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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 2023-08-10T14:46:28+00:00.
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 X, Zhang Q, Li S, Devarajan R, Luo B, Tan Z, Wang Z, Giannareas N, Wenta T, Ma W, Li Y, Yang Y, Manninen A, Wu S, Wei GH. GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression
J Exp Clin Cancer Res, 42, pp. 198.
doi:10.1186/s13046-023-02745-7 (8 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)
Kulus J, Kranc W, Kulus M, Dzięgiel P, Bukowska D, Mozdziak P, Kempisty B, Antosik P. Expression of genes regulating cell division in porcine follicular granulosa cells
Cell Div, 18, pp. 12.
doi:10.1186/s13008-023-00094-7 (7 August 2023)
Boso D, Tognon M, Curtarello M, Minuzzo S, Piga I, Brillo V, Lazzarini E, Carlet J, Marra L, Trento C, Rasola A, Masgras I, Caporali L, Del Ben F, Brisotto G, Turetta M, Pastorelli R, Brunelli L, Navaglia F, Esposito G, Grassi A, Indraccolo S. Anti-VEGF therapy selects for clones resistant to glucose starvation in ovarian cancer xenografts
J Exp Clin Cancer Res, 42, pp. 196.
doi:10.1186/s13046-023-02779-x (7 August 2023)
Zhu XY, Li Y, Xue CX, Lidbury ID, Todd JD, Lea-Smith DJ, Tian J, Zhang XH, Liu J. Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems
Microbiome, 11, pp. 175.
doi:10.1186/s40168-023-01618-7 (7 August 2023)
Wang C, Amini H, Xu Z, Peralta AA, Yazdi MD, Qiu X, Wei Y, Just A, Heiss J, Hou L, Zheng Y, Coull BA, Kosheleva A, Baccarelli AA, Schwartz JD. Long-term exposure to ambient fine particulate components and leukocyte epigenome-wide DNA Methylation in older men: the Normative Aging Study
Environ Health, 22, pp. 54.
doi:10.1186/s12940-023-01007-5 (7 August 2023)
Castiglioni A, Yang Y, Williams K, Gogineni A, Lane RS, Wang AW, Shyer JA, Zhang Z, Mittman S, Gutierrez A, Astarita JL, Thai M, Hung J, Yang YA, Pourmohamad T, Himmels P, De Simone M, Elstrott J, Capietto AH, Cubas R, Modrusan Z, Sandoval W, Ziai J, Gould SE, Fu W, Wang Y, Koerber JT, Sanjabi S, Mellman I, Turley SJ, Müller S. Combined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors
Nat Commun, 14, pp. 4703.
doi:10.1038/s41467-023-40398-4 (5 August 2023)
Ware AP, Satyamoorthy K, Paul B. Integrated multiomics analysis of chromosome 19 miRNA cluster in bladder cancer
Funct Integr Genomics, 23(3), pp. 266.
doi:10.1007/s10142-023-01191-0 (5 August 2023)
Mäkinen AI, Pappalardo VY, Buijs MJ, Brandt BW, Mäkitie AA, Meurman JH, Zaura E. Salivary microbiome profiles of oral cancer patients analyzed before and after treatment
Microbiome, 11, pp. 171.
doi:10.1186/s40168-023-01613-y (5 August 2023)
Huang F, Wang X, Zhong J, Chen H, Song D, Xu T, Tian K, Sun P, Sun N, Qin J, Song Y, Ma W, Liu Y, Yu D, Meng X, Jiang C, Xuan H, Qian D, Cai J. Using integrated analysis from multicentre studies to identify RNA methylation-related lncRNA risk stratification systems for glioma
Cancer Cell Int, 23, pp. 156.
doi:10.1186/s12935-023-03001-w (5 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)
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)
Wang Y, Pan Y, Luo Y, Wu J, Fang Z, Teng W, Guan Y, Li Y. Elucidation of the anti-lung cancer mechanism of Juan-Liu-San-Jie prescription based on network pharmacology and experimental validation
Heliyon, 9(8), pp. e18298.
doi:10.1016/j.heliyon.2023.e18298 (23 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)
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)
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)
Liao Y, Raghu D, Pal B, Mielke LA, Shi W. cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data.
Bioinformatics, 39(7).
doi:10.1093/bioinformatics/btad439 (1 July 2023)
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