The following publications are from BSPC’s collaborations since 2018. BSPC members are indicated in bold.

2021

• Beck DB, Basar MA, Asmar AJ, Thompson JJ, Oda H, Uehara DT, Saida K, Pajusalu S, Talvik I, D'Souza P, Bodurtha J, Mu W, Barañano KW, Miyake N, Wang R, Kempers M, Tamada T, Nishimura Y, Okada S, Kosho T, Dale R, Mitra A, Macnamara E, Undiagnosed Diseases Network, Matsumoto N, Inazawa J, et al. [7 more authors] (2021). Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. Sci Adv 7. https://doi.org/10.1126/sciadv.abe2116
• Gaikwad S, Ghobakhlou F, Young DJ, Visweswaraiah J, Zhang H, Hinnebusch AG (2021). Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs. Elife 10. https://doi.org/10.7554/eLife.64283
• Lee D, Rhodes CT, Mitra AK, Zhang Y, Maric D, Dale RK, Petros TJ (2021). Transcriptional heterogeneity of ventricular zone cells throughout the embryonic mouse forebrain. bioRxiv . https://doi.org/10.1101/2021.07.05.451224
• Li F, Hung S, Esnault C, Levin HL (2021). A protocol for transposon insertion sequencing in Schizosaccharomyces pombe to identify factors that maintain heterochromatin. STAR Protoc 2, 100392. https://doi.org/10.1016/j.xpro.2021.100392
• Mahadevan V, Mitra AK, Zhang Y, Yuan X, Peltekian AA, Chittajallu VK, Esnault CM, Maric D, Rhodes CT, Pelkey KA, Dale RK, Petros T, McBain CJ (2021) NMDARs drive the expression of neuropsychiatric disorder risk genes within GABAergic interneurons subtypes in the juvenile brain. Frontiers in Molecular Neuroscience, in press. https://doi.org/10.3389/fnmol.2021.712609
• Rodriguez-Gil JL, Baxter LL, Watkins-Chow DE, Johnson NL, Davidson CD, Carlson SR, Incao AA, NISC Comparative Sequencing Program (Mullikin JC, member), Wallom KL, Farhat NY, Platt FM, Dale RK, Porter FD, Pavan WJ (2021) Transcriptome of HPβCD-treated Niemann-pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics. Hum Mol Genet, in press (e-pub ahead of print) https://doi.org/10.1093/hmg/ddab194
• Shibata Y, Tanizaki Y, Zhang H, Lee H, Dasso M, Shi YB (2021). Thyroid Hormone Receptor Is Essential for Larval Epithelial Apoptosis and Adult Epithelial Stem Cell Development but Not Adult Intestinal Morphogenesis during Xenopus tropicalis Metamorphosis. Cells 10. https://doi.org/10.3390/cells10030536
• Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT (2021). Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. Elife 10. https://doi.org/10.7554/eLife.62438
• Tseng WC, Johnson Escauriza AJ, Tsai-Morris CH, Feldman B, Dale RK, Wassif CA, Porter FD (2021). The role of Niemann-Pick type C2 in zebrafish embryonic development. Development 148. https://doi.org/10.1242/dev.194258

2020

• Chang E, Fu C, Coon SL, Alon S, Bozinoski M, Breymaier M, Bustos DM, Clokie SJ, Gothilf Y, Esnault C, Michael Iuvone P, Mason CE, Ochocinska MJ, Tovin A, Wang C, Xu P, Zhu J, Dale R, Klein DC (2020) Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. J Pineal Res, in press (e-pub ahead of print) https://doi.org/10.1111/jpi.12673
• Kang H, Jha S, Ivovic A, Fratzl-Zelman N, Deng Z, Mitra A, Cabral WA, Hanson EP, Lange E, Cowen EW, Katz J, Roschger P, Klaushofer K, Dale RK, Siegel RM, Bhattacharyya T, Marini JC (2020). Somatic SMAD3-activating mutations cause melorheostosis by up-regulating the TGF-β/SMAD pathway. J Exp Med 217. https://doi.org/10.1084/jem.20191499
• Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H, Levin HL (2020). Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Rep 30, 2686-2698.e8. https://doi.org/10.1016/j.celrep.2020.01.094
• Li L, Mitra A, Cui K, Zhao B, Choi S, Lee JY, Stamos DB, El-Khoury D, Warzecha C, Pfeifer K, Hardwick J, Zhao K, Venters B, Davé UP, Love PE (2020). Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood 135, 2252-2265. https://doi.org/10.1182/blood.2019000794
• Martin KB, Williams IM, Cluzeau CV, Cougnoux A, Dale RK, Iben JR, Cawley NX, Wassif CA, Porter FD (2020). Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1. Int J Mol Sci 21. https://doi.org/10.3390/ijms21010292
• Matson CA, Choi S, Livak F, Zhao B, Mitra A, Love PE, Singh NJ (2020). CD5 dynamically calibrates basal NF-κB signaling in T cells during thymic development and peripheral activation. Proc Natl Acad Sci U S A 117, 14342-14353. https://doi.org/10.1073/pnas.1922525117
• Tanizaki Y, Shibata Y, Zhang H, Shi YB (2020) Analysis of Thyroid Hormone Receptor α-Knockout Tadpoles Reveals That the Activation of Cell Cycle Program Is Involved in Thyroid Hormone-Induced Larval Epithelial Cell Death and Adult Intestinal Stem Cell Development During Xenopus tropicalis Metamorphosis. Thyroid, in press (e-pub ahead of print) https://doi.org/10.1089/thy.2020.0022
• Wolf G, de Iaco A, Sun MA, Bruno M, Tinkham M, Hoang D, Mitra A, Ralls S, Trono D, Macfarlan TS (2020). KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage. Elife 9. https://doi.org/10.7554/eLife.56337
• Zhou F, Zhang H, Kulkarni SD, Lorsch JR, Hinnebusch AG (2020). eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA 26, 419-438. https://doi.org/10.1261/rna.073536.119

2019

• Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG, Lorsch JR (2019). Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 17, 101. https://doi.org/10.1186/s12915-019-0718-5
• Melamed S, Adams PP, Zhang A, Zhang H, Storz G (2019). RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles. Mol Cell 77, 411-425.e7. https://doi.org/10.1016/j.molcel.2019.10.022
• Nakajima K, Tanizaki Y, Luu N, Zhang H, Shi YB (2019). Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption. Gen Comp Endocrinol 287, 113349. https://doi.org/10.1016/j.ygcen.2019.113349
• Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods 15, 475-476. https://doi.org/10.1038/s41592-018-0046-7