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📖 Bioconductor Publications

Publications

This is a select list of featured and recent publications that cite Bioconductor, along with select books, book chapters, and original Bioconductor technical reports.

Featured

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

10 most recent PubMed and PubMed Central citations mentioning "*Bioconductor*". For a complete list, go to PubMed and PubMed Central. Last updated 2024-10-09T22:00:13-04:00.

Ghosh A, Rogers KL Jr, Gallant SC, Kim YH, Rager JE, Gilmour MI, Randell SH, Jaspers I. Effects of simulated smoke condensate generated from combustion of selected military burn pit contents on human airway epithelial cells Part Fibre Toxicol, 21, pp. 41. doi:10.1186/s12989-024-00604-7 (8 October 2024)

Rong S, Dai B, Yang C, Lan Z, Wang L, Xu L, Chen W, Chen J, Wu Z. HNRNPC modulates PKM alternative splicing via m6A methylation, upregulating PKM2 expression to promote aerobic glycolysis in papillary thyroid carcinoma and drive malignant progression J Transl Med, 22, pp. 914. doi:10.1186/s12967-024-05668-9 (8 October 2024)

Liao Y, Cavalcante RG, Waller JB, Deng F, Scruggs AM, Huang YJ, Atasoy U, Chen Y, Huang SK. Differences in the DNA methylome of T cells in adults with asthma of varying severity Clin Epigenetics, 16, pp. 139. doi:10.1186/s13148-024-01750-7 (8 October 2024)

Laddach A, Pachnis V, Shapiro M. TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations NAR Genom Bioinform, 6(4), pp. lqae139. doi:10.1093/nargab/lqae139 (8 October 2024)

Chen Y, Cao S, Shao S, Tong Z. Identifying prothrombin and bone sialoprotein as potential drug targets for idiopathic pulmonary fibrosis BMC Pulm Med, 24, pp. 488. doi:10.1186/s12890-024-03289-y (7 October 2024)

Javanmardifard Z, Rahmani S, Bayat H, Mirtavoos-Mahyari H, Ghanei M, Mowla SJ. A comprehensive in silico analysis and experimental validation of miRNAs capable of discriminating between lung adenocarcinoma and squamous cell carcinoma Front Genet, 15, pp. 1419099. doi:10.3389/fgene.2024.1419099 (23 September 2024)

Kabakibo TS, Arnold E, Padhan K, Lemieux A, Ortega-Delgado GG, Routy JP, Shoukry N, Dubé M, Kaufmann DE. Artificial antigen-presenting cell system reveals CD28’s role in modulating T cell functions during human immunodeficiency virus infection iScience, 27(10), pp. 110947. doi:10.1016/j.isci.2024.110947 (13 September 2024)

Safavi K, Hajibabaie F, Abedpoor N. Bioinformatics and Chemoinformatics Analysis Explored the Role of Linum usitatissimum in Diabetic Heart Conditions: Experimental Analysis in H9c2 Rat Embryonic Cardiomyocytes Cell Lines J Med Signals Sens, 14, pp. 27. doi:10.4103/jmss.jmss_4_24 (2 September 2024)

Hickman E, Frey J, Wylie A, Hartwell HJ, Herkert NJ, Short SJ, Mills-Koonce WR, Fry RC, Stapleton HM, Propper C, Rager JE. Chemical and non-chemical stressors in a postpartum cohort through wristband and self report data: Links between increased chemical burden, economic, and racial stress Environ Int, 191, pp. 108976. doi:10.1016/j.envint.2024.108976 (23 August 2024)

de Nonneville A, Kalbacher E, Cannone F, Guille A, Adelaïde J, Finetti P, Cappiello M, Lambaudie E, Ettore G, Charafe E, Mamessier E, Provansal M, Bertucci F, Sabatier R. Endometrioid ovarian carcinoma landscape: pathological and molecular characterization Mol Oncol, 18(10), pp. 2586-2600. doi:10.1002/1878-0261.13679 (25 June 2024)