CIBCB 2015 Program

Tutorial TUT1: A Survey of Representations for Applying Evolutionary Computation to Bioinformatics
Wednesday, August 12, 8:30AM-10:00AM, Room: Niagara, Instructor: Daniel Ashlock

CB1: Coffee Break
Wednesday, August 12, 10:00AM-10:30AM, Room: Niagara

Tutorial TUT2: Bioinformatics on the Epigenome
Wednesday, August 12, 10:30AM-12:00PM, Room: Niagara, Instructor: Wendy Ashlock

Tutorial TUT3: Applications of Bayesian Model Averaging in Personalized Medicine and Systems Biology
Wednesday, August 12, 1:30PM-3:00PM, Room: Niagara, Instructor: Ka Yee Yeung

CB2: Coffee Break
Wednesday, August 12, 3:00PM-3:30PM, Room: Niagara

Tutorial TUT4: The Identification of cis-Regulatory Elements: A Tutorial From the Machine-Learning Perspective
Wednesday, August 12, 3:30PM-5:00PM, Room: Niagara, Instructor: Yifeng Li

Plenary Talk PT1: Uncommon Use of Common Data (in BioMedicine)
Thursday, August 13, 9:00AM-10:00AM, Room: Niagara, Speaker: Hagit Shatkay

CB3: Coffee Break
Thursday, August 13, 10:00AM-10:20AM, Room: Niagara

Session A: Gene Expression Analysis
Thursday, August 13, 10:20AM-12:00PM, Room: Niagara, Chair: Kay C. Wiese

10:20AM  Detecting Protein Complexes using Gene Expression Biclusters [#15003]
Eileen Marie Hanna and Nazar Zaki
UAEU, United Arab Emirates
10:40AM  Heuristic Principal Component Analysis Based unsupervised Feature Extraction and its Application to Gene Expression Analysis of Amyotrophic Lateral Sclerosis [#15009]
Y-h. Taguchi, Mitsuo Iwadate and Hideaki Umeyama
Chuo University, Japan
11:00AM  Digitization of Trait Representation in Microarray Data Analysis of Wheat Infected by Fusarium graminearum [#15050]
Youlian Pan, Therese Ouellet, Sieu Phan, Alain Tchagang, Francois Fauteux and Dan Tulpan
Information and Communications Technologies, NRC, Canada; Eastern Cereal and Oilseed Research Centre, AAFC, Canada
11:20AM  Towards Large Scale Genetic Network Modeling [#15092]
Rubaiya Rahtin Khan and Madhu Chetty
Federation University Australia, Australia
11:40AM  Lexicode Crossover for Embeddable Biomarkers [#15034]
Daniel Ashlock and Sheridan Houghten
University of Guelph, Canada; Brock University, Canada

Special Session Z3.1: Pattern Recognition, Data Mining and Image Processing for Bioinformatics, Computational Biology, and Medicine
Thursday, August 13, 1:30PM-3:30PM, Room: Niagara, Chair: Fazel Zarandi

1:30PM  Systematic Bone Infection Detection in Axial Diabetic Foot MRI [#15011]
Maede Maftouni, Mohammad hossein Fazel Zarandi, Burhan Turksen and Niloofar Ayubi Yazdi
Department of Industrial Engineering, Amirkabir University of technology, Iran; Knowledge Intelligent System Laboratory University of Toronto, Canada; Advanced Diagnostic and Interventional Radiology Research Center, Tehran University of Medical Science, Iran
1:50PM  Lung Nodule Diagnosis from CT Images Based on Ensemble Learning [#15018]
Farzad Vasheghani Farahani, Abbas Ahmadi and Mohammad hossein Fazel Zarandi
Department of Industrial Engineering and Management Systems, Amirkabir University of Technology, Iran
2:10PM  Fuzzy Rule-based Expert System for Diagnosis of Thyroid Disease [#15093]
Sajjad Amrollahi Biyouki, Mohammad Hossein Fazel Zarandi and Ismail Burhan Turksen
Department of Industrial Engineering, Amirkabir University of Technology, Iran; Department of Mechanical and Industrial Engineering, University of Toronto, Canada
2:30PM  Classification via Correlation-based Feature Grouping [#15036]
Mina Maleki and Luis Rueda
University of Windsor, Canada
2:50PM  A Novel Gene Selection Algorithm for cancer identification based on Random Forest and Particle Swarm Optimization [#15102]
Elnaz Pashaei, Mustafa Ozen and Nizamettin Aydin
Yildiz Technical University, Turkey; Biruni University, Turkey
3:10PM  New Approaches to Identify Cancer Heterogeneity in DNA Methylation Studies Using the Lepage Test and Multinomial Logistic Regression [#15076]
Seongkeon Lee, Youngjun Piao, Huidong Shi and Jeong-Hyeon Choi
Sungshin Women's University, Korea, Republic of; Chungbuk National University, Korea, Republic of; Georgia Regents University, United States

