The following publications are from BSPC’s collaborations since 2018. BSPC members in bold; post-bacs are indicated with an additional ‘*’.

2025

Alkaslasi, M.R., Lloyd, E.Y.H., Gable, A.S., Silberberg, H., Yarur, H.E., Tsai, V.S., Sohn, M., Margolin, G., Tejeda, H.A., Le Pichon, C.E.. 2025. The transcriptional response of cortical neurons to concussion reveals divergent fates after injury. Nature Communications 16 (1) 1097. https://doi.org/10.1038/s41467-025-56292-0.

Barnes, A.M., Mitra, A., Knue, M.M., Derkyi, A., Dang Do, A., Dale, R.K., Marini, J.C.. 2025. CRTAP-Null Osteoblasts Have Increased Proliferation, Protein Secretion, and Skeletal Morphogenesis Gene Expression with Downregulation of Cellular Adhesion. Cells 14 (7) 518. https://doi.org/10.3390/cells14070518.

Bruno, M., Farhana, S.M., Mitra, A., Costello, K., Watkins-Chow, D.E., Logsdon, G.A., Gambogi, C.W., Dumont, B.L., Black, B.E., Keane, T.M., Ferguson-Smith, A.C., Dale, R.K., Macfarlan, T.S.. 2025. Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice. Nature Communications 16 (1) 9608. https://doi.org/10.1038/s41467-025-64609-2.

Chakraborty, S., Wenzlitschke, N., Anderson, M.J., Eraso, A., Baudic, M., Thompson, J.J., Evans, A.A., *Shatford-Adams, L.M., Chari, R., Awasthi, P., Dale, R.K., Lewandoski, M., Petros, T.J., Rocha, P.P.. 2025. Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development. Developmental Cell 60 (13) 1838-1853.e9. https://doi.org/10.1016/j.devcel.2025.02.002.

Elizondo, D.M., Patel, T.P., Cole, B.T., Jansujwicz, E.A., Chen, J., Hollis, M.C., Mitra, A., Yanovski, J.A.. 2025. Transglutaminase 2-expressing macrophages modulate adipose tissue inflammation. Communications Biology 8 (1) 859. https://doi.org/10.1038/s42003-025-08199-1.

Evans, A., Farrell, J.A.. 2025. DaniocellDesktop: for Interactive Reanalysis of Wild-Type Zebrafish Single-Cell Genomic Data. Zebrafish 22 (6) 230-232. https://doi.org/10.1177/15458547251376181.

Gupta, T., Margolin, G., Burgess, H.A.. 2025. Mutations in the microexon splicing regulator srrm4 have minor phenotypic effects on zebrafish neural development. G3 (Bethesda, Md.) 15 (5) jkaf052. https://doi.org/10.1093/g3journal/jkaf052.

Jovanovic, M., Mitra, A., Stephan, C., Wong, K.W., Talvacchio, S., Forlino, A., To, M., Kozloff, K.M., Dale, R.K., Marini, J.C.. 2025. The Role of Osteoblasts in Phenotypic Variability of Dominant Osteogenesis Imperfecta: Evidence from Patients and Murine Models. International Journal of Molecular Sciences 26 (23) 11722. https://doi.org/10.3390/ijms262311722.

Kessler, A.C., Mattijssen, S., Margolin, G.H., Prochnau, J.Y., Iben, J.R., Li, T., Gaidamakov, S., Schowe, I.P., Hafner, M., Maraia, R.J.. 2025. A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB. Nucleic Acids Research 53 (13) gkaf513. https://doi.org/10.1093/nar/gkaf513.

Kunselman, J.M., Williamson, C.D., Golding, A.E., Jia, R., Sohn, M., Dale, R.K., Bonifacino, J.S.. 2025. The hereditary spastic paraplegia type 21 (SPG21) protein is a RAB7A effector that promotes noncanonical mTORC1-catalyzed TFEB phosphorylation and cytoplasmic retention. Molecular Biology of the Cell 36 (10) ar123. https://doi.org/10.1091/mbc.E25-07-0346.

Luo, X., Zhang, A., Esnault, C., De Mets, F., Adams, P.P., Dale, R.K., Storz, G., Gottesman, S.. 2025. RNA-RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA-mRNA pairing. Nucleic Acids Research 53 (22) gkaf1313. https://doi.org/10.1093/nar/gkaf1313.

