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Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

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Dual RNA-seq of pathogen and host

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Calculating Sample Size Estimates for RNA Sequencing Data

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Effect of different carbon sources on denitrification performance, microbial community structure and denitrification genes

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Finding the active genes in deep RNA-seq gene expression studies

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Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

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Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin

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Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysisPreprint

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Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes

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RNA-seq and microarray complement each other in transcriptome profiling

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Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals

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Human tRNA synthetase catalytic nulls with diverse functions

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Research Resource: RNA-Seq Reveals Unique Features of the Pancreatic β-Cell Transcriptome

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Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

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Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

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Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species

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Transcriptome sequencing in Sézary syndrome identifies Sézary cell and mycosis fungoides-associated lncRNAs and novel transcripts

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Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

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A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat

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Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

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Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma

Lock, F. E., Rebollo, R., Miceli-Royer, K., Gagnier, L., Kuah, S., Babaian, A., Sistiaga-Poveda, M., Lai, C. B., Nemirovsky, O., Serrano, I., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405507111 · Cited by 78

Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose

Liu, Y., Ferguson, J. F., Xue, C., Silverman, I. M., Gregory, B., Reilly, M. P., & Li, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066883 · Cited by 74

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

Cumbie, J. S., Kimbrel, J. A., Di, Y., Schafer, D. W., Wilhelm, L., Fox, S. E., Sullivan, C. M., Curzon, A. D., Carrington, J. C., Mockler, T. C., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025279 · Cited by 73

MHC I–associated peptides preferentially derive from transcripts bearing miRNA response elements

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RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk

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Splicing in immune cells—mechanistic insights and emerging topics

Schaub, A., & Glasmacher, E. (2017) · International Immunology · doi:10.1093/intimm/dxx026 · Cited by 68

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

Greiff, V., Menzel, U., Haessler, U., Cook, S. C., Friedensohn, S., Khan, T. A., Pogson, M., Hellmann, I., & Reddy, S. T. (2014) · BMC Immunology · doi:10.1186/s12865-014-0040-5 · Cited by 64

Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

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Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians

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Correlation between RNA-Seq and microarrays results using TCGA data

Chen, L., Sun, F., Yang, X., Jin, Y., Shi, M., Wang, L., Shi, Y., Zhan, C., & Wang, Q. (2017) · Gene · doi:10.1016/j.gene.2017.07.056 · Cited by 62

Transcriptome-wide analysis of protein–RNA interactions using high-throughput sequencing

Milek, M., Wyler, E., & Landthaler, M. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.12.001 · Cited by 64

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling

Robinson, D. G., & Storey, J. D. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu552 · Cited by 57

The autoimmunity-associated BLK haplotype exhibits cis-regulatory effects on mRNA and protein expression that are prominently observed in B cells early in development

Simpfendorfer, K. R., Olsson, L. M., Manjarrez‐Orduño, N., Khalili, H., Simeone, A. M., Katz, M. S., Lee, A. T., Diamond, B., & Gregersen, P. K. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds220 · Cited by 52

Alternative Transcript Initiation and Splicing as a Response to DNA Damage

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Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing

Lin, K.-T., Shann, Y.-J., Chau, G.-Y., Hsu, C.-N., & Huang, C.-Y. F. (2013) · Oncogene · doi:10.1038/onc.2013.424 · Cited by 50

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

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Local and global factors affecting RNA sequencing analysis

Sendler, E. D., Johnson, G. D., & Krawetz, S. A. (2011) · Analytical Biochemistry · doi:10.1016/j.ab.2011.08.013 · Cited by 49

Long noncoding RNAs in psychiatric disorders

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A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly and Utility for RNA-Seq in a Non-Model Bird

Finseth, F. R., & Harrison, R. G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108550 · Cited by 46

Latency-Associated Nuclear Antigen of Kaposi Sarcoma–Associated Herpesvirus Promotes Angiogenesis through Targeting Notch Signaling Effector Hey1

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Transcriptomes of Mouse Olfactory Epithelium Reveal Sexual Differences in Odorant Detection

Shiao, M., Chang, A. Y.-F., Liao, B., Ching, Y., Lu, M. J., Chen, S. M., & Li, W. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs039 · Cited by 46

Accuracy of RNA-Seq and its dependence on sequencing depth

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PLK2 Plays an Essential Role in High D-Glucose-Induced Apoptosis, ROS Generation and Inflammation in Podocytes

