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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 2022-10-06T13:00:10-04:00.

Herrera M, Keynan Y, McLaren PJ, Isaza JP, Abrenica B, López L, Marin D, Rueda ZV. Gene expression profiling identifies candidate biomarkers for new latent tuberculosis infections. A cohort study. PLoS One, 17(9), pp. e0274257. doi:10.1371/journal.pone.0274257 (28 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)
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)
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)
Guo Z, Shafik AM, Jin P, Wu H. Differential RNA Methylation Analysis for MeRIP-seq Data under General Experimental Design. Bioinformatics. doi:10.1093/bioinformatics/btac601 (5 September 2022)
Lee DY, Hah JH, Jeong WJ, Chung EJ, Kwon TK, Ahn SH, Sung MW, Kwon SK. Expression of defensin-associated gene can be correlated with lymph node metastasis of early stage tongue cancer. Clin Exp Otorhinolaryngol. doi:10.21053/ceo.2022.00150 (30 August 2022)
Patil AH, Baran A, Brehm ZP, McCall MN, Halushka MK. A curated human cellular microRNAome based on 196 primary cell types. Gigascience, 11. doi:10.1093/gigascience/giac083 (25 August 2022)
Wei H, Zhou L, Zhao X, Xie F. Network-Based Pharmacological Study on the Mechanism of Action of Buxue Liqi Huatan Decoction in the Treatment of Lung Cancer. Comput Intell Neurosci, 2022, pp. 3418687. doi:10.1155/2022/3418687 (19 August 2022)
Wang K, Wang Z, Wang Z, Xie X, Zang L, Wang L, Che F. Stellera chamaejasme L. extracts in the treatment of glioblastoma cell lines: Biological verification based on a network pharmacology approach. Front Oncol, 12, pp. 962970. doi:10.3389/fonc.2022.962970 (17 August 2022)
Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I. Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER. Bioinformatics. doi:10.1093/bioinformatics/btac555 (12 August 2022)
Wang XW, Zhang CA, Ye M. Study on the Mechanism of Xiaotan Sanjie Recipe in the Treatment of Colon Cancer Based on Network Pharmacology. Biomed Res Int, 2022, pp. 9498109. doi:10.1155/2022/9498109 (5 August 2022)
Bürger A, Dugas M. Cogito: automated and generic comparison of annotated genomic intervals. BMC Bioinformatics, 23(1), pp. 315. doi:10.1186/s12859-022-04853-1 (4 August 2022)
Iida K, Kondo J, Wibisana JN, Inoue M, Okada M. ASURAT: Functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinformatics. doi:10.1093/bioinformatics/btac541 (4 August 2022)
Zhang W, Shi G, Wang H, Feng M, Gao X, Xie Q, Zhang N, Lv Z. Molecular Mechanism of Xingnao Kaiqiao Pill for Perioperative Neurocognitive Disorder and Its Correlation With Immune and Inflammatory Signaling Pathways Based on Network Pharmacology and Molecular Docking. Front Aging Neurosci, 14, pp. 925072. doi:10.3389/fnagi.2022.925072 (3 August 2022)
Bennett AN, Rainford J, Huang X, He Q, Chan KHK. Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files. BMC Bioinformatics, 23(1), pp. 304. doi:10.1186/s12859-022-04822-8 (27 July 2022)
Wang L, Yuan L. Analysis of ginseng in the treatment of Interstitial Cystitis/Bladder Pain Syndrome based on network pharmacology. Eur Rev Med Pharmacol Sci, 26(13), pp. 4709-4720. doi:10.26355/eurrev_202207_29196 (21 July 2022)
Qian X, Zhang L, Xie F, Cheng Y, Cui D. Network-Based Pharmacological Study on the Mechanism of Guishao-Liujun Decoction in the Treatment of Gastric Cancer. Front Pharmacol, 13, pp. 937439. doi:10.3389/fphar.2022.937439 (5 July 2022)
Macedo-da-Silva J, Coutinho JVP, Rosa-Fernandes L, Marie SKN, Palmisano G. Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data. Adv Protein Chem Struct Biol, 131, pp. 311-339. doi:10.1016/bs.apcsb.2022.04.002 (12 May 2022)

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