Miller, M.F., Greenspan, L.J., Gildea, D.E., Monzo, K., Margolin, G., Pham, V.N., Ameyaw, K.K., Price, L., Aloi, N., Stratman, A.N., Davis, A.E., Cisneros, I., Mertus, C.A., Dale, R.K., Baxevanis, A.D., Weinstein, B.M.. 2025. In vivo profiling of the endothelium using ‘AngioTag’ zebrafish. Angiogenesis 28 (3) 40. https://doi.org/10.1007/s10456-025-09990-8.

Semenova, S.A., Nammi, D., Garrett, G.B., Margolin, G., Sinclair, J.L., Maroofian, R., Caldecott, K.W., Burgess, H.A.. 2025. Parp1 deletion rescues cerebellar hypotrophy in xrcc1 mutant zebrafish. Scientific Reports 15 (1) 17043. https://doi.org/10.1038/s41598-025-01870-x.

Tanizaki, Y., Zhang, H., Shi, Y.. 2025. Complementary and additive functions of TRα and TRβ during intestinal remodeling as revealed by ChIP-Seq analysis on wild type and TR knockout animals. General and Comparative Endocrinology 360 114645. https://doi.org/10.1016/j.ygcen.2024.114645.

Thongdee, N., Alaniz, M.M., Samatova, E., Zhong, A., Esnault, C., Zhang, H., Dale, R.K., Rodnina, M.V., Storz, G.. 2025. Modulation of protein activity by small RNA base pairing internal to coding sequences. Molecular Cell 85 (9) 1824-1837.e7. https://doi.org/10.1016/j.molcel.2025.03.014.

2024

De Pace, R., Ghosh, S., Ryan, V.H., Sohn, M., Jarnik, M., Rezvan Sangsari, P., Morgan, N.Y., Dale, R.K., Ward, M.E., Bonifacino, J.S.. 2024. Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration. Nature Neuroscience 27 (6) 1087-1102. https://doi.org/10.1038/s41593-024-01619-1.

Gaikwad, S., Ghobakhlou, F., Zhang, H., Hinnebusch, A.G.. 2024. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo. eLife 12 RP92916. https://doi.org/10.7554/eLife.92916.

Rhodes, C.T., Asokumar, D., Sohn, M., Naskar, S., Elisha, L., Stevenson, P., Lee, D.R., Zhang, Y., Rocha, P.P., Dale, R.K., Lee, S., Petros, T.J.. 2024. Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles. Frontiers in Cellular Neuroscience 18 1334244. https://doi.org/10.3389/fncel.2024.1334244.

2023

Anbazhagan, R., Kavarthapu, R., Dale, R., *Campbell, K., Faucz, F.R., Dufau, M.L.. 2023. miRNA Expression Profiles of Mouse Round Spermatids in GRTH/DDX25-Mediated Spermiogenesis: mRNA-miRNA Network Analysis. Cells 12 (5) 756. https://doi.org/10.3390/cells12050756.

*Campbell, K., Cawley, N.X., Luke, R., Scott, K.E.J., *Johnson, N., Farhat, N.Y., Alexander, D., Wassif, C.A., Li, W., Cologna, S.M., Berry-Kravis, E., Do, A.D., Dale, R.K., Porter, F.D.. 2023. Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1. Biomarker Research 11 (1) 14. https://doi.org/10.1186/s40364-023-00448-x.

Chakraborty, S., Kopitchinski, N., Zuo, Z., Eraso, A., Awasthi, P., Chari, R., Mitra, A., Tobias, I.C., Moorthy, S.D., Dale, R.K., Mitchell, J.A., Petros, T.J., Rocha, P.P.. 2023. Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nature Genetics 55 (2) 280-290. https://doi.org/10.1038/s41588-022-01295-6.

Dang Do, A.N., Sleat, D.E., *Campbell, K., *Johnson, N.L., Zheng, H., Wassif, C.A., Dale, R.K., Porter, F.D.. 2023. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. Journal of Proteome Research 22 (7) 2493-2508. https://doi.org/10.1021/acs.jproteome.3c00199.

