Associate Professor Mikael Boden
Associate Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
Affiliate Research Fellow
Institute for Molecular Bioscience
| Featured projects | Duration |
|---|---|
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Deciphering the epitranscriptome machinery using direct native RNA sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2021 |
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High-throughput sequencing of protein variant libraries Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2023 |
Book Chapters
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
Zaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. Directed evolution library creation: methods and protocols. (pp. 315-333) edited by Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-1053-3_21
Tino, P., Hammer, B. and Boden, M. (2007). Markovian bias of neural-based architectures with feedback connections. Perspectives of Neural-Symbolic Integration. (pp. 95-133) edited by Hammer, B. and Hitzler, P.. Heidelberg, Germany: Springer-Verlag. doi: 10.1007/978-3-540-73954-8_5
Wiles, J. H., Blair, A. D. and Boden, M. B. (2001). Representation beyond finite states: Alternatives to pushdown automata. A Field Guide to Dynamical Recurrent Networks. (pp. 129-142) edited by J.J. Kolen and S.C. Kremer. Piscataway, New Jersey, U.S.A.: IEEE.
Journal Articles
Joshi, 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
Prabhu, 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) ARTN ycae067. doi: 10.1093/ismeco/ycae067
Teshima, 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
Balderson, Brad, Fane, Mitchell, Harvey, Tracey J, Piper, Michael, Smith, Aaron and Bodén, Mikael (2024). Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Briefings in Functional Genomics. doi: 10.1093/bfgp/elad055
Balderson, 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
Sun, 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
Afonso, 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
Bayaraa, 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
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
Lv, 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
Harris, 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
Yaghmaeian 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
Mora, 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
Wilson, 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
Newell, 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
Kojic, 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
Shim, 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
Lai, 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
O’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
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
Fraser, 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
Horsefield, 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
Foley, 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
Sützl, 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
Littmann, 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
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
Fraser, 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
Gumulya, 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
Fletcher, 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
Zaugg, 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
Zaugg, 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
Bernhofer, 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
Essebier, 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
Patrick, 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
Williams, 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
Patrick, 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
O'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
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
Essebier, 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
Cao, 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
Huang, 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
Fraser, 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
Cao, 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
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
Roona, 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
Patrick, 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
Chang, Chiung-Wen, Couñago, Rafael, Williams, Simon, Bodén, Mikael and Kobe, Boštjan (2014). Importin alpha and nonclassical nuclear localization signal. Acta Crystallographica Section A Foundations and Advances, 70 (a1), C1634-C1634. doi: 10.1107/s205327331408365x