CB4: Coffee Break
Thursday, August 13, 3:30PM-3:50PM, Room: Niagara

Special Session Z4: Computational Intelligence in Ecoinformatics
Thursday, August 13, 3:50PM-5:30PM, Room: Niagara, Chair: Daniel Ashlock

3:50PM  Stress and Productivity Performance in the Workforce Modelled with Binary Decision Automata [#15035]
Matthew Page and Daniel Ashlock
CIBC Bank, Canada; University of Guelph, Canada
4:10PM  FragGeneScan-Plus for scalable high-throughput short-read open reading frame prediction [#15109]
Dongjae Kim, Aria Hahn, Shang-Ju Wu, Niels Hanson, Kishori Konwar and Steven Hallam
University of British Columbia, Canada
4:30PM  A Comparison of Incremental Community Assembly with Evolutionary Community Selection [#15065]
Daniel Ashlock and Meghan Timmins
University of Guelph, Canada
4:50PM  Assembly independent functional annotation of short-read data using SOFA: Short-ORF Functional Annotation [#15083]
Aria Hahn, Niels Hanson, Dongjae Kim, Kishori Konwar and Steven Hallam
University of British Columbia, Canada
5:10PM  Varying Decision Inputs in Prisoner's Dilemma [#15041]
Lee-Ann Barlow and Daniel Ashlock
University of Guelph, Canada

Plenary Poster Session P1: Reception and Poster Session
Thursday, August 13, 6:00PM-8:00PM, Room: Rainbow Salon, Chair: Sheridan Houghten

