Detecting and correcting systematic variation in large-scale RNA sequencing data

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Items 101–175 of 175

1. Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis
   Kamil Antoszewski, Klaudia Chmielewska, Karolina Jagiełło, Tomasz Puzyn · 2025 · Computational and Structural Biotechnology Journal
2. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
   Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban · 2016 · PLoS ONE
3. RNA-Seq Data Analysis, Applications and Challenges
   Anna Esteve‐Codina · 2018 · Comprehensive analytical chemistry
4. Interactions between genetic variation and cellular environment in skeletal muscle gene expression
   D. Leland Taylor, David A. Knowles, Laura J. Scott, Andrea H. Ramirez, Francesco Paolo Casale, Brooke N. Wolford, Li Guan, Arushi Varshney, Ricardo D’Oliveira Albanus, Stephen C.J. Parker et al. · 2018 · PLoS ONE
5. Local sequence and sequencing depth dependent accuracy of RNA-seq reads
   Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao · 2017 · BMC Bioinformatics
6. Standardization Efforts Enabling Next-Generation Sequencing and Microarray Based Biomarkers for Precision Medicine
   Yuanting Zheng, Tao Qing, Xue Song, Jinhang Zhu, Ying Yu, Weiwei Shi, Lajos Pusztai, Leming M. Shi · 2015 · Biomarkers in Medicine
7. Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
   Binsheng Gong, Dan Li, Paweł P. Łabaj, Bohu Pan, Natalia Novoradovskaya, Danielle Thierry‐Mieg, Jean Thierry‐Mieg, Guangchun Chen, Anne Bergstrom Lucas, Jennifer S. LoCoco et al. · 2024 · Scientific Data
8. Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
   Mengjie Chen, Qi Zhang, Zepeng Mu, Lili Wang, Zhaohui Zheng, Jinlin Miao, Ping Zhu, Yang Li · 2021 · Genome Research
9. Depth normalization of small RNA sequencing: using data and biology to select a suitable method
   Yannick Düren, Johannes Lederer, Li‐Xuan Qin · 2022 · Nucleic Acids Research
10. Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq
    Hefei Zhang, Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural, Jingyi Jessica Li, Manuel G. Garber, Albertha J.M. Walhout · 2025 · Nature Communications
11. A large-scale genome-wide gene expression analysis in peripheral blood identifies very few differentially expressed genes related to antidepressant treatment and response in patients with major depressive disorder
    Anne Krogh Nøhr, Morten Lindow, Annika Forsingdal, Samuel Demharter, Troels T. Nielsen, R. Buller, Ida Moltke, Morana Vitezic, Anders Albrechtsen · 2021 · Neuropsychopharmacology
12. Artificial intelligence-based non-small cell lung cancer transcriptome RNA-sequence analysis technology selection guide
    Min Soo Joo, Kyoung‐Ho Pyo, Jong-Moon Chung, Byoung Chul Cho · 2023 · Frontiers in Bioengineering and Biotechnology
13. Inference of differentially expressed genes using generalized linear mixed models in a pairwise fashion
    Douglas Terra Machado, Otávio J. B. Brustolini, Yasmmin Martins, Marco Antonio Grivet Mattoso Maia, Ana Tereza Ribeiro de Vasconcelos · 2023 · PeerJ
14. AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
    Sara Ballouz, Jesse A Gillis · 2016 · PLoS Computational Biology
15. RNA Sequencing Data from Human Intracranial Aneurysm Tissue Reveals a Complex Inflammatory Environment Associated with Rupture
    Vincent M. Tutino, Haley R. Zebraski, Hamidreza Rajabzadeh-Oghaz, Lee Daniel Chaves, Adam Andrew Dmytriw, Adnan Hussain Siddiqui, John J. Kolega, Kerry E. Poppenberg · 2021 · Molecular Diagnosis & Therapy
16. Bottlenecks in advancing and applying multiomic data integration—common data resources as rate-limiting drivers—the high-impact use case of atherosclerotic cardiovascular disease
    Stephanie Bezzina Wettinger, Kanita Karađuzović-Hadžiabdić, R. Attard, Rosienne C. Farrugia, Brooke N. Wolford, Marco Chierici, Giuseppe Jurman, Panagiotis Alexiou, José Luis Peñalvo, Rafael S. Costa et al. · 2025 · Briefings in Bioinformatics
17. Gene expression signatures from whole blood predict amyotrophic lateral sclerosis case status and survival
    Yue Zhao, Masha G. Savelieff, Xiayan Li, Kai Guo, Kai Wang, Minghua Li, Bo Li, Gayatri R. Iyer, Stacey A. Sakowski, Lili Zhao et al. · 2025 · Nature Communications
18. Integrated systems‐genetic analyses reveal a network target for delaying glioma progression
    Liisi Laaniste, Prashant Kumar Srivastava, Julianna Stylianou, Nelofer Syed, Silvia Cases‐Cunillera, Kirill Shkura, Qingyu Zeng, Owen J. L. Rackham, Sarah R. Langley, Andrée Delahaye‐Duriez et al. · 2019 · Annals of Clinical and Translational Neurology
19. Characterizing batch effects and binding site-specific variability in ChIP-seq data
    Mingxiang Teng, Dongliang Du, Danfeng Chen, Rafael A. Irizarry · 2021 · NAR Genomics and Bioinformatics
