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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 2024-05-07T16:00:10-04:00.

König E, Beasley S, Heponiemi P, Kivinen S, Räkköläinen J, Salminen S, Collado MC, Borman T, Lahti L, Piirainen V, Valros A, Heinonen M. Fecal microbiota profiles of growing pigs and their relation to growth performance PLoS One, 19(5), pp. e0302724. doi:10.1371/journal.pone.0302724 (6 May 2024)

Xu K, Zhang L, Wang T, Yu T, Zhao X, Zhang Y. Transcriptomics reveals dynamic changes in the “gene profiles” of rat supraspinatus tendon at three different time points after diabetes induction BMC Med Genomics, 17, pp. 122. doi:10.1186/s12920-024-01899-3 (6 May 2024)

Jurburg SD, Blowes SA, Shade A, Eisenhauer N, Chase JM. Synthesis of recovery patterns in microbial communities across environments Microbiome, 12, pp. 79. doi:10.1186/s40168-024-01802-3 (6 May 2024)

Shui YB, Liu Y, Huang AJ, Siegfried CJ. SDPR expression in human trabecular meshwork and its potential role in racial disparities of glaucoma Sci Rep, 14, pp. 10258. doi:10.1038/s41598-024-61071-w (4 May 2024)

Xu Z, Niu L, Kresvich JK, Taylor JA. Methscore: a comprehensive R function for DNA methylation-based health predictors. Bioinformatics. doi:10.1093/bioinformatics/btae302 (3 May 2024)

Meng G, Pan Y, Tang W, Zhang L, Cui Y, Schumacher FR, Wang M, Wang R, He S, Krischer J, Li Q, Feng H. imply: improving cell-type deconvolution accuracy using personalized reference profiles. Genome Med, 16(1), pp. 65. doi:10.1186/s13073-024-01338-z (29 April 2024)

Pan Y, Wang X, Sun J, Liu C, Peng J, Li Q. Multimodal joint deconvolution and integrative signature selection in proteomics. Commun Biol, 7(1), pp. 493. doi:10.1038/s42003-024-06155-z (24 April 2024)

Dirkx L, Van Acker SI, Nicolaes Y, Cunha JL, Ahmad R, Hendrickx R, Caljon B, Imamura H, Ebo DG, Jeffares DC, Sterckx YG, Maes L, Hendrickx S, Caljon G. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites PLoS Pathog, 20(4), pp. e1012181. doi:10.1371/journal.ppat.1012181 (24 April 2024)

Qin Q, Liu R, Li Z, Liu M, Wu X, Wang H, Yang S, Sun X, Yi X. Resolving candidate genes of duck ovarian tissue transplantation via RNA-Seq and expression network analyses Poult Sci, 103(7), pp. 103788. doi:10.1016/j.psj.2024.103788 (21 April 2024)

Díaz-Varela M, Sanchez-Hidalgo A, Calderon-Copete S, Tacchini V, Shipley TR, Ramírez LG, Marquis J, Fernández OL, Saravia NG, Tacchini-Cottier F. The different impact of drug-resistant Leishmania on the transcription programs activated in neutrophils iScience, 27(5), pp. 109773. doi:10.1016/j.isci.2024.109773 (18 April 2024)