|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
2017 Journal Article Bioinformatics approaches to predict target genes from transcription factor binding dataEssebier, Alexandra, Lamprecht, Marnie, Piper, Michael and Bodén, Mikael (2017). Bioinformatics approaches to predict target genes from transcription factor binding data. Methods (San Diego, Calif.), 131, 111-119. doi: 10.1016/j.ymeth.2017.09.001 |
|
2017 Journal Article PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylationPatrick, Ralph, Kobe, Bostjan, Lê Cao, Kim-Anh and Bodén, Mikael (2017). PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. Bioinformatics, 33 (12), 1773-1781. doi: 10.1093/bioinformatics/btx072 |
|
2016 Journal Article Structure and function of the TIR domain from the grape NLR protein RPV1Williams, Simon J., Yin, Ling, Foley, Gabriel, Casey, Lachlan W., Outram, Megan A., Ericsson, Daniel J., Lu, Jiang, Boden, Mikael, Dry, Ian B. and Kobe, Bostjan (2016). Structure and function of the TIR domain from the grape NLR protein RPV1. Frontiers in Plant Science, 7 (DECEMBER2016) 1850, 1850. doi: 10.3389/fpls.2016.01850 |
|
2016 Journal Article Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequencePatrick, Ralph, Horin, Coralie, Kobe, Bostjan, Cao, Kim-Anh Le and Bodén, Mikael (2016). Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence. Biochimica et Biophysica Acta, 1864 (11), 1599-1608. doi: 10.1016/j.bbapap.2016.08.001 |
|
2016 Journal Article CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq dataO'Connor, Timothy, Boden, Mikael and Bailey, Timothy L. (2016). CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data. Nucleic Acids Research, 45 (4), e19. doi: 10.1093/nar/gkw956 |
|
2016 Journal Article Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-alpha (vol 14, pg 1144, 2013)Chang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2016). Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-alpha (vol 14, pg 1144, 2013). Traffic, 17 (6), 704-704. doi: 10.1111/tra.12395 |
|
2016 Journal Article Statistical enrichment of epigenetic states around triplet repeats that can undergo expansionsEssebier, Alexandra, Wolf, Patricia Vera, Cao, Minh Duc, Carroll, Bernard J., Balasubramanian, Sureshkumar and Boden, Mikael (2016). Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions. Frontiers in Neuroscience, 10 (MAR) 92, 92.1-92.12. doi: 10.3389/fnins.2016.00092 |
|
2016 Journal Article Robust estimation of evolutionary distances with information theoryCao, Minh Duc, Allison, Lloyd, Dix, Trevor I. and Boden, Mikael (2016). Robust estimation of evolutionary distances with information theory. Molecular Biology and Evolution, 33 (5), 1349-1357. doi: 10.1093/molbev/msw019 |
