Journal Articles
Vo, Tuan, Balderson, Brad, Jones, Kahli, Ni, Guiyan, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Singleton, Matthew, Kojic, Marija, Robertson, Thomas, Walters, Shaun, Mulay, Onkar, Bhuva, Dharmesh D., Davis, Melissa J., Wainwright, Brandon J., Nguyen, Quan and Genovesi, Laura A. (2023). Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition. Genome Medicine, 15 (1) 29. doi: 10.1186/s13073-023-01185-4
Gaik, Monika, Kojic, Marija, Stegeman, Megan R., Öncü‐Öner, Tülay, Kościelniak, Anna, Jones, Alun, Mohamed, Ahmed, Chau, Pak Yan Stefanie, Sharmin, Sazia, Chramiec‐Głąbik, Andrzej, Indyka, Paulina, Rawski, Michał, Biela, Anna, Dobosz, Dominika, Millar, Amanda, Chau, Vann, Ünalp, Aycan, Piper, Michael, Bellingham, Mark C., Eichler, Evan E., Nickerson, Deborah A., Güleryüz, Handan, Abbassi, Nour El Hana, Jazgar, Konrad, Davis, Melissa J., Mercimek‐Andrews, Saadet, Cingöz, Sultan, Wainwright, Brandon J. and Glatt, Sebastian (2022). Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Molecular Medicine, 14 (7) e15608, e15608. doi: 10.15252/emmm.202115608
El-Saafin, Farrah, Bergamasco, Maria I., Chen, Yunshun, May, Rose E., Esakky, Prabagaran, Hediyeh-zadeh, Soroor, Dixon, Mathew, Wilcox, Stephen, Davis, Melissa J., Strasser, Andreas, Smyth, Gordon K., Thomas, Tim and Voss, Anne K. (2022). Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death. Cell Death and Differentiation, 29 (5), 1013-1027. doi: 10.1038/s41418-022-00982-5
Sangar, Michelle L. Cook, Genovesi, Laura A., Nakamoto, Madison W., Davis, Melissa J., Knobluagh, Sue E., Ji, Pengxiang, Millar, Amanda, Wainwright, Brandon J. and Olson, James M. (2017). Inhibition of CDK4/6 by palbociclib significantly extends survival in medulloblastoma patient-derived xenograft mouse models. Clinical Cancer Research, 23 (19), 5802-5813. doi: 10.1158/1078-0432.CCR-16-2943
Lim, Yenkai, Wan, Yunxia, Vagenas, Dimitrios, Ovchinnikov, Dmitry A., Perry, Chris F. L., Davis, Melissa J. and Punyadeera, Chamindie (2016). Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers. BMC Cancer, 16 (1) 749, 1-12. doi: 10.1186/s12885-016-2785-0
Skalamera, Dubravka, Dahmer-Heath, Mareike, Stevenson, Alexander J., Pinto, Cletus, Shah, Esha T., Daignault, Sheena M., Said, Nur Akmarina B. M., Davis, Melissa, Haass, Nikolas K., Williams, Elizabeth D., Hollier, Brett G., Thompson, Erik W., Gabrielli, Brian and Gonda, Thomas J. (2016). Genome-wide gain-of-function screen for genes that induce epithelial-to-mesenchymal transition in breast cancer. Oncotarget, 7 (38), 61000-61020. doi: 10.18632/oncotarget.11314
Shah, Anup D., Inder, Kerry L., Shah, Alok K, Cristino, Alexandre S., McKie, Arthur B., Gabra, Hani, Davis, Melissa J. and Hill, Michelle M. (2016). Integrative analysis of subcellular quantitative proteomics studies reveals functional cytoskeleton membrane-lipid raft interactions in cancer. Journal of Proteome Research, 15 (10), 3451-3462. doi: 10.1021/acs.jproteome.5b01035
Shah, Anup, Chen, David, Boda, Akash R., Foster, Leonard J., Davis, Melissa J. and Hill, Michelle M. (2015). RaftProt: mammalian lipid raft proteome database. Nucleic Acids Research, 43 (D1), D335-D338. doi: 10.1093/nar/gku1131
Mond, Michael, Alexiadis, Maria, Eriksson, Natalie, Davis, Melissa J., Muscat, George E. O., Fuller, Peter J. and Gilfillan, Christopher (2014). Nuclear receptor expression in human differentiated thyroid tumors. Thyroid, 24 (6), 1000-1011. doi: 10.1089/thy.2013.0509
