Publications

2011

  • Genome Annotation Test with Validation on Transcription Start Site and ChIP-Seq for Pol-II Binding Data, Bedo, Justin and Kowalczyk, Adam, Bioinformatics, 2011, DOI: 10.1093/bioinformatics/btr263
  • Meta-analysis of gene expression microarrays with missing replicates, Shi, Fan, Abraham, Gad, Leckie, Christopher, Haviv, Izhak, and Kowalczyk, Adam, BMC Bioinformatics, 12, pp. 84, 2011, DOI: 10.1186/1471-2105-12-84
  • Epigenetic Regulation of Cell Type-Specific Expression Patterns in the Human Mammary Epithelium, Maruyama, Reo, Choudhury, Sibgat, Kowalczyk, Adam, Bessarabova, Marina, Beresford-Smith, Bryan, Conway, Thomas, Kaspi, Antony, Wu, Zhenhua, Nikolskaya, Tatiana, Merino, Vanessa F., Lo, Pang-Kuo, Liu, X. Shirley, Nikolsky, Yuri, Sukumar, Saraswati, Haviv, Izhak, and Polyak, Kornelia, PLoS Genet, 7, pp. e1001369, 2011, DOI: 10.1371/journal.pgen.1001369
  • Optimized Relative Lempel-Ziv Compression of Genomes, Kuruppu, Shanika, Puglisi, Simon J., and Zobel, Justin, ACSC2011
  • Succint Data Structures for Assembling Large Genomes, Conway, Thomas and Bromage, Andrew, Bioinformatics, 27, pp. 479--486, 2011, DOI: 10.1093/bioinformatics/btq697

2010

  • Blood borne A-beta dimer correlates with clinical markers of Alzheimer's disease, Villemagne, Victor, Perez, Keyla, Pike, Kerryn, Kok, W, Rowe, Christopher, White, Anthony, Bourgeat, Pierrick, Salvado, Olivier, Bedo, Justin, Hutton, Craig, Faux, Noel G., Masters, Colin L., and Barnham, Kevin, Journal of Neuroscience, 30, pp. 6315--6322, 2010
  • A fast indexing approach for protein structure comparison, Zhang, Lei, Bailey, James, Konagurthu, Arun S., and Ramamohanarao, Kotagiri, BMC Bioinformatics, 11 (Suppl 1), pp. S46, 2010, DOI: 10.1186/1471-2105-11-S1-S46
  • Space-Efficient Fragment Assembly using Succinct Data Structures, Bromage, Andrew, Conway, Thomas, and Zobel, Justin, EAS/WABI 2010
  • MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography, Konagurthu, Arun S., Reboul, Cyril F., Schmidberger, Jason W., Irving, James A., Lesk, Arthur M., Stuckey, Peter J., Whisstock, James C., and Buckle, Ashley M. PLoS ONE, 5, pp. e10048, 2010, DOI: 10.1371/journal.pone.0010048
  • EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes, Mahmood, Khalid, Konagurthu, Arun S., Song, Jiangning, Buckle, Ashley M., Webb, Geoffrey I., and Whisstock, James C., Bioinformatics, 26, pp. 2076--2084, 2010, DOI: 10.1093/bioinformatics/btq339
  • Reference-Free Validation of Short Read Data, Schroeder, Jan, Bailey, James, Conway, Thomas, and Zobel, Justin, PLoS ONE, 5, pp. e12681, 2010, DOI: 10.1371/journal.pone.0012681
  • MIRAGAA --- a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer, Gaire, Raj K., Bailey, James, Bearfoot, Jennifer, Campbell, Ian G., Stuckey, Peter J., and Haviv, Izhak, Bioinformatics, 26, pp. 161--167, 2010 , DOI: 10.1093/bioinformatics/btp654
  • Cataloging topologies of protein folding patterns, Konagurthu, Arun S. and Lesk, Arthur M., Journal of Molecular Recognition, 23, pp. 253--257, 2010, DOI: 10.1002/jmr.1006
  • Design of an efficient out-of-core read alignment algorithm, Konagurthu, Arun S., Allison, Lloyd, Conway, Thomas, Beresford-Smith, Bryan, and Zobel, Justin, Proceedings of the Tenth WABI International Workshop on Bioinformatics
  • is-rSNP: a novel technique for in silico regulatory SNP detection, Macintyre, Geoff, Bailey, James, Haviv, Izhak, and Kowalczyk, Adam, Bioinformatics, 26 ECCB 2010, pp. i524--i530, 2010, DOI: 10.1093/bioinformatics/btq378
  • Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations, Wong, Gerard, Leckie, Christopher, Gorringe, Kylie L., Haviv, Izhak, Campbell, Ian G., and Kowalczyk, Adam, Bioinformatics, 26, pp. 1007--1014, 2010, DOI: 10.1093/bioinformatics/btq088
  • Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context, Abraham, Gad, Kowalczyk, Adam, Loi, Sherene, Haviv, Izhak, and Zobel, Justin, BMC Bioinformatics, 11, pp. 277, 2010, DOI: 10.1186/1471-2105-11-277
  • The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data, Kowalczyk, Adam, Bedo, Justin, Conway, Thomas, and Beresford-Smith, Bryan, RECOMB 2010
  • The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data, Kowalczyk, Adam, Bedo, Justin, Conway, Thomas, and Beresford-Smith, Bryan, Lecture notes in Computer Science, 6004 , pp. 297--309, 2010
  • Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval, Kuruppu, Shanika, Puglisi, Simon J., and Zobel, Justin, SPIRE2010
  • A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer, Shi, Fan, Leckie, Christopher, Macintyre, Geoff, Haviv, Izhak, Boussioutas, Alex, and Kowalczyk, Adam, BMC Bioinformatics, 11, pp. 477, 2010, DOI: 10.1186/1471-2105-11-477
  • Using Gene Ontology annotations in exploratory microarray clustering to understand cancer etiology, Macintyre, Geoff, Bailey, James, Gustafsson, Daniel, Haviv, Izhak, and Kowalczyk, Adam, Pattern Recognition Letters, 13, pp. 2138--2146, 2010, DOI: 10.1016/j.patrec.2010.01.006
  • PBT2 Rapidly Improves Cognition in Alzheimer's Disease: Additional Phase II Analyses, Faux, Noel G., Ritchie, Craig W., Gunn, Adam, Rembach, Alan, Tsatsanis, Andrew, Bedo, Justin, Harrison, John, Lannfelt, Lars, Blennow, Kaj, Zetterberg, Henrik, Ingelsson, Martin, Masters, Colin L., Tanzi, Rudolph E., Cummings, Jeffrey L., Herd, Caroline M., and Bush., Ashley I., Journal of Alzheimer's Disease, 20 2010