Mazgut, 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
Mehdi, Ahmed M., Patrick, Ralph, Bailey, Timothy L. and Boden, Mikael (2014). Predicting the dynamics of protein abundance. Molecular and Cellular Proteomics, 13 (5), 1330-1340. doi: 10.1074/mcp.M113.033076
Cao, Minh Duc, Tasker, Edward, Willadsen, Kai, Imelfort, Michael, Vishwanathan, Sailaja, Sureshkumar, Sridevi, Balasubramanian, Sureshkumar and Bodén, Mikael (2014). Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Research, 42 (3) ARTN e16, e16.1-e16.11. doi: 10.1093/nar/gkt1313
Chang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2013). Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α. Traffic, 14 (11), 1144-1154. doi: 10.1111/tra.12098
Oyarzun, Patricio, Ellis, Jonathan J., Boden, Mikael and Kobe, Bostjan (2013). PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinformatics, 14 (1) 52, 52. doi: 10.1186/1471-2105-14-52
Willadsen, Kai, Minh Duc Cao, Wiles, Janet, Balasubramanian, Sureshkumar and Boden, Mikael (2013). Repeat-encoded poly-Q tracts show statistical commonalities across species. Bmc Genomics, 14 (1) 76, 76.1-76.10. doi: 10.1186/1471-2164-14-76
Chang, Chiung-Wen, Counago, Rafael Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2013). The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site in plant nuclear import factor importin-α. Plant Signaling and Behavior, 8 (10), e25976.1-e25976.6. doi: 10.4161/psb.25976
Mehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2013). DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. Bioinformatics, 29 (1), 39-46. doi: 10.1093/bioinformatics/bts654
Chang, Chiung-Wen, Counago, Rafael Lemos Miguez, Williams, Simon J., Boden, Mikael and Kobe, Bostjan (2012). Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signals. Plant Cell, 24 (12), 5074-5088. doi: 10.1105/tpc.112.104422
Willadsen, Kai, Mohamad, Nurul and Boden, Mikael (2012). NSort/DB: an intra-nuclear compartment protein database. Genomics, Proteomics & Bioinformatics, 10 (4), 226-229. doi: 10.1016/j.gpb.2012.07.001
Kobe, Bostjan and Boden, Mikael (2012). Computational modelling of linear motif-mediated protein interactions. Current Topics in Medicinal Chemistry, 12 (14), 1553-1561. doi: 10.2174/156802612802652439
Patrick, Ralph, Cao, Kim-Anh L., Davis, Melissa, Kobe, Bostjan and Bodén, Mikael (2012). Mapping the stabilome: a novel computational method for classifying metabolic protein stability. BMC Systems Biology, 6 (1) 60, 60.1-60.15. doi: 10.1186/1752-0509-6-60
Madala, Praveen K., Fairlie, David P. and Bodén, Mikael (2012). Matching cavities in G protein-coupled receptors to infer ligand-binding sites. Journal of Chemical Information and Modeling, 52 (5), 1401-1410. doi: 10.1021/ci2005498
Marfori, Mary, Mynott, Andrew, Ellis, Jonathan J., Mehdi, Ahmed M., Saunders, Neil F. W., Curmi, Paul M., Forwood, Jade K., Bodén, Mikael and Kobe, Bostjan (2011). Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochimica et Biophysica Acta (BBA): Molecular Cell Research, 1813 (9), 1562-1577. doi: 10.1016/j.bbamcr.2010.10.013
Bauer, Denis C., Willadsen, Kai, Buske, Fabian A., Lê Cao, Kim-Anh, Bailey, Timothy L., Dellaire, Graham and Bodén, Mikael (2011). Sorting the nuclear proteome. Bioinformatics, 27 (13) btr217, i7-i14. doi: 10.1093/bioinformatics/btr217
Mehdi, Ahmed M., Sehgal, Muhammad Shoaib B., Kobe, Bostjan, Bailey, Timothy L. and Boden, Mikael (2011). A probabilistic model of nuclear import of proteins. Bioinformatics, 27 (9) btr121, 1239-1246. doi: 10.1093/bioinformatics/btr121
You, Liwen, Brusic, Vladimir, Gallagher, Marcus and Boden, Mikael (2010). Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomes. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 7 (4) 4695825, 741-751. doi: 10.1109/TCBB.2008.131
Bauer, Denis C., Buske, Fabian A., Bailey, Timothy L. and Boden, Mikael (2010). Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. Neurocomputing, 73 (13-15), 2300-2307. doi: 10.1016/j.neucom.2010.01.022
Mohamad, Nurul and Bodén, Mikael (2010). The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression. BMC Systems Biology, 4 (44) 44, 1-12. doi: 10.1186/1752-0509-4-44
Bailey, Timothy L., Bodén, Mikael, Whitington, Tom and Machanick, Philip (2010). The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics, 11 (179) 179, 1-14. doi: 10.1186/1471-2105-11-179