Jovanovic, M., Mitra, A., Besio, R., Contento, B.M., Wong, K.W., Derkyi, A., To, M., Forlino, A., Dale, R.K., Marini, J.C.. 2023. Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study. Matrix Biology: Journal of the International Society for Matrix Biology 121 127-148. https://doi.org/10.1016/j.matbio.2023.06.004.

Melamed, S., Zhang, A., Jarnik, M., Mills, J., Silverman, A., Zhang, H., Storz, G.. 2023. σ28-dependent small RNA regulation of flagella biosynthesis. eLife 12 RP87151. https://doi.org/10.7554/eLife.87151.

Petroni, E., Esnault, C., Tetreault, D., Dale, R.K., Storz, G., Adams, P.P.. 2023. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nature Communications 14 (1) 3931. https://doi.org/10.1038/s41467-023-39576-1.

Piña, J.O., Raju, R., Roth, D.M., Winchester, E.W., Chattaraj, P., Kidwai, F., Faucz, F.R., Iben, J., Mitra, A., *Campbell, K., *Fridell, G., Esnault, C., Cotney, J.L., Dale, R.K., D’Souza, R.N.. 2023. Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis. Nature Communications 14 (1) 5687. https://doi.org/10.1038/s41467-023-41349-9.

Raju, R., Piña, J.O., Roth, D.M., Chattaraj, P., Kidwai, F.K., Faucz, F.R., Iben, J., *Fridell, G., Dale, R.K., D’Souza, R.N.. 2023. Profiles of Wnt pathway gene expression during tooth morphogenesis. Frontiers in Physiology 14 1316635. https://doi.org/10.3389/fphys.2023.1316635.

Sharma, V.K., *Campbell, K., Yang, X., Dale, R., Loh, Y.P.. 2023. Characterization of serotonin-5-HTR1E signaling pathways and its role in cell survival. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 37 (5) e22925. https://doi.org/10.1096/fj.202300128R.

Sur, A., Wang, Y., Capar, P., Margolin, G., Prochaska, M.K., Farrell, J.A.. 2023. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. Developmental Cell 58 (24) 3028-3047.e12. https://doi.org/10.1016/j.devcel.2023.11.001.

Tanizaki, Y., Wang, S., Zhang, H., Shibata, Y., Shi, Y.. 2023. Liver development during Xenopus tropicalis metamorphosis is controlled by T3-activation of WNT signaling. iScience 26 (4) 106301. https://doi.org/10.1016/j.isci.2023.106301.

Tanizaki, Y., Zhang, H., Shibata, Y., Shi, Y.. 2023. Organ-specific effects on target binding due to knockout of thyroid hormone receptor α during Xenopus metamorphosis. Development, Growth & Differentiation 65 (1) 23-28. https://doi.org/10.1111/dgd.12825.

Trivellin, G., Daly, A.F., Hernández-Ramírez, L.C., Araldi, E., Tatsi, C., Dale, R.K., *Fridell, G., Mittal, A., Faucz, F.R., Iben, J.R., Li, T., Vitali, E., Stojilkovic, S.S., Kamenicky, P., Villa, C., Baussart, B., Chittiboina, P., Toro, C., Gahl, W.A., Eugster, E.A., Naves, L.A., Jaffrain-Rea, M., de Herder, W.W., Neggers, S.J., Petrossians, P., Beckers, A., Lania, A.G., Mains, R.E., Eipper, B.A., Stratakis, C.A.. 2023. Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion. Frontiers in Endocrinology 14 1166076. https://doi.org/10.3389/fendo.2023.1166076.

Wang, S., Shibata, Y., Tanizaki, Y., Zhang, H., Yan, W., Fu, L., Shi, Y.. 2023. Comparative Analysis of Transcriptome Profiles Reveals Distinct and Organ-Dependent Genomic and Nongenomic Actions of Thyroid Hormone in Xenopus tropicalis Tadpoles. Thyroid: Official Journal of the American Thyroid Association 33 (4) 511-522. https://doi.org/10.1089/thy.2022.0469.

Zheng, Q., Qiu, H., Zhang, H., Hinnebusch, A.G.. 2023. Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes. Nucleic Acids Research 51 (8) 3696-3721. https://doi.org/10.1093/nar/gkad099.