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J., Reverter, Antonio and Ragan, Mark A. (2014). INsPeCT: INtegrative Platform for Cancer Transcriptomics. Cancer Informatics, 13, 59-66. doi: 10.4137/CIN.S13630
Maetschke, Stefan R., Madhamshettiwar, Piyush B., Davis, Melissa J. and Ragan, Mark A. (2014). Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Briefings in Bioinformatics, 15 (2) bbt034, 195-211. doi: 10.1093/bib/bbt034
Genovesi, Laura A., Ng, Ching Ging, Davis, Melissa J., Remke, Marc, Taylor, Michael D., Adams, David J., Rust, Alistair G., Ward, Jerrold M., Ban, Kenneth H., Jenkins, Nancy A., Copeland, Neal G. and Wainwright, Brandon J. (2013). Sleeping Beauty mutagenesis in a mouse medulloblastoma model defines networks that discriminate between human molecular subgroups. Proceedings of the National Academy of Sciences of the United States of America, 110 (46), E4325-E4334. doi: 10.1073/pnas.1318639110
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J. and Ragan, Mark A. (2013). RMaNI: Regulatory module network inference framework. BMC Bioinformatics, 14 (Suppl. 16) S14, S14.1-S14.10. doi: 10.1186/1471-2105-14-S16-S14
Fearnley, Liam, Davis, Melissa, Ragan, Mark A. and Nielsen, Lars K. (2013). Extracting reaction networks from databases-opening Pandora's box. Briefings in Bioinformatics, 15 (6), 973-983. doi: 10.1093/bib/bbt058
Davis, Melissa J. and Ragan, Mark A. (2013). Understanding cellular function and disease with comparative pathway analysis. Genome Medicine, 5 (7) 64, 64.1-64.2. doi: 10.1186/gm468
Primmer, C. R., Papakostas, S., Leder, E. H., Davis, M. J. and Ragan, M. A. (2013). Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology, 22 (12), 3216-3241. doi: 10.1111/mec.12309
Inder, Kerry L., Davis, Melissa and Hill, Michelle M. (2013). Ripples in the pond - using a systems approach to decipher the cellular functions of membrane microdomains. Molecular Biosystems, 9 (3), 330-338. doi: 10.1039/c2mb25300c
Wang, Chenwei, Taciroglu, Alperen, Maetschke, Stefan R., Nelson, Colleen C., Ragan, Mark A. and Davis, Melissa J. (2012). mCOPA: analysis of heterogeneous features in cancer expression data. Journal of Clinical Bioinformatics, 2 (1) 22, 22.1-22.11. doi: 10.1186/2043-9113-2-22
Gonzalez, Ignacio, Le Cao, Kim-Anh, Davis, Melissa J. and Dejean, Sebastien (2012). Visualising associations between paired 'omics' data sets. BioData Mining, 5 (1) 19, 1-23. doi: 10.1186/1756-0381-5-19
Collins, Brett, Davis, Melissa, Hancock, John F. and Parton, Robert G. (2012). Structure-based reassessment of the caveolin signalling model: Do caveolae regulate signaling through caveolin-protein interactions. Developmental Cell, 23 (1), 11-20. doi: 10.1016/j.devcel.2012.06.012
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
Madhamshettiwar, Piyush B., Maetschke, Stefan R., Davis, Melissa J., Reverter, Antonio and Ragan, Mark A. (2012). Gene regulatory network inference: Evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Medicine, 4 (5) 41, 41.1-41.15. doi: 10.1186/gm340
Inder, Kerry L., Zheng, Yu Zi, Davis, Melissa J., Moon, Hyeongsun, Loo, Dorothy, Nguyen, Hien, Clements, Judith A., Parton, Robert G., Foster, Leonard J. and Hill, Michelle M. (2012). Expression of PTRF in PC-3 cells modulates cholesterol dynamics and the actin cytoskeleton impacting secretion pathways. Molecular and Cellular Proteomics, 11 (2) M111.012245, M111.012245. doi: 10.1074/mcp.M111.012245
Maetschke, Stefan R., Simonsen, Martin, Davis, Melissa J. and Ragan, Mark A. (2012). Gene Ontology-driven inference of protein-protein interaction using inducers. Bioinformatics, 28 (1) btr610, 69-75. doi: 10.1093/bioinformatics/btr610
