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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 2018-07-16T19:40:06-04:00.

Zhang Y, Jenkins DF, Manimaran S, Johnson WE. Alternative empirical Bayes models for adjusting for batch effects in genomic studies BMC Bioinformatics, 19, pp. 262. doi:10.1186/s12859-018-2263-6 (13 July 2018)

Zhang T, Zhang SW, Zhang L, Meng J. trumpet: transcriptome-guided quality assessment of m6A-seq data BMC Bioinformatics, 19, pp. 260. doi:10.1186/s12859-018-2266-3 (13 July 2018)

Gerhard GS, Malenica I, Llaci L, Chu X, Petrick AT, Still CD, DiStefano JK. Differentially methylated loci in NAFLD cirrhosis are associated with key signaling pathways Clin Epigenetics, 10, pp. 93. doi:10.1186/s13148-018-0525-9 (13 July 2018)

Eguchi R, Karim MB, Hu P, Sato T, Ono N, Kanaya S, Altaf-Ul-Amin M. An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease BMC Bioinformatics, 19, pp. 264. doi:10.1186/s12859-018-2251-x (13 July 2018)

Zhao XC, Yang SH, Yan YQ, Zhang X, Zhang L, Jiao B, Jiang S, Yu ZB. Identification of differential gene expression profile from peripheral blood cells of military pilots with hypertension by RNA sequencing analysis BMC Med Genomics, 11, pp. 59. doi:10.1186/s12920-018-0378-2 (11 July 2018)

Chen LF, Han XL, Li FX, Yao YY, Fang JP, Liu XJ, Li XC, Wu K, Liu M, Chen XG. Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing Parasit Vectors, 11, pp. 402. doi:10.1186/s13071-018-2983-5 (11 July 2018)

Dykes IM, Szumska D, Kuncheria L, Puliyadi R, Chen CM, Papanayotou C, Lockstone H, Dubourg C, David V, Schneider JE, Keane TM, Adams DJ, Brown SD, Mercier S, Odent S, Collignon J, Bhattacharya S. A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity Sci Rep, 8, pp. 10439. doi:10.1038/s41598-018-28714-1 (11 July 2018)

Roychoudhury P, De Silva Feelixge H, Reeves D, Mayer BT, Stone D, Schiffer JT, Jerome KR. Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir BMC Biol, 16, pp. 75. doi:10.1186/s12915-018-0544-1 (11 July 2018)

Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Detection and removal of barcode swapping in single-cell RNA-seq data Nat Commun, 9, pp. 2667. doi:10.1038/s41467-018-05083-x (10 July 2018)

Takahashi K, Wang F, Morita K, Yan Y, Hu P, Zhao P, Zhar AA, Wu CJ, Gumbs C, Little L, Tippen S, Thornton R, Coyle M, Mendoza M, Thompson E, Zhang J, DiNardo CD, Jain N, Ravandi F, Cortes JE, Garcia-Manero G, Kornblau S, Andreeff M, Jabbour E, Bueso-Ramos C, Takaori-Kondo A, Konopleva M, Patel K, Kantarjian H, Futreal PA. Integrative genomic analysis of adult mixed phenotype acute leukemia delineates lineage associated molecular subtypes Nat Commun, 9, pp. 2670. doi:10.1038/s41467-018-04924-z (10 July 2018)

Schulze M, Sommer A, Plötz S, Farrell M, Winner B, Grosch J, Winkler J, Riemenschneider MJ. Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs Acta Neuropathol Commun, 6, pp. 58. doi:10.1186/s40478-018-0561-x (10 July 2018)

Catoni M, Tsang JM, Greco AP, Zabet NR. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. doi:10.1093/nar/gky602 (9 July 2018)

Solomon P, Dong Y, Dogra S, Gupta R. Interleukin 8 is a biomarker of telomerase inhibition in cancer cells BMC Cancer, 18, pp. 730. doi:10.1186/s12885-018-4633-x (9 July 2018)

Huang J, Hao X, Jin Y, Guo X, Shao Q, Kumar KS, Ahlawat YK, Harry DE, Joshi CP, Zheng Y. Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata) BMC Plant Biol, 18, pp. 140. doi:10.1186/s12870-018-1356-8 (9 July 2018)

Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development Nat Commun, 9, pp. 2656. doi:10.1038/s41467-018-04966-3 (9 July 2018)

Torralba D, Baixauli F, Villarroya-Beltri C, Fernández-Delgado I, Latorre-Pellicer A, Acín-Pérez R, Martín-Cófreces NB, Jaso-Tamame ÁL, Iborra S, Jorge I, González-Aseguinolaza G, Garaude J, Vicente-Manzanares M, Enríquez JA, Mittelbrunn M, Sánchez-Madrid F. Priming of dendritic cells by DNA-containing extracellular vesicles from activated T cells through antigen-driven contacts Nat Commun, 9, pp. 2658. doi:10.1038/s41467-018-05077-9 (9 July 2018)

Taipale T, Seppälä I, Raitoharju E, Mononen N, Lyytikäinen LP, Illig T, Waldenberger M, Juonala M, Hutri-Kähönen N, Oksala N, Kähönen M, Raitakari O, Lehtimäki T. Fatty liver is associated with blood pathways of inflammatory response, immune system activation and prothrombotic state in Young Finns Study Sci Rep, 8, pp. 10358. doi:10.1038/s41598-018-28563-y (9 July 2018)

Zhao M, Svensson MN, Venken K, Chawla A, Liang S, Engel I, Mydel P, Day J, Elewaut D, Bottini N, Kronenberg M. Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70 Nat Commun, 9, pp. 2627. doi:10.1038/s41467-018-05095-7 (6 July 2018)

Kok YL, Schmutz S, Inderbitzin A, Neumann K, Kelley A, Jörimann L, Shilaih M, Vongrad V, Kouyos RD, Günthard HF, Berens C, Metzner KJ. Spontaneous reactivation of latent HIV-1 promoters is linked to the cell cycle as revealed by a genetic-insulators-containing dual-fluorescence HIV-1-based vector Sci Rep, 8, pp. 10204. doi:10.1038/s41598-018-28161-y (5 July 2018)

Sjöström M, Staaf J, Edén P, Wärnberg F, Bergh J, Malmström P, Fernö M, Niméus E, Fredriksson I. Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors Breast Cancer Res, 20, pp. 64. doi:10.1186/s13058-018-0978-y (4 July 2018)