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Journal Contents: International Journal of Knowledge Discovery in Bioinformatics (IJKDB)

Volume 4 (2014)
Issue 1
1.
Towards a Mixed Approach to Extract Biomedical Terms from Text Corpus (pages 1-15)
Juan Antonio Lossio Ventura (LIRMM, University Montpellier 2, Montpellier, France & CNRS, Paris, France), Clement Jonquet (LIRMM, University Montpellier 2, Montpellier, France & CNRS, Paris, France), Mathieu Roche (UMR TETIS, Cirad, Irstea, AgroParisTech, Montpellier, France) and Maguelonne Teisseire (UMR TETIS, Cirad, Irstea, AgroParisTech, Montpellier, France)
2.
Property and Personality Rights with Regard to Biobanks: A Layered System with Germany as an Example (pages 16-23)
Jürgen Robienski (Centre for Ethics and Law in the Life Sciences (CELLS), Medical University Hannover, Hannover, Germany) and Jürgen Simon (Centre for Ethics and Law in the Life Sciences (CELLS), Medical University Hannover, Hannover, Germany)
3.
Domain-Based Approaches to Prediction and Analysis of Protein-Protein Interactions (pages 24-41)
Morihiro Hayashida (Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan) and Tatsuya Akutsu (Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan)
4.
Biological and Medical Big Data Mining (pages 42-56)
George Tzanis (Aristotle University of Thessaloniki, Thessaloniki, Greece)
Volume 3 (2012)
Issue 1
1.
Improved Feature Selection by Incorporating Gene Similarity into the LASSO (pages 1-22)
Christopher E. Gillies (Department of Computer Science and Engineering, Oakland University, Rochester, MI, USA), Xiaoli Gao (Department of Mathematics and Statistics, Oakland University, Rochester, MI, USA), Nilesh V. Patel (Department of Computer Science and Engineering, Oakland University, Rochester, MI, USA), Mohammad-Reza Siadat (Department of Computer Science and Engineering, Oakland University, Rochester, MI, USA) and George D. Wilson (Radiation Oncology Department and BioBank Department Beaumont Health System, Royal Oak, MI, USA)
2.
Insight into Disrupted Spatial Patterns of Human Connectome in Alzheimer’s Disease via Subgraph Mining (pages 23-38)
Junming Shao (Department of Neuroradiology, Technische Universität München, Munich, Germany, & Institute for Computer Science, Johannes Gutenberg-Universität Mainz, Mainz, Germany), Qinli Yang (Institute for Computer Science, Ludwig-Maximilians-Universität München, Munich, Germany), Afra Wohlschläger (Department of Neuroradiology, Technische Universität München, Munich, Germany) and Christian Sorg (Department of Neuroradiology and Psychiarty, Technische Universität München, Munich, Germany)
3.
Figure Based Biomedical Document Retrieval System using Structural Image Features (pages 39-58)
Harikrishna G. N. Rai (Infosys Labs, Infosys Limited, Bangalore, India), K Sai Deepak (Infosys Labs, Infosys Limited, Bangalore, India) and P. Radha Krishna (Infosys Labs, Infosys Limited, Hyderabad, India)
4.
Exerting Cost-Sensitive and Feature Creation Algorithms for Coronary Artery Disease Diagnosis (pages 59-79)
Roohallah Alizadehsani (Department of Computer Engineering, Sharif University of Technology, Tehran, Iran), Mohammad Javad Hosseini (Department of Computer Engineering, Sharif University of Technology, Tehran, Iran), Reihane Boghrati (Department of Computer Engineering, Sharif University of Technology, Tehran, Iran), Asma Ghandeharioun (Department of Computer Engineering, Sharif University of Technology, Tehran, Iran), Fahime Khozeimeh (Mashhad University of Medical Science, Mashhad, Iran) and Zahra Alizadeh Sani (Tehran University of Medical Science, Tehran, Iran)
Issue 2
1.
Classifier Ensemble Methods for Diagnosing COPD from Volatile Organic Compounds in Exhaled Air (pages 1-15)
Ludmila Ilieva Kuncheva (School of Computer Science, Bangor University, Bangor Gwynedd, UK), Juan Jose Rodríguez (Escuela Politécnica Superior, Universidad de Burgos, Burgos, Spain), Yasir Iftikhar Syed (Respiratory Department, Prince Philip Hospital, Dafen, Llanelli, UK), Christopher O. Phillips (Welsh Centre for Printing and Coating, College of Engineering, Swansea University, Swansea, UK) and Keir Edward Lewis (Respiratory Department, Prince Philip Hospital, & College of Medicine, Swansea University, Llanelli, UK)
2.
