The University of Queensland

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

Computational tools for directed evolution: a comparison of prospective and retrospective strategies

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

Markovian bias of neural-based architectures with feedback connections

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

Representation beyond finite states: Alternatives to pushdown automata

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.

Development of a Highly Selective NAD+‐Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell‐Free Enzyme Cascades

Teshima, Mariko, Sutiono, Samuel, Döring, Manuel, Beer, Barbara, Boden, Mikael, Schenk, Gerhard and Sieber, Volker (2023). Development of a Highly Selective NAD+‐Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell‐Free Enzyme Cascades. ChemSusChem. doi: 10.1002/cssc.202301132

Cytocipher determines significantly different populations of cells in single cell RNA-seq data

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

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

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

Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle

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

Structural and functional insight into the mechanism of the Fe‐S cluster‐dependent dehydratase from Paralcaligenes ureilyticus

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

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

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

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

Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates

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

Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes

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

Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2

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

Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid

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

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

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

Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype

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

Conserved epigenetic regulatory logic infers genes governing cell identity

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

Evolutionary model of protein secondary structure capable of revealing new biological relationships

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

T-Gene: improved target gene prediction

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

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

Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development

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

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

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

SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications

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

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases

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

Detailed prediction of protein sub-nuclear localization

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

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

Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development

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

Engineering highly functional thermostable proteins using ancestral sequence reconstruction

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

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization

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

Effect of Binding on Enantioselectivity of Epoxide Hydrolase

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

Learning epistatic interactions from sequence-activity data to predict enantioselectivity

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

NLSdb-major update for database of nuclear localization signals and nuclear export signals

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

Bioinformatics approaches to predict target genes from transcription factor binding data

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

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

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

Structure and function of the TIR domain from the grape NLR protein RPV1

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

Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

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

CISMAPPER: predicting regulatory interactions from transcription factor ChIP-seq data

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

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

Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions

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

Robust estimation of evolutionary distances with information theory

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

ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries

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

Cell-type-specific expression of NFIX in the developing and adult cerebellum

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

Sequencing technologies and tools for short tandem repeat variation detection

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

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

Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation

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

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

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

Importin alpha and nonclassical nuclear localization signal

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

Dimensionality reduction and topographic mapping of binary tensors

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

Predicting the dynamics of protein abundance

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

Inferring short tandem repeat variation from paired-end short reads

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), e16.1-e16.11. doi: 10.1093/nar/gkt1313

Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α

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

PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

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

Repeat-encoded poly-Q tracts show statistical commonalities across species

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

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

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

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

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

Crystal structure of rice importin-alpha and structural basis of its interaction with plant-specific nuclear localization signals

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

NSort/DB: an intra-nuclear compartment protein database

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

Computational modelling of linear motif-mediated protein interactions

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

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

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

Matching cavities in G protein-coupled receptors to infer ligand-binding sites

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

Molecular basis for specificity of nuclear import and prediction of nuclear localization

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

Sorting the nuclear proteome

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

A probabilistic model of nuclear import of proteins

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

Using Gaussian process with test rejection to detect T-Cell epitopes in pathogen genomes

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

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

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

The proteins of intra-nuclear bodies: A data-driven analysis of sequence, interaction and expression

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

The value of position-specific priors in motif discovery using MEME

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

A bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies

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

Assigning roles to DNA regulatory motifs using comparative genomics

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

In silico characterization of protein chimeras: Relating sequence and function within the same fold

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

It's about time: Signal recognition in staged models of protein translocation

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

MEME suite: Tools for motif discovery and searching

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

Determining nucleolar association from sequence by leveraging protein-protein interactions

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

Associating transcription factor-binding site motifs with target GO terms and target genes

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

Network: Computation in Neural Systems: Editorial

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

Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programming

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

Evolving spelling exercises to suit individual student needs

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

Identifying novel peroxisomal proteins

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

Predicting Nuclear Localization

Hawkins, John, Davis, Lynne and Boden, Mikael (2007). Predicting Nuclear Localization. Journal of Proteome Research, 6 (4), 1402-1409. doi: 10.1021/pr060564n

Detecting and sorting targeting peptides wtih neural networks and support vector machines

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

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

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

Predicting the solvent accessibility of transmembrane residues from protein sequence

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

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

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

STAR: predicting recombination sites from amino acid sequence

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

Prediction of subcellular localization using sequence-biased recurrent networks

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

Improved Access To Sequential Motifs: A Note On The Architectural Bias Of Recurrent Networks

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

The applicability of recurrent neural networks for biological sequence analysis

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

Generalization by symbolic abstraction in cascaded recurrent networks

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

Learning the dynamics of embedded clauses

Boden, M. and Blair, A. (2003). Learning the dynamics of embedded clauses. Applied Intelligence, 19 (1-2), 51-63. doi: 10.1023/A:1023816706954

On learning context-free and context-sensitive languages

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

Context-free and context-sensitive dynamics in recurrent neural networks

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

Semantic systematicity and context in connectionist networks

Boden, Mikael and Niklasson, Lars (2000). Semantic systematicity and context in connectionist networks. Connection Science, 12 (2), 111-142. doi: 10.1080/09540090050129754

Connectionism

Boden, MB and Niklasson, LF (1993). Connectionism. Artificial Intelligence Review, 7 (5), 259-260. doi: 10.1007/BF00849053

553. H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle

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). 553. H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle. The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_553

Common regulatory targets of NFIA and NFIX mediate postnatal cerebellar development

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

Multilinear decomposition and topographic mapping of binary tensors

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

Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes

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

Predicting SUMOylation sites

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

A comparison of sequence kernels for localization prediction of transmembrane proteins

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

Decoupling signal recognition from sequence models of protein secretion

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

Predicting nucleolar proteins using support-vector machines

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

Reducing the number of support vectors to allay inefficiency of large-scale models in computational biology

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

Understanding prediction systems for HLA-binding peptides and t-cell epitope identification

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

Comparing SVM sequence kernels: A protein subcellular localization theme

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..

Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway

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

Higher order HMMs for localization prediction of transmembrance proteins

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..

Multi-stage redundancy reduction: effective utilisation of small protein data sets

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..

Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

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

Predicting peroxisomal proteins

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

Predicting structural disruption of proteins caused by crossover

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

BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction

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

Detecting residues in targeting peptides

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

Exploiting sequence dependencies in the prediction of peroxisomal proteins

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

Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

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.

Predicting peroxisomal proteins

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.

Predicting structural disruption of proteins caused by crossover

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.

Using evolutionary noise to improve prediction of rapidly evolving targeting peptides

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

An experimental comparison of weight evolution in neural control architectures for a 'Garbage-Collecting' Khepera robot

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.

Content, context and connectionist networks

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.

Learning to predict a context-free language: Analysis of dynamics in recurrent hidden units

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

On the ability of recurrent nets to learn deeply embedded structures

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.

A connectionist variation on inheritance

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

Features of distributed representations for tree-structures: A study of RAAM

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.

A Representational Architecture for Nonmonotonic Inheritance Structures

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

Proceedings of the A1 2006 Workshop on Intelligent Systems of Bioinformatics (WISB 2006)

Mikael Boden and Timothy L. Bailey eds. (2006). Proceedings of the A1 2006 Workshop on Intelligent Systems of Bioinformatics (WISB 2006). Intelligent Systems for Bioinformatics 2006, Hobart, Australia, 4 December, 2006. New South Wales, Australia: Australian Computer Society Inc..