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📖 Bioconductor Publications

Publications

This is a select list of featured and recent publications that cite Bioconductor, along with select books, book chapters, and original Bioconductor technical reports.

Featured

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

10 most recent PubMed and PubMed Central citations mentioning "*Bioconductor*". For a complete list, go to PubMed and PubMed Central. Last updated 2026-09-29T01:00:10-04:00.

Ma S, Kang C, Liu X, Yang L, Li M, Ye Y, Zhang J, Li Y, Jin G, Liu Y, Chen X, Wang K, Yang Z. NS1-Induced PARP1 Phase Transitions Prolongs Host Transcriptional Pausing to Promote Influenza A Virus Replication. Adv Sci (Weinh), pp. e77883. doi:10.1002/advs.77883 (27 September 2026)

Huang Y, Hu Z, Liao J, Huang L, Liu J, Tu C, Li Y, Xie L, Bi S, Fang X, Chen J, Du L, Sun W, Wang H, Zhang S, Chen D, Tu Z. CHD8-Dependent Chromatin Licensing Sustains Trophoblast Stem Cell Transcriptional Programs. Adv Sci (Weinh), pp. e77823. doi:10.1002/advs.77823 (27 September 2026)

Zhang N, Wan T, Zhang S, Jiang Y, Su P, Liu J, Chen Z, Hao J, Wang H, Chen B, Zhao W, Wang L, Xing T, Zhang Q, Schmitz U, Ding Z, Crosetto N, Liu B, Yang Q. Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC. Adv Sci (Weinh), pp. e77897. doi:10.1002/advs.77897 (27 September 2026)

Huang Y, Liu Y, Peng H, Ni Y, Jiang Z, Yu C, Zhang X, Kang H, Liu Y, Chen J, Zhao K, Han L, Zou X, Shu K, Wang X, Wang JZ, Lei T, Gan C, Liu J, Zhang H. AI-Designed TREM1-Targeted LYTAC Nanoparticles Reprogram the Neuroimmune Microenvironment in Traumatic Brain Injury. Adv Sci (Weinh), pp. e77972. doi:10.1002/advs.77972 (27 September 2026)

Wang J, Tang X, Li Z, Qi Q, Sun C, Sun W, Zhang W, Yin Y, Deng Y, Ling P, Xu Y, Sun G, Ren Y, Pan H, Wang S, Zhou W. CXCL3 Antagonism Reverses Systemic Antitumor Immune Memory Impairment Associated With High Tumor Burden and Sensitizes Anti-PD-1 Therapy. Adv Sci (Weinh), pp. e77976. doi:10.1002/advs.77976 (27 September 2026)

Dou J, Liao Y, Shen X, Huang X, Tang Z, Gou Y, Zhou H, Xu J, Liu H, Wang Y, Liang K, Liu J, Zhang X, Li C, Wang S, Fu L, Yin L, Li X, Zhao S, Liu X, Li J, Fu Y. Multi-Layer Transcriptomic Comparison Across Human, Pig, and Mouse Informs Tissue- and Trait-Specific Animal Model Selection. Adv Sci (Weinh), pp. e77881. doi:10.1002/advs.77881 (27 September 2026)

Meng YX, Joo J, Li YM, Li CJ, Taghizadeh A, Shin SJ, Bayarkhangai B, Ha TW, Lee S, Chung J, Yoon BE, Kim HS, Jung I, Lee JH, Leong KW, Kim HW. Matrix Rigidity Mechanoprimes Microglia for Inflammation Through Cytoskeletal-to-Nuclear Signaling and 3D Spatio-Epigenomic Remodeling. Adv Sci (Weinh), pp. e77736. doi:10.1002/advs.77736 (27 September 2026)

Sun C, Wei S, Tao J, Chen H, Yan C, Wang J, Xu J, Duan L, Zhan Y, Zou Y, Li R, Yuan L, She W, Lu S, Wang N, Ren Q, Guo Y, Xu Y, Wang C, Tian H, Zhang C, Dong Y, Tang G, Shang Z, Jiang Y, Lv W, Zhang M, Lyu H. Integrating Genetics With Epidemiological Measurements Identifies Burden QTLs of Inflammatory Bowel Disease across 20 Countries. Adv Sci (Weinh), pp. e19007. doi:10.1002/advs.202519007 (27 September 2026)

Azevedo MIG, Neves-da-Rocha J, Sanches PR, Petrucelli MF, Santos-Saboya MJ, Martinez-Rossi NM, Rossi A. Genome-wide analysis of alternative splicing associated with the transcription factor StuA in Trichophyton rubrum. Fungal Genet Biol, 186, pp. 104120. doi:10.1016/j.fgb.2026.104120 (26 September 2026)

Gunz S, Crowell HL, Robinson MD. Analysis of multicellular anatomical structures from spatial omics data using sosta. PLoS Comput Biol, 22(9), pp. e1014551. doi:10.1371/journal.pcbi.1014551 (10 September 2026)