Publications

To date, I have nearly 200 publications and presentations in journals and conferences among the top in the fields. I am thankful to my students, fellows and collaborators for making it happen. Below is a list of the most recent and/or relevant publications.

Books

  1. L. Rueda. Microarray Image and Data Analysis: Theory and Practice, CRC Press, 2014. More details can be found here.
  2. D. Mery, L. Rueda. Advances in Image and Video Technology. Proceedings of the IEEE Pacific-Rim Symposium on Image and Video Technology (PSIVT 2007). Lecture Notes in Computer Science (LNCS), Vol. 4872, Springer, 2007.
  3. L. Rueda, D. Mery, J. Kittler. Progress in Pattern Recognition, Image Analysis and Applications. Proceedings of the 12th Iberoamerican Congress on Pattern Recognition (CIARP 2007), Lecture Notes in Computer Science (LNCS), Vol. 4756, Springer, 2007.

Book Chapters

  1. M. Maleki, M. Hall, L. Rueda, Structural Domains in Prediction of Biological Protein-Protein InteractionsStructural Domains in Prediction of Biological Protein-Protein Interactions, Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, Wiley, 2015, pp. 291-314.
  2. L. Rueda, A. Ali. Introduction to Microarrays. Microarray Image and Data Analysis: Theory and Practice, CRC Press, 2014, pp. 1-40.
  3. I. Rezaeian, L. Rueda. Gridding Methods for DNA Microarray Images. Microarray Image and Data Analysis: Theory and Practice, CRC Press, 2014, pp. 77-108.
  4. D. Rojas, L. Rueda, H. Urrutia, A. Ngom, and G. Carcamo. Automatic Segmentation Methods and Applications to Biofilm Image Analysis. Imaging and Systems, CRC Press, 2011.
  5. N. Subhani, L. Rueda, A. Ngom. On Clustering Gene Expression Time-series Signals. Data Mining in Biomedical Signaling, Imaging and Systems, CRC Press, 2011.
  6. B. John Oommen and L. Rueda. Stochastic Learning-based Weak Estimation of Multinomials and Its Applications to Pattern Recognition and Data Compression. Knowledge-Based Intelligent System Advancements: Systemic and Cybernetic Approaches, IGI Global Publishers, ISBN 978-1-61692-811-7, 2010, pp. 1-29.
  7. L. Rueda and A. Bari. Clustering Time-series Gene Expression Data. Oligonucleotide Array Sequence Analysis, Nova Science Publishers, ISBN 978-1-60456-542-3, 2008, pp. 121-159.

