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2025 Journal Article Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressureShen, Sophie, Werner, Tessa, Lukowski, Samuel W., Andersen, Stacey, Sun, Yuliangzi, Shim, Woo Jun, Mizikovsky, Dalia, Kobayashi, Sakurako, Outhwaite, Jennifer, Chiu, Han Sheng, Chen, Xiaoli, Chapman, Gavin, Martin, Ella M. M. A., Xia, Di, Pham, Duy, Su, Zezhuo, Kim, Daniel, Yang, Pengyi, Tan, Men Chee, Sinniah, Enakshi, Zhao, Qiongyi, Negi, Sumedha, Redd, Meredith A., Powell, Joseph E., Dunwoodie, Sally L., Tam, Patrick P. L., Bodén, Mikael, Ho, Joshua W. K., Nguyen, Quan and Palpant, Nathan J. (2025). Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. Nature Communications, 16 (1) 1356, 1356-1. doi: 10.1038/s41467-025-56533-2 |
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2025 Journal Article Do protein language models learn phylogeny?Tule, Sanjana, Foley, Gabriel and Bodén, Mikael (2025). Do protein language models learn phylogeny?. Briefings in Bioinformatics, 26 (1) bbaf047. doi: 10.1093/bib/bbaf047 |
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2025 Journal Article TRIAGE: an R package for regulatory gene analysisZhao, Qiongyi, Shim, Woo Jun, Sun, Yuliangzi, Sinniah, Enakshi, Shen, Sophie, Boden, Mikael and Palpant, Nathan J. (2025). TRIAGE: an R package for regulatory gene analysis. Briefings in Bioinformatics, 26 (1) bbaf004, 1-13. doi: 10.1093/bib/bbaf004 |
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2025 Journal Article Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticityBalderson, Brad, Fane, Mitchell, Harvey, Tracey J., Piper, Michael, Smith, Aaron and Bodén, Mikael (2025). Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Briefings in Functional Genomics, 24 elad055. doi: 10.1093/bfgp/elad055 |
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2024 Journal Article SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancerMora, Ariane, Schmidt, Christina, Balderson, Brad, Frezza, Christian and Bodén, Mikael (2024). SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer. Genome Medicine, 16 (1) 144. doi: 10.1186/s13073-024-01415-3 |
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2024 Journal Article Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam AntibioticsJoshi, Pallav, Krco, Stefan, Davis, Samuel J., Asser, Lachlan, Brück, Thomas, Soo, Rochelle M., Bodén, Mikael, Hugenholtz, Philip, Wilson, Liam A., Schenk, Gerhard and Morris, Marc T. (2024). Phage Anti-Pycsar Proteins Efficiently Degrade β-Lactam Antibiotics. Applied Biosciences, 3 (4), 438-449. doi: 10.3390/applbiosci3040028 |
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2024 Journal Article Optimal phylogenetic reconstruction of insertion and deletion eventsTule, Sanjana, Foley, Gabriel, Zhao, Chongting, Forbes, Michael and Bodén, Mikael (2024). Optimal phylogenetic reconstruction of insertion and deletion events. Bioinformatics, 40 (s1), i277-i286. doi: 10.1093/bioinformatics/btae254 |
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2024 Journal Article Development of a highly selective NAD+‐dependent glyceraldehyde dehydrogenase and its application in minimal cell‐free enzyme cascadesTeshima, Mariko, Sutiono, Samuel, Döring, Manuel, Beer, Barbara, Boden, Mikael, Schenk, Gerhard and Sieber, Volker (2024). Development of a highly selective NAD+‐dependent glyceraldehyde dehydrogenase and its application in minimal cell‐free enzyme cascades. ChemSusChem, 17 (4) e202301132, 1-13. doi: 10.1002/cssc.202301132 |
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2024 Journal Article Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuaryPrabhu, Apoorva, Tule, Sanjana, Chuvochina, Maria, Bodén, Mikael, McIlroy, Simon J., Zaugg, Julian and Rinke, Christian (2024). Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary. ISME Communications, 4 (1) ycae067, ycae067. doi: 10.1093/ismeco/ycae067 |
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2023 Journal Article Cytocipher determines significantly different populations of cells in single cell RNA-seq dataBalderson, Brad, Piper, Michael, Thor, Stefan and Boden, Mikael (2023). Cytocipher determines significantly different populations of cells in single cell RNA-seq data. Bioinformatics, 39 (7) btad435. doi: 10.1093/bioinformatics/btad435 |
