Home
Help
Publications

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 2023-11-29T07:00:07-05:00.

Rossi N, Gigante N, Vitacolonna N, Piazza C. Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE. IEEE/ACM Trans Comput Biol Bioinform, PP. doi:10.1109/TCBB.2023.3337258 (28 November 2023)

Drummond RD, Defelicibus A, Meyenberg M, Valieris R, Dias-Neto E, Rosales RA, da Silva IT. Relating mutational signature exposures to clinical data in cancers via signeR 2.0. BMC Bioinformatics, 24(1), pp. 439. doi:10.1186/s12859-023-05550-3 (22 November 2023)

Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res. doi:10.1093/nar/gkad1059 (14 November 2023)

Schwarzl T, Sahadevan S, Lang B, Miladi M, Backofen R, Huber W, Hentze MW, Tartaglia GG. Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Nucleic Acids Res. doi:10.1093/nar/gkad998 (14 November 2023)

Liu N, Bhuva DD, Mohamed A, Bokelund M, Kulasinghe A, Tan CW, Davis MJ. standR: spatial transcriptomic analysis for GeoMx DSP data. Nucleic Acids Res. doi:10.1093/nar/gkad1026 (11 November 2023)

Williams JJ, Tractenberg RE, Batut B, Becker EA, Brown AM, Burke ML, Busby B, Cooch NK, Dillman AA, Donovan SS, Doyle MA, van Gelder CWG, Hall CR, Hertweck KL, Jordan KL, Jungck JR, Latour AR, Lindvall JM, Lloret-Llinares M, McDowell GS, Morris R, Mourad T, Nisselle A, Ordóñez P, Paladin L, Palagi PM, Sukhai MA, Teal TK, Woodley L. An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. PLoS One, 18(11), pp. e0293879. doi:10.1371/journal.pone.0293879 (9 November 2023)

Tsuyuzaki K, Ishii M, Nikaido I. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC Bioinformatics, 24(1), pp. 420. doi:10.1186/s12859-023-05490-y (7 November 2023)

Malinverni R, Corujo D, Gel B, Buschbeck M. regioneReloaded: evaluating the association of multiple genomic region sets. Bioinformatics, 39(11). doi:10.1093/bioinformatics/btad704 (1 November 2023)

Cascianelli S, Ceddia G, Marchesi A, Masseroli M. Identification of transcription factor high accumulation DNA zones. BMC Bioinformatics, 24(1), pp. 395. doi:10.1186/s12859-023-05528-1 (20 October 2023)

Huuki-Myers LA, Montgomery KD, Kwon SH, Page SC, Hicks SC, Maynard KR, Collado-Torres L. Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue. Genome Biol, 24(1), pp. 233. doi:10.1186/s13059-023-03066-w (16 October 2023)

Nedwed AS, Helbich SS, Braband KL, Volkmar M, Delacher M, Marini F. Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues. Front Immunol, 14, pp. 1241283. doi:10.3389/fimmu.2023.1241283 (12 October 2023)

Windhager J, Zanotelli VRT, Schulz D, Meyer L, Daniel M, Bodenmiller B, Eling N. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc, 18(11), pp. 3565-3613. doi:10.1038/s41596-023-00881-0 (10 October 2023)

Willie E, Yang P, Patrick E. The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data. Bioinform Adv, 3(1), pp. vbad141. doi:10.1093/bioadv/vbad141 (9 October 2023)

Zhang A, Tian S. Integrative Analyses of Mendelian Randomization and Transcriptomic Data Reveal No Association between Leptin and Chronic Obstructive Pulmonary Disease. COPD, 20(1), pp. 321-326. doi:10.1080/15412555.2023.2260890 (9 October 2023)

Naake T, Rainer J, Huber W. MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. Bioinformatics, 39(10). doi:10.1093/bioinformatics/btad618 (3 October 2023)

McLean C, Sorokin A, Simpson TI, Armstrong JD, Sorokina O. BioNAR: an integrated biological network analysis package in bioconductor. Bioinform Adv, 3(1), pp. vbad137. doi:10.1093/bioadv/vbad137 (29 September 2023)

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. bioRxiv. doi:10.1101/2023.09.27.559579 (29 September 2023)

Naderi Yeganeh P, Teo YY, Karagkouni D, Pita-Juárez Y, Morgan SL, Slack FJ, Vlachos IS, Hide WA. PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs. Brief Bioinform, 24(6). doi:10.1093/bib/bbad418 (22 September 2023)

Nikolaienko O, Lønning PE, Knappskog S. epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data. Gigascience, 12. doi:10.1093/gigascience/giad087 (28 December 2022)

Hazelaar DM, van Riet J, Hoogstrate Y, van de Werken HJG. Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection. Gigascience, 12. doi:10.1093/gigascience/giad081 (28 December 2022)