Patents

Journal Publications - most recent

  1. S. Jubair, A. Alkhateeb, A. Abou Tabl, L. Rueda, A. Ngom (2019). Identifying subtype specific network-biomarkers of breast cancer survivability. BMC Bioinformatics Suppl, 2019. In Press.
  2. A. Abou Tabl, A. Alkhateeb, W. El-Maraghy L. Rueda, A. Ngom. A machine learning approach for identifying gene biomarkers guiding the treatment of breast cancer. Frontiers in Genetics, 2019. In Press.
  3. A. Alkhateeb, I. Rezaeian, S. Reddy, D. Cavallo-Medved, L. Porter, L. Rueda. "Transcriptomics signature from next-generation sequencing data reveals new transcriptomic biomarkers related to prostate cancer". Cancer Informatics, 2019. In Press.
  4. A. Abou Tabl, A. Alkhateeb, L. Rueda, W. El-Maraghy, A. Ngom. A novel approach for identifying relevant genes for breast cancer survivability on specific therapies. Evolutionary Bioinformatics, 2018, 14:1176934318790266. doi: 10.1177/1176934318790266.
  5. S. Peelar, J. Urbanic, B. Hedrick, L. Rueda. "Real-Time Visualization of Bead Based Additive Manufacturing Toolpaths Using Implicit Boundary Representations", Computer-Aided Design and Applications, 2018, pp. 322-326.
  6. Y. Li, M. Maleki, N. Carruthers, P. Stemmer, A. Ngom, L. Rueda. "The predictive performance of short-linear motif features in the prediction of Calmodulin-binding proteins", BMC Bioinformatics, 2018, 19 (Suppl 14) :410.
  7. F. Firoozbakht, I. Rezaeian, M. D’Agnillo, L. Porter, L. Rueda, A. Ngom. "An integrative approach for identifying network biomarkers of breast cancer subtypes using genomics, interactomics and transcriptomics data", Journal of Computational Biology, 2017, 24(8):756-766, doi: 10.1089/cmb.2017.0010.
  8. A. Alkhateeb, L. Rueda. "Zseq : an approach for preprocessing next generation sequencing data", Journal of Computational Biology, 2017, 24(8):746-755, doi: 10.1089/cmb.2017.0021.
  9. E.J. Mucaki, K. Baranova, H.P. Quang, I. Rezaeian, D. Angelov, A. Ngom, L. Rueda, P.K. Rogan. "Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Machine Learning". F1000Research, 2017, 5:2124. (doi: 10.12688/f1000research.9417.2).
  10. M. Alshehri, I. Rezaeian, A. Alkhateeb, L. Rueda. "Potential protein isoforms reveal additional information on biomarkers obtained from RNA-Seq data" [v1; not peer reviewed]. F1000Research 2016, 5(ISCB Comm J):1820 (poster) (doi: 10.7490/f1000research.1112702.1).
  11. I. Rezaeian, A. Tavakoli, D. Cavallo-Medved, L. Porter, L. Rueda. "A model used to detect differential splice junctions as biomarkers in prostate cancer from RNA-seq data", Journal of Biomedical Informatics, 2016, 60:422-30. doi: 10.1016/j.jbi.2016.03.010.
  12. Y. Li, B. J. Oommen, A. Ngom, L. Rueda. "Pattern Classification Using a New Border Identification Paradigm: The Nearest Border Technique", Neurocomputing, Vol. 157, 2015, pp. 105--117.
  13. I. Rezaeian, L. Rueda. "CMT: A Constrained Multi-level Thresholding Approach for ChIP-Seq Data Analysis", PLoS ONE, 2014, 9(4): e93873. doi:10.1371/journal.pone.0093873.
  14. M. Maleki, M. Hall, L. Rueda. "The Role of Structural Domains in Prediction of Protein-protein Interaction Types". Network Modeling Analysis in Health Informatics and Bioinformatics, 2013, 2(4):267-275. DOI 10.1007/s13721-013-0043-9.
  15. M. Maleki, G. Vasudev, L. Rueda. "The role of electrostatic energies in prediction of obligate protein-protein interactions". Proteome Science, 2013, 11(Suppl 1):S11.
  16. N. Shakiba, L. Rueda. "MicroRNA Identification Using Linear Dimensionality Reduction with Explicit Feature Mapping". BMC Proceedings (Supplements), 2013, 7(Suppl 7):S8.
  17. Md. Aziz, M. Maleki, L. Rueda, M. Raza, S. Banerjee, "Prediction of Biological Protein-protein Interactions using Atom-type and Amino Acid Properties", Proteomics, 2011, 11(19):3802--3810, DOI: 10.1002/pmic.201100186.
  18. L. Rueda, I. Rezaeian, "A Fully Automatic Gridding Method for cDNA Microarray Images", BMC Bioinformatics, 2011, 12:113.