Buske, Fabian A., Boden, Mikael, Bauer, Denis C. and Bailey, Timothy L. (2010). Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics, 26 (7) btq049, 860-866. doi: 10.1093/bioinformatics/btq049
Boden, Mikael, Dellaire, Graham, Burrage, Kevin and Bailey, Timothy L. (2010). A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies. Journal of Computational Biology, 17 (4), 617-630. doi: 10.1089/cmb.2009.0140
Buske, Fabian A., Their, Ricarda, Gillam, Elizabeth M. J. and Boden, Mikael (2009). In silico characterization of protein chimeras: Relating sequence and function within the same fold. Proteins: Structure, Function, and Bioinformatics, 77 (1), 111-120. doi: 10.1002/prot.22422
Buske, Fabian A., Maetschke, Stefan and Boden, Mikael (2009). It's about time: Signal recognition in staged models of protein translocation. Pattern Recognition, 42 (4), 567-574. doi: 10.1016/j.patcog.2008.09.020
Bailey, T. L., Boden, M. B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J. Y., Li, W. W. and Noble, W. S. (2009). MEME suite: Tools for motif discovery and searching. Nucleic Acids Research, 37 (Suppl. 2), W202-W208. doi: 10.1093/nar/gkp335
Boden, M. and Teasdale, R. D. (2008). Determining nucleolar association from sequence by leveraging protein-protein interactions. Journal of Computational Biology, 15 (3), 291-304. doi: 10.1089/cmb.2007.0163
Boden, M. and Bailey, T. L. (2008). Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Research, 36 (12), 4108-4117. doi: 10.1093/nar/gkn374
Goodhill, Geoff, Baker, Curtis, Balasubramanian, Vijay, Bazhenov, Maxim, Beck, Jeffrey, Becker, Sue, Bethge, Matthias, Boahen, Kwabena, Boden, Mikael, Bonin, Vincent, Bouret, Sebastien, Fairhall, Adrienne, Flash, Tamar, French, Robert, Gillies, Andrew, Gollisch, Tim, Gurney, Kevin, Gutkin, Boris, Hayhoe, Mary, Hunt, Jonathan, Ibbotson, Michael, Kepecs, Adam, Kingdom, Fred, Kropff, Emilio, Longden, Kit, Marder, Eve, Miikkulainen, Risto, Oliva, Aude, Olshausen, Bruno ... Zhaoping, Li (2008). Network: Computation in Neural Systems: Editorial. Network: Computation in Neural Systems, 19 (1), 1-2. doi: 10.1080/09548980801915409
Suksawatchon, J., Lursinsap, C. and Boden, M. (2007). Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programming. Journal of Bioinformatics and Computational Biology, 5 (1), 117-133. doi: 10.1142/S0219720007002552
Boden, Marie and Boden, Mikael (2007). Evolving spelling exercises to suit individual student needs. Applied Soft Computing, 7 (1), 126-135. doi: 10.1016/j.asoc.2005.03.001
Hawkins, J., Mahony, D., Maetschke, S., Wakabayashi, M., Teasdale, R. D. and Boden, M. (2007). Identifying novel peroxisomal proteins. Proteins: Structure Function and Bioinformatics, 69 (3), 606-616. doi: 10.1002/prot.21420
Hawkins, John, Davis, Lynne and Boden, Mikael (2007). Predicting Nuclear Localization. Journal of Proteome Research, 6 (4), 1402-1409. doi: 10.1021/pr060564n
Hawkins, John and Boden, Mikael (2006). Detecting and sorting targeting peptides wtih neural networks and support vector machines. Journal of Bioinformatics and Computational Biology, 4 (1), 1-18. doi: 10.1142/S0219720006001771
Bauer, Denis C., Boden, Mikael, Thier, Ricarda and Gillam, Elizabeth M. (2006). STAR: predicting recombination sites from amino acid sequence. BMC Bioinformatics, 7 (437) 437, 437. doi: 10.1186/1471-2105-7-437
Boden, M., Yuan, Z. and Bailey, T. L. (2006). Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. Bmc Bioinformatics, 7 (68) 68, 1-12. doi: 10.1186/1471-2105-7-68
Yuan, Z., Zhang, F. S., Davis, M. J., Boden, M. and Teasdale, R. D. (2006). Predicting the solvent accessibility of transmembrane residues from protein sequence. Journal of Proteome Research, 5 (5), 1063-1070. doi: 10.1021/pr050397b
Boden, M. and Bailey, T. L. (2006). Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics, 22 (15), 1809-1814. doi: 10.1093/bioinformatics/btl198
Boden, Mikael and Hawkins, John (2005). Prediction of subcellular localization using sequence-biased recurrent networks. Bioinformatics, 21 (10), 2279-2286. doi: 10.1093/bioinformatics/bti372
Boden, Mikael and Hawkins, John (2005). Improved Access To Sequential Motifs: A Note On The Architectural Bias Of Recurrent Networks. IEEE Transactions on Neural Networks, 16 (2), 491-494. doi: 10.1109/TNN.2005.844086
Hawkins, J. and Boden, M. (2005). The applicability of recurrent neural networks for biological sequence analysis. IEEE-ACM Transactions on Computational Biology and Bioinformatiocs, 2 (3), 243-253. doi: 10.1109/TCBB.2005.44
Boden, Mikael (2004). Generalization by symbolic abstraction in cascaded recurrent networks. Neurocomputing, 57 (1-4), 87-104. doi: 10.1016/j.neucom.2004.01.006
