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 2023-09-25T01:00:09-04:00.

Bao Y, Ma Y, Liu W, Li X, Li Y, Zhou P, Feng Y, Delgado-Baquerizo M. Innovative strategy for the conservation of a millennial mausoleum from biodeterioration through artificial light management NPJ Biofilms Microbiomes, 9, pp. 69. doi:10.1038/s41522-023-00438-9 (23 September 2023)

Séraudie I, Pillet C, Cesana B, Bazelle P, Jeanneret F, Evrard B, Chalmel F, Bouzit A, Battail C, Long JA, Descotes JL, Cochet C, Filhol O. A new scaffold-free tumoroid model provides a robust preclinical tool to investigate invasion and drug response in Renal Cell Carcinoma Cell Death Dis, 14(9), pp. 622. doi:10.1038/s41419-023-06133-z (22 September 2023)

Laddach A, Chng SH, Lasrado R, Progatzky F, Shapiro M, Erickson A, Sampedro Castaneda M, Artemov AV, Bon-Frauches AC, Amaniti EM, Kleinjung J, Boeing S, Ultanir S, Adameyko I, Pachnis V. A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia Nat Commun, 14, pp. 5904. doi:10.1038/s41467-023-41492-3 (22 September 2023)

Rohatgi N, Zou W, Li Y, Cho K, Collins PL, Tycksen E, Pandey G, DeSelm CJ, Patti GJ, Dey A, Teitelbaum SL. BAP1 promotes osteoclast function by metabolic reprogramming Nat Commun, 14, pp. 5923. doi:10.1038/s41467-023-41629-4 (22 September 2023)

Ni P, Wu S, Su Z. Underlying causes for prevalent false positives and false negatives in STARR-seq data NAR Genom Bioinform, 5(3), pp. lqad085. doi:10.1093/nargab/lqad085 (22 September 2023)

Wang W, Wu B, Liu Z, Sun X, Zhou L, Xu W, Yu T, Zheng Y, Zhang S. Comprehensive analysis on the regulation of differentially expressed of mRNA and ncRNA in different ovarian stages of ark shell Scapharca broughtonii BMC Genomics, 24, pp. 563. doi:10.1186/s12864-023-09648-z (22 September 2023)

Yamashita A, Ignatenko O, Nguyen M, Lambert R, Watt K, Daneault C, Robillard-Frayne I, Topisirovic I, Rosiers CD, McBride HM. Depletion of LONP2 unmasks differential requirements for peroxisomal function between cell types and in cholesterol metabolism Biol Direct, 18, pp. 60. doi:10.1186/s13062-023-00416-3 (22 September 2023)

Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages Mol Biol Evol, 40(9), pp. msad188. doi:10.1093/molbev/msad188 (21 September 2023)

Rzasa P, Whelan S, Farahmand P, Cai H, Guterman I, Palacios-Gallego R, Undru SS, Sandford L, Green C, Andreadi C, Mintseva M, Parrott E, Jin H, Hey F, Giblett S, Sylvius NB, Allcock NS, Straatman-Iwanowska A, Feuda R, Tufarelli C, Brown K, Pritchard C, Rufini A. BRAFV600E-mutated serrated colorectal neoplasia drives transcriptional activation of cholesterol metabolism Commun Biol, 6, pp. 962. doi:10.1038/s42003-023-05331-x (21 September 2023)

Vitting-Seerup K. Most protein domains exist as variants with distinct functions across cells, tissues and diseases NAR Genom Bioinform, 5(3), pp. lqad084. doi:10.1093/nargab/lqad084 (20 September 2023)

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)

Li J, Sheng Y, Xu H, Li Q, Lin X, Zhou Y, Zhao Y, Song X, Wang J. Transcriptome and hormone metabolome reveal the mechanism of stem bending in water lily (Nymphaea tetragona) cut-flowers Front Plant Sci, 14, pp. 1195389. doi:10.3389/fpls.2023.1195389 (8 September 2023)

Yu X, Guo Z, Fang Z, Yang K, Liu C, Dong Z, Liu C. Identification and validation of disulfidptosis-associated molecular clusters in non-alcoholic fatty liver disease Front Genet, 14, pp. 1251999. doi:10.3389/fgene.2023.1251999 (8 September 2023)

Wang M, An K, Huang J, Mprah R, Ding H. A novel model based on necroptosis to assess progression for polycystic ovary syndrome and identification of potential therapeutic drugs Front Endocrinol (Lausanne), 14, pp. 1193992. doi:10.3389/fendo.2023.1193992 (7 September 2023)

Schiebout C, Lust H, Huang Y, Frost HR. Cell type-specific interaction analysis using doublets in scRNA-seq Bioinform Adv, 3(1), pp. vbad120. doi:10.1093/bioadv/vbad120 (6 September 2023)

Li J, Wu X, Ji XB, He C, Xu S, Xu X. Biphasic function of GSK3β in gefitinib‑resistant NSCLC with or without EGFR mutations Exp Ther Med, 26(4), pp. 488. doi:10.3892/etm.2023.12187 (4 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)

Bosnakovski D, Toso EA, Ener ET, Gearhart MD, Yin L, Lüttmann FF, Magli A, Shi K, Kim J, Aihara H, Kyba M. Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein iScience, 26(10), pp. 107823. doi:10.1016/j.isci.2023.107823 (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)