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2021 Journal Article Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acidWilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21 |
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2021 Journal Article ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicatesNewell, Rhys, Pienaar, Richard, Balderson, Brad, Piper, Michael, Essebier, Alexandra and Bodén, Mikael (2021). ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates. Genomics, 113 (4), 1855-1866. doi: 10.1016/j.ygeno.2021.04.026 |
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2021 Journal Article Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotypeKojic, Marija, Gawda, Tomasz, Gaik, Monika, Begg, Alexander, Salerno-Kochan, Anna, Kurniawan, Nyoman D., Jones, Alun, Drożdżyk, Katarzyna, Kościelniak, Anna, Chramiec-Głąbik, Andrzej, Hediyeh-Zadeh, Soroor, Kasherman, Maria, Shim, Woo Jun, Sinniah, Enakshi, Genovesi, Laura A., Abrahamsen, Rannvá K., Fenger, Christina D., Madsen, Camilla G., Cohen, Julie S., Fatemi, Ali, Stark, Zornitza, Lunke, Sebastian, Lee, Joy, Hansen, Jonas K., Boxill, Martin F., Keren, Boris, Marey, Isabelle, Saenz, Margarita S., Brown, Kathleen ... Wainwright, Brandon J. (2021). Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nature Communications, 12 (1) 2678, 2678. doi: 10.1038/s41467-021-22888-5 |
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2020 Journal Article Conserved epigenetic regulatory logic infers genes governing cell identityShim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001 |
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2020 Journal Article Evolutionary model of protein secondary structure capable of revealing new biological relationshipsLai, Jhih‐Siang, Rost, Burkhard, Kobe, Bostjan and Bodén, Mikael (2020). Evolutionary model of protein secondary structure capable of revealing new biological relationships. Proteins: Structure, Function, and Bioinformatics, 88 (9) prot.25898, 1251-1259. doi: 10.1002/prot.25898 |
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2020 Journal Article T-Gene: improved target gene predictionO’Connor, Timothy, Grant, Charles E, Bodén, Mikael and Bailey, Timothy L (2020). T-Gene: improved target gene prediction. Bioinformatics, 36 (12), 3902-3904. doi: 10.1093/bioinformatics/btaa227 |
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2019 Journal Article Correction to: Detailed prediction of protein sub-nuclear localization (BMC Bioinformatics (2019) 20 (205) DOI: 10.1186/s12859-019-2790-9)Littmann, Maria, Goldberg, Tatyana, Seitz, Sebastian, Bodén, Mikael and Rost, Burkhard (2019). Correction to: Detailed prediction of protein sub-nuclear localization (BMC Bioinformatics (2019) 20 (205) DOI: 10.1186/s12859-019-2790-9). BMC Bioinformatics, 20 (1) 727, 727. doi: 10.1186/s12859-019-3305-4 |
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2019 Journal Article Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar DevelopmentFraser, James, Essebier, Alexandra, Brown, Alexander S., Davila, Raul Ayala, Harkins, Danyon, Zalucki, Oressia, Shapiro, Lauren P., Penzes, Peter, Wainwright, Brandon J., Scott, Matthew P., Gronostajski, Richard M., Bodén, Mikael, Piper, Michael and Harvey, Tracey J. (2019). Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development. Cerebellum, 19 (1), 89-101. doi: 10.1007/s12311-019-01089-3 |
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2019 Conference Publication Common regulatory targets of NFIA and NFIX mediate postnatal cerebellar developmentHarvey, Tracey, Fraser, James, Essebier, Alexandra, Brown, Alexander, Davila, Raul, Boden, Mikael, Gronostajski, Richard and Piper, Michael (2019). Common regulatory targets of NFIA and NFIX mediate postnatal cerebellar development. 10th IBRO World Congress of Neuroscience, Daegu, South Korea, 21-25 September 2019. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.ibror.2019.07.1042 |
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2019 Journal Article NAD+ cleavage activity by animal and plant TIR domains in cell death pathwaysHorsefield, Shane, Burdett, Hayden, Zhang, Xiaoxiao, Manik, Mohammad K., Shi, Yun, Chen, Jian, Qi, Tiancong, Gilley, Jonathan, Lai, Jhih-Siang, Rank, Maxwell X., Casey, Lachlan W., Gu, Weixi, Ericsson, Daniel J., Foley, Gabriel, Hughes, Robert O., Bosanac, Todd, von Itzstein, Mark, Rathjen, John P., Nanson, Jeffrey D., Boden, Mikael, Dry, Ian B., Williams, Simon J., Staskawicz, Brian J., Coleman, Michael P., Ve, Thomas, Dodds, Peter N. and Kobe, Bostjan (2019). NAD+ cleavage activity by animal and plant TIR domains in cell death pathways. Science, 365 (6455), 793-799. doi: 10.1126/science.aax1911 |
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2019 Journal Article SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applicationsFoley, Gabriel, Sützl, Leander, D'Cunha, Stephlina A., Gillam, Elizabeth M.J. and Bodén, Mikael (2019). SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications. BioTechniques, 67 (2), 50-54. doi: 10.2144/btn-2018-0188 |
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2019 Journal Article The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductasesSützl, Leander, Foley, Gabriel, Gillam, Elizabeth M J, Bodén, Mikael and Haltrich, Dietmar (2019). The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. Biotechnology for Biofuels, 12 (1) 118, 118. doi: 10.1186/s13068-019-1457-0 |
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2019 Journal Article Detailed prediction of protein sub-nuclear localizationLittmann, Maria, Goldberg, Tatyana, Seitz, Sebastian, Bodén, Mikael and Rost, Burkhard (2019). Detailed prediction of protein sub-nuclear localization. BMC Bioinformatics, 20 (1) 205. doi: 10.1186/s12859-019-2790-9 |
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2019 Journal Article Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE)Gumulya, Yosephine, Huang, Weiliang, D'Cunha, Stephlina A., Richards, Katelyn E., Thomson, Raine E.S., Hunter, Dominic J.B., Baek, Jong-Min, Harris, Kurt L., Boden, Mikael, De Voss, James J., Hayes, Martin A., Isin, Emre M., Andersson, Shalini, Jurva, Ulrik and Gillam, Elizabeth (2019). Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE). ChemCatChem, 11 (2) cctc.201801644, 841-850. doi: 10.1002/cctc.201801644 |
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2018 Journal Article Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar developmentFraser, James, Essebier, Alexandra, Brown, Alexander S., Davila, Raul Ayala, Sengar, Ameet S., Tu, YuShan, Ensbey, Kathleen S., Day, Bryan W., Scott, Matthew P., Gronostajski, Richard M., Wainwright, Brandon J., Boden, Mikael, Harvey, Tracey J. and Piper, Michael (2018). Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development. Brain Structure and Function, 224 (2), 811-827. doi: 10.1007/s00429-018-1801-3 |
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2018 Journal Article Engineering highly functional thermostable proteins using ancestral sequence reconstructionGumulya, Yosephin, Baek, Jong-Min, Wun, Shun-Jie, Thomson, Raine E. S., Harris, Kurt L., Hunter, Dominic J. B., Behrendorff, James B. Y. H., Kulig, Justyna, Zheng, Shan, Wu, Xueming, Wu, Bin, Stok, Jeanette E., De Voss, James J., Schenk, Gerhard, Jurva, Ulrik, Andersson, Shalini, Isin, Emre M., Bodén, Mikael, Guddat, Luke and Gillam, Elizabeth M. J. (2018). Engineering highly functional thermostable proteins using ancestral sequence reconstruction. Nature Catalysis, 1 (11), 878-888. doi: 10.1038/s41929-018-0159-5 |
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2018 Journal Article SCRAM: a pipeline for fast index-free small RNA read alignment and visualizationFletcher, Stephen J., Boden, Mikael, Mitter, Neena and Carroll, Bernard J. (2018). SCRAM: a pipeline for fast index-free small RNA read alignment and visualization. Bioinformatics, 34 (15), 2670-2672. doi: 10.1093/bioinformatics/bty161 |
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2018 Journal Article Effect of Binding on Enantioselectivity of Epoxide HydrolaseZaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018). Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 (3), 630-640. doi: 10.1021/acs.jcim.7b00353 |
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2017 Journal Article Learning epistatic interactions from sequence-activity data to predict enantioselectivityZaugg, Julian, Gumulya, Yosephine, Malde, Alpeshkumar K and Bodén, Mikael (2017). Learning epistatic interactions from sequence-activity data to predict enantioselectivity. Journal of computer-aided molecular design, 31 (12), 1085-1096. doi: 10.1007/s10822-017-0090-x |
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2017 Journal Article NLSdb-major update for database of nuclear localization signals and nuclear export signalsBernhofer, Michael, Goldberg, Tatyana, Wolf, Silvana, Ahmed, Mohamed, Zaugg, Julian, Boden, Mikael and Rost, Burkhard (2017). NLSdb-major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Research, 46 (D1), D503-D508. doi: 10.1093/nar/gkx1021 |
