Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · see citing works

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829 · see citing works

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works

Summaries of Affymetrix GeneChip probe level data

Irizarry, R. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng015 · Cited by 4,906 · see citing works

RSeQC: quality control of RNA-seq experiments

Wang, L., Wang, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts356 · Cited by 2,813 · see citing works

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

Bullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-94 · Cited by 1,680 · see citing works

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

Nair, R. P., Duffin, K. C., Helms, C. A., Ding, J., Stuart, P. E., Goldgar, D. E., Gudjonsson, J. E., Li, Y., Tejasvi, T., Feng, B., et al. (2009) · Nature Genetics · doi:10.1038/ng.311 · Cited by 1,414 · see citing works

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Anders, S., McCarthy, D. J., Chen, Y., Okoniewski, M. J., Smyth, G. K., Huber, W. K., & Robinson, M. D. (2013) · Nature Protocols · doi:10.1038/nprot.2013.099 · Cited by 1,129 · see citing works

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn425 · Cited by 1,088 · see citing works

Database resources of the National Center for Biotechnology Information

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1000 · Cited by 1,007 · see citing works

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

Zhao, S., Fung‐Leung, W., Bittner, A., Ngo, K., & Liu, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0078644 · Cited by 945 · see citing works

Summarizing and correcting the GC content bias in high-throughput sequencing

Benjamini, Y., & Speed, T. P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks001 · Cited by 913 · see citing works

Camera: a competitive gene set test accounting for inter-gene correlation

Wu, D., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks461 · Cited by 880 · see citing works

Coupling mRNA processing with transcription in time and space

Bentley, D. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3662 · Cited by 828 · see citing works

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.

't Hoen, P. A. C., Ariyurek, Y., Thygesen, H. H., Vreugdenhil, E., Vossen, R. H. A. M., de Menezes, R. X., Boer, J. M., van Ommen, G.-J. B., & den Dunnen, J. T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn705 · Cited by 742 · see citing works

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C. E., Socci, N. D., & Betel, D. (2013) · Genome Biology · doi:10.1186/gb-2013-14-9-r95 · Cited by 733 · see citing works

Biases in Illumina transcriptome sequencing caused by random hexamer priming

Hansen, K. D., Brenner, S. E., & Dudoit, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq224 · Cited by 713 · see citing works

Transcript length bias in RNA-seq data confounds systems biology

Oshlack, A., & Wakefield, M. J. (2009) · Biology Direct · doi:10.1186/1745-6150-4-14 · Cited by 497 · see citing works

Statistical inferences for isoform expression in RNA-Seq

Jiang, H., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp113 · Cited by 453 · see citing works

RNase 7, a Novel Innate Immune Defense Antimicrobial Protein of Healthy Human Skin

Harder, J., & Schröder, J. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207587200 · Cited by 425 · see citing works

Library preparation methods for next-generation sequencing: Tone down the bias

van Dijk, E., Jaszczyszyn, Y., & Thermes, C. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.01.008 · Cited by 411 · see citing works

Transcriptome Analysis of Psoriasis in a Large Case–Control Sample: RNA-Seq Provides Insights into Disease Mechanisms

Li, B., Tsoi, L. C., Swindell, W. R., Gudjonsson, J. E., Tejasvi, T., Johnston, A. W. B., Ding, J., Stuart, P. E., Xing, X., Kochkodan, J. J., et al. (2014) · Journal of Investigative Dermatology · doi:10.1038/jid.2014.28 · Cited by 393 · see citing works

Interferon action—sequence specificity of the ppp(A2′p)nA-dependent ribonuclease

Wreschner, D. H., McCauley, J. W., Skehel, J. J., & Kerr, I. M. (1981) · Nature · doi:10.1038/289414a0 · Cited by 321 · see citing works

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M., & Nielsen, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks804 · Cited by 309 · see citing works

Type I Interferon: Potential Therapeutic Target for Psoriasis?

