Publications

Bioconductor F1000 Research Channel launched!

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

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2022-09-28T10:30:08-04:00.

Clark SJ, Argelaguet R, Lohoff T, Krueger F, Drage D, Göttgens B, Marioni JC, Nichols J, Reik W. Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis Genome Biol, 23, pp. 202. doi:10.1186/s13059-022-02762-3 (26 September 2022)
Ahmadi-Balootaki S, Doosti A, Jafarinia M, Goodarzi HR. Targeting the MALAT1 gene with the CRISPR/Cas9 technique in prostate cancer Genes Environ, 44, pp. 22. doi:10.1186/s41021-022-00252-3 (26 September 2022)
Muhammad JS, ElGhazali G, Shafarin J, Mohammad MG, Abu-Qiyas A, Hamad M. SARS-CoV-2-induced hypomethylation of the ferritin heavy chain (FTH1) gene underlies serum hyperferritinemia in severe COVID-19 patients Biochem Biophys Res Commun. doi:10.1016/j.bbrc.2022.09.083 (25 September 2022)
Sánchez-Baizán N, Ribas L, Piferrer F. Improved biomarker discovery through a plot twist in transcriptomic data analysis BMC Biol, 20, pp. 208. doi:10.1186/s12915-022-01398-w (24 September 2022)
Li L, Yang L, Chen X, Chen X, Diao L, Zeng Y, Xu J. TNFAIP6 defines the MSC subpopulation with enhanced immune suppression activities Stem Cell Res Ther, 13, pp. 479. doi:10.1186/s13287-022-03176-5 (24 September 2022)
Zehetmayer S, Posch M, Graf A. Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments BMC Bioinformatics, 23, pp. 388. doi:10.1186/s12859-022-04928-z (24 September 2022)
Mishra N, Aden K, Blase JI, Baran N, Bordoni D, Tran F, Conrad C, Avalos D, Jaeckel C, Scherer M, Sørensen SB, Overgaard SH, Schulte B, Nikolaus S, Rey G, Gasparoni G, Lyons PA, Schultze JL, Walter J, Andersen V, Dermitzakis ET, Schreiber S, Rosenstiel P. Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease Genome Med, 14, pp. 110. doi:10.1186/s13073-022-01112-z (24 September 2022)
Wen Q, Verheijen M, Wittens MM, Czuryło J, Engelborghs S, Hauser D, van Herwijnen MH, Lundh T, Bergdahl IA, Kyrtopoulos SA, de Kok TM, Smeets HJ, Briedé JJ, Krauskopf J. Lead-exposure associated miRNAs in humans and Alzheimer’s disease as potential biomarkers of the disease and disease processes Sci Rep, 12, pp. 15966. doi:10.1038/s41598-022-20305-5 (24 September 2022)
Sohl J, Hartmann AK, Hahlbrock J, Bartneck J, Stassen M, Klein M, Bros M, Grabbe S, Marini F, Woods K, Guezguez B, Mack M, Schild H, Muth S, Melchior F, Probst HC, Langguth P, Radsak MP. Dithranol as novel co-adjuvant for non-invasive dermal vaccination NPJ Vaccines, 7, pp. 112. doi:10.1038/s41541-022-00530-9 (24 September 2022)
Xu J, Chen WJ, Wang Z, Xin MY, Gao SH, Liu WJ, Wang KK, Ma JW, Yan XZ, Ren YM. Profiles of transcriptome and metabolic pathways after hypobaric hypoxia exposure Proteome Sci, 20, pp. 16. doi:10.1186/s12953-022-00198-y (24 September 2022)
Huang X, Wang X, Huang G, Li R, Liu X, Cao L, Ye J, Zhang P. Bioinformatic identification of differentially expressed genes associated with hepatocellular carcinoma prognosis Medicine (Baltimore), 101(38), pp. e30678. doi:10.1097/MD.0000000000030678 (23 September 2022)
Gómez-Carballa A, Pardo-Seco J, Pischedda S, Rivero-Calle I, Butler-Laporte G, Richards JB, Viz-Lasheras S, Martinón-Torres F, Salas A. Sex-biased expression of the TLR7 gene in severe COVID-19 patients: Insights from transcriptomics and epigenomics Environ Res, pp. 114288. doi:10.1016/j.envres.2022.114288 (21 September 2022)
Chan MM, Sadeghi-Alavijeh O, Lopes FM, Hilger AC, Stanescu HC, Voinescu CD, Beaman GM, Newman WG, Zaniew M, Weber S, Ho YM, Connolly JO, Wood D, Maj C, Stuckey A, Kousathanas A, Kleta R, Woolf AS, Bockenhauer D, Levine AP, Gale DP. Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves eLife, 11, pp. e74777. doi:10.7554/eLife.74777 (20 September 2022)
Li D, Zand MS, Dye TD, Goniewicz ML, Rahman I, Xie Z. An evaluation of RNA-seq differential analysis methods. PLoS One, 17(9), pp. e0264246. doi:10.1371/journal.pone.0264246 (16 September 2022)
Showpnil IA, Selich-Anderson J, Taslim C, Boone MA, Crow JC, Theisen ER, Lessnick SL. EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma Nucleic Acids Res, 50(17), pp. 9814-9837. doi:10.1093/nar/gkac747 (16 September 2022)
Ferrer-Bonsoms JA, Gimeno M, Olaverri D, Sacristan P, Lobato C, Castilla C, Carazo F, Rubio A. EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains. NAR Genom Bioinform, 4(3), pp. lqac067. doi:10.1093/nargab/lqac067 (15 September 2022)
Friskes A, Koob L, Krenning L, Severson TM, Koeleman ES, Vergara X, Schubert M, van den Berg J, Evers B, Manjón AG, Joosten S, Kim Y, Zwart W, Medema RH. Double-strand break toxicity is chromatin context independent Nucleic Acids Res, 50(17), pp. 9930-9947. doi:10.1093/nar/gkac758 (15 September 2022)
Gründing AR, Schneider MA, Richtmann S, Kriegsmann M, Winter H, Martinez-Delgado B, Varona S, Liu B, DeLuca DS, Held J, Wrenger S, Muley T, Meister M, Welte T, Janciauskiene S. Lung Adenocarcinoma Cell Sensitivity to Chemotherapies: A Spotlight on Lipid Droplets and SREBF1 Gene. Cancers (Basel), 14(18). doi:10.3390/cancers14184454 (14 September 2022)
Visentin L, Scarpellino G, Chinigò G, Munaron L, Ruffinatti FA. BioTEA: Containerized Methods of Analysis for Microarray-Based Transcriptomics Data. Biology (Basel), 11(9). doi:10.3390/biology11091346 (13 September 2022)
Shao Z, Chwa M, Atilano SR, Park J, Karageozian H, Karageozian V, Kenney MC. The Transcriptome Profile of Retinal Pigment Epithelium and Müller Cell Lines Protected by Risuteganib Against Hydrogen Peroxide Stress J Ocul Pharmacol Ther, 38(7), pp. 513-526. doi:10.1089/jop.2022.0015 (12 September 2022)

Books

Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers

Compendia

Literature Search »

 

Courses & Conferences »

Bioconductor courses and conferences explore R programming and the analysis of genomic data. View catalog of a recent course material.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available viaDocker Images and for use in the AnVIL.