2022

Baxter, L.L., Watkins-Chow, D.E., *Johnson, N.L., Farhat, N.Y., Platt, F.M., Dale, R.K., Porter, F.D., Pavan, W.J., Rodriguez-Gil, J.L.. 2022. Correlation of age of onset and clinical severity in Niemann-Pick disease type C1 with lysosomal abnormalities and gene expression. Scientific Reports 12 (1) 2162. https://doi.org/10.1038/s41598-022-06112-y.

El-Gazzar, A., Kang, H., Fratzl-Zelman, N., Webb, E., Barnes, A.M., Jovanovic, M., Mehta, S.G., Datta, V., Saraff, V., Dale, R.K., Rauch, F., Marini, J.C., Högler, W.. 2022. SMAD3 mutation in LDS3 causes bone fragility by impairing the TGF-β pathway and enhancing osteoclastogenesis. Bone Reports 17 101603. https://doi.org/10.1016/j.bonr.2022.101603.

Kean, C.M., Tracy, C.J., Mitra, A., Rahat, B., Van Winkle, M.T., Gebert, C.M., Noeker, J.A., Calof, A.L., Lander, A.D., Kassis, J.A., Pfeifer, K.. 2022. Decreasing Wapl dosage partially corrects embryonic growth and brain transcriptome phenotypes in Nipbl+/- embryos. Science Advances 8 (48) eadd4136. https://doi.org/10.1126/sciadv.add4136.

Lee, D.R., Rhodes, C., Mitra, A., Zhang, Y., Maric, D., Dale, R.K., Petros, T.J.. 2022. Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain. eLife 11 e71864. https://doi.org/10.7554/eLife.71864.

Li, F., Lee, M., Esnault, C., Wendover, K., Guo, Y., Atkins, P., Zaratiegui, M., Levin, H.L.. 2022. Identification of an integrase-independent pathway of retrotransposition. Science Advances 8 (26) eabm9390. https://doi.org/10.1126/sciadv.abm9390.

Rhodes, C.T., Thompson, J.J., Mitra, A., Asokumar, D., Lee, D.R., Lee, D.J., Zhang, Y., *Jason, E., Dale, R.K., Rocha, P.P., Petros, T.J.. 2022. An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nature Communications 13 (1) 4196. https://doi.org/10.1038/s41467-022-31793-4.

Tanizaki, Y., Shibata, Y., Zhang, H., Shi, Y.. 2022. Thyroid Hormone Receptor α Controls the Hind Limb Metamorphosis by Regulating Cell Proliferation and Wnt Signaling Pathways in Xenopus tropicalis. International Journal of Molecular Sciences 23 (3) 1223. https://doi.org/10.3390/ijms23031223.

Tanizaki, Y., Zhang, H., Shibata, Y., Shi, Y.. 2022. Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway. Communications Biology 5 (1) 112. https://doi.org/10.1038/s42003-022-03061-0.

Thompson, J.J., Lee, D.J., Mitra, A., Frail, S., Dale, R.K., Rocha, P.P.. 2022. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nature Communications 13 (1) 4257. https://doi.org/10.1038/s41467-022-31938-5.

Walling, L.R., Kouse, A.B., Shabalina, S.A., Zhang, H., Storz, G.. 2022. A 3’ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria. Nucleic Acids Research 50 (17) 10093-10109. https://doi.org/10.1093/nar/gkac748.

2021

Adams, P.P., Baniulyte, G., Esnault, C., Chegireddy, K., Singh, N., Monge, M., Dale, R.K., Storz, G., Wade, J.T.. 2021. Regulatory roles of Escherichia coli 5’ UTR and ORF-internal RNAs detected by 3’ end mapping. eLife 10 e62438. https://doi.org/10.7554/eLife.62438.

Beck, D.B., Basar, M.A., Asmar, A.J., Thompson, J.J., Oda, H., Uehara, D.T., Saida, K., Pajusalu, S., Talvik, I., D’Souza, P., Bodurtha, J., Mu, W., Barañano, K.W., 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., Walkiewicz, M., Õunap, K., Tifft, C.J., Aksentijevich, I., Kastner, D.L., Rocha, P.P., Werner, A.. 2021. Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. Science Advances 7 (4) eabe2116. https://doi.org/10.1126/sciadv.abe2116.

