situ hybridization in Caenorhabditis elegans, combined with RNA-seq, identifies germline-enriched microRNAs
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   Vladimir B. Teif, Jan‐Philipp Mallm, Tanvi Sharma, David B. Mark Welch, Karsten Rippe, Roland Eils, Jörg Langowski, Ada L. Olins, Donald E. Olins · 2017 · Nucleus
10. Patterns of Gene Expression in Western Corn Rootworm (Diabrotica virgifera virgifera) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing
    Haichuan Wang, Seong‐il Eyun, Kanika S. Arora, Sek Yee Tan, Premchand Gandra, Etsuko N. Moriyama, Chitvan Khajuria, Jessica Jurzenski, Huarong Li, Maia Donahue et al. · 2017 · Toxins
11. Genome-Wide Constitutively Expressed Gene Analysis and New Reference Gene Selection Based on Transcriptome Data: A Case Study from Poplar/Canker Disease Interaction
    Jiaping Zhao, Fan Yang, Jinxia Feng, Yanli Wang, Barbara Lachenbruch, Jiange Wang, Xianchong Wan · 2017 · Frontiers in Plant Science
12. Getting the most out of RNA-seq data analysis
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13. A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials
    Duo Wang, Yaqing Liu, Yuanfeng Zhang, Qingwang Chen, Yanxi Han, Wanwan Hou, Cong Liu, Ying Yu, Ziyang Li, Ziqiang Li et al. · 2024 · Nature Communications
14. Oxidative stress in northern elephant seals: Integration of omics approaches with ecological and experimental studies
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15. Circulating microRNAs in Fabry Disease
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16. Valproic acid induces prosurvival transcriptomic changes in swine subjected to traumatic injury and hemorrhagic shock
    Patrick E. Georgoff, Vahagn C. Nikolian, Gerald A. Higgins, Kiril Chtraklin, Hassan Eidy, Mohamed H. Ghandour, Aaron M. Williams, Brian Athey, Hasan Badre Alam · 2017 · The Journal of Trauma: Injury, Infection, and Critical Care
17. Comparison of multi-tissue aging between human and mouse
    Jujuan Zhuang, Lijun Zhang, Shuang Dai, Lingyu Cui, Cheng Guo, Laura Gail Sloofman, Jialiang Yang · 2019 · Scientific Reports
18. A comprehensive workflow for optimizing RNA-seq data analysis
    Jiang Gao, Juan-Yu Zheng, Shu-Ning Ren, Weilun Yin, Xinli Xia, Yun Li, Hou‐Ling Wang · 2024 · BMC Genomics
19. Antiviral Activity of Belladonna During Japanese Encephalitis Virus Infection via Inhibition of Microglia Activation and Inflammation Leading to Neuronal Cell Survival
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20. A Five-lncRNAs Signature-Derived Risk Score Based on TCGA and CGGA for Glioblastoma: Potential Prospects for Treatment Evaluation and Prognostic Prediction
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21. Identification of Cancer-Associated Fibroblast Subtype of Triple-Negative Breast Cancer
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22. Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways
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23. A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
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24. Allele‐specific expression and gene regulation help explain transgressive thermal tolerance in non‐native hybrids of the endangered California tiger salamander ( Ambystoma californiense )
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25. Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges
    Krishanpal Anamika, Srikant Prasad Verma, Abhay Jere, Aarti Desai · 2016 · InTech eBooks
26. Dysregulation of miRNA isoform level at 5ʹ end in Alzheimer's disease
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27. A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
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28. Bioinformatic analysis of retinal gene function and expression in diabetic rats
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29. SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud
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30. Integrated COVID-19 Predictor: Differential expression analysis to reveal potential biomarkers and prediction of coronavirus using RNA-Seq profile data
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31. Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema
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32. Potential anti‐cancer effect of curcumin in human lung squamous cell carcinoma
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33. Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei
    Uriel Alonso Hurtado Paez, Ibonne Aydee García Romero, Silvia Restrepo, Fabio Aristizábal, Dolly Montoya Castaño · 2015 · PLoS ONE
34. Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
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35. Transcriptome analysis after PPARγ activation in human meibomian gland epithelial cells (hMGEC)
    Sun Woong Kim, Donald J. Brown, James V. Jester · 2019 · The Ocular Surface
36. Early social experience alters transcriptomic responses to species-specific song stimuli in female songbirds
    Matthew I. M. Louder, Márk E. Hauber, Christopher N. Balakrishnan · 2018 · Behavioural Brain Research
37. Transcriptomic and Metabolomic Response to High Light in the Charophyte Alga Klebsormidium nitens
    Emma Serrano-Pérez, Ana B. Romero–Losada, María Morales-Pineda, M. Elena García‐Gómez, Inmaculada Couso, Mercedes García‐González, Francisco J. Romero–Campero · 2022 · Frontiers in Plant Science
38. Improving the reliability of peer-reviewed publications: We are all in it together
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39. Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014–2015
    Justin C. Havird, Scott R. Santos · 2016 · Integrative and Comparative Biology
40. Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems
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41. RNA-Seq-Based Comparative Transcriptomics: RNA Preparation and Bioinformatics
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42. DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
    Zhihua Gao, Zhiying Zhao, Wenqiang Tang · 2018 · Frontiers in Genetics
43. Extent of foetal exposure to maternal elexacaftor/tezacaftor/ivacaftor during pregnancy
    Danni Li, Martin Donnelley, David Parsons, Mark D. Habgood, Elena K. Schneider‐Futschik · 2024 · British Journal of Pharmacology
44. Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection
    Humaira Lambarey, Naadirah Moola, Amy Veenstra, Shane L. Murray, Mohamed Suhail Rafudeen · 2020 · Plants
45. Purkinje Neurons with Loss of STIM1 Exhibit Age-Dependent Changes in Gene Expression and Synaptic Components
    Sreeja Kumari Dhanya, Gaiti Hasan · 2021 · Journal of Neuroscience
46. Efflux transporters in rat placenta and developing brain: transcriptomic and functional response to paracetamol
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47. Chronic Inhibition of STAT3/STAT5 in Treatment-Resistant Human Breast Cancer Cell Subtypes: Convergence on the ROS/SUMO Pathway and Its Effects on xCT Expression and System xc- Activity
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48. Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types
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49. (Post-)Genomics approaches in fungal research
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50. Novel molecules lncRNAs, tRFs and circRNAs deciphered from next-generation sequencing/RNA sequencing: computational databases and tools
    A Saleembhasha, Seema Mishra · 2017 · Briefings in Functional Genomics