Conference Publications, Presentations and Posters - most recent

  1. S. Peelar, J. Urbanic, L. Rueda, B. Hedrick. "Real-Time Visualization of Bead Based Additive Manufacturing Toolpaths Using Implicit Boundary Representations". 15th Annual International CAD Conference (CAD 2018), Paris, France, 2018, pp. 322-326.
  2. O. Hamzeh, T. Zhang, B. Fifield, Y. El-Gohary, R. Goel, T. Deklaj, R. Sorenson, T. Eldson, J. Mathews, A. Ghafoor, G. Atikukke, D. Cavallo-Medved, L. Porter, L. Rueda, S. Kanjeekal. "Muscle invasion in bladder cancer is associated with copy number alterations of TP53, DDR2 and MLL2", 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), Chicago, IL, USA, 2018. Poster presentation, peer-reviewed.
  3. H. Pham, J. Guba, L. Porter, L. Rueda, A. Ngom. "A Sub-network Selection Approach for Identifying Biomarkers to Predict Breast Cancer Outcomes", 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), Chicago, IL, USA, 2018. Poster presentation, peer-reviewed.
  4. S. Jubair, L. Rueda, A. Ngom. "Identifying subtype specific network-biomarkers of breast cancer survivability", IEEE World Congress on Computational Intelligence/International Joint Conference on Neural Networks (WCCI 2018)/IJCNN 2018), Rio de Janeiro, Brazil, 2018, pp. 1-8.
  5. S. Krishnamoorthy, L. Rueda, S. Saad, H. Elmiligi. "Identification of User Behavioral Biometrics for Authentication using Keystroke Dynamics and Machine Learning", 2nd International Conference on Biometric Engineering and Applications (ICBEA 2018), Amsterdam, The Netherlands, 2018, pp. 50-57.
  6. O. Hamzeh, A. Alkhateeb, L. Rueda. "Predicting Tumor Locations in Prostate Cancer Tissue Using Gene Expression". 6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2018), Granada, Spain, 2018, pp. 343-351.
  7. A. Abou Tabl, A. Alkhateeb, L. Rueda, W. Elmaraghy, A. Ngom. "Identification of the Treatment Survivability Gene Biomarkers of Breast Cancer Patients via a Tree-Based Approach". 6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2018), Granada, Spain, 2018, pp. 166-176.
  8. A. Abou Tabl, A. Alkhateeb, W. El-Maraghy, L. Rueda, A. Ngom. "Identifying Gene Biomarkers for Breast Cancer Survival Using a Tree-based Approach". IEEE Biomedical and Health Informatics (BHI 2018), Las Vegas, NV, 2018. Poster presentation.
  9. R. Razavi-Far, E. Hallaji, M. Saif, L. Rueda. "A Hybrid Scheme for Fault Diagnosis with Partially Labeled Sets of Observations", 16th IEEE International Conference on Machine Learning and Applications (ICMLA 2017), Cancun, Mexico, 2017, pp. 61-67.
  10. H. Quang, L. Rueda, A. Ngom. "Predicting Breast Cancer Outcome under Different Treatments by Feature Selection Approaches", ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2017), 2017, Boston, MA, USA, pp. 617-617.
  11. N. Mangalakumar, H. Quang, A. Alkhateeb, L. Rueda, A. Ngom. "Outlier Genes as Biomarkers of Breast Cancer Survivability in Time-Series Data", ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2017), 2017, Boston, MA, USA, pp. 594-594.
  12. W. Xu, L. Rueda, A. Ngom. "Drug-Target Interaction Networks Prediction using Short-Linear Motifs", 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology (ISMB/ECCB 2017), Prague, Czech Republic, 2017. Poster presentation, peer-reviewed.
  13. A. Karkar, O. Hamzeh, A. Alkhateeb, L. Rueda, "Finding Biomarkers Associated with Prostate Cancer Gleason Stages using Next Generation Sequencing and Machine Learning Techniques", 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology (ISMB/ECCB 2017), Prague, Czech Republic, 2017. Poster presentation, peer-reviewed.
  14. N. Mangalakumar, A. Alkhateeb, H. Quang, L. Rueda, A. Ngom. "Identifying Gene Biomarkers of Breast Cancer Survivability from Time-Series Data", 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology (ISMB/ECCB 2017), Prague, Czech Republic, 2017. Poster presentation, peer-reviewed.
  15. H. Ahmed, O. Hamzeh, A. Alkhateeb, L. Rueda. "An Open Source Machine Learning Tool for Identifying Biomarkers in Next Generation Sequencing", The Great Lakes Bioinformatics Conference (GLBIO 2017), 2017, Chicago, IL, USA. Poster presentation.
  16. S. Chakrabarti, R. Razavi-Far, M. Saif, L. Rueda. "'Multi-Class Heteroscedastic Linear Dimensionality Reduction Scheme for Diagnosing Process Faults", 30th Canadian IEEE Conference on Electrical and Computer Engineering (CCECE 2017), Windsor, ON, Canada, 2017.
  17. O. Hamzeh, A. Alkhateeb, I. Rezaeian, A. Karkar, L. Rueda. "Finding Transcripts Associated with Prostate Cancer Gleason Stages Using Next Generation Sequencing and Machine Learning Techniques". 5th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2017), Granada, Spain, 2017, pp. 337-348.
  18. Y. Li, M. Maleki, N.J. Carruthers, L. Rueda, P.M. Stemmer, A. Ngom. "Prediction of Calmodulin Binding Proteins Using Short Linear Motifs". 5th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2017), Granada, Spain, 2017, pp. 107-117.