Gaikwad, S., Ghobakhlou, F., Young, D.J., Visweswaraiah, J., Zhang, H., Hinnebusch, A.G.. 2021. Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs. eLife 10 e64283. https://doi.org/10.7554/eLife.64283.

Li, F., Hung, S., Esnault, C., Levin, H.L.. 2021. A protocol for transposon insertion sequencing in Schizosaccharomyces pombe to identify factors that maintain heterochromatin. STAR protocols 2 (2) 100392. https://doi.org/10.1016/j.xpro.2021.100392.

Mahadevan, V., Mitra, A., Zhang, Y., Yuan, X., Peltekian, A., Chittajallu, R., Esnault, C., Maric, D., Rhodes, C., Pelkey, K.A., Dale, R., Petros, T.J., McBain, C.J.. 2021. NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile Brain. Frontiers in Molecular Neuroscience 14 712609. https://doi.org/10.3389/fnmol.2021.712609.

Park, K., Rahat, B., Lee, H.C., Yu, Z., Noeker, J., Mitra, A., Kean, C.M., Knutsen, R.H., Springer, D., Gebert, C.M., Kozel, B.A., Pfeifer, K.. 2021. Cardiac pathologies in mouse loss of imprinting models are due to misexpression of H19 long noncoding RNA. eLife 10 e67250. https://doi.org/10.7554/eLife.67250.

Rodriguez-Gil, J.L., Baxter, L.L., Watkins-Chow, D.E., *Johnson, N.L., Davidson, C.D., Carlson, S.R., Incao, A.A., NISC Comparative Sequencing Program, Wallom, K.L., Farhat, N.Y., Platt, F.M., Dale, R.K., Porter, F.D., Pavan, W.J.. 2021. Transcriptome of HPβCD-treated Niemann-Pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics. Human Molecular Genetics 30 (24) 2456-2468. https://doi.org/10.1093/hmg/ddab194.

Sen, N.D., Zhang, H., Hinnebusch, A.G.. 2021. Down-Regulation of Yeast Helicase Ded1 by Glucose Starvation or Heat-Shock Differentially Impairs Translation of Ded1-Dependent mRNAs. Microorganisms 9 (12) 2413. https://doi.org/10.3390/microorganisms9122413.

Shibata, Y., Tanizaki, Y., Zhang, H., Lee, H., Dasso, M., Shi, Y.. 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 (3) 536. https://doi.org/10.3390/cells10030536.

Stamos, D.B., Clubb, L.M., Mitra, A., Chopp, L.B., Nie, J., Ding, Y., Das, A., Venkataganesh, H., Lee, J., El-Khoury, D., Li, L., Bhandoola, A., Bosselut, R., Love, P.E.. 2021. The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. The Journal of Experimental Medicine 218 (12) e20202012. https://doi.org/10.1084/jem.20202012.

Storz, G., Adams, P.P., Baniulyte, G., Esnault, C., Chegireddy, K., Singh, N., Monge, M., Dale, R.K., Wade, J.T.. 2021. Correction: Regulatory roles of Escherichia coli 5’ UTR and ORF-internal RNAs detected by 3’ end mapping. eLife 10 e69260. https://doi.org/10.7554/eLife.69260.

Tanizaki, Y., Shibata, Y., Zhang, H., Shi, Y.. 2021. 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: Official Journal of the American Thyroid Association 31 (1) 128-142. https://doi.org/10.1089/thy.2020.0022.

Tseng, W., *Johnson Escauriza, A.J., Tsai-Morris, C., Feldman, B., Dale, R.K., Wassif, C.A., Porter, F.D.. 2021. The role of Niemann-Pick type C2 in zebrafish embryonic development. Development (Cambridge, England) 148 (7) dev194258. https://doi.org/10.1242/dev.194258.

2020

Aksenova, V., Smith, A., Lee, H., Bhat, P., Esnault, C., Chen, S., Iben, J., Kaufhold, R., Yau, K.C., Echeverria, C., Fontoura, B., Arnaoutov, A., Dasso, M.. 2020. Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway. Nature Communications 11 (1) 4577. https://doi.org/10.1038/s41467-020-18266-2.