20. Evolutionary context of psoriatic immune skin response
    Izzy Starr, Kristina Seiffert-Sinha, Animesh A. Sinha, Ömer Gökçümen · 2021 · Evolution Medicine and Public Health
21. Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling
    Ying Yu, Wanwan Hou, Haiyan Wang, Lianhua Dong, Yaqing Liu, Shanyue Sun, Jingcheng Yang, Zehui Cao, Peipei Zhang, Yi Zi et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
22. Comparative transcript profiling reveals the mechanism of female sterility associated with seedless Ponkan mandarin (Citrus reticulata Blanco)
    Jinping Xiao, Lanlan Zhang, Fangjuan Fan, Xubo Liu · 2018 · Genome
23. Deep learning of representations for transcriptomics-based phenotype prediction
    Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter V. Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
24. Bias-invariant RNA-sequencing metadata annotation
    Hannes Wartmann, Sven Heins, Karin Kloiber, Stefan Bonn · 2021 · GigaScience
25. Intron retention as a novel source of cancer neoantigens
    Alicia Smart, Claire A. Margolis, Harold Pimentel, Meng Xiao He, Diana Miao, Dennis O. Adeegbe, Tim Fugmann, Kwok‐Kin Wong, Eliezer M. Van Allen · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
26. CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders
    Stepan A. Nersisyan, Phillipe Loher, Isidore Rigoutsos · 2025 · Nucleic Acids Research
27. Credentialing Individual Samples for Proteogenomic Analysis
    Wei Zhao, Jun Li, Rehan Akbani, Han Liang, Gordon Brent Mills · 2018 · Molecular & Cellular Proteomics
28. Systems Pharmacology: Enabling Multidimensional Therapeutics
    Stuart R. Maudsley, Hanne Leysen, Jaana van Gastel, Bronwen Martin · 2021 · Elsevier eBooks
29. RNA-seq reproducibility of Pseudomonas aeruginosa in laboratory models of cystic fibrosis
    Rebecca P. Duncan, Gina R. Lewin, Daniel M. Cornforth, Frances L. Diggle, Ananya Kapur, Dina A. Moustafa, Yasmin Hilliam, Jennifer M. Bomberger, Marvin Whiteley, Joanna B. Goldberg · 2024 · Microbiology Spectrum
30. The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies
    Johannes B. Goll, Steven E. Bosinger, Travis Lee Jensen, Hasse Walum, Tyler Grimes, Gregory K. Tharp, Muktha S. Natrajan, Azra Blazevic, Richard D. Head, Casey E. Gelber et al. · 2023 · Frontiers in Immunology
31. Hierarchical clustering of DNA k-mer counts in RNA-seq fastq files reveals batch effects
    Wolfgang Kaisers, Holger R. Schwender, Heiner Schaal · 2014 · arXiv (Cornell University)
32. Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
    Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta S. Byrska‐Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
33. Integrating genomics, transcriptomics, proteomics, metabolomics, and other omics
    Panagiotis Alexiou, Aleksandra Gruca, José Basílio, Kanita Karađuzović-Hadžiabdić, David Philip Kreil, Stephanie Bezzina Wettinger · 2025 · Elsevier eBooks
34. GeneCompete: an integrative tool of a novel union algorithm with various ranking techniques for multiple gene expression data
    Panisa Janyasupab, Apichat Suratanee, Kitiporn Plaimas · 2023 · PeerJ Computer Science
35. On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves
    Diana Lobo, Raquel S. Linheiro, Raquel Godinho, John Patrick Archer · 2022 · PLoS ONE
36. Nonparametric analysis of contributions to variance in genomics and epigenomics data
    David M. Moskowitz, William James Greenleaf · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
37. Integrative RNA-Seq and TCGA-BRCA Analyses Highlight the Role of LINC01133 in Triple-Negative Breast Cancer
    Leandro Teodoro Júnior, Henrique César Jesus-Ferreira, Mari Cleide Sogayar, Milton Yutaka Nishiyama · 2026 · Biomedicines
38. PAXgene-fixed paraffin-embedded sample is applicable to laser capture microdissection with well-balanced RNA quality and tissue morphology
    Masaki Yamazaki, Nami Yabuki, Yasunori Suzuki, Mayumi Ito, Asuka Ikeda, Osamu Natori, Masami Suzuki, Atsuhiko Kato · 2018 · Journal of Toxicologic Pathology
39. Better together: multiplexing samples to improve the preparation and reliability of gene expression studies
    Ali Mortazavi · 2015 · Nature Methods
40. Application of Transcriptomics in Exposed Human Populations: Benzene as an Example
    Cliona M. McHale, Martyn T. Smith, Luoping Zhang · 2016 · Royal Society of Chemistry eBooks
41. Lossy Compression of Quality Scores in Differential Gene Expression: A First Assessment and Impact Analysis
    Ana A. Hernandez-Lopez, Jan Voges, Claudio Alberti, Marco Mattavelli, Jörn Östermann · 2018 · DCC
42. Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data
    Omar Alaqeeli, Li Xing, Xuekui Zhang · 2021 · Microbiology Research
43. Critical view on oligo(dT)-based RNA-seq: bias arising, modeling, and mitigating