  19. R. Etemadi, A. Alkhateeb, I. Rezaeian, L. Rueda, "Identification of Discriminative Genes for Predicting Breast Cancer Subtypes", Workshop on Health Informatics and Data Science (HI-DS 2016) - IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Shenzhen, China, 2016, pp: 1184-1188.
  20. H. Quang, A. Ngom, L. Rueda, "A new feature selection approach for optimizing prediction models, applied to breast cancer subtype classification", IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Shenzhen, China, 2016, pp. 1535-1541.
  21. H. Quang, I. Rezaeian, E. Mucaki, A. Ngom, L. Rueda, P. Rogan. "Predicting Breast Cancer Drug Response via an Apriori-like Gene Selection Approach", The Fourth International Society for Computational Biology Latin America Bioinformatics Conference (ISCB-LA 2016), Buenos Aires, Argentina. Poster presentation.
  22. M. Alsheri, A. Alkhateeb, I. Rezaeian, L. Rueda. "Discovery of Protein Isoforms for Different Stages of Prostate Cancer", The Fourth International Society for Computational Biology Latin America Bioinformatics Conference (ISCB-LA 2016), Buenos Aires, Argentina. Oral presentation.
  23. H. Pham, A. Ngom, L. Rueda, "AFSP -- an efficient method for classifier-specific feature selection", IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2016), Athens, Greece, 2016, pp. 1-8.
  24. M. Alshehri, I. Rezaeian, A. Alkhateeb, L. Rueda. "A Machine Learning Model for Discovery of Protein Isoforms as Biomarkers", ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACMBCB 2016), Seattle, WA, USA, 2016, pp. 474-475.
  25. F. Firoozbakht, I. Rezaeian, A. Ngom, L. Rueda, "An Integrative Approach for Identification of Network Biomarkers in Breast Cancer Subtypes", 12th International Symposium on Bioinformatics Research and Applications (ISBRA 2016), Minsk, Belarus, 2016, pp. 1-4.
  26. M. Alshehri, A. Alkhateeb, I. Rezaeian, L. Rueda, "Potential Protein Isoforms Reveal Additional Information on Biomarkers Obtained from RNA-Seq Data", 24th Conference on Intelligent Systems for Molecular Biology (ISMB 2016), Orlando, Florida, USA, 2016. Poster presentation, peer-reviewed.
  27. B. Elkarami, A. Alkhateeb, L. Rueda, "Cost-Sensitive Classification on Class-balanced Ensembles for Imbalanced Non-coding RNA Data", The IEEE Engineering in Medicine and Biology Society (EMBS) International Student Conference (ISC) 2016, Ottawa, Canada, pp. 1-4.
  28. M. Kordestani, A. Alkhateeb, I. Rezaeian, L. Rueda, M. Saif. "A new clustering method using wavelet based probability density functions for identifying patterns in time-series data", The IEEE Engineering in Medicine and Biology Society (EMBS) International Student Conference (ISC) 2016, Ottawa, Canada, pp. 1-4.
  29. M. D'Agnillo, I. Rezaeian, A. Ngom, L. Rueda, "Machine Learning Approaches for Breast Cancer Subtypes Reveal Key Genes as Potential Biomarkers", The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016, Toronto, Canada. Poster presentation.
  30. Y. Li, L. Rueda, A. Ngom, "Prediction of High-throughput Protein-protein Interactions Using Short Linear Motifs", The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016, Toronto, Canada. Poster presentation.
  31. A. Alkhateeb, I. Rezaeian, L. Rueda, "Hierarchal Clustering based on Non-negative Matrix Factorization for Time Series transcriptomes profiles", The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016, Toronto, Canada. Poster presentation.
  32. I. Rezaeian, E. Mucaki, K. Baranova, H.P. Quang, D. Angelov, L. Ilie, A. Ngom, L. Rueda, P. Rogan, "Predicting patient outcomes of hormone therapy in the METABRIC breast cancer study", The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016, Toronto, Canada. Poster presentation.
  33. M. Pandit, M. Maleki, N. J. Carruthers, P. Stemmer, L. Rueda, "Prediction of Calmodulin-binding Proteins Using Canonical Motifs", The GLBIO/CCBC Great Lakes Bioinformatics and the Canadian Computational Biology Conference, 2016, Toronto, Canada. Poster presentation.
  34. M. Farajzadeh-Zanjani, R. Razavi-Far, M. Saif, L. Rueda, "Efficient feature extraction of vibration signals for diagnosing bearing defects in induction motors", The Annual International Joint Conference on Neural Networks (IJCNN 2016), Vancouver, Canada, 2016, pp. 4504-4511.
  35. F. Firoozbakht, I. Rezaeian, A. Ngom, L. Rueda, "Breast Cancer Network Biomarker Identification by Incorporating Genomics, Transcriptomics and Proteomics Data", 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2016), Santa Monica, CA, USA, 2016. Poster and Oral presentation, peer-reviewed.
  36. A. Alkhateeb, I. Rezaeian, L. Rueda, "Nonnegative Matrix Factorization Clustering for Time Series Cancer Progression Data", 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2016), Santa Monica, CA, USA, 2016. Poster and Oral presentation, peer-reviewed.
  37. M. Alsheri, A. Alkhateeb, I. Rezaeian, L. Rueda, "A standalone tool for finding ORFs and reconstructing potential protein isoforms from RNA-Seq data", Next Generation Sequencing 2016 (NGS 2016), Barcelona, Spain, 2016, Poster presentation -- peer reviewed.

A full list of my publications can also be found in the main public scholar databases: