Publications in Bioinformatics in the past 3 years --->

Books and Book Chapters

  • Robin Gras, Study of Genetic algorithms behavior for high epitasis and high dimensional deceptive functions, Evolutionary Computation, (2009), In Press, Editor(s) - IN-TECH, Vienna, Austria.
  • Elham Salehi, Jayashree Nyayachavadi and Robin Gras, (2009) Une étude comparative pour la détection de dépendances multiples In Régis Gras, Fabrice Guillet and Jean-Claude Régnier, Analyse Statistique Implicative. Une méthode d'analyse de données pour la recherche de causalite, 251-270, Editor(s) - Cépaduès, Revue des Nouvelles Technologies de l'Information.
  • 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.

Journals

  • Devaurs D., Gras R., (2009) Studying species abundance distributions in an individual-based simulated ecosystem through Fishers log-series, Simulation Modelling Practice and Theory, In Press.
  • Ngom A. Wang L., Rueda L., and Gras R., (2009) Non-Unique Oligonucleotide Probe Selection using Evolutionary Methods, "Special Issue on Computational Intelligence Methods in Bioinformatics" Neurocomputing, In Press.
  • Ngom A., L. Wang L. Rueda L., and Gras R., (2009) Selection Based Heuristics for the Non-Unique Oligonucleotide Probe Selection Problem in Microarray Design, “Special Issue on Pattern Recognition Methods in Bioinformatics”, Pattern Recognition Letters, In Press.
  • Gras R., Devaurs D., Wozniak A., Aspinall A., (2009) An agent-based evolving predator-prey ecosystem simulation using a Fuzzy Cognitive Map model of behavior, Artificial Life, 15(4), 423-463
  • Hernandez, D.; Gras, R., Appel, R.D., (2008) Neighborhood Functions and Hill-Climbing Stragegies dedicated to the Generalized Ungapped Local Multiple alignment, European Journal of Operational Research, 185, 1276-1284
  • Wang L., Ngom A., Gras R., Rueda L., (2008) An Evolutionary Approach to the Non-Unique Oligonucleotide Probe Selection Problem, Transactions on Computational System Biology, 10 (1974), 143-162
  • Deon, C.; Bienvenut, W.; Sanchez, J.C.; Hochstrasser, D.F.; Muller, M.; Gras, R., Appel, R.D., (2007) Analysis of Proteomes Using the Molecular Scanner, Cold Spring Harbor Protocols (pdb.prot4592)
  • P. Jopia, N. Ruiz-Tagle, M. Villagrán, K. Sossa, S. Pantoja, L. Rueda, H. Urrutia, Biofilm Growth Kinetics of a Monomethylamine Producing Alphaproteobacteria Strain Isolated from an Anaerobic Reactor. Anaerobe, 2009. In press.
  • L. Rueda, A. Bari, A. Ngom, Clustering Time-series Gene Expression Data with Unequal Time Intervals, Springer Trans. on Computational Systems Biology, Springer, LNBI 5410, 2008, pp. 100-123.
  • Jakupciak, John, P; Maggrah, Andrea; Maragh, Samantha; Maki, Jennifer; Reguly, Brian; Maki, Katrina; Wittock, Roy; Robinson, Kerry; Wagner, Paul, D; Thayer, Robert, E; Gehman, Ken; Gehman, Theresa; Srivastava, Sudhir; Ngom, Alioune; Dakubo, Gabriel, D; Parr, Ryan, L, Facile whole mitochondrial genome resequencing from nipple aspirate ?uid using MitoChip v2.0, BMC Cancer, 8(95), pp.1471-2407, 2008, April, BioMed Central Online Journal.
  • L. Rueda and M. Herrera, Linear Dimensionality Reduction by Maximizing the Chernoff Distance in the Transformed Space, Pattern Recognition, Vol. 41, Issue 10, 2008, pp. 3138-3152.

