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 2023-08-10T14:55:35+00:00.
Wang Y, Wu T, Tsai MC, Rezzonico MG, Abdel-Haleem AM, Xie L, Gandham VD, Ngu H, Stark K, Glock C, Xu D, Foreman O, Friedman BA, Sheng M, Hanson JE. TPL2 kinase activity regulates microglial inflammatory responses and promotes neurodegeneration in tauopathy mice
eLife, 12, pp. e83451.
doi:10.7554/eLife.83451 (9 August 2023)
Jiang B, Zhong Z, Su J, Zhu T, Yueh T, Bragasin J, Bu V, Zhou C, Lin C, Wang X. Co-condensation with photoexcited cryptochromes facilitates MAC3A to positively control hypocotyl growth in Arabidopsis
Sci Adv, 9(32), pp. eadh4048.
doi:10.1126/sciadv.adh4048 (9 August 2023)
Pickles OJ, Wanigasooriya K, Ptasinska A, Patel AJ, Robbins HL, Bryer C, Whalley CM, Tee L, Lal N, Pinna CM, Elzefzafy N, Taniere P, Beggs AD, Middleton GM. MHC Class II is Induced by IFNγ and Follows Three Distinct Patterns of Expression in Colorectal Cancer Organoids
Cancer Res Commun, 3(8), pp. 1501-1513.
doi:10.1158/2767-9764.CRC-23-0091 (9 August 2023)
Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community
Nat Commun, 14, pp. 4780.
doi:10.1038/s41467-023-40372-0 (8 August 2023)
Feng B, Feng X, Yu Y, Xu H, Ye Q, Hu R, Fang X, Gao F, Wu J, Pan Q, Yu J, Lang G, Li L, Cao H. Mesenchymal stem cells shift the pro-inflammatory phenotype of neutrophils to ameliorate acute lung injury
Stem Cell Res Ther, 14, pp. 197.
doi:10.1186/s13287-023-03438-w (8 August 2023)
Schactler SA, Scheuerman SJ, Lius A, Altemeier WA, An D, Matula TJ, Mikula M, Kulecka M, Denisenko O, Mar D, Bomsztyk K. CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis
BMC Genomics, 24, pp. 446.
doi:10.1186/s12864-023-09527-7 (8 August 2023)
Yang H, Wang Z, Xiao J, Hu J, Tu X, Gu Z. Integrated morphological and transcriptome profiles reveal a highly-developed extrusome system associated to virulence in the notorious fish parasite, Ichthyophthirius multifiliis
Virulence, 14(1), pp. 2242622.
doi:10.1080/21505594.2023.2242622 (7 August 2023)
Xie S, Zhong J, Zhang Z, Huang W, Lin X, Pan Y, Kong X, Xia H, Yu Z, Ni H, Xia J. Novel risk model based on angiogenesis-related lncRNAs for prognosis prediction of hepatocellular carcinoma
Cancer Cell Int, 23, pp. 159.
doi:10.1186/s12935-023-02975-x (7 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)
Gui C, Wei J, Mo C, Liang Y, Cen J, Chen Y, Wang D, Luo J. Therapeutic implications for localized prostate cancer by multiomics analyses of the ageing microenvironment landscape
Int J Biol Sci, 19(12), pp. 3951-3969.
doi:10.7150/ijbs.85209 (31 July 2023)
Wei KH, Lin IT, Chowdhury K, Lim KL, Liu KT, Ko TM, Chang YM, Yang KC, Lai SL. Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration
eLife, 12, pp. e84679.
doi:10.7554/eLife.84679 (27 July 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)
Benoit S, Henry M, Fneich S, Mathou A, Xia L, Foury A, Jouin M, Junien C, Capuron L, Jouneau L, Moisan MP, Delpierre C, Gabory A, Darnaudéry M. Strain-specific changes in nucleus accumbens transcriptome and motivation for palatable food reward in mice exposed to maternal separation
Front Nutr, 10, pp. 1190392.
doi:10.3389/fnut.2023.1190392 (26 July 2023)
Avanthay R, Garcia-Nicolas O, Zimmer G, Summerfield A. NS1 and PA-X of H1N1/09 influenza virus act in a concerted manner to manipulate the innate immune response of porcine respiratory epithelial cells
Front Cell Infect Microbiol, 13, pp. 1222805.
doi:10.3389/fcimb.2023.1222805 (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)
Ali L, Raza AA, Zaheer AB, Alhomrani M, Alamri AS, Alghamdi SA, Almalki AA, Alghamdi AA, Khawaja I, Alhadrami M, Ramzan F, Jamil M, Ali M, Jabeen N. In vitro analysis of PI3K pathway activation genes for exploring novel biomarkers and therapeutic targets in clear cell renal carcinoma
Am J Transl Res, 15(7), pp. 4851-4872.
doi: (15 July 2023)
Agarwal T, Wang X, Mildenhall F, Ibrahim IM, Puthiyaveetil S, Varala K. Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato
Hortic Res, 10(8), pp. uhad137.
doi:10.1093/hr/uhad137 (11 July 2023)
Weber LM, Saha A, Datta A, Hansen KD, Hicks SC. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
Nat Commun, 14(1), pp. 4059.
doi:10.1038/s41467-023-39748-z (10 July 2023)
Valenzi E, Bahudhanapati H, Tan J, Tabib T, Sullivan DI, Nouraie M, Sembrat J, Fan L, Chen K, Liu S, Rojas M, Lafargue A, Felsher DW, Tran PT, Kass DJ, Lafyatis R. Single-Nucleus Chromatin Accessibility Identifies a Critical Role for TWIST1 in IPF Myofibroblast Activity
Eur Respir J, 62(1), pp. 2200474.
doi:10.1183/13993003.00474-2022 (7 July 2023)
Ruiz-Arenas C, Abarrategui L, Hernandez-Ferrer C, Escribà-Montagut X, Pelegrí-Sisó D, Ryser-Welch P, Vrijheid M, Bustamante M, Grazuleviciene R, Lepeule J, Mathai M, Vafeiadi M, Beltran S, Pérez-Jurado LA, González JR. Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package.
Epigenetics, 18(1), pp. 2230670.
doi:10.1080/15592294.2023.2230670 (6 July 2023)
Books
