|
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 |
|
2016 Journal Article ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein librariesHuang, Weiliang, Johnston, Wayne A., Boden, Mikael and Gillam, Elizabeth M.J. (2016). ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries. BioTechniques, 60 (2), 91-94. doi: 10.2144/000114381 |
|
2016 Journal Article Cell-type-specific expression of NFIX in the developing and adult cerebellumFraser, James, Essebier, Alexandra, Gronostajski, Richard M., Boden, Mikael, Wainwright, Brandon J., Harvey, Tracey J. and Piper, Michael (2016). Cell-type-specific expression of NFIX in the developing and adult cerebellum. Brain Structure and Function, 222 (5), 1-20. doi: 10.1007/s00429-016-1340-8 |
|
2015 Journal Article Sequencing technologies and tools for short tandem repeat variation detectionCao, Minh Duc, Balasubramanian, Sureshkumar and Boden, Mikael (2015). Sequencing technologies and tools for short tandem repeat variation detection. Briefings in Bioinformatics, 16 (2) bbu001, 193-204. doi: 10.1093/bib/bbu001 |
|
2015 Journal Article A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases.Oyarzun, Patricio, Ellis, Jonathan J., Gonzalez-Galarza, Faviel F., Jones, Andrew R, Middleton, Derek, Boden, Mikael and Kobe, Bostjan (2015). A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases.. Vaccine, 33 (10), 1267-1273. doi: 10.1016/j.vaccine.2015.01.040 |
|
2014 Journal Article Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylationRoona, Gergely, Borsos, Mate, Ellis, Jonathan J., Mehdi, Ahmed M., Christie, Mary, Koornyei, Zsuzsanna, Neubrandt, Mate, Tooth, Judit, Bozooky, Zoltan, Buday, Laszlo, Madaraasz, Emilia, Bodaen, Mikael, Kobe, Bostjan and Veertessy, Beata G. (2014). Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle, 13 (22), 3551-3564. doi: 10.4161/15384101.2014.960740 |
|
2014 Journal Article PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation eventsPatrick, Ralph, Lê Cao, Kim-Anh, Kobe, Bostjan and Bodén, Mikael (2014). PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. Bioinformatics, 31 (3), 382-389. doi: 10.1093/bioinformatics/btu663 |
|
2014 Conference Publication Importin alpha and nonclassical nuclear localization signalChang, Chiung-Wen, Couñago, Rafael, Williams, Simon, Bodén, Mikael and Kobe, Boštjan (2014). Importin alpha and nonclassical nuclear localization signal. XXIII IUCr Congress, Montreal, Canada, 5-12 August 2014. Hoboken, NJ United States: Wiley-Blackwell. doi: 10.1107/s205327331408365x |
|
2014 Journal Article Dimensionality reduction and topographic mapping of binary tensorsMazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2014). Dimensionality reduction and topographic mapping of binary tensors. Pattern Analysis and Applications, 17 (3), 497-515. doi: 10.1007/s10044-013-0317-y |