P101  Protein Secondary Structure Prediction Using an Evolutionary Computation Method and Clustering [#15086]
Masood Zamani and Kremer Stefan
University of Guelph, Canada
P102  Taenia Biomolecular Phylogeny and the Impact of Mitochondrial Genes on this Latter [#15010]
Huda Al-Nayyef, Christophe Guyeux and Jacques M. Bahi
University of Franche-Comte, France
P103  Protein Structure Similarity using Recurrence Relation Technique [#15088]
S. Jahnavi Somavarapu, Dr. K. Suvarna Vani Koneru and Praveen Kumar Kollu
V.R.Siddhartha Engineering College, India
P104  LargeDEL: A Tool for Identifying Large Deletions in the Whole Genome Sequencing Data [#15017]
Pinar Kavak and Huseyin Demirci
Advanced Genomics and Bioinformatics Research Group, BILGEM, TUBITAK, Turkey
P105  Novel Domain Identification Approach for Protein-Protein Interaction Prediction [#15105]
Maad Shatnawi and Nazar Zaki
United Arab Emirates University, United Arab Emirates
P106  TSC_ATP: A Two-Stage Classifier For Predicting Protein-ATP Binding Sites From Protein Sequence [#15090]
Bryan Andrews and Jing Hu
Franklin and Marshall College, United States
P107  Analysis of Gene Mutation that cause Lung Cancer by using Data miningand Study of Common Remedy [#15054]
Chaewon Ham, Jiwoo Kim, Seojung Ahn, Yebin Kim, Sewon Kim and Taeseon Yoon
Department of International, Hankuk Academy of Foreign Studies, Korea (South); Department of Natural Science, Hankuk Academy of Foreign Studies, Korea (South)
P108  Prediction of High-Throughput Protein-Protein Interactions based on Protein Sequence Information [#15062]
Yixun Li, Behzad Rezaei, Alioune Ngom and Luis Rueda
University of Windsor, Canada
P109  The impact of particles initialization in PSO: parameter estimation as a case in point [#15031]
Paolo Cazzaniga, Marco S. Nobile and Daniela Besozzi
University of Bergamo, Italy; University of Milano-Bicocca, Italy; University of Milano, Italy
P110  Interactive Evolution Instead of Default Parameters [#15042]
Daniel Ashlock, Cameron McGuinness and Joseph O'Neill
University of Guelph, Canada
P111  On predicting transport proteins and their substrates for the reconstruction of metabolic networks [#15043]
Faizah Aplop and Gregory Butler
Universiti Malaysia Terengganu, Malaysia; Concordia University, Canada
P112  A Neural Network Approach to Retinal Layer Boundary Identification From Optical Coherence Tomography Images [#15045]
Kevin McDonough, Ilya Kolmanovsky and Inna Glybina
University of Michigan, United States; Wayne State University, School of Medicine, United States
P113  Dimensionality Reduction Approach for Genotypic Data [#15051]
Luluah Al-Husain and Alaaeldin Hafez
King Saud University, Saudi Arabia
P114  Reconstruction of a GRN model of salt stress response in Arabidopsis using genetic algorithms [#15053]
Gonzalo Ruz, Tania Timmermann and Eric Goles
Universidad Adolfo Ibanez, Chile
P115  A Multi-Scale Evolutionary Algorithm for Engineering Bacterial Populations [#15104]
Jennifer Hallinan and Anil Wipat
Macquarie University, Australia; Newcastle University, United Kingdom
P116  An Information Extraction System for Protein Function Prediction [#15046]
Kamal Taha and Paul Yoo
Khalifa University, United Arab Emirates; Bournemouth University, United Kingdom
P117  An Intelligent Multi-Agent System Architecture for enhancing Self-Management of Type 2 Diabetic Patients [#15007]
Zahra Darabi, Saba Shokoohisolgi, Mohammadhosein Fazel Zarandi and Burhan Turksen
Department of Industrial Engineering Sharif University of Technology, Iran; Department of Industrial Engineering Amir-Kabir University of Technology, Iran; Department of Mechanical and Industrial Engineering University of Toronto, Canada
P118  Analysis of Cell Migration Patterns in Time Lapse Microscopy Using Texture Features [#15060]
Jiang Ching-Fen, Chiu Tzeng-Shiang and Tsai Ming-Hong
Department of Biomedical Engineering, I-Shou University, Taiwan
P119  A Complexity Measurement for de novo Protein Folding [#15021]
Michael Brown, Olivia Hua and James Coker
University of Maryland, University College, United States; Saint Mary's College of California, United States
P120  Epilepsy Detection using Ensemble methods: A Novel Hybrid Classifiers based Model for mining in Neuro-imaging [#15005]
A.B.N. Alvi and Usman Qamar
NUST, Pakistan
P121  A Novel Approach for Finding Informative Genes in Ten Subtypes of Breast Cancer [#15047]
Forough Firoozbakht, Iman Rezaeian, Lisa Porter, Alioune Ngom and Luis Rueda
University of Windsor, Canada
P122  Hybrid Feature Selection Methods for Online Biomedical Publication Classification [#15079]
Long Ma, Yanqing Zhang, Raj Sunderraman, Peter T. Fox, Angela R. Laird, Jessica A. Turner and Matthew D. Turner
Department of Computer Science, Georgia State University, Atlanta, United States; University of Texas Health Science Center San Antonio (UTHSCSA), United States; Department of Physics, Florida International University, Miami, United States; Department of Psychology and the Neuroscience Institute, Georgia State University, Atlanta, United States
P123  Predicting Time Sequences in Gene expression Using Dynamic Neuro-fuzzy Networks [#15095]
Ali Ahmadi and Sadaf Iranpour Tari
K.N.Toosi University of Technolog, Iran

Session C: Structure Prediction and Folding
Friday, August 14, 8:00AM-10:00AM, Room: Niagara, Chair: Kay C. Wiese

8:00AM  Genetic Operators Based on Backbone Constraint Angles for Protein Structure Prediction [#15027]
Karina Santos, Fabio Custodio, Helio Barbosa and Laurent Dardenne
National Laboratory for Scientific Computing (LNCC), Brazil
8:20AM  Classification of RNA sequences with pseudoknots using features based on partial sequences [#15012]
Kwok-Kit Tong, Kwan-Yau Cheung, Kin-Hong Lee and Kwong-Sak Leung
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin N.T. Hong Kong, Hong Kong
8:40AM  Computational approach for GRP78-NFKB binding interactions in the context of neuroprotective pathway in brain injuries [#15016]
Janneth Gonzalez
Assistant Professor, Colombia
9:00AM  A Multiobjective Approach for Protein Structure Prediction Using a Steady-State Genetic Algorithm with Phenotypic Crowding [#15026]
Gregorio Rocha, Fabio Custodio, Helio Barbosa and Laurent Dardenne
The National Laboratory for Scientific Computing (LNCC), Brazil
9:20AM  Side-Chain Flexibility in Protein Docking [#15072]
Hui Liu, Feng Lin, Jianli Yang and Xiuling Liu
Nanyang Technological University, Singapore; Hebei University, China
9:40AM  O-glycosylation Sites Prediction using the Meta-Prediction Approach [#15084]
Wei-Fu Lu and Yi-Hou Chen
Department of CSIE, Asia University, Taiwan; Department of Biomedical Science, Asia University, Taiwan