Boden, M. and Blair, A. (2003). Learning the dynamics of embedded clauses. Applied Intelligence, 19 (1-2), 51-63. doi: 10.1023/A:1023816706954
Boden, Mikael and Wiles, Janet (2002). On learning context-free and context-sensitive languages. IEEE Transactions on Neural Networks, 13 (2), 491-493. doi: 10.1109/72.991436
Boden, Mikael and Wiles, Janet (2000). Context-free and context-sensitive dynamics in recurrent neural networks. Connection Science: journal of neural computing, artificial intelligence, and cognitive research, 12 (3-4), 197-210. doi: 10.1080/095400900750060122
Boden, Mikael and Niklasson, Lars (2000). Semantic systematicity and context in connectionist networks. Connection Science, 12 (2), 111-142. doi: 10.1080/09540090050129754
Boden, MB and Niklasson, LF (1993). Connectionism. Artificial Intelligence Review, 7 (5), 259-260. doi: 10.1007/BF00849053
Conference Papers
Tule, Sanjana, Foley, Gabriel, Zhao, Chongting, Forbes, Michael and Bodén, Mikael (2024). Optimal phylogenetic reconstruction of insertion and deletion events. 32nd International Conference on Intelligent Systems for Molecular Biology 2024, Montreal, QC Canada, 12-16 July 2024. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/bioinformatics/btae254
Afonso, 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
Harvey, 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
Mazgut, Jakub, Tino, Peter, Boden, Mikael and Yan, Hong (2010). Multilinear decomposition and topographic mapping of binary tensors. 20th International Conference on Artificial Neural Networks (ICANN 2010), Thessaloniki, Greece, 15-18 September 2010. Heidelberg, Germany: Springer. doi: 10.1007/978-3-642-15819-3_42
Arieshanti, I., Boden, M., Maetschke, S and Buske, F. A. (2009). Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2009, Nashville, Tennessee, U.S.A., 30 March - 2 April , 2009. United States of America: IEEE. doi: 10.1109/CIBCB.2009.4925706
Bauer, Denis C., Buske, Fabian A. and Boden, Mikael (2008). Predicting SUMOylation sites. 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, Melbourne, Australia, 15-17 October, 2008. Berlin, Germany: Springer-Verlag Berlin. doi: 10.1007/978-3-540-88436-1-3
Buske, Fabian and Boden, Mikael (2007). Decoupling signal recognition from sequence models of protein secretion. Computational Models for Life Sciences - CMLS'07, Gold Coast, QLD, Australia, 17 - 19 December 2007. Melville, NY, U.S.A.: American Institute of Physics. doi: 10.1063/1.2816618
Dufton, L. and Boden, M. (2007). Reducing the number of support vectors to allay inefficiency of large-scale models in computational biology. Computational Models for Life Sciences - CMLS'07, Queensland, Australia, 17-19 December, 2007. New York: American Institute of Physics. doi: 10.1063/1.2816639
Bodén, Mikael (2007). Predicting nucleolar proteins using support-vector machines. 6th Asia-Pacific Bioinformatics Conference, Kyoto, Japan, 14-17 January, 2008. London, U.K.: Imperial College Press. doi: 10.1142/9781848161092_0005
Maetschke, S., Gallagher, M. and Boden, M. (2007). A comparison of sequence kernels for localization prediction of transmembrane proteins. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2007 (CIBCB 2007), Honolulu, Hawaii, 1-5 April 2007. Piscataway, NJ, U.S.A.: IEEE - Institute of Electrical Electronics Engineers Inc.. doi: 10.1109/cibcb.2007.4221246
You, L., Zhang, P., Boden, M. and Brusic, V. (2007). Understanding prediction systems for HLA-binding peptides and t-cell epitope identification. Pattern Recognition in Bioinformatics (PRIB 2007), Singapore, 1-2 October 2007. Heidelberg, Germany: Springer. doi: 10.1007/978-3-540-75286-8_32
Maetschke, S. R., Boden, M B and Gallagher, M R (2006). Higher order HMMs for localization prediction of transmembrance proteins. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia, 4 December, 2006. New South Wales, Australia: Australian Computer Society Inc..
Hawkins, J. and Boden, M. (2006). Multi-stage redundancy reduction: effective utilisation of small protein data sets. Intelligent Systems for Bioinformatics 2006, Hobart, Australia, 4 December, 2006. New South Wales, Australia: Australian Computer Society Inc..
Davis, L., Hawkins, J. C., Maetschke, S. R. and Boden, M B (2006). Comparing SVM sequence kernels: A protein subcellular localization theme. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Tas, Australia, 4 December, 2006. New South Wales, Australia: Australian Computer Society Inc..
Boden, M. B. and Hawkins, J. C. (2006). Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway. 2006 IEEE Congress on Evolutionary Computation, Vancouver, BC, Canada, 16-21 July, 2006. Piscataway, N.J., USA: IEEE. doi: 10.1109/cec.2006.1688653
Bauer, Denis C., Bodén, Mikael, Thier, Ricarda and Yuan, Zheng (2005). Predicting structural disruption of proteins caused by crossover. IEEE Computer Society. doi: 10.1109/cibcb.2005.1594962
Suksawatchon, J., Lursinsap, C. and Bodén, M. (2005). Heuristic algorithm for computing reversal distance with multigene families via binary integer programming. IEEE Computer Society. doi: 10.1109/cibcb.2005.1594916
Hawkins, John and Bodén, Mikael (2005). Predicting peroxisomal proteins. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05, , , November 14, 2005-November 15, 2005. IEEE Computer Society. doi: 10.1109/cibcb.2005.1594956
Boden, M. B. and Hawkins, J. C. (2005). Detecting residues in targeting peptides. 3rd Asia-Pacific Bioinformatics Conference, Singapore, 17-21 January, 2005. London, United Kingdom: Imperial College Press. doi: 10.1142/9781860947322_0013
Maetschke, S. R., Towsey, M. and Boden, M. B. (2005). BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. 3rd Asia Pacific Bioinformatics Conference, Singapore, 17-21 January 2005. London, UK: Imperial College Press. doi: 10.1142/9781860947322_0014
Hawkins, J. C. and Boden, M. B. (2005). Predicting peroxisomal proteins. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, USA, 14-15 November, 2005. Piscataway, NJ, USA: IEEE Press.
Suksawatchon, J., Lursinsap, C. and Boden, M. B. (2005). Heuristic algorithm for computing reversal distance with multigene families via binary integer programming. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, U.S.A., 14-15 November 2005. Piscataway, NJ, U.S.A.: IEEE Press.
Bauer, Denis C., Boden, Mikael, Thier, Ricarda and Yuan, Zheng (2005). Predicting structural disruption of proteins caused by crossover. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, U.S.A., 14-15 November 2005. Piscataway, NJ, U.S.A.: IEEE Press.
Wakabayashi, M., Hawkins, J. C., Maetschke, S. R. and Boden, M. B. (2005). Exploiting sequence dependencies in the prediction of peroxisomal proteins. Intelligent Data Engineering and Automated Learning - IDEAL2005, Brisbane, Australia, 6-8 July 2005. Berlin, Germany: Springer-Verlag. doi: 10.1007/11508069_59
Boden, M. B. (2003). Using evolutionary noise to improve prediction of rapidly evolving targeting peptides. 2003 Congress on Evolutionary Computation, Canberra, 8-12 December, 2003. Australia: The Institute of Electrical and Electronics Engineers. doi: 10.1109/CEC.2003.1299446
Boden, M. B., Wiles, J. H., Tonkes, B. and Blair, A. D. (1999). On the ability of recurrent nets to learn deeply embedded structures. IJCAI'99, Stockholm, 31 July - 6 August 1999. Stockholm: IJCAII.
Ziemke, T., Carlsson, J. and Boden, M. (1999). An experimental comparison of weight evolution in neural control architectures for a 'Garbage-Collecting' Khepera robot. 1st International Khepera Workshop, Paderborn, Germany, 10-11 December 1999. Paderborn, Germany: HNI-Verlagsschrittenreihe.
Niklasson, L. and Boden, M. B. (1999). Content, context and connectionist networks. 21st Annual Meeting of the Cognitive Science Society, Vancouver, August 1999. New York, NY, United States: Lawrence Erlbaum.
Boden, M. B., Wiles, J. H., Tonkes, B. and Blair, A. D. (1999). Learning to predict a context-free language: Analysis of dynamics in recurrent hidden units. ICANN'99, Edinburgh, Scotland, 7-10 September, 1999. London, United Kingdom: IEE. doi: 10.1049/cp:19991135
Bodén, Mikael (1996). A connectionist variation on inheritance. 1996 International Conference on Artificial Neural Networks, ICANN 1996, , , July 16, 1996-July 19, 1996. Springer Verlag. doi: 10.1007/3-540-61510-5_62
Boden, M and Niklasson, L (1995). Features of distributed representations for tree-structures: A study of RAAM. Swedish Conference on Connectionism, Skovde Sweden, Mar 02-03, 1995. MAHWAH: LAWRENCE ERLBAUM ASSOC PUBL.
Bodén, Mikael and Narayanan, Ajit (1993). A Representational Architecture for Nonmonotonic Inheritance Structures. ICANN 1993: International Conference on Artificial Neural Networks, Amsterdam, The Netherlands, 13-16 September, 1993. London, United Kingdom: Springer London. doi: 10.1007/978-1-4471-2063-6_79