Yao, Y., Richman, L. K., Morehouse, C., Reyes, M. D. L., Higgs, B. W., Boutrin, A., White, B., Coyle, A. J., Krueger, J. G., Kiener, P. A., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002737 · Cited by 309 · see citing works

Expanding the Psoriasis Disease Profile: Interrogation of the Skin and Serum of Patients with Moderate-to-Severe Psoriasis

Suárez‐Fariñas, M., Li, K., Fuentes‐Duculan, J., Hayden, K. E., Brodmerkel, C. M., & Krueger, J. G. (2012) · Journal of Investigative Dermatology · doi:10.1038/jid.2012.184 · Cited by 308 · see citing works

Effective treatment of psoriasis with etanercept is linked to suppression of IL-17 signaling, not immediate response TNF genes

Zaba, L. C., Suárez‐Fariñas, M., Fuentes‐Duculan, J., Nograles, K. E., Guttman‐Yassky, E., Cardinale, I. R., Lowes, M. A., & Krueger, J. G. (2009) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2009.08.046 · Cited by 303 · see citing works

A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data

Kvam, V. M., Liu, P., & Si, Y. (2012) · American Journal of Botany · doi:10.3732/ajb.1100340 · Cited by 281 · see citing works

Enhanced Expression and Secretion of Antimicrobial Peptides in Atopic Dermatitis and after Superficial Skin Injury

Harder, J., Dressel, S., Wittersheim, M., Cordes, J., Meyer‐Hoffert, U., Mrowietz, U., Fölster‐Holst, R., Proksch, E., Schröder, J., Schwarz, T., et al. (2010) · Journal of Investigative Dermatology · doi:10.1038/jid.2009.432 · Cited by 258 · see citing works

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

Joyce, C. E., Zhou, X., Xia, J., Ryan, C., Thrash, B., Menter, A., Zhang, W., & Bowcock, A. M. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr331 · Cited by 240 · see citing works

Effects of filtering by Present call on analysis of microarray experiments

McClintick, J. N., & Edenberg, H. J. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-49 · Cited by 236 · see citing works

Psoriatic scales: a promising source for the isolation of human skin-derived antimicrobial proteins

Harder, J., & Schröder, J. (2005) · Journal of Leukocyte Biology · doi:10.1189/jlb.0704409 · Cited by 227 · see citing works

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

Bottomly, D., Walter, N. A. R., Hunter, J. E., Darakjian, P., Kawane, S., Buck, K. J., Searles, R. P., Mooney, M. A., McWeeney, S. K., & HITZEMANN, R. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017820 · Cited by 225 · see citing works

MicroRNAs and potential target interactions in psoriasis

Zibert, J. R., Løvendorf, M. B., Litman, T., Olsen, J., Kaczkowski, B., & Skov, L. (2010) · Journal of Dermatological Science · doi:10.1016/j.jdermsci.2010.03.004 · Cited by 218 · see citing works

Impact of RNA degradation on gene expression profiling

Opitz, L., Salinas, G., Grade, M., Jung, K., Jo, P., Emons, G., Ghadimi, Β. M., Beißbarth, T., & Gaedcke, J. (2010) · BMC Medical Genomics · doi:10.1186/1755-8794-3-36 · Cited by 208 · see citing works

Quality Assessment of Affymetrix GeneChip Data

Bolstad, B. M., Collin, F., Brettschneider, J. A., Simpson, K., Cope, L., Irizarry, R. A., & Speed, T. P. (2005) · Springer eBooks · doi:10.1007/0-387-29362-0_3 · Cited by 197 · see citing works

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

Paulsen, M. T., Veloso, A., Prasad, J., Bedi, K., Ljungman, E. A., Magnuson, B., Wilson, T. E., & Ljungman, M. E. (2013) · Methods · doi:10.1016/j.ymeth.2013.08.015 · Cited by 194 · see citing works

RNA-seq and microarray complement each other in transcriptome profiling

Kogenaru, S., Yan, Q., Guo, Y., & Wang, N. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-629 · Cited by 157 · see citing works

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

Bradford, J. R., Hey, Y., Yates, T., Li, Y., Pepper, S. D. V., & Miller, C. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-282 · Cited by 145 · see citing works

Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients

Swindell, W. R., Johnston, A. W. B., Voorhees, J. J., Elder, J. T., & Gudjonsson, J. E. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-527 · Cited by 135 · see citing works

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

Xu, X., Zhang, Y., Williams, J. L., Antoniou, E., McCombie, W. R., Wu, S., Zhu, W., Davidson, N. O., Denoya, P. I., & Li, E. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s9-s1 · Cited by 129 · see citing works

Methodological considerations for gene expression profiling of human brain

Atz, M. E., Walsh, D. M. A., Cartagena, P. M., Li, J. Z., Evans, S. J., Choudary, P. V., Overman, K., Stein, R., Tomita, H., Potkin, S. G., et al. (2007) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2007.03.022 · Cited by 115 · see citing works

