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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 2023-09-24T00:00:08-04:00.

Eagles NJ, Wilton R, Jaffe AE, Collado-Torres L. BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. BMC Bioinformatics, 24(1), pp. 340. doi:10.1186/s12859-023-05461-3 (13 September 2023)

Movassagh M, Schiff SJ, Paulson JN. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics, 39(9). doi:10.1093/bioinformatics/btad565 (2 September 2023)

Peters Couto BZ, Robertson N, Patrick E, Ghazanfar S. MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor. Bioinformatics, 39(9). doi:10.1093/bioinformatics/btad550 (2 September 2023)

Taguchi YH, Turki T. Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction. Front Artif Intell, 6, pp. 1237542. doi:10.3389/frai.2023.1237542 (1 September 2023)

Rodríguez-García A, Sola-Landa A, Barreiro C. RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics. Methods Mol Biol, 2704, pp. 99-113. doi:10.1007/978-1-0716-3385-4_6 (29 August 2023)

Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L. Curated single cell multimodal landmark datasets for R/Bioconductor. PLoS Comput Biol, 19(8), pp. e1011324. doi:10.1371/journal.pcbi.1011324 (25 August 2023)

Wang Y, Wei Z, Su J, Coenen F, Meng J. RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity. Comput Struct Biotechnol J, 21, pp. 4110-4117. doi:10.1016/j.csbj.2023.08.021 (24 August 2023)

Peixoto PM, Bromfield JJ, Ribeiro ES, Santos JEP, Thatcher WW, Bisinotto RS. Transcriptome changes associated with elongation of bovine conceptuses II: differentially expressed transcripts in the endometrium on day 17 after insemination. J Dairy Sci. doi:10.3168/jds.2023-23399 (23 August 2023)

Peixoto PM, Bromfield JJ, Ribeiro ES, Santos JEP, Thatcher WW, Bisinotto RS. Transcriptome changes associated with elongation of bovine conceptuses I: differentially expressed transcripts in the conceptus on day 17 after insemination. J Dairy Sci. doi:10.3168/jds.2023-23398 (23 August 2023)

Moses L, Einarsson PH, Jackson K, Luebbert L, Booeshaghi AS, Antonsson S, Bray N, Melsted P, Pachter L. Voyager: exploratory single-cell genomics data analysis with geospatial statistics. bioRxiv. doi:10.1101/2023.07.20.549945 (19 August 2023)

Zare H, Sajedi S, Ebrahimi G, Roudi R, Mehta I, Samimi H, Kazempour S, Zainulabadeen A, Docking T, Arora S, Cigarroa F, Seshadri S, Karsan A. "iNETgrate": integrating DNA methylation and gene expression data in a single gene network. Res Sq. doi:10.21203/rs.3.rs-3246325/v1 (18 August 2023)

Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes. bioRxiv. doi:10.1101/2023.08.17.553679 (17 August 2023)

Jablonski KP, Beerenwinkel N. Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. Bioinformatics, 39(8). doi:10.1093/bioinformatics/btad522 (1 August 2023)

Manukonda R, Jakati S, Attem J, Mishra DK, Mocherla TR, Reddy MM, Gulati K, Poluri KM, Vemuganti GK, Kaliki S. Identifying Treatment Resistance Related Pathways by Analyzing Serum Extracellular Vesicles of Patients With Resistant Versus Regressed Retinoblastoma. Invest Ophthalmol Vis Sci, 64(11), pp. 26. doi:10.1167/iovs.64.11.26 (1 August 2023)

Klein HU. demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models. Bioinformatics, 39(8). doi:10.1093/bioinformatics/btad481 (1 August 2023)

Feng H, Meng G, Lin T, Parikh H, Pan Y, Li Z, Krischer J, Li Q. ISLET: individual-specific reference panel recovery improves cell-type-specific inference. Genome Biol, 24(1), pp. 174. doi:10.1186/s13059-023-03014-8 (26 July 2023)

Huang T, Staniak M, Veiga Leprevost FD, Figueroa-Navedo AM, Ivanov AR, Nesvizhskii AI, Choi M, Vitek O. Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling. J Proteome Res, 22(8), pp. 2641-2659. doi:10.1021/acs.jproteome.3c00155 (19 July 2023)

Liao Y, Raghu D, Pal B, Mielke LA, Shi W. cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data. Bioinformatics, 39(7). doi:10.1093/bioinformatics/btad439 (1 July 2023)

Liu R, Xu J, Lu Q. A study on the mechanism of action of YiQiYangYindecotion for the treatment of diabetes based on network pharmacology. Cell Mol Biol (Noisy-le-grand), 69(6), pp. 198-202. doi:10.14715/cmb/2023.69.6.30 (30 June 2023)

Hernández HG, Aranzazu-Moya GC, Pinzón-Reyes EH. Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers. Biomedicines, 11(7). doi:10.3390/biomedicines11071797 (23 June 2023)