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Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 1:kxab030. doi: 10.1093/biostatistics/kxab030. Epub ahead of print. PMID: 34467372.

Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3. PMID: 35760813; PMCID: PMC9237024

Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan 12;2(1):100085. doi: 10.1016/j.xgen.2021.100085. Epub 2022 Jan 13. PMID: 35199087; PMCID: PMC8863334

He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. PMID: 35277707; PMCID: PMC8933848

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2023-06-07T00:00:10-04:00.

Park HJ, Bang YJ, Kwon SP, Kwak W, Park SI, Roh G, Bae SH, Kim JY, Kwak HW, Kim Y, Yoo S, Kim D, Keum G, Bang EK, Hong SH, Nam JH. Analyzing immune responses to varied mRNA and protein vaccine sequences NPJ Vaccines, 8, pp. 84. doi:10.1038/s41541-023-00684-0 (5 June 2023)

Zong C, Zhang Z, Gao L, He J, Wang Y, Li Q, Liu X, Yang J, Chen D, Huang R, Zheng G, Jin X, Wei W, Jia R, Shen J. APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors Cell Death Dis, 14(6), pp. 348. doi:10.1038/s41419-023-05867-0 (3 June 2023)

Zaghi M, Banfi F, Massimino L, Volpin M, Bellini E, Brusco S, Merelli I, Barone C, Bruni M, Bossini L, Lamparelli LA, Pintado L, D’Aliberti D, Spinelli S, Mologni L, Colasante G, Ungaro F, Cioni JM, Azzoni E, Piazza R, Montini E, Broccoli V, Sessa A. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition Nat Commun, 14, pp. 3212. doi:10.1038/s41467-023-39043-x (3 June 2023)

Yu JC, Zeng Y, Zhao K, Lu T, Oros Klein K, Colmegna I, Lora M, Bhatnagar SR, Leask A, Greenwood CM, Hudson M. Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data Clin Epigenetics, 15, pp. 96. doi:10.1186/s13148-023-01513-w (3 June 2023)

Kurniansyah N, Goodman MO, Khan AT, Wang J, Feofanova E, Bis JC, Wiggins KL, Huffman JE, Kelly T, Elfassy T, Guo X, Palmas W, Lin HJ, Hwang SJ, Gao Y, Young K, Kinney GL, Smith JA, Yu B, Liu S, Wassertheil-Smoller S, Manson JE, Zhu X, Chen YD, Lee IT, Gu CC, Lloyd-Jones DM, Zöllner S, Fornage M, Kooperberg C, Correa A, Psaty BM, Arnett DK, Isasi CR, Rich SS, Kaplan RC, Redline S, Mitchell BD, Franceschini N, Levy D, Rotter JI, Morrison AC, Sofer T. Evaluating the use of blood pressure polygenic risk scores across race/ethnic background groups Nat Commun, 14, pp. 3202. doi:10.1038/s41467-023-38990-9 (2 June 2023)

Ryaboshapkina M, Azzu V. Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease Sci Rep, 13, pp. 8943. doi:10.1038/s41598-023-36187-0 (2 June 2023)

Phillips IR, Veeravalli S, Khadayate S, Shephard EA. Metabolomic and transcriptomic analyses of Fmo5-/- mice reveal roles for flavin-containing monooxygenase 5 (FMO5) in NRF2-mediated oxidative stress response, unfolded protein response, lipid homeostasis, and carbohydrate and one-carbon metabolism PLoS One, 18(6), pp. e0286692. doi:10.1371/journal.pone.0286692 (2 June 2023)

Zeng B, Liu Z, Lu Y, Zhong S, Qin S, Huang L, Zeng Y, Li Z, Dong H, Shi Y, Yang J, Dai Y, Ma Q, Sun L, Bian L, Han D, Chen Y, Qiu X, Wang W, Marín O, Wu Q, Wang Y, Wang X. The single-cell and spatial transcriptional landscape of human gastrulation and early brain development Cell Stem Cell, 30(6), pp. 851-866.e7. doi:10.1016/j.stem.2023.04.016 (1 June 2023)

Soneson C, Bendel AM, Diss G, Stadler MB. mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data Genome Biol, 24, pp. 132. doi:10.1186/s13059-023-02967-0 (1 June 2023)

Lima DA, Gonçalves LO, Reis-Cunha JL, Guimarães PAS, Ruiz JC, Liarte DB, Murta SMF. Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations. Parasit Vectors, 16(1), pp. 167. doi:10.1186/s13071-023-05775-4 (22 May 2023)

Zhou X, Cao J, Zhu L, Farrell K, Wang M, Guo L, Yang J, McKenzie A, Crary JF, Cai D, Tu Z, Zhang B. Molecular differences in brain regional vulnerability to aging between males and females Front Aging Neurosci, 15, pp. 1153251. doi:10.3389/fnagi.2023.1153251 (22 May 2023)

DeBerardine M. BRGenomics for analyzing high resolution genomics data in R. Bioinformatics. doi:10.1093/bioinformatics/btad331 (19 May 2023)

Ramos M, Morgan M, Geistlinger L, Carey VJ, Waldron L. RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor. Bioinformatics. doi:10.1093/bioinformatics/btad330 (19 May 2023)

Wang W, Zhang TN, Yang N, Wen R, Wang YJ, Zhang BL, Yang YH, Liu CF. Transcriptome-wide identification of altered RNA m6A profiles in cardiac tissue of rats with LPS-induced myocardial injury Front Immunol, 14, pp. 1122317. doi:10.3389/fimmu.2023.1122317 (19 May 2023)

Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci, 24(10). doi:10.3390/ijms24108961 (18 May 2023)

Liang H, Kong X, Cao Z, Wang H, Liu E, Sun F, Qi J, Zhang Q, Zhou Y. Bioinformatics and Raman spectroscopy-based identification of key pathways and genes enabling differentiation between acute myeloid leukemia and T cell acute lymphoblastic leukemia. Front Immunol, 14, pp. 1194353. doi:10.3389/fimmu.2023.1194353 (17 May 2023)

Zhao HC, Chen CZ, Tian YZ, Song HQ, Wang XX, Li YJ, He JF, Zhao HL. CD168+ macrophages promote hepatocellular carcinoma tumor stemness and progression through TOP2A/β-catenin/YAP1 axis iScience, 26(6), pp. 106862. doi:10.1016/j.isci.2023.106862 (12 May 2023)

Alghamdi MA, Al-Eitan LN, Tarkhan AH. Integrative analysis of gene expression and DNA methylation to identify biomarkers of non-genital warts induced by low-risk human papillomaviruses infection. Heliyon, 9(5), pp. e16101. doi:10.1016/j.heliyon.2023.e16101 (7 May 2023)

Boniolo F, Hoffmann M, Roggendorf N, Tercan B, Baumbach J, Castro MAA, Robertson AG, Saur D, List M. spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinformatics, 39(5). doi:10.1093/bioinformatics/btad276 (4 May 2023)

Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH. matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling. Bioinformatics, 39(5). doi:10.1093/bioinformatics/btad197 (4 May 2023)