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2023 Journal Article Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identitySun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D., Ho, Joshua W. K., Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J (2023). Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Research, 51 (11), e62-e62. doi: 10.1093/nar/gkad307 |
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2023 Journal Article Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattleAfonso, Juliana, Shim, Woo Jun, Boden, Mikael, Salinas Fortes, Marina Rufino, da Silva Diniz, Wellison Jarles, de Lima, Andressa Oliveira, Rocha, Marina Ibelli Pereira, Cardoso, Tainã Figueiredo, Bruscadin, Jennifer Jessica, Gromboni, Caio Fernando, Nogueira, Ana Rita Araujo, Mourão, Gerson Barreto, Zerlotini, Adhemar, Coutinho, Luiz Lehmann and de Almeida Regitano, Luciana Correia (2023). Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochemistry and Biophysics Reports, 33 101420, 1-9. doi: 10.1016/j.bbrep.2023.101420 |
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2023 Journal Article Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticusBayaraa, Tenuun, Lonhienne, Thierry, Sutiono, Samuel, Melse, Okke, Brück, Thomas B., Marcellin, Esteban, Bernhardt, Paul V., Boden, Mikael, Harmer, Jeffrey R., Sieber, Volker, Guddat, Luke W. and Schenk, Gerhard (2023). Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticus. Chemistry: A European Journal, 29 (9) e202203140, 1-13. doi: 10.1002/chem.202203140 |
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2022 Conference Publication H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscleAfonso, J., Shim, W.J., Boden, M., Palpant, N., Fortes, M.R.S., Diniz, W.J.S., Lima, A.O., Rocha, M.I.P., Cardoso, T.F., Bruscadin, J.J., Gromboni, C.F., Nogueira, A.R.A., Mourão, G.B., Zerlotini, A., Coutinho, L.L. and Regitano, L.C.A. (2022). H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_553 |
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2022 Journal Article Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633 |
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2022 Journal Article Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform ChemicalsLv, You, Zheng, Shan, Goldenzweig, Adi, Liu, Fengjiang, Gao, Yan, Yang, Xiuna, Kandale, Ajit, McGeary, Ross P., Williams, Simon, Kobe, Bostjan, Schembri, Mark A., Landsberg, Michael J., Wu, Bin, Brück, Thomas B., Sieber, Volker, Boden, Mikael, Rao, Zihe, Fleishman, Sarel J., Schenk, Gerhard and Guddat, Luke W. (2022). Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals. Applied Biosciences, 1 (2), 163-178. doi: 10.3390/applbiosci1020011 |
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2022 Journal Article Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebratesHarris, Kurt L., Thomson, Raine E.S., Gumulya, Yosephine, Foley, Gabriel, Carrera-Pacheco, Saskya E., Syed, Parnayan, Janosik, Tomasz, Sandinge, Ann-Sofie, Andersson, Shalini, Jurva, Ulrik, Bodén, Mikael and Gillam, Elizabeth M.J. (2022). Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Molecular Biology and Evolution, 39 (6) msac116. doi: 10.1093/molbev/msac116 |
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2022 Journal Article Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypesYaghmaeian Salmani, Behzad, Balderson, Brad, Bauer, Susanne, Ekman, Helen, Starkenberg, Annika, Perlmann, Thomas, Piper, Michael, Bodén, Mikael and Thor, Stefan (2022). Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes. Development, 149 (5) dev200076. doi: 10.1242/dev.200076 |
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2022 Journal Article Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2Mora, Ariane, Rakar, Jonathan, Cobeta, Ignacio Monedero, Salmani, Behzad Yaghmaeian, Starkenberg, Annika, Thor, Stefan and Bodén, Mikael (2022). Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2. Nucleic Acids Research, 50 (3), 1280-1296. doi: 10.1093/nar/gkac006 |
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2022 Book Chapter Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP)Ross, Connie M., Foley, Gabriel, Boden, Mikael and Gillam, Elizabeth M. J. (2022). Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP). Enzyme engineering. (pp. 85-110) edited by Francesca Magnani, Chiara Marabelli and Francesca Paradisi. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-1826-4_6 |