CB5: Coffee Break
Friday, August 14, 10:00AM-10:20AM, Room: Niagara

Session S: Big Data Analysis and Tools for Biological and Medical Data
Friday, August 14, 10:20AM-12:00PM, Room: Niagara, Chair: Ananya Das Christman

10:20AM  A Biomarker Ensemble Ranking Framework for Prioritizing Depression Candidate Genes [#15029]
Abu Chowdhury, Md Alam and Yanqing Zhang
Georgia State University, United States
10:40AM  Evolutionary Computation for Disease Gene Association [#15091]
Ashkan Entezari Heravi, Koosha Tahmasebipour and Sheridan Houghten
Brock University, Canada
11:00AM  A Study of Comparing the Ambiguity of Existing Virus Taxonomy Structures Using Protein's Region Names in the Vector Space Model [#15004]
Jing-Doo Wang
Asia University, Taiwan
11:20AM  REFBSS: Reference Based Similarity Search in Biological Network Databases [#15014]
Arda Soylev and Osman Abul
Necmettin Erbakan University, Turkey; TOBB University, Turkey
11:40AM  Significance Testing for Variable Selection in High-Dimension [#15069]
Jean-Michel Becu, Christophe Ambroise, Cyril Dalmasso and Yves Grandvalet
Heudiasyc, UTC, France; LaMME, UEVE, France

Plenary Talk PT2: Computational Approaches to Identify Functional Genetic Variants in Cancer
Friday, August 14, 1:30PM-2:30PM, Room: Niagara, Speaker: Gary Bader

CB6: Coffee Break
Friday, August 14, 2:30PM-2:50PM, Room: Niagara

Special Session Z3.2: Pattern Recognition, Data Mining and Image Processing for Bioinformatics, Computational Biology, and Medicine
Friday, August 14, 2:50PM-4:30PM, Room: Niagara, Chair: Fazel Zarandi

2:50PM  A Benchmark for Automated Peak Picking of Protein NMR Spectra [#15049]
Piotr Klukowski, Adam Gonczarek and Michal Walczak
Wroclaw University of Technology, Poland; ETH Zurich, Switzerland
3:10PM  A High-Speed Real-Time Nanopore Signal Detector [#15073]
Yiyun Huang, Sebastian Magierowski, Ebrahim Ghafar-Zadeh and Chengjie Wang
York University, Canada
3:30PM  Semi-Automated Patient-Specific Scalp EEG Seizure Detection with Unsupervised Machine Learning [#15028]
Otis Smart and Michael Chen
Emory University, United States; Georgia Institute of Technology, United States
3:50PM  Dynamic Ensemble Selection with Local Expertise Consistency [#15100]
Yun Zhu, Yanqing Zhang and Yi Pan
Georgia State University, United States
4:10PM  Identifying Differentially Expressed Transcripts Associated with Prostate Cancer Progression using RNA-Seq and Machine Learning Techniques [#15048]
Siva Singireddy, Abed Alkhateeb, Iman Rezaeian, Dora Cavallo-Medved, Lisa Porter and Luis Rueda
University of Windsor, Canada

CB7: Coffee Break
Friday, August 14, 4:30PM-4:50PM, Room: Niagara

Session J: Modeling, Simulation, and Optimization of Biological Systems
Friday, August 14, 4:50PM-6:30PM, Room: Niagara, Chair: Ananya Das Christman

4:50PM  Inferring the Dynamics of Gene Regulatory Networks via Optimized Recurrent Neural Network and Dynamic Bayesian Network [#15081]
Arinze Akutekwe and Huseyin Seker
University of Northumbria at Newcastle, United Kingdom
5:10PM  Bridging the Multiscale Gap: Identifying Cellular Parameters from Multicellular Data [#15082]
Qanita Bani Baker, Gregory J. Podgorski, Christopher D. Johnson, Elizabeth Vargis and Nicholas S. Flann
Utah State University, United States
5:30PM  Matching Models of HIV-1 Viral Dynamics to Clinical Data [#15085]
Andrew Adams, Zabrina Brumme, Alexander Rutherford and Ralf Wittenberg
Simon Fraser University, Canada
5:50PM  Iterative learning cascaded multiclass kernel based support vector machine for neural spike data classification [#15013]
Amir Zjajo and Rene van Leuken
Delft University of Technology, Netherlands
6:10PM  Multimodal Medical Image Registration Using Particle Swarm Optimization with Influence of the Data's Initial Orientation [#15071]
Lydia Schwab, Manuel Schmitt and Rolf Wanka
Department of Computer Science, University of Erlangen-Nuremberg, Germany

