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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 2017-12-15T17:40:06-05:00.

Ruiz-Arenas C, González JR. Redundancy analysis allows improved detection of methylation changes in large genomic regions. BMC Bioinformatics, 18(1), pp. 553. doi:10.1186/s12859-017-1986-0 (14 December 2017)
Li Y, Li Y, Bai Z, Pan J, Wang J, Fang F. Identification of potential transcriptomic markers in developing pediatric sepsis: a weighted gene co-expression network analysis and a case-control validation study. J Transl Med, 15(1), pp. 254. doi:10.1186/s12967-017-1364-8 (13 December 2017)
Knoll M, Winther S, Natarajan A, Yang H, Jiang M, Thiru P, Shahsafaei A, Chavarria TE, Lamming DW, Sun L, Hansen JB, Lodish HF. SYK kinase mediates brown fat differentiation and activation Nat Commun, 8, pp. 2115. doi:10.1038/s41467-017-02162-3 (13 December 2017)
Kling S, Hammer A, Netto EA, Hafezi F. Differential Gene Transcription of Extracellular Matrix Components in Response to In Vivo Corneal Crosslinking (CXL) in Rabbit Corneas Transl Vis Sci Technol, 6(6), pp. 8. doi:10.1167/tvst.6.6.8 (12 December 2017)
Veltsos P, Fang Y, Cossins AR, Snook RR, Ritchie MG. Mating system manipulation and the evolution of sex-biased gene expression in Drosophila Nat Commun, 8, pp. 2072. doi:10.1038/s41467-017-02232-6 (12 December 2017)
Söllner JF, Leparc G, Hildebrandt T, Klein H, Thomas L, Stupka E, Simon E. An RNA-Seq atlas of gene expression in mouse and rat normal tissues Sci Data, 4, pp. 170185. doi:10.1038/sdata.2017.185 (12 December 2017)
Yang H, Zhao L, Zhao S, Wang J, Shi H. Biochemical and transcriptomic analyses of drought stress responses of LY1306 tobacco strain Sci Rep, 7, pp. 17442. doi:10.1038/s41598-017-17045-2 (12 December 2017)
Yamazaki S, Tanaka Y, Araki H, Kohda A, Sanematsu F, Arasaki T, Duan X, Miura F, Katagiri T, Shindo R, Nakano H, Ito T, Fukui Y, Endo S, Sumimoto H. The AP-1 transcription factor JunB is required for Th17 cell differentiation Sci Rep, 7, pp. 17402. doi:10.1038/s41598-017-17597-3 (12 December 2017)
Wenric S, ElGuendi S, Caberg JH, Bezzaou W, Fasquelle C, Charloteaux B, Karim L, Hennuy B, Frères P, Collignon J, Boukerroucha M, Schroeder H, Olivier F, Jossa V, Jerusalem G, Josse C, Bours V. Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer Sci Rep, 7, pp. 17452. doi:10.1038/s41598-017-17811-2 (12 December 2017)
Chiesa M, Colombo GI, Piacentini L. DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification. Bioinformatics. doi:10.1093/bioinformatics/btx795 (11 December 2017)
Shi Y, He G, Lee WC, McKenzie JA, Silva MJ, Long F. Gli1 identifies osteogenic progenitors for bone formation and fracture repair Nat Commun, 8, pp. 2043. doi:10.1038/s41467-017-02171-2 (11 December 2017)
Athanasiadis EI, Botthof JG, Andres H, Ferreira L, Lio P, Cvejic A. Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis Nat Commun, 8, pp. 2045. doi:10.1038/s41467-017-02305-6 (11 December 2017)
Oldrini B, Hsieh WY, Erdjument-Bromage H, Codega P, Carro MS, Curiel-García A, Campos C, Pourmaleki M, Grommes C, Vivanco I, Rohle D, Bielski CM, Taylor BS, Hollmann TJ, Rosenblum M, Tempst P, Blenis J, Squatrito M, Mellinghoff IK. EGFR feedback-inhibition by Ran-binding protein 6 is disrupted in cancer Nat Commun, 8, pp. 2035. doi:10.1038/s41467-017-02185-w (11 December 2017)
Hassan MA, Vasquez JJ, Guo-Liang C, Meissner M, Nicolai Siegel T. Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii BMC Genomics, 18, pp. 961. doi:10.1186/s12864-017-4362-6 (11 December 2017)
Metri R, Mohan A, Nsengimana J, Pozniak J, Molina-Paris C, Newton-Bishop J, Bishop D, Chandra N. Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach Sci Rep, 7, pp. 17314. doi:10.1038/s41598-017-17330-0 (11 December 2017)
Pegolo S, Dadousis C, Mach N, Ramayo-Caldas Y, Mele M, Conte G, Schiavon S, Bittante G, Cecchinato A. SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile Sci Rep, 7, pp. 17317. doi:10.1038/s41598-017-17434-7 (11 December 2017)
Capobianco E, Valdes C, Sarti S, Jiang Z, Poliseno L, Tsinoremas NF. Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes Sci Rep, 7, pp. 17344. doi:10.1038/s41598-017-17337-7 (11 December 2017)
Zhang J, Wallace SJ, Shiu MY, Smith I, Rhind SG, Langlois VS. Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low‐volume, high‐intensity interval training Physiol Rep, 5(23), pp. e13534. doi:10.14814/phy2.13534 (7 December 2017)
de Oliveira LS, Tschoeke DA, Magalhães Lopes AC, Sudatti DB, Meirelles PM, Thompson CC, Pereira RC, Thompson FL. Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea mSphere, 2(6), pp. e00094-17. doi:10.1128/mSphere.00094-17 (6 December 2017)
Delabrière A, Hohenester UM, Colsch B, Junot C, Fenaille F, Thévenot EA. proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry. Bioinformatics, 33(23), pp. 3767-3775. doi:10.1093/bioinformatics/btx458 (1 December 2017)

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