51. MicroRNAs as Biomarkers and Therapeutic Targets in Female Infertility
    Lucía Chico-Sordo, Juan Antonio García-Velasco · 2024 · International Journal of Molecular Sciences
52. Comparative expression analysis in small cell lung carcinoma reveals neuroendocrine pattern change in primary tumor versus lymph node metastases
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53. Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
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54. Bioinformatics for RNA‐Seq Data Analysis
    Shanrong Zhao, Baohong Zhang, Ying Zhang, William Gordon, Sarah Du, Theresa Paradis, Michael S. Vincent, David von Schack · 2016 · InTech eBooks
55. Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference
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56. Blood Transcriptome Profiling in Myasthenia Gravis Patients to Assess Disease Activity: A Pilot RNA-seq Study
    Kee Hong Park, Junghee Jung, Jung-Hee Lee, Yoon‐Ho Hong · 2016 · Experimental Neurobiology
57. RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis
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58. Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome
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59. TRIM67 promotes NF‑κB pathway and cell apoptosis in GA‑13315‑treated lung cancer cells
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60. An improved understanding of cancer genomics through massively parallel sequencing.
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61. Transcriptomic profiling of high- and low-spiking regions reveals novel epileptogenic mechanisms in focal cortical dysplasia type II patients
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62. Effect of high variation in transcript expression on identifying differentially expressed genes in RNA‐seq analysis
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63. A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
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64. Explaining the optimistic performance evaluation of newly proposed methods: A cross‐design validation experiment
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65. Locomotion and brain gene expression exhibit sex-specific non-monotonic dose-response to HFPO-DA during Drosophila melanogaster lifespan
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66. Transcriptional response to West Nile virus infection in the zebra finch ( Taeniopygia guttata )
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67. Transcriptome profile of Carrizo citrange roots in response to Phytophthora parasitica infection
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68. Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets
    Oluwasegun Olalekan Kuloyo, Ruan Fourie, Errol Duncan Cason, Jacobus Albertyn, Carolina Henritta Pohl · 2020 · G3 Genes Genomes Genetics
69. rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data
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70. The importance of study design for detecting differentially abundant features in high-throughput experiments
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71. Molecular Genetic Analysis of Human Endometrial Mesenchymal Stem Cells That Survived Sublethal Heat Shock
    Alexander E. Vinogradov, М. А. Шилина, Olga V. Anatskaya, Alekseenko Lp, Irina I. Fridlyanskaya, Anna Krasnenko, A. Kim, Dmitriy O. Korostin, Valery Vladimirovich Ilinsky, Artem U. Elmuratov et al. · 2017 · Stem Cells International
72. Identification of cancer prognosis-associated functional modules using differential co-expression networks
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73. Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review)
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74. Identifying Breast Cancer-induced Gene Perturbations and its Application in Guiding Drug Repurposing
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75. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin
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76. Construction of an integrated gene regulatory network link to stress-related immune system in cattle
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77. AIDE: annotation-assisted isoform discovery with high precision
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78. Transcriptome analysis during fruit developmental stages in durian (Durio zibethinus Murr.) var. D24
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79. Changes in Corticotrope Gene Expression Upon Increased Expression of Peptidylglycine α-Amidating Monooxygenase
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80. CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
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81. Methadone alters transcriptional programs associated with synapse formation in human cortical organoids
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82. Phenotypic and molecular analysis of the effect of 20-hydroxyecdysone on the human filarial parasite Brugia malayi
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83. What Is the Transcriptome and How it is Evaluated?
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84. An automated RNA‐Seq analysis pipeline to identify and visualize differentially expressed genes and pathways in CHO cells
    Chun Chen, Huong Le, Chetan T. Goudar · 2015 · Biotechnology Progress
85. B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data
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86. Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets
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87. CANEapp: a user-friendly application for automated next generation transcriptomic data analysis
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88. Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs
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89. miRNA repertoires of cystic fibrosis ex vivo models highlight miR‐181a and miR ‐101 that regulate WISP1 expression
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90. How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
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91. Altered Steroid Milieu in AI-Resistant Breast Cancer Facilitates AR Mediated Gene-Expression Associated with Poor Response to Therapy
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92. RNA-seq 2G: online analysis of differential gene expression with comprehensive options of statistical methods
    Zhe Zhang, Yuanchao Zhang, Perry Evans, Asif Chinwalla, Deanne M. Taylor · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
93. A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
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94. Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
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95. Transcriptome software results show significant variation among different commercial pipelines
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96. Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens
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97. Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach
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98. BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
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99. Impact of human gene annotations on RNA-seq differential expression analysis
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100. Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
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