Zou, H., Yang, P.-P., Huang, T.-L., Zheng, X.-X., & Xu, G.-S. (2017) · Scientific Reports · doi:10.1038/s41598-017-00686-8 · Cited by 38

Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach

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Long Noncoding RNA Expression Profiling Using Arraystar LncRNA Microarrays

Shi, Y., & Shang, J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3378-5_6 · Cited by 36

DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression

George, N. I., & Chang, C. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-92 · Cited by 31

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

Rallapalli, G., Kemen, E. M., Robert‐Seilaniantz, A., Segonzac, C., Etherington, G., Sohn, K. H., MacLean, D., & Jones, J. D. G. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-341 · Cited by 34

Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection

Postler, T. S., Pantry, S. N., Desrosiers, R. C., & Ghosh, S. (2017) · Virology · doi:10.1016/j.virol.2017.08.006 · Cited by 34

Alternative Splicing in Cancer and Immune Cells

Bernard, A., Boidot, R., & Végran, F. (2022) · Cancers · doi:10.3390/cancers14071726 · Cited by 33

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

Ni, Y., Hall, A. W., Battenhouse, A. M., & Iyer, V. R. (2012) · BMC Genetics · doi:10.1186/1471-2156-13-46 · Cited by 32

Transcriptome Sequencing of and Microarray Development for a Helicoverpa zea Cell Line to Investigate In Vitro Insect Cell-Baculovirus Interactions

Nguyen, Q. H., Palfreyman, R. W., Chan, L. C. L., Reid, S., & Nielsen, L. K. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036324 · Cited by 31

High-throughput sequencing reveals differing immune responses in the intestinal mucosa of two inbred lines afflicted with necrotic enteritis

Truong, A. D., Hong, Y. H., & Lillehoj, H. S. (2015) · Veterinary Immunology and Immunopathology · doi:10.1016/j.vetimm.2015.06.008 · Cited by 31

Transcriptional profiling of adult Drosophila antennae by high-throughput sequencing

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Transcriptome analysis of human colorectal cancer biopsies reveals extensive expression correlations among genes related to cell proliferation, lipid metabolism, immune response and collagen catabolism

Xu, L., Wang, R., Ziegelbauer, J. M., Wu, W. W., Shen, R., Juhl, H. H., Zhang, Y., Pelosof, L. C., & Rosenberg, A. S. (2017) · Oncotarget · doi:10.18632/oncotarget.20345 · Cited by 28

Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments

Marsh, J. W., Hayward, R. J., Shetty, A. C., Mahurkar, A., Humphrys, M. S., & Myers, G. S. A. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx043 · Cited by 29

Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: Applying RNA-sequencing analysis on archived specimens

Lin, X. S., Hu, L., Sandy, K. Y. P., Correll, M., Quackenbush, J. F., Wu, C., & McDougal, W. S. (2013) · Urologic Oncology Seminars and Original Investigations · doi:10.1016/j.urolonc.2013.06.014 · Cited by 27

Transcriptional profiles of virulent and precocious strains of Eimeria tenella at sporozoite stage; novel biological insight into attenuated asexual development

Matsubayashi, M., Kawahara, F., Hatta, T., Yamagishi, J., Miyoshi, T., Anisuzzaman, A., Sasai, K., Isobe, T., Kita, K., & Tsuji, N. (2016) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2016.02.021 · Cited by 27

UBR5 HECT domain mutations identified in mantle cell lymphoma control maturation of B cells

Swenson, S. A., Gilbreath, T. J., Vahle, H., Hynes-Smith, R. W., Graham, J. H., Law, H. C.-H., Amador, C., Woods, N. T., Green, M. R., & Buckley, S. M. (2020) · Blood · doi:10.1182/blood.2019002102 · Cited by 27

Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses

Chen, G., Wang, C., Shi, L. M., Qu, X., Chen, J., Yang, J., Shi, C., Chen, L., Zhou, P., Ning, B., et al. (2013) · RNA · doi:10.1261/rna.037473.112 · Cited by 27

RNA-binding protein Ptbp1 is essential for BCR-mediated antibody production

Sasanuma, H., Ozawa, M., & Yoshida, N. (2018) · International Immunology · doi:10.1093/intimm/dxy077 · Cited by 25