    Qiang Su, Jun Wang, Kang Kang, Yanqin Niu, Shujin Li, Deming Gou · 2023 · Genetics
44. Transcriptomics
    Lora E. Liharska, Alexander W. Charney · 2024 · Current topics in behavioral neurosciences
45. Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples
    Samuel Hamilton, Gaurav T. Gadhvi, Tyler Therron, Deborah R. Winter, SCRIPT Study Investigators · 2026 · BMC Bioinformatics
46. Genes, Behavior, and Next-Generation Sequencing
    ROBERT J. HITZEMANN, Priscila Darakjian, Denesa L. Oberbeck, CHRISTINA L. ZHENG, Nikki Walter, Ovidiu D. Iancu, Robert P. Searles, Christina A. Harrington, Shannon K. McWeeney · 2018 · Elsevier eBooks
47. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns
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48. Gene Expression and Profiling
    Yu Guo Zhou, Chao Xu, Jigang Zhang, Hong‐Wen Deng · 2016 · Translational bioinformatics
49. Variation-preserving normalization unveils blind spots in gene expression profiling
    Carlos P. Roca, Susana I.L. Gomes, Mónica J.B. Amorim, Janeck James Scott-Fordsmand · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
50. Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples
    Marie-Ange Palomares, Cyril Dalmasso, Éric Bonnet, Céline Derbois, Solène Brohard, Christophe Ambroise, Christophe Battail, Jean‐François Deleuze, Robert Olaso · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
51. Bias invariant RNA-seq metadata annotation
    Hannes Wartmann, Sven Heins, Karin Kloiber, Stefan Bonn · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
52. transcript usage from RNA-seq data: isoform pre-ltering improves performance of count-based methods
    Charlotte Soneson, Katarina Luise Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson · 2015
53. Side-by-side analysis of alternative approaches on multi-level RNA-seq data
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54. What are the most influencing factors in reconstructing a reliable transcriptome assembly?
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55. Genome-Wide Scanning of Gene Expression
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56. Single-Cell, Human Sperm Transcriptomes and Variants from Fathers of Autistic and Healthy Children
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57. TVScript: A Tool for Exploring the Effects of Intra-Condition Variation on the Detection of Differentially Expressed Genes
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58. Taming of the wild: a new method for cross study RNA-seq analysis
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59. Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns
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60. Ribosome Profiling
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61. Translational tidbits
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62. Faculty Opinions recommendation of Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study.
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63. Towards reproducible, transparent, and systematic benchmarking of omics computational tools
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64. A Toxicogenomics Study of the Hepatocarcinogen Furan
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65. Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference Materials
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66. Deep Learning Prediction of Exonic Sequence
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67. Genome-Wide Scanning of Gene Expression
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68. Additional file 1 of Genomic reproducibility in the bioinformatics era
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69. Additional file 1 of Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses
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70. Additional file 1 of Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
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71. Additional file 1 of Spatial omics technologies at multimodal and single cell/subcellular level
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72. Additional file 2 of Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
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73. Additional file 2 of Genomic reproducibility in the bioinformatics era
    Pelin Icer Baykal, Pawel Labaj, Florian M. Markowetz, Lynn M. Schriml, Daniel Johannes Stekhoven, Mangul, Serghei, Niko Beerenwinkel · 2024 · Figshare
74. Additional file 1 of Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
    Yu, Ying, Zhang, Naixin, Yuanbang Mai, Luyao Ren, Chen, Qiaochu, Zehui Cao, Chen, Qingwang, Liu, Yaqing, Wanwan Hou, Yang, Jingcheng et al. · 2023 · Figshare
75. Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants
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