Home
Help
Publications

Publications

Bioconductor F1000 Research Channel launched!

Featured

Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344

Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468

Huber W, et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115-121; doi:10.1038/nmeth.3252 (full-text free with registration).

Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi: 10.1371/journal.pcbi.1003118

Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2019-07-17T00:20:08-04:00.

Cardenas A, Sordillo JE, Rifas-Shiman SL, Chung W, Liang L, Coull BA, Hivert MF, Lai PS, Forno E, Celedón JC, Litonjua AA, Brennan KJ, DeMeo DL, Baccarelli AA, Oken E, Gold DR. The nasal methylome as a biomarker of asthma and airway inflammation in children Nat Commun, 10, pp. 3095. doi:10.1038/s41467-019-11058-3 (12 July 2019)

Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O. Retention of paternal DNA methylome in the developing zebrafish germline Nat Commun, 10, pp. 3054. doi:10.1038/s41467-019-10895-6 (11 July 2019)

Batlle R, Andrés E, Gonzalez L, Llonch E, Igea A, Gutierrez-Prat N, Berenguer-Llergo A, Nebreda AR. Regulation of tumor angiogenesis and mesenchymal–endothelial transition by p38α through TGF-β and JNK signaling Nat Commun, 10, pp. 3071. doi:10.1038/s41467-019-10946-y (11 July 2019)

Jakobsen JS, Laursen LG, Schuster MB, Pundhir S, Schoof E, Ge Y, d’Altri T, Vitting-Seerup K, Rapin N, Gentil C, Jendholm J, Theilgaard-Mönch K, Reckzeh K, Bullinger L, Döhner K, Hokland P, Fitzgibbon J, Porse BT. Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML Sci Adv, 5(7), pp. eaaw4304. doi:10.1126/sciadv.aaw4304 (10 July 2019)

Todd EV, Ortega-Recalde O, Liu H, Lamm MS, Rutherford KM, Cross H, Black MA, Kardailsky O, Marshall Graves JA, Hore TA, Godwin JR, Gemmell NJ. Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change Sci Adv, 5(7), pp. eaaw7006. doi:10.1126/sciadv.aaw7006 (10 July 2019)

Yu R, Sun L, Sun Y, Han X, Qin L, Dang W. Cellular response to moderate chromatin architectural defects promotes longevity Sci Adv, 5(7), pp. eaav1165. doi:10.1126/sciadv.aav1165 (10 July 2019)

Bonnal RJP, Yates A, Goto N, Gautier L, Willis S, Fields C, Katayama T, Prins P. Sharing Programming Resources Between Bio* Projects. Methods Mol Biol, 1910, pp. 747-766. doi:10.1007/978-1-4939-9074-0_25 (7 July 2019)

Ravegnini G, Sammarini G, Moran S, Calice G, Indio V, Urbini M, Astolfi A, Zanotti F, Pantaleo MA, Hrelia P, Angelini S. Mechanisms of resistance to a PI3K inhibitor in gastrointestinal stromal tumors: an omic approach to identify novel druggable targets Cancer Manag Res, 11, pp. 6229-6244. doi:10.2147/CMAR.S189661 (5 July 2019)

Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genet, 15(7), pp. e1008203. doi:10.1371/journal.pgen.1008203 (3 July 2019)

Kegerreis B, Catalina MD, Bachali P, Geraci NS, Labonte AC, Zeng C, Stearrett N, Crandall KA, Lipsky PE, Grammer AC. Machine learning approaches to predict lupus disease activity from gene expression data Sci Rep, 9, pp. 9617. doi:10.1038/s41598-019-45989-0 (3 July 2019)

Francisco CS, Ma X, Zwyssig MM, McDonald BA, Palma-Guerrero J. Morphological changes in response to environmental stresses in the fungal plant pathogen Zymoseptoria tritici Sci Rep, 9, pp. 9642. doi:10.1038/s41598-019-45994-3 (3 July 2019)

Plancade S, Clark A, Philippe C, Helbling JC, Moisan MP, Esquerré D, Moyec LL, Robert C, Barrey E, Mach N. Unraveling the effects of the gut microbiota composition and function on horse endurance physiology Sci Rep, 9, pp. 9620. doi:10.1038/s41598-019-46118-7 (3 July 2019)

Tu J, Chen J, He M, Tong H, Liu H, Zhou B, Liao Y, Wang Z. Bioinformatics analysis of molecular genetic targets and key pathways for hepatocellular carcinoma Onco Targets Ther, 12, pp. 5153-5162. doi:10.2147/OTT.S198802 (2 July 2019)

Woo J, Winterhoff BJ, Starr TK, Aliferis C, Wang J. De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments Life Sci Alliance, 2(4), pp. e201900443. doi:10.26508/lsa.201900443 (2 July 2019)

Fasterius E, Uhlén M, Al-Khalili Szigyarto C. Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer Sci Rep, 9, pp. 9524. doi:10.1038/s41598-019-45934-1 (2 July 2019)

Sivaprakasam B, Sadagopan P. Development of an Interactive Web Application "Shiny App for Frequency Analysis on Homo sapiens Genome (SAFA-HsG)". Interdiscip Sci. doi:10.1007/s12539-019-00340-z (1 July 2019)

Crotti A, Sait HR, McAvoy KM, Estrada K, Ergun A, Szak S, Marsh G, Jandreski L, Peterson M, Reynolds TL, Dalkilic-Liddle I, Cameron A, Cahir-McFarland E, Ransohoff RM. BIN1 favors the spreading of Tau via extracellular vesicles Sci Rep, 9, pp. 9477. doi:10.1038/s41598-019-45676-0 (1 July 2019)

Klinge CM, Piell KM, Tooley CS, Rouchka EC. HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells Sci Rep, 9, pp. 9430. doi:10.1038/s41598-019-45636-8 (1 July 2019)

Roser LG, Agüero F, Sánchez DO. FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files. BMC Bioinformatics, 20(1), pp. 361. doi:10.1186/s12859-019-2961-8 (28 June 2019)

Chagas VS, Groeneveld CS, Oliveira KG, Trefflich S, de Almeida RC, Ponder BAJ, Meyer KB, Jones SJM, Robertson AG, Castro MAA. RTNduals: An R/Bioconductor package for analysis of co-regulation and inference of dual regulons. Bioinformatics. doi:10.1093/bioinformatics/btz534 (28 June 2019)