Predicting Aging-Genes in Drosophila Melanogaster by Integrating Network Topological Features and Functional Categories (pages 16-26)
Yan-Hui Li (Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Beijing, China), Jian-Hui Li (Computer Network Information Center Chinese Academy of Sciences, Beijing, China), Xin Song (Computer Network Information Center Chinese Academy of Sciences, Beijing, China), Kai Feng (Computer Network Information Center Chinese Academy of Sciences, Beijing, China) and Yuan-Chun Zhou (Computer Network Information Center Chinese Academy of Sciences, Beijing, China)
3.
Evidence-Based Combination of Weighted Classifiers Approach for Epileptic Seizure Detection using EEG Signals (pages 27-44)
Abduljalil Mohamed (Computer Science and Engineering Department, College of Engineering, Qatar University, Qatar), Khaled Bashir Shaban (Computer Science and Engineering Department, College of Engineering, Qatar University, Qatar) and Amr Mohamed (Computer Science and Engineering Department, College of Engineering, Qatar University, Qatar)
4.
Perspective Wall Technique for Visualizing and Interpreting Medical Data (pages 45-61)
Hela Ltifi (REsearch Group on Intelligent Machines, National School of Engineers, University of Sfax, Sfax, Tunisia), Mounir Ben Ayed (REsearch Group on Intelligent Machines, National School of Engineers, University of Sfax, Sfax, Tunisia), Ghada Trabelsi (REsearch Group on Intelligent Machines, National School of Engineers, University of Sfax, Sfax, Tunisia) and Adel M. Alimi (REsearch Group on Intelligent Machines, National School of Engineers, University of Sfax, Sfax, Tunisia)
Issue 3
1.
Classification of Tandem Repeats in the Human Genome (pages 1-21)
Yupu Liang (Department of Computer Science, City University of New York, New York, NY, USA), Dina Sokol (Department of Computer and Information Science, Brooklyn College of CUNY, Brooklyn, NY, USA), Sarah Zelikovitz (Department of Computer Science, College of Staten Island of CUNY, Staten Island, NY, USA) and Sarah Ita Levitan (Department of Computer Science, Brooklyn College of CUNY, Brooklyn, NY, USA)
2.
Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics (pages 22-43)
Evrim Acar (Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark), Gozde Gurdeniz (Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark), Morten A. Rasmussen (Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark), Daniela Rago (Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark), Lars O. Dragsted (Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark) and Rasmus Bro (Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark)
3.
Healthcare Data Mining: Predicting Hospital Length of Stay (PHLOS) (pages 44-66)
Ali Azari (Information System department, University of Maryland, Baltimore County (UMBC), Baltimore, MD, USA), Vandana P. Janeja (Information System department, University of Maryland, Baltimore County (UMBC), Baltimore, MD, USA) and Alex Mohseni (Emergency Medicine Associates, Potomac, MD, USA)
4.
Dis2PPI: A Workflow Designed to Integrate Proteomic and Genetic Disease Data (pages 67-85)
Daniel Luis Notari (Centro de Computação e Tecnologia da Informação, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil), Samuel Brando Oldra (Centro de Computação e Tecnologia da Informação, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil), Mauricio Adami Mariani (Centro de Computação e Tecnologia da Informação, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil), Cristian Reolon (Centro de Computação e Tecnologia da Informação, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil) and Diego Bonatto (Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil)
Issue 4
1.
Data Mining for Biologists (pages 1-14)
Koji Tsuda (Max Planck Institute for Biological Cybernetics, Tübingen, Germany)
2.
Protein Interactions for Functional Genomics (pages 15-30)
Pablo Minguez (Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain) and Joaquin Dopazo (Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain)
3.
Prioritizing Disease Genes and Understanding Disease Pathways (pages 31-49)
Xiaoyue Zhao (Bionovo Inc., Emeryville, CA, USA), Lilia M. Iakoucheva (Rockefeller University, New York, NY, USA) and Michael Q. Zhang (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA)
4.
Predicting Protein Functions from Protein Interaction Networks (pages 50-70)
Hon Nian Chua (Institute for Infocomm Research, Singapore) and Limsoon Wong (National University of Singapore, Singapore)
Volume 2 (2011)
Issue 1
1.
Combinatorial Optimization Algorithms for Metabolic Networks Alignments and Their Applications (pages 1-23)
Qiong Cheng (University of Miami, FL) and Alexander Zelikovsky (Georgia State University, GA)
2.