The relationship between mRNA stability and length inSaccharomyces cenvisiae

Santiago, T. C., Purvis, I. J., Bettany, A. J. E., & Brown, A. J. P. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.21.8347 · Cited by 115 · see citing works

Transcriptional Profiling of Psoriasis Using RNA-seq Reveals Previously Unidentified Differentially Expressed Genes

Jabbari, A., Suárez‐Fariñas, M., Dewell, S. B., & Krueger, J. G. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.267 · Cited by 98 · see citing works

Heterogeneity of Inflammatory and Cytokine Networks in Chronic Plaque Psoriasis

Swindell, W. R., Xing, X., Stuart, P. E., Chen, C. S., Aphale, A., Nair, R. P., Voorhees, J. J., Elder, J. T., Johnston, A. W. B., & Gudjonsson, J. E. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034594 · Cited by 93 · see citing works

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

Su, Z., Li, Z., Chen, T., Li, Q., Fang, H., Ding, D., Ge, W., Ning, B., Hong, H., Perkins, R., et al. (2011) · Chemical Research in Toxicology · doi:10.1021/tx200103b · Cited by 85 · see citing works

Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

Stalteri, M. A., & Harrison, A. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-13 · Cited by 82 · see citing works

IFN-α Enhances Poly-IC Responses in Human Keratinocytes by Inducing Expression of Cytosolic Innate RNA Receptors: Relevance for Psoriasis

Prens, E. P., Kant, M., van Dijk, G., van der Wel, L. I., Mourits, S., & van der Fits, L. (2007) · Journal of Investigative Dermatology · doi:10.1038/sj.jid.5701087 · Cited by 79 · see citing works

Cross-Study Homogeneity of Psoriasis Gene Expression in Skin across a Large Expression Range

Bigler, J., Rand, H. A., Kerkof, K., Timour, M., & Russell, C. B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0052242 · Cited by 76 · see citing works

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

Popova, T. G., Mennerich, D., Weith, A., & Quast, K. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-91 · Cited by 69 · see citing works

Comparison of Microarrays and RNA-Seq for Gene Expression Analyses of Dose-Response Experiments

Black, M. B., Parks, B., Pluta, L., Chu, T., Allen, B. C., Wolfinger, R. D., & Thomas, R. S. (2013) · Toxicological Sciences · doi:10.1093/toxsci/kft249 · Cited by 64 · see citing works

Hepatitis C virus RNA: Dinucleotide frequencies and cleavage by RNase L

Washenberger, C. L., Han, J.-Q., Kechris, K. J., Jha, B. K., Silverman, R. H., & Barton, D. J. (2007) · Virus Research · doi:10.1016/j.virusres.2007.05.020 · Cited by 63 · see citing works

Modulation of Epidermal Transcription Circuits in Psoriasis: New Links between Inflammation and Hyperproliferation

Swindell, W. R., Johnston, A. W. B., Xing, X., Voorhees, J. J., Elder, J. T., & Gudjonsson, J. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079253 · Cited by 63 · see citing works

Sensitivity of Hepatitis C Virus RNA to the Antiviral Enzyme Ribonuclease L Is Determined by a Subset of Efficient Cleavage Sites

Han, J.-Q., Wroblewski, G., Xu, Z., Silverman, R. H., & Barton, D. J. (2004) · Journal of Interferon & Cytokine Research · doi:10.1089/jir.2004.24.664 · Cited by 62 · see citing works

Early tissue responses in psoriasis to the antitumour necrosis factor-α biologic etanercept suggest reduced interleukin-17 receptor expression and signalling

Johnston, A. W. B., Guzman, A. M., Swindell, W. R., Wang, F., Kang, S., & Gudjonsson, J. E. (2014) · British Journal of Dermatology · doi:10.1111/bjd.12937 · Cited by 56 · see citing works

Transcription Poisoning by Topoisomerase I Is Controlled by Gene Length, Splice Sites, and miR-142-3p

Solier, S., Ryan, M., Martin, S. E., Varma, S., Kohn, K. W., Liu, H., Zeebèrg, B. R., & Pommier, Y. G. (2013) · Cancer Research · doi:10.1158/0008-5472.can-12-3504 · Cited by 54 · see citing works

IL-17A and IFN-γ Synergistically Induce RNase 7 Expression via STAT3 in Primary Keratinocytes