2009

  • A voting approach to identify a small number of highly predictive genes using multiple classifiers, Hassan, Md. Rafiul, Hossain, M. Maruf, Bailey, James, Macintyre, Geoff, Ho, Joshua W. K., and Ramamohanarao, Kotagiri, BMC Bioinformatics, 10 (Suppl 1), pp. S19, 2009, DOI: 10.1186/1471-2105-10-S1-S19

2008

  • PConPy --- a Python module for generating 2D protein maps, Ho, Hui Kian, Kuiper, Michael J., and Kotagiri, Ramamohanarao, Bioinformatics, 24, pp. 2934--2935, 2008
  • Microarray Design using the Hilbert--Schmidt Independence Criterion, Bedo, Justin, Lecture notes in Bioinformatics, pp. 288--298, 2008
  • A Bi-ordering approach to Linking Gene Expression with Clinical Annotations in Cancer, Shi, Fan, Macintyre, Geoff, Leckie, Christopher, Haviv, Izhak, Boussioutas, Alex, and Kowalczyk, Adam, Proceedings of the second International Workshop on Machine Learning in Systems Biology
  • Gene Ontology Assisted Exploratory Microarray Clustering and its Application to Cancer, Macintyre, Geoff, Bailey, James, Gustafsson, Daniel, Kowalczyk, Adam, Boussioutas, Alex, and Haviv, Izhak, Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB)
  • Precision-mapping and statistical validation of quantitative trait loci by machine learning, Bedo, Justin, Wenzl, Peter, Kowalczyk, Adam, and Kilian, Andrzej, BMC Genetics, 9, pp. 35, 2008
  • Structural search and retrieval using a tableau representation of protein folding patterns, Konagurthu, Arun S., Stuckey, Peter J., and Lesk, Arthur M., Bioinformatics, 24, pp. 645--651, 2008, DOI: 10.1093/bioinformatics/btm641

2007

  • Classification of Anti-learnable Biological and Synthetic Data, Kowalczyk, Adam, KDD, 4702, pp. 176, 2007
  • Supervised feature selection via dependence estimation, Song, Le, Smola, Alex, Gretton, Arthur, Borgwardt, K, and Bedo, Justin, Proceedings of the 24th international conference on Machine Learning, 2007
  • Stratification bias in low signal microarray studies, Parker, Brian J., Gunter, Simon, and Bedo, Justin, BMC Bioinformatics, 8, pp. 326, 2007
  • Pretreatment Gene Expression Profiles can be Used to Predict Response to Neoadjuvant Chemoradiotherapy in Esophagael Cancer, Greenawalt, Danielle M, Kowalczyk, Adam, and Ciavarella, M, Annals of Surgical Oncology, 14 , pp. 3602--3609, 2007
  • Continuity of Performance Metrics for Thin Feature Maps, Kowalczyk, Adam, ALT, 2007
  • Gene selection via the BAHSIC family of algorithms, Song, Le, Bedo, Justin, Borgwardt, K, Gretton, Arthur, and Smola, Alex, Bioinformatics, 23, pp. i490--i498, 2007
  • Large Validation of Anti-learnable Signature in Classification of Response to Chemoradiotherapy in Esophageal Adenocarcinoma Patients, Kowalczyk, Adam, Greenawalt, Danielle M, Bedo, Justin, Cuong, Duong, Raskutti, Garvesh, Thomas, Robert JS, and Phillips, Wayne A, Lecture Notes in Operations Research, 7, pp. 213--221, 2007

2006

  • An Efficient Alternative to SVM Based Recursive Feature Elimination with Applications in Natural Language Processing and Bioinformatics, Bedo, Justin, Sanderson, Conrad, and Kowalczyk, Adam, AI206 Proceedings of the Australian Joint Conference on Artifical Intelligence, 2006

2005

  • An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin, Tothill, Richard W, Kowalczyk, Adam, Rischin, Danny, Boussioutas, Alex, Haviv, Izhak, Laar, Ryan K van, Waring, Paul M, Zalcberg, John, Ward, Robyn, Biankin, Andrew, Sutherland, Robert L, Henshall, Susan M, Fong, Kwun, Pollack, Jonathan R, Bowtell, David, and Holloway, Andrew, J Cancer Research, 65, pp. 4031--40, 2005 ,
  • An Analysis of the Anti-Learning Phenomenon for the Class Symmetric Polyhedron, Kowalczyk, Adam and Chapelle, Olivier, Proceedings of the 16th International Conference on Algorithmic Learning Theory

2002

  • One class SVM for yeast regulation prediction, Kowalczyk, Adam and Raskutti, Bhavani, ACM SIGKDD Explorations Newsletter, 4, pp. 99--100, 2002
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