Influence of Genomic and Other Biological Data Sets in the Understanding of Protein Structures, Functions and Interactions (pages 24-44)
N. Srinivasan (Indian Institute of Science, India), G. Agarwal (Indian Institute of Science, India), R. M. Bhaskara (Indian Institute of Science, India), R. Gadkari (Indian Institute of Science, India), O. Krishnadev (University of Georgia, USA), B. Lakshmi (National Centre for Biological Sciences, India), S. Mahajan (National Centre for Biological Sciences, India), S. Mohanty (Indian Institute of Science, India), R. Mudgal (Indian Institute of Science, India), R. Rakshambikai (Indian Institute of Science, India), S. Sandhya (Indian Institute of Science, India), G. Sudha (Indian Institute of Science, India), L. Swapna (Indian Institute of Science, India) and N. Tyagi (Indian Institute of Science, India)
3.
Scaling Unsupervised Risk Stratification to Massive Clinical Datasets (pages 45-59)
Zeeshan Syed (University of Michigan, USA) and Ilan Rubinfeld (Henry Ford Hospital, USA)
4.
Medical Domain Knowledge and Associative Classification Rules in Diagnosis (pages 60-73)
Sung Ho Ha (Kyungpook National University, Korea)
Issue 2
1.
Transcriptome-To-Metabolome™ Biosimulation Reveals Human Hippocampal Hypometabolism with Age and Alzheimer’s Disease (pages 1-18)
Clyde F. Phelix (University of Texas at San Antonio and AL Phahelix Biometrics, Inc., USA), Richard G. LeBaron (University of Texas at San Antonio and AL Phahelix Biometrics, Inc., USA), Dawnlee J. Roberson (AL Phahelix Biometrics, Inc., USA), Rosa E. Villanueva (SouthWest Clinical Laboratory Consultants, USA), Greg Villareal (CFPAL Biomedical Consultants, USA), Omid B. Rahimi (University of Texas Health Science Center, USA), Sandra Siedlak (Case Western Reserve University, USA), Xiongwei Zhu (Case Western Reserve University, USA) and George Perry (University of Texas at San Antonio, USA)
2.
Graph-Based Shape Analysis for MRI Classification (pages 19-33)
Seth Long (Washington State University, USA) and Lawrence B. Holder (Washington State University, USA)
3.
Association Rule Mining Based HotSpot Analysis on SEER Lung Cancer Data (pages 34-54)
Ankit Agrawal (Northwestern University, USA) and Alok Choudhary (Northwestern University, USA)
4.
Search for Protein Sequence Homologues that Display Considerable Domain Length Variations (pages 55-77)
Eshita Mutt (National Centre for Biological Sciences (TIFR) and International Institute of Information Technology Hyderabad, India), Abhijit Mitra (International Institute of Information Technology Hyderabad, India) and R. Sowdhamini (National Centre for Biological Sciences (TIFR), India)
Issue 3
1.
Early Deterioration Warning for Hospitalized Patients by Mining Clinical Data (pages 1-20)
Yi Mao (Washington University in St. Louis, USA and Xidian University, China), Yixin Chen (Washington University in St. Louis, USA), Gregory Hackmann (Washington University in St. Louis, USA), Minmin Chen (Washington University in St. Louis, USA), Chenyang Lu (Washington University in St. Louis, USA), Marin Kollef (Washington University School of Medicine, USA) and Thomas C. Bailey (Washington University School of Medicine, USA)
2.
BioTextRetriever: A Tool to Retrieve Relevant Papers (pages 21-36)
Célia Talma Gonçalves (Instituto Superior de Contabilidade e Administração do Porto & CEISE-STI, Portugal), Rui Camacho (Universidade do Porto, Portugal) and Eugénio Oliveira (Universidade do Porto, Portugal)
3.
Trend Analysis of Length of Stay Data via Phase-Type Models (pages 37-51)
Truc Viet Le (Nanyang Technological University, Singapore), Chee Keong Kwoh (Nanyang Technological University, Singapore), Kheng Hock Lee (Singapore General Hospital, Singapore) and Eng Soon Teo (Nanyang Technological University, Singapore)
4.
Medical Survival Analysis Through Transduction of Semi-Supervised Regression Targets (pages 52-65)
Faisal M. Khan (Rutgers University, USA) and Qiuhua Liu (Schlumberger Limited, USA)
Issue 4
1.