Simanski, M., Rademacher, F., Schröder, L. C., Schumacher, H. M., Gläser, R., & Harder, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059531 · Cited by 50 · see citing works

Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

Veloso, A., Biewen, B., Paulsen, M. T., Berg, N. K., Lima, L. C. D. A., Prasad, J., Bedi, K., Magnuson, B., Wilson, T. E., & Ljungman, M. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078190 · Cited by 48 · see citing works

Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin

Xia, J., Joyce, C. E., Bowcock, A. M., & Zhang, W. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds481 · Cited by 47 · see citing works

Integrative Biology Approach Identifies Cytokine Targeting Strategies for Psoriasis

Perera, G. K., Ainali, C., Semenova, E., Hundhausen, C., Barinaga, G., Kassen, D., Williams, A. E., Mirza, M. M., Balázs, M., Wang, X., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3007217 · Cited by 44 · see citing works

Cytokine modulation of retinoic acid-inducible gene-I (RIG-I) expression in human epidermal keratinocytes

Kitamura, H., Matsuzaki, Y., Kimura, K., Nakano, H., Imaizumi, T., Satoh, K., & Hanada, K. (2006) · Journal of Dermatological Science · doi:10.1016/j.jdermsci.2006.11.003 · Cited by 42 · see citing works

Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods

Landau, W. M., & Liu, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081415 · Cited by 34 · see citing works

Differential expression analysis for paired RNA-seq data

Chung, L. M., Ferguson, J. P., Zheng, W., Qian, F., Bruno, V. M., Montgomery, R. R., & Zhao, H. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-110 · Cited by 32 · see citing works

Method for Improved Illumina Sequencing Library Preparation Using NuGEN Ovation RNA-Seq System

Head, S. R., Komori, H. K., Hart, T., Shimashita, J., Schaffer, L., Salomon, D. R., & Ordoukhanian, P. T. (2011) · BioTechniques · doi:10.2144/000113613 · Cited by 30 · see citing works

Transcriptional regulatory network for psoriasis

Lu, X., Du, J., Liang, J. F., Zhu, X., Yang, Y., & Xu, J. (2012) · The Journal of Dermatology · doi:10.1111/1346-8138.12000 · Cited by 29 · see citing works

A central role for RNA in the induction and biological activities of type 1 interferons

Li, X., Ezelle, H. J., Hsi, T. Y., & Hassel, B. A. (2010) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.32 · Cited by 26 · see citing works

Creation of Differentiation-Specific Genomic Maps of Human Epidermis through Laser Capture Microdissection

Gulati, N., Krueger, J. G., Suárez‐Fariñas, M., & Mitsui, H. (2013) · Journal of Investigative Dermatology · doi:10.1038/jid.2013.190 · Cited by 19 · see citing works

Towards the integration, annotation and association of historical microarray experiments with RNA-seq

Chavan, S. S., Bauer, M., Peterson, E. A., Heuck, C. J., & Johann, D. J. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s14-s4 · Cited by 18 · see citing works

Subcellular distribution of phosphatases, proteinases, and ribonucleases in normal human stratum corneum and psoriatic scales

F�rster, F. J., Neufahrt, A., Stockum, G., Bauer, K., Frenkel, S., Fertig, U., & Leonhardi, G. (1975) · Archives of Dermatological Research · doi:10.1007/bf00561530 · Cited by 12 · see citing works

The Pre-mRNA Splicing Reaction

Wongpalee, S. P., & Sharma, S. (2014) · Methods in molecular biology · doi:10.1007/978-1-62703-980-2_1 · Cited by 8 · see citing works

III. THE RIBONUCLEASES OF HUMAN EPIDERMIS

Melbye, S. W., Brant, B. A., & Freedberg, I. M. (1977) · British Journal of Dermatology · doi:10.1111/j.1365-2133.1977.tb14242.x · Cited by 7 · see citing works

On the length, weight and GC content of the human genome

Piovesan, A., Pelleri, M. C., Antonaros, F., Strippoli, P., Caracausi, M., & Vitale, L. (2019) · BMC Research Notes · doi:10.1186/s13104-019-4137-z · Cited by 283 · see citing works

RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

Suárez‐Fariñas, M., Ungar, B., da Rosa, J. C., Ewald, D. A., Rozenblit, M., Gonzalez, J., Xu, H., Zheng, X., Peng, X., Estrada, Y. D., et al. (2015) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2015.03.003 · Cited by 270 · see citing works