Davis, Melissa J., Shin, Chang Jin, Jing, Ning and Ragan, Mark A. (2012). Rewiring the dynamic interactome. Molecular Biosystems, 8 (8), 2054-2066. doi: 10.1039/c2mb25050k
Alexiadis, Maria, Eriksson, Natalie, Jamieson, Stacey, Davis, Melissa, Drummond, Ann E., Chu, Simon, Clyne, Colin D., Muscat, George E. and Fuller, Peter J. (2011). Nuclear receptor profiling of ovarian granulosa cell tumors. Hormones and Cancer, 2 (3), 157-169. doi: 10.1007/s12672-011-0069-3
Davis, Melissa J., Sehgal, Muhammad Shoaib B. and Ragan, Mark A. (2010). Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics, 11 (1) 498, 498-1-498-13. doi: 10.1186/1471-2105-11-498
Choi, JooYoung, Davis, Melissa J., Newman, Andrew F. and Ragan, Mark A. (2010). A semantic web ontology for small molecules and their biological targets. Journal of Chemical Information and Modeling, 50 (5), 732-741. doi: 10.1021/ci900461j
Shin, C. J., Davis, M. J. and Ragan, M. A. (2009). Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics, 9 (23), 5256-5266. doi: 10.1002/pmic.200900262
Shin, Chang Jin, Wong, Simon, Davis, Melissa J. and Ragan, Mark A. (2009). Protein-protein interaction as a predictor of subcellular location. BMC Systems Biology, 3 (1) 28, x-x. doi: 10.1186/1752-0509-3-28
Martinez, Gemma, Georgas, Kylie, Challen, Grant A., Rumballe, Bree, Davis, Melissa J., Taylor, Darrin, Teasdale, Rohan D., Grimmond, Sean M. and Little, Melissa H. (2006). Definition and spatial annotation of the dynamic secretome during early kidney development. Developmental Dynamics, 235 (6), 1709-1719. doi: 10.1002/dvdy.20740
Davis, Melissa J., Hanson, Kelly A., Clark, Francis, Fink, J. Lynn, Zhang, Fasheng, Kasukawa, Takeya, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006). Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. Plos Genetics, 2 (4) e46, 554-563. doi: 10.1371/journal.pgen.0020046
Mitchell, E. K. L., Taylor, D. F., Woods, K., Davis, M. J., Nelson, A. L., Teasdale, R. D., Grimmond, S. M., Little, M. H., Bertram, J. F. and Caruana, G. (2006). Differential gene expression in the developing mouse ureter. Gene Expression Patterns, 6 (5), 519-538. doi: 10.1016/j.modgep.2005.10.008
Caruana, Georgina, Cullen-McEwen, Luise, Nelson, Amy L., Kostoulias, Xenia, Woods, Kyra, Gardiner, Brooke, Davis, Melissa J., Taylor, Darrin F., Teasdale, Rohan D., Grimmond, Sean M., Little, Melissa H. and Bertram, John F. (2006). Spatial gene expression in the T-stage mouse metanephros. Gene Expression Patterns, 6 (8), 807-825. doi: 10.1016/j.modgep.2006.02.001
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
Aturaliya,Rajith N., Fink, J. Lynn, Davis, Melissa J., Hanson, Kelly A., Miranda,Kevin C., Forrest,Alistair R. R., Grimmond, Sean M., Suzuki,Harukazu, Kanamori,Mutsumi, Kai,Chikatoshi, Kawai,Jun, Carninci,Piero, Hayashizaki,Yoshihide and Teasdale,Rohan D. (2006). Subcellular localization of mammalian type II membrane proteins. Traffic, 7 (5), 613-625. doi: 10.1111/j.1600-0854.2006.00407.x
Fink, J. Lynn, Aturaliya, Rajith N., Davis, Melissa J., Zhang, Fasheng, Hanson, Kelly, Teasdale, Melvena S., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006). LOCATE: a mouse protein subcellular localization database. Nucleic Acids Research, 34 (Supp. 1), D213-D217. doi: 10.1093/nar/gkj069
Davis, Melissa J., Zhang, Fasheng, Yuan, Zheng and Teasdale, Rohan D. (2006). MemO: A Consensus Approach to the Annotation of a Protein's Membrane Organization. In Silico Biology, 6 (5), 387-399.