Chang, E., Fu, C., Coon, S.L., Alon, S., Bozinoski, M., Breymaier, M., Bustos, D.M., Clokie, S.J., Gothilf, Y., Esnault, C., Michael Iuvone, P., Mason, C.E., Ochocinska, M.J., Tovin, A., Wang, C., Xu, P., Zhu, J., Dale, R., Klein, D.C.. 2020. Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. Journal of Pineal Research 69 (3) e12673. https://doi.org/10.1111/jpi.12673.

Guo, X., Plank-Bazinet, J., Krivega, I., Dale, R.K., Dean, A.. 2020. Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Research 48 (18) 10226-10240. https://doi.org/10.1093/nar/gkaa736.

Kang, H., Jha, S., Ivovic, A., Fratzl-Zelman, N., Deng, Z., Mitra, A., Cabral, W.A., Hanson, E.P., Lange, E., Cowen, E.W., Katz, J., Roschger, P., Klaushofer, K., Dale, R.K., Siegel, R.M., Bhattacharyya, T., Marini, J.C.. 2020. Somatic SMAD3-activating mutations cause melorheostosis by up-regulating the TGF-β/SMAD pathway. The Journal of Experimental Medicine 217 (5) e20191499. https://doi.org/10.1084/jem.20191499.

Lee, S.Y., Hung, S., Esnault, C., Pathak, R., *Johnson, K.R., Bankole, O., Yamashita, A., Zhang, H., Levin, H.L.. 2020. Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Reports 30 (8) 2686-2698.e8. https://doi.org/10.1016/j.celrep.2020.01.094.

Li, L., Mitra, A., Cui, K., Zhao, B., Choi, S., Lee, J.Y., Stamos, D.B., El-Khoury, D., Warzecha, C., Pfeifer, K., Hardwick, J., Zhao, K., Venters, B., Davé, U.P., Love, P.E.. 2020. Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood 135 (25) 2252-2265. https://doi.org/10.1182/blood.2019000794.

Matson, C.A., Choi, S., Livak, F., Zhao, B., Mitra, A., Love, P.E., Singh, N.J.. 2020. CD5 dynamically calibrates basal NF-κB signaling in T cells during thymic development and peripheral activation. Proceedings of the National Academy of Sciences of the United States of America 117 (25) 14342-14353. https://doi.org/10.1073/pnas.1922525117.

Miller, B.F., Pisanic Ii, T.R., Margolin, G., Petrykowska, H.M., Athamanolap, P., Goncearenco, A., Osei-Tutu, A., Annunziata, C.M., Wang, T., Elnitski, L.. 2020. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clinical Epigenetics 12 (1) 154. https://doi.org/10.1186/s13148-020-00939-w.

Wolf, G., de Iaco, A., Sun, M., Bruno, M., Tinkham, M., Hoang, D., Mitra, A., Ralls, S., Trono, D., Macfarlan, T.S.. 2020. KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage. eLife 9 e56337. https://doi.org/10.7554/eLife.56337.

Zhou, F., Zhang, H., Kulkarni, S.D., Lorsch, J.R., Hinnebusch, A.G.. 2020. eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA (New York, N.Y.) 26 (4) 419-438. https://doi.org/10.1261/rna.073536.119.

2019

Esnault, C., Lee, M., Ham, C., Levin, H.L.. 2019. Transposable element insertions in fission yeast drive adaptation to environmental stress. Genome Research 29 (1) 85-95. https://doi.org/10.1101/gr.239699.118.

Martin, K.B., Williams, I.M., Cluzeau, C.V., Cougnoux, A., Dale, R.K., Iben, J.R., Cawley, N.X., Wassif, C.A., Porter, F.D.. 2019. Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1. International Journal of Molecular Sciences 21 (1) 292. https://doi.org/10.3390/ijms21010292.

2018

Grüning, B., Dale, R., Sjödin, A., Chapman, B.A., Rowe, J., Tomkins-Tinch, C.H., Valieris, R., Köster, J., Bioconda Team. 2018. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods 15 (7) 475-476. https://doi.org/10.1038/s41592-018-0046-7.

Grüning, B., Chilton, J., Köster, J., Dale, R., Soranzo, N., van den Beek, M., Goecks, J., Backofen, R., Nekrutenko, A., Taylor, J.. 2018. Practical Computational Reproducibility in the Life Sciences. Cell Systems 6 (6) 631-635. https://doi.org/10.1016/j.cels.2018.03.014.