Conferences

  • Yifeng Li, Numanul Subhani, Alioune Ngom, and Luis Rueda: Alignment-based versus Variation-based Transformation Methods for Clustering Microarray Time-Series Data, Proceedings of the Conference On Bioinformatics and Computational Biology (ACM-BCB 2010). August 2010 (Accepted).
  • Numanul Subhani, Yifeng Li, Alioune Ngom, and Luis Rueda: Alignment versus variation vector Methods for Clustering Microarray Time-Series Data, Proceedings of the IEEE World Congress on Computational Intellegence (WCCI 2010). July 2010 (To Appear).
  • Numanul Subhani, Luis Rueda, Alioune Ngom and Conrad Burden: New Approaches to Clustering Microarray Time-Series Data Using Multiple Expression Profile Alignment, Proceedings of the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2010). Pages 170-176, May 2010.
  • Yifeng Li, Alioune Ngom and Luis Rueda: Missing Value Imputation Methods for Gene-Sample-Time Microarray Data Analysis, Proceedings of the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2010). Pages 183-189, May 2010.
  • Soltan Ghoraie L., Gras R., Wang L., Ngom A., (2009) Bayesian Optimization Algorithm for the Non-unique Oligonucleotide Probe Selection Problem, Pattern Recognition in Bioinformatics, LNCS 5780, 2009, pp. 365-376.
  • Saheli E., Gras R., (2009) An empirical comparison of the efficiency of several local search heuristics algorithms for Bayesian network structure learning, Learning and Intelligent OptimizatioN IEEE international conference, In Press
  • Z. Ibrahim, A. Ngom and A. Tawfik, Qualitative Motif Detection in Gene Regulatory Networks, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009, Washington DC, USA, November 1-4, To Appear.
  • Z. Ibrahim, A. Taw?k and A. Ngom, Surprise-based Qualitative Probabilistic Networks, The 10th European Conference on Symbolic and Quantitative Approaches to Reasoning with Uncertainty, ECSQARU 2009, Verona, Italy, July 1-3, Lecture Notes in Arti?cial Intelligence 5590, pp.228-239, 2009.
  • Z. Ibrahim, A. Taw?k and A. Ngom, A Surprise-based Qualitative Calculus, FLAIRS 2009, pp.573-574, 2009.
  • X. Wu, A. Jaekel, A. Bari and A. Ngom, Optimized hybrid resource allocation in wireless cellular networks with and without channel reassignment, The 6-th IEEE International Conference on Information Technology: New Generations, ITNG 2009, Las Vegas, Nevada, USA, April 27-29, pp.1146-1151, 2009.
  • D. Rojas, L. Rueda, A. Ngom, H. Urrutia, G. Carcamo, Biofilm Image Segmentation Using Optimal Multi-Level Thresholding, IEEE International Conference on Bioinformatics & Biomedicine, Washington, D.C., USA, 2009. In Press.
  • L. Rueda, J. Rojas, A Pattern Classification Approach to DNA Microarray Image Segmentation, 4th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2009), Sheffield, UK, Springer, 2009, LNCS 5780, pp. 319-330.
  • D. Rojas, L. Rueda, H. Urrutia, A. Ngom, Efficient Optimal Multi-Level Thresholding for Biofilm Image Segmentation, 4th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2009), Sheffield, UK, 2009, LNCS 5780, 2009, pp. 307-318.
  • N. Subhani, L. Rueda, A. Ngom and C.J. Burden, Clustering Microarray Time-Series Data using Expectation Maximization and Multiple Profile Alignment, IEEE International Conference on Bioinformatics and Biomedicine – Workshop on Applications of Machine Learning in Bioinformatics, (BIBM-AMLB 2009), Washington DC, USA, November 1-4, pp. 2-7
  • N. Subhani, A. Ngom, L. Rueda, C. Burden, Microarray Time-Series Data Clustering via Multiple Alignment of Gene Expression Profiles, 4th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2009), Sheffield, UK, 2009, LNCS 5780, 2009, pp. 377-390.
  • M. Pinninghoff, R. Contreras, L. Rueda, An Evolutionary Approach for Correcting Random Amplified Polymorphism DNA Images, to be presented at the 3rd International Work Conference on the Interplay between Natural and Artificial Computation (IWINAC 2009), Santiago de Compostela, Spain, 2009.
  • V.A. Gallardo, H. Urrutia, N. Ruiz-Tagle, C. Espinoza, L. Rueda, A. Ngom, C. Monsalve, A. Fonseca, J. Gutierrez, S. Rojas and L. Abarzua, High Throughput Sequencing to Assess Benthic Bacteria Biodiversity off Central Chile, Census of Marine Life Synthesis Workshop, (CoML 2009), February 1-5, Long Beach, California, 2009.
  • L. Rueda, An Efficient Algorithm for Optimal Multilevel Thresholding of Irregularly Sampled Histograms, 7th International Workshop on Statistical Pattern Recognition (S+SSPR 2008), Orlando, Florida, USA, Springer, LNCS 5432, 2008, pp. 612-621.
  • A. Bari, L. Rueda, A. Ngom, Microarray Time-Series Data Classification via Multiple Alignment of Gene Expression Profiles, Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, Australia, 2008, Springer, LNBI 5265, pp. 25-36.
  • L. Wang, A. Ngom, L. Rueda, Sequential Forward Selection Approach to the Non-Unique Oligonucleotide Probe Selection Problem, Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, Australia, 2008, Springer, LNBI 5265, pp. 262-275.
  • V. Gallardo, A. Teske, J. L. Nielsen, H. Urrutia, N. Ruiz-Tagle, C. Espinoza, L. Abarzua, D. Andrades, L. Rueda, C. Monsalve, 16S Ribosomal RNA Gene Sequence Analysis of Sediment Macrobacteria from the Central Chile Oxygen Minimum Zone, 12th Biennial Symposium on Microbial Ecology (ISME-12), Cairns, Australia, 2008. Poster presentation.
  • X. Li, A. Ngom and L. Rueda, Minimal siRNA Set Cover Heuristic for Gene Family Knockdown, The 3-rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008, Melbourne, Australia, October 15-17, ISBN 978-0-7326-2226-8.
  • Z. Ibrahim, A. Taw?k and A. Ngom, Qualitative Hidden Markov Models for Classifying Gene Expression Data, The 28-th Conference on Innovative Techniques and Applications of Arti?cial Intelligence, Italy, Lecture Notes in Arti?cial Intelligence, pp.47-60, 2008.
  • Gras R., How efficient are genetic algorithms to solve high epistasis deceptive problems?, (2008), IEEE World Congress on Computational Intelligence, IEEE World Congress on Computational Intelligence, 242-249
  • Wang L., Ngom A., Gras R., (2008) Non-Unique Oligonucleotide Microarray Probe Selection Method Based on Genetic Algorithms, 1004-1011, IEEE World Congress on Computational Intelligence, IEEE World Congress on Computational Intelligence
  • L. Wang, A. Ngom, R. Gras, L. Rueda, Evolution Strategy with Greedy Probe Selection Heuristics for the Non-Unique Oligonucleotide Probe Selection Problem, 5th Conference on Computational Intelligence in Bioinformatics and Bioengineering (CIBCB 2008), Sun Valley, Idaho, USA, 2008, pp. 54-61. Recognized for the Overall Best Paper Award.
Bioinfo Header CS website