IL-17A inhibition by secukinumab induces early clinical, histopathologic, and molecular resolution of psoriasis

Krueger, J. G., Wharton, K. A., Schlitt, T., Suprun, M., Torene, R. I., Jiang, X., Wang, C. Q. F., Fuentes‐Duculan, J., Hartmann, N., Peters, T., et al. (2019) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2019.04.029 · Cited by 190 · see citing works

Aquaporin-3 in the epidermis: more than skin deep

Bollag, W. B., Aitkens, L., White, J. D., & Hyndman, K. A. (2020) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00075.2020 · Cited by 149 · see citing works

IFN-γ and TNF-α synergism may provide a link between psoriasis and inflammatory atherogenesis

Mehta, N. N., Teague, H., Swindell, W. R., Baumer, Y., Ward, N. L., Xing, X., Baugous, B., Johnston, A., Joshi, A. A., Silverman, J. I. M., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-14365-1 · Cited by 123 · see citing works

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

Swindell, W. R., Remmer, H. A., Sarkar, M. K., Xing, X., Barnes, D. H., Wolterink, L., Voorhees, J. J., Nair, R. P., Johnston, A. W. B., Elder, J. T., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0208-5 · Cited by 103 · see citing works

Human Aquaporins: Functional Diversity and Potential Roles in Infectious and Non-infectious Diseases

Azad, A. K., Raihan, T., Ahmed, J., Hakim, A., Emon, T. H., & Chowdhury, P. A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.654865 · Cited by 103 · see citing works

NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis

Tervaniemi, M. H., Katayama, S., Skoog, T., Siitonen, H. A., Vuola, J., Nuutila, K., Sormunen, R. T., Johnsson, A., Linnarsson, S., Suomela, S., et al. (2016) · Scientific Reports · doi:10.1038/srep22745 · Cited by 96 · see citing works

Transcriptional landscape of psoriasis identifies the involvement of IL36 and IL36RN

Keermann, M., Kõks, S., Reimann, E., Prans, E., Abram, K., & Kingo, K. (2015) · BMC Genomics · doi:10.1186/s12864-015-1508-2 · Cited by 91 · see citing works

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples

Nazarov, P. V., Muller, A., Kaoma, T., Nicot, N., Máximo, C., Birembaut, P. L., Tran, N. L., Dittmar, G. A. G., & Vallar, L. (2017) · BMC Genomics · doi:10.1186/s12864-017-3819-y · Cited by 88 · see citing works

Review—Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis

Schwingen, J., Kaplan, M., & Kurschus, F. C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21030699 · Cited by 76 · see citing works

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs

Ahn, R. S., Gupta, R., Lai, K., Chopra, N., Arron, S. T., & Liao, W. J. (2016) · BMC Genomics · doi:10.1186/s12864-016-3188-y · Cited by 76 · see citing works

Cross-Disease Transcriptomics: Unique IL-17A Signaling in Psoriasis Lesions and an Autoimmune PBMC Signature

Swindell, W. R., Sarkar, M. K., Liang, Y., Xing, X., & Gudjonsson, J. E. (2016) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2016.04.035 · Cited by 73 · see citing works

Induction of Alternative Proinflammatory Cytokines Accounts for Sustained Psoriasiform Skin Inflammation in IL-17C+IL-6KO Mice

Fritz, Y., Klenotic, P. A., Swindell, W. R., Yin, Z. Q., Groft, S. G., Zhang, L., Baliwag, J., Camhi, M. I., Diaconu, D., Young, A. B., et al. (2016) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2016.10.021 · Cited by 53 · see citing works

Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

Egatz-Gómez, A., Wang, C., Klacsmann, F., Pan, Z., Marczak, S. P., Wang, Y., Sun, G., Senapati, S., & Chang, H. (2016) · Biomicrofluidics · doi:10.1063/1.4948525 · Cited by 48 · see citing works

Keratinocytes Derived from Patient-Specific Induced Pluripotent Stem Cells Recapitulate the Genetic Signature of Psoriasis Disease

Ali, G., Elsayed, A. K., Nandakumar, M., Bashir, M., Younis, I., Aqel, Y. W. A., Memon, B., Temanni, R., Abubaker, F., Taheri, S., et al. (2020) · Stem Cells and Development · doi:10.1089/scd.2019.0150 · Cited by 47 · see citing works

Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites

Swindell, W. R., Sarkar, M. K., Stuart, P. E., Voorhees, J. J., Elder, J. T., Johnston, A., & Gudjonsson, J. E. (2015) · Clinical and Translational Medicine · doi:10.1186/s40169-015-0054-5 · Cited by 46 · see citing works

Comparison of microarray and RNA-Seq analysis of mRNA expression in dermal mesenchymal stem cells

Li, J., Hou, R., Niu, X., Liu, R., Wang, Q., Wang, C., Li, X., Hao, Z., Yin, G., & Zhang, K. (2015) · Biotechnology Letters · doi:10.1007/s10529-015-1963-5 · Cited by 44 · see citing works

Aquaporins in the Skin

Patel, R. R., Heard, L. K., Chen, X., & Bollag, W. B. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-94-024-1057-0_11 · Cited by 38 · see citing works

Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster

Payne, B. L., & Alvarez‐Ponce, D. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz051 · Cited by 21 · see citing works

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation

Dom, G., Dmitriev, P., Lambot, M.-A., Vliet, G. V., Glinoer, D., Libert, F., Lefort, A., Dumont, J. E., & Maenhaut, C. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.669354 · Cited by 20 · see citing works

Transcriptomic Profiling of Peripheral Edge of Lesions to Elucidate the Pathogenesis of Psoriasis Vulgaris

Boonpethkaew, S., Meephansan, J., Jumlongpim, O., Tangtanatakul, P., Soonthornchai, W., Wongpiyabovorn, J., Vipanurat, R., & Komine, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094983 · Cited by 19 · see citing works

Know your enemy – transcriptome of myxozoanTetracapsuloides bryosalmonaereveals potential drug targets against proliferative kidney disease in salmonids

Ahmad, F., Debes, P. V., Pukk, L., Kahar, S., Hartikainen, H., Gross, R., & Vasemägi, A. (2021) · Parasitology · doi:10.1017/s003118202100010x · Cited by 15 · see citing works

Microfluidic Electrokinetic Preconcentration Chips: Enhancing the detection of nucleic acids and exosomes

Kim, J., Sahloul, S., Orozaliev, A., Do, V. Q., Pham, V.-S., Martins, D., Wei, X., Levicky, R., & Song, Y. (2020) · IEEE Nanotechnology Magazine · doi:10.1109/mnano.2020.2966064 · Cited by 14 · see citing works

Analysis of psoriasis‐relevant gene expression and exon usage alterations after silencing of SR ‐rich splicing regulators

Szlávicz, E., Oláh, P., Szabó, K., Pagani, F., Bata‐Csörgõ, Z., Kemény, L. V., & Széll, M. (2018) · Experimental Dermatology · doi:10.1111/exd.13530 · Cited by 13 · see citing works

Aquaporins in Skin

Yin, Z., & Ren, H. (2023) · Advances in experimental medicine and biology · doi:10.1007/978-981-19-7415-1_15 · Cited by 11 · see citing works

Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis

Zhang, Y., Akintola, O. S., Liu, K. J. A., & Sun, B. (2015) · Gene · doi:10.1016/j.gene.2015.09.041 · Cited by 11 · see citing works

Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level

Yan, S., Liu, R., Mao, M., Liu, Z., Zhang, W., Zhang, Y., Li, J., Peng, C., & Chen, X. (2019) · PeerJ · doi:10.7717/peerj.7404 · Cited by 11 · see citing works

Rapid detection of exosomal microRNA biomarkers by electrokinetic concentration for liquid biopsy on chip

Cheung, L. S., Wei, X., Martins, D., & Song, Y. (2018) · Biomicrofluidics · doi:10.1063/1.5009719 · Cited by 10 · see citing works

Exploratory analysis of genetic variants influencing molecular traits in cerebral cortex of suicide completers

Rodríguez-López, M. L., Martínez‐Magaña, J. J., Cabrera‐Mendoza, B., Mendoza, A. D. G., García‐Dolores, F., López‐Armenta, M., Flores, G., Vázquez‐Roque, R. A., & Nicolini, H. (2019) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32752 · Cited by 10 · see citing works

Transcriptome dynamics of human pluripotent stem cell-derived contracting cardiomyocytes using an embryoid body model with fetal bovine serum

Jung, K. B., Son, Y. S., Lee, H., Jung, C., Kim, J., & Son, M. (2017) · Molecular BioSystems · doi:10.1039/c7mb00174f · Cited by 9 · see citing works