BAN: Banquet
Friday, August 14, 7:00PM-9:00PM, Room: Rainbow Salon, Chair: Sheridan Houghten

Special Session Z1&Z5: Multiobjective Optimization and Decision-Making in Bioinformatics and Bioengineering & Side Effect Machines for Sequence Analysis
Saturday, August 15, 8:00AM-9:40AM, Room: Niagara, Chair: Richard Allmendinger

8:00AM  Evolving DNA Classifiers with Extinction Based Ring Optimization [#15068]
Daniel Ashlock, Sierra Gillis, Jennifer Garner and Gary Fogel
University of Guelph, Canada; Natural Selection Incorporated, United States
8:20AM  On Side Effect Machines as a Representation for Evolutionary Algorithms [#15096]
Joseph Brown
Innopolis University, Russia
8:40AM  Chaos Automata for Sequence Visualization [#15103]
Daniel Ashlock, Cameron McGuinness and Wendy Ashlock
University of Guelph, Canada; York University, Canada
9:00AM  A Multi objective Approach to Evolving Artificial Neural Networks for Coronary Heart Disease Classification [#15040]
Alex Shenfield and Shahin Rostami
Sheffield Hallam University, United Kingdom; Bournemouth University, United Kingdom
9:20AM  Using Multi-Objective Genetic Programming to Evolve Stochastic Logic Gate Circuits [#15025]
Brian Ross
Brock University, Canada

CB8: Coffee Break
Saturday, August 15, 9:40AM-10:00AM, Room: Niagara

Special Session Z2: Gene Ontology and Applications
Saturday, August 15, 10:00AM-11:40AM, Room: Niagara, Chair: Anurag Nagar

10:00AM  A Visual Spreadsheet using HTML5 for Whole Genome Display [#15044]
Nada Alhirabi and Gregory Butler
King Saud University, Saudi Arabia; Concordia University, Canada
10:20AM  Association Rule Mining of Gene Ontology Annotation Terms for SGD [#15032]
Anurag Nagar, Michael Hahsler and Hisham Al-Mubaid
University of Houston - Clear Lake, United States; Southern Methodist University, United States
10:40AM  A Hybrid Semantic Similarity Measure for Gene Ontology Based On Offspring and Path Length [#15033]
Anurag Nagar and Hisham Al-Mubaid
University of Houston - Clear Lake, United States
11:00AM  Exploiting Information Content and Semantics to Accurately Computing Similarity of GO-based Annotated Entities [#15059]
Ignacio Traverso-Ribon and Maria-Esther Vidal
FZI Research Center for Information Technology, Germany; Universidad Simon Bolivar, Venezuela
11:20AM  Exploiting Modularity and Hierarchical Modularity to Infer Large Causal Gene Regulatory Network [#15075]
Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee and Kwong-Sak Leung
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, Hong Kong; Department of Computing and Decision Sciences, Lingnan University, Tuen Mun, Hong Kong, Hong Kong

CB9: Coffee Break
Saturday, August 15, 11:40AM-12:00PM, Room: Niagara

Session P: Biomedical Data Modeling and Mining
Saturday, August 15, 12:00PM-1:20PM, Room: Niagara, Chair: Steven Corns

12:00PM  Automated Classification of Author's Sentiments in Citation Using Machine Learning Techniques: A Preliminary Study [#15077]
In Cheol Kim and George Thoma
Lister Hill National Center for Biomedical Communications, National Library of Medicine, United States
12:20PM  Predicting Cassette Exons Using Transductive Learning Approaches [#15080]
Ana Stanescu and Doina Caragea
Kansas State University, United States
12:40PM  Sorting the Phenotypic Heterogeneity of Autism Spectrum Disorders: a Hierarchical Clustering Model [#15101]
Tayo Obafemi-Ajayi, Dao Lam, T. Nicole Takahashi, Stephen Kanne and Donald Wunsch
Missouri University of Science and Technology, United States; University of Missouri Thompson Center for Autism and Neurodevelopmental Disorders, United States
1:00PM  Granular Computing Approach for the Design of Medical Data Classification Systems [#15087]
Mohammed Al-Shammaa and Maysam F. Abbod
Brunel University, United Kingdom