Mining Medical Data to Develop Clinical Decision Making Tools in Hemodialysis: Prediction of Cardiovascular Events and Feature Selection using a Random Forest Approach (pages 1-17)
Jasmine Ion Titapiccolo (Politecnico di Milano, Italy), Manuela Ferrario (Politecnico di Milano, Italy), Sergio Cerutti (Politecnico di Milano, Italy), Carlo Barbieri (Fresenius Medical Care, Germany), Flavio Mari (Fresenius Medical Care, Germany), Emanuele Gatti (Fresenius Medical Care, Germany) and Maria G. Signorini (Politecnico di Milano, Italy)
2.
Knowledge Discovery and Multimodal Inputs for Driving an Intelligent Wheelchair (pages 18-34)
Brígida Mónica Faria (University of Aveiro, Institute of Electronics and Telematics Engineering of Aveiro, Polytechnic Institute of Porto & Artificial Intelligence and Computer Science Laboratory of University, Porto, Portugal), Luís Paulo Reis (University of Minho & Artificial Intelligence and Computer Science Laboratory of University, Porto, Portugal) and Nuno Lau (University of Aveiro & Institute of Electronics and Telematics Engineering of Aveiro, Portugal)
3.
Identification Methods of G Protein-Coupled Receptors (pages 35-52)
Meriem Zekri (Badji Mokhtar-Annaba University, Algeria), Karima Alem (Badji Mokhtar-Annaba University, Algeria) and Labiba Souici-Meslati (Badji Mokhtar-Annaba University, Algeria)
4.
PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies (pages 53-66)
Karuppiah Kanagarajadurai (Madurai Kamaraj University, India), Singaravelu Kalaimathy (Biotechnologisches Zentrum, Germany), Paramasivam Nagarajan (Max Planck Institute for Developmental Biology, Germany) and Ramanathan Sowdhamini (National Centre for Biological Sciences, India)
Volume 1 (2010)
Issue 1
1.
Prediction of Protein-Protein Interactions Between Human Host and Two Mycobacterial Organisms (pages 1-13)
Oruganty Krishnadev (Indian Institute of Science, India), Shveta Bisht (Indian Institute of Science, India) and Narayanaswamy Srinivasan (Indian Institute of Science, India)
2.
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets (pages 14-31)
Takeyuki Tamura (Kyoto University, Japan), Kazuhiro Takemoto (Graduate School of Frontier Sciences, Japan) and Tatsuya Akutsu (Kyoto University, Japan)
3.
Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map (pages 32-47)
Lee Sael (Purdue University, USA) and Daisuke Kihara (University, USA)
4.
Mapping Affymetrix Microarray Probes to the Rat Genome via a Persistent Index (pages 48-65)
Susan Fairley (University of Glasgow, UK), John D. McClure (University of Glasgow, UK), Neil Hanlon (University of Glasgow, UK), Rob Irving (University of Glasgow, UK), Martin W. McBride (University of Glasgow, UK), Anna F. Dominiczak (University of Glasgow UK) and Ela Hunt (University of Strathclyde, UK)
5.
A Transfer Learning Approach and Selective Integration of Multiple Types of Assays for Biological Network Inference (pages 66-80)
Tsuyoshi Kato (AIST Computational Biology Research Center, Japan and Ochanomizu University, Japan), Kinya Okada (KO Institute for Medical Bioinformatics, Japan), Hisashi Kashima (IBM Research, Japan) and Masashi Sugiyama (Tokyo Institute of Technology, Japan)
6.
New Trends in Graph Mining: Structural and Node-Colored Network Motifs (pages 81-99)
Francesco Bruno (DEIS, Università della Calabria, Italy), Luigi Palopoli (DEIS, Università della Calabria, Italy) and Simona E. Rombo (DEIS, Università della Calabria, Italy)
Issue 2
1.
SPCCTDM, a Catalogue for Analysis of Therapeutic Drug Monitoring Related Contents in the Drug Prescription Information (pages 1-11)
Sven Ulrich (Pharmaceutical Consultant, Germany), Pierre Baumann (University of Lausanne, Switzerland), Andreas Conca (Regional Hospital of Bolzano, Italy), Hans-Joachim Kuss (University of Munich, Germany), Viktoria Stieffenhofer (University of Mainz, Germany) and Christoph Hiemke (University of Mainz, Germany)
2.
Clustering Genes Using Heterogeneous Data Sources (pages 12-28)
Erliang Zeng (University of Notre Dame, USA), Chengyong Yang (Life Technologies Inc., USA), Tao Li (