NGS Evaluation of Colorectal Cancer Reveals Interferon Gamma Dependent Expression of Immune Checkpoint Genes and Identification of Novel IFNγ Induced Genes

Xu, L., Pelosof, L., Wang, R., Mcfarland, H. I., Wu, W. W., Phue, J., Lee, C.-T., Shen, R.-F., Juhl, H., Wu, L., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00224 · Cited by 20

Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders

Wang, O., Liang, G., McAllister, T. A., Plastow, G. S., Stanford, K., Selinger, L. B., & Guan, L. L. (2016) · PLoS ONE · doi:10.1371/journal.pone.0151284 · Cited by 25

Hypoxia-Induced miR-148a Downregulation Contributes to Poor Survival in Colorectal Cancer

Nersisyan, S. A., Galatenko, A. V., Chekova, M., & Tonevitsky, A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.662468 · Cited by 25

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro

Marsh, J. W., Humphrys, M. S., & Myers, G. S. A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01830 · Cited by 25

Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome

Zheng, H., Liu, E., Shi, T., Ye, L., Konno, T., Oda, M., & Ji, Z. (2015) · Molecular BioSystems · doi:10.1039/c5mb00547g · Cited by 26

ADAR1-mediated RNA editing promotes B cell lymphomagenesis

Pecori, R., Ren, W., Pirmoradian, M., Wang, X., Liu, D., Berglund, M., Li, W., Tasakis, R. N., Giorgio, S. D., Ye, X., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106864 · Cited by 23

Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK)

Li, J., Lai, K. P., Ching, A. K.-K., & Chan, T.-F. (2014) · Genomics · doi:10.1016/j.ygeno.2013.12.005 · Cited by 23

Molecular cloning of novel transcripts of human kallikrein-related peptidases 5, 6, 7, 8 and 9 (KLK5 – KLK9), using Next-generation sequencing

Adamopoulos, P. G., Kontos, C. K., & Scorilas, A. (2017) · Scientific Reports · doi:10.1038/s41598-017-16269-6 · Cited by 22

An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis

Normand, R., & Yanai, I. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-514-9_1 · Cited by 22

Small Nucleolar RNAs: Biological Functions and Diseases

Wang, Y., Fu, M., Zheng, Z., Feng, J., & Zhang, C. (2025) · MedComm · doi:10.1002/mco2.70257 · Cited by 23

The RNA regulatory programs that govern lymphocyte development and function

Díaz‐Muñoz, M. D., & Osma-García, I. C. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1683 · Cited by 22

Transcriptomic Profile of Whole Blood Cells from Elderly Subjects Fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label Study

Solano-Aguilar, G. I., Molokin, A., Botelho, C. A., Fiorino, A., Vinyard, B. T., Li, R., Chen, C. T., Urban, J. F., Dawson, H. D., Andreyeva, I., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0147426 · Cited by 21

Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

Díez, P., Droste, C., Dégano, R. M., González-Muñoz, M., Ibarrola, N., Pérez‐Andrés, M., Garín-Muga, A., Segura, V., Marko‐Varga, G., LaBaer, J., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00474 · Cited by 20

Clinical Genomics: Challenges and Opportunities

Vijay, P., McIntyre, A. B. R., Mason, C. E., Greenfield, J. P., & Li, S. (2016) · Critical Reviews in Eukaryotic Gene Expression · doi:10.1615/critreveukaryotgeneexpr.2016015724 · Cited by 18

Identification and Validation of Gene Expression Pattern and Signature in Patients with Immune Thrombocytopenia

Ye, Q., Jiang, H., Liao, X.-L., Chen, K., & Li, S.-S. (2016) · SLAS DISCOVERY · doi:10.1177/1087057116664029 · Cited by 16

Deep Sequencing of Cardiac MicroRNA-mRNA Interactomes in Clinical and Experimental Cardiomyopathy

Matkovich, S. J., & Dorn, G. W. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2572-8_3 · Cited by 17

The dynamic mechanisms underpinning symbiotic Epichloë–grass interactions: implications for sustainable and resilient agriculture

Johnson, L. J., Bastías, D. A., Caradus, J. R., Chettri, P., Forester, N. T., Mace, W. J., Miller, T. A., Moon, C. D., Voisey, C. R., Zhang, W., et al. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822122-8.00008-x · Cited by 17

Single Nucleotide Variants in Transcription Factors Associate More Tightly with Phenotype than with Gene Expression

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Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design

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