The FANTOM Consortium, Gough, J., Frith, M. C., Ravasi, T., Wells, C., Forrest, A. R. R., Davis, M. J., Aturaliya, R. N., Bailey, T. L., Crowe, M. L., Faulkner, G., Pang, K. C., Teasdale, R. D., Grimmond, S. M., Mattick, J. S., Hume, D. A. and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Core Team) (2005). The transcriptional landscape of the mammalian genome. Science, 309 (5740), 1559-1563. doi: 10.1126/science.1112014
Challen, G. A., Martinez, G., Davis, M. J., Taylor, D. F., Crowe, M., Teasdale, R. D., Grimmond, S. M. and Little, M. H. (2004). Identifying the molecular phenotype of renal progenitor cells. Journal of The American Society of Nephrology, 15 (9), 2344-2357. doi: 10.1097/01.ASN.0000136779.17837.8F
Kanapin, A., Batalov, S., Davis, M., Gough, J., Grimmond, S. M., Kawaji, H., Magrane, M., Matsuda, H., Schonbach, C., Teasdale, R. D., RIKEN GER Group,, GSL Members, and Yuan, Z. (2003). Mouse proteome analysis. Genome Research, 13 (6B), 1335-1344. doi: 10.1101/gr.978703
Grimmond, Sean M., Miranda, Kevin C., Yuan, Zheng, Davis, Melissa J., Hume, David A., Yagi, Ken, Tominaga, Naoko, Bono, Hidemasa, Hayashizaki, Yoshihide, Okazaki, Yasushi, RIKEN GER Group,, GSL Members, and Teasdale, Rohan D. (2003). The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Research, 13 (6B), 1350-1359. doi: 10.1101/gr.983703
Yuan, Z., Davis, M. J., Zhang, F. S. and Teasdale, R. D. (2003). Computational differentiation of N-terminal signal peptides and transmembrane helices. Biochemical And Biophysical Research Communications, 312 (4), 1278-1283. doi: 10.1016/j.bbrc.2003.11.069
Conference Papers
van den Bergen, Glen, Inglis, Josha, Ling, Jun, Thompson, Jake, Emerson, Marisa and Davis, Melissa J. (2014). Identification of common disrupted protein networks in metastasis across multiple cancer types. MRS 2014: 15th International Biennial Congress of the Metastasis Research Society, Heidelberg, Germany, 28 June-1 July, 2014. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/s10585-015-9708-3
Wang, Chenwei, Taciroglu, Alperen, Maetschke, Stefan, Nelson, Colleen, Ragan, Mark and Davis, Melissa (2013). mCOPA : analysis of heterogeneous features in cancer expression data. The Prostate Cancer World Congress and 14th Australasian Prostate Cancer Conference, Melbourne, VIC Australia, 6-10 August 2013. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing Ltd.. doi: 10.1111/bju.12293
Newman, Andrew, Hunter, Jane, Li, Yuan-Fang, Bouton, Chris and Davis, Melissa (2008). BioMANTA Ontology: The integration of protein-protein interaction data. The Third Interdisciplinary Ontology Conference, Tokyo, Japan, 26-27 February, 2008. not found: not found.
Newman, Andrew, Hunter, Jane, Li, Yuan-Fang, Bouton, Chris and Davis, Melissa (2008). A scale-out RDF molecule store for distributed processing of biomedical data. Semantic Web for Health Care and Life Sciences Workshop, Beijing, China, 22 April, 2008.
Newman, Andrew, Li, Yuan-Fang, Hunter, Jane, Bouton, Chris and Davis, Melissa (2008). A scale-out RDF molecule store for distributed processing of biomedical data. Semantic Web for Health Care and Life Sciences Workshop, held in conjunction with The 17th International World Wide Web Conference (HCLS/WWW2008), Beijing, China, 22 April 2008. New York, U.S.A.: Semantic Web Health Care and Life Sciences Interest Group.
Davis, M., Newman, A., Khan, I., Hunter, J. and Ragan, M. A. (2007). Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions. 6th Asia Pacific Bioinformatics Conference (APBC'08), Kyoto, Japan, 14-17 January 2008. London, U.K.: Imperial College Press. doi: 10.1142/9781848161092_0017