Identification of biomarkers of acne based on transcriptome analysis and combined with network pharmacology to explore the therapeutic mechanism of Jinhuang ointment

Li, M., Gao, X., Miao, T., & Sun, H. (2023) · Medicine · doi:10.1097/md.0000000000035642 · Cited by 5 · see citing works

Empirical Bayes analysis of RNA sequencing experiments with auxiliary information

Liang, K. (2019) · The Annals of Applied Statistics · doi:10.1214/19-aoas1270 · Cited by 5 · see citing works

Meta-Analysis of Gene Expression in Bulk-Processed Post-Mortem Spinal Cord from ALS Patients and Normal Controls

Swindell, W. R. (2025) · NeuroSci · doi:10.3390/neurosci6030065 · Cited by 3 · see citing works

Integrative leaf transcriptomic and physiological insights into salt stress responses in Eucalyptus: A comparative analysis of two contrasting clones

Tadiya, R., Barthwal, S., Ginwal, H. S., Singh, H., & Singh, F. (2025) · Plant Gene · doi:10.1016/j.plgene.2025.100551 · Cited by 3 · see citing works

Exploring the role of growth factors as potential regulators in psoriatic plaque formation

Boonpethkaew, S., Meephansan, J., Ponnikorn, S., Jumlongpim, O., Juntongjin, P., Chakkavittumrong, P., Wongpiyabovorn, J., Morita, A., & Komine, M. (2023) · Experimental Dermatology · doi:10.1111/exd.14918 · Cited by 3 · see citing works

Transcriptomic signatures of prostate cancer progression: a comprehensive RNA-seq study

Modanwal, S., Mulpuru, V., Mishra, A., & Mishra, N. (2025) · 3 Biotech · doi:10.1007/s13205-025-04297-3 · Cited by 2 · see citing works

Data Wisdom in Computational Genomics Research

Huang, H., & Yu, B. (2017) · Statistics in Biosciences · doi:10.1007/s12561-016-9173-9 · Cited by 1 · see citing works

Declining RNA integrity in control autopsy brain tissue is robustly and asymmetrically associated with selective neuronal mRNA signal lossPreprint

Johnson, E. S., Stenzel, K. E., Lee, S., & Blalock, E. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.07.459326 · Cited by 1 · see citing works

Gene expression and functional studies on psoriatic epidermis

Tervaniemi, M. H. (2016) · Työväentutkimus Vuosikirja

Transcriptome profiling research in urothelial cell carcinoma

Ahmad, U., Ibrahim, B., Mohammed, M., Aldoghachi, A. F., Usman, M., Yakubu, A. H., Tanko, A. S., Bobbo, K. A., Garkuwa, ⁠. A., Faggo, A. A., et al. (2023) · Applied Research · doi:10.1002/appl.202300002

Comment on “Melanoma microsatellites exhibit a metastatic signature by spatial transcriptomics and overexpress mediators of immune evasion”

Satapathy, P., Mehta, R., & Sah, R. (2025) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-025-04305-0

Transcriptome Analysis of Psoriasis in a Large Case–Control Sample: RNA-Seq Provides Insights into Disease Mechanisms

Li, B., Tsoi, L. C., Swindell, W. R., Gudjonsson, J. E., Tejasvi, T., Johnston, A. W. B., Ding, J., Stuart, P. E., Xing, X., Kochkodan, J. J., et al. (2014) · Journal of Investigative Dermatology · doi:10.1038/jid.2014.28 · Cited by 393 · see citing works

Comparisons of gene expression in normal, lesional, and non‐lesional psoriatic skin using DNA microarray techniques

Xie, S., Chen, Z., Wang, Q., Song, X., & Zhang, L. (2014) · International Journal of Dermatology · doi:10.1111/ijd.12476 · Cited by 27 · see citing works

Cross-Study Homogeneity of Psoriasis Gene Expression in Skin across a Large Expression Range

Bigler, J., Rand, H. A., Kerkof, K., Timour, M., & Russell, C. B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0052242 · Cited by 76 · see citing works

Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (gsea). PLoS ONE 5:e10247. doi: 10.1371/journal.pone.0010247

Lowes, M. A., Zaba, L. C., & Krueger, J. G. (2010)

Evaluation of the Psoriasis Transcriptome across Different Studies by Gene Set Enrichment Analysis (GSEA)

Suárez‐Fariñas, M., Lowes, M. A., Zaba, L. C., & Krueger, J. G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010247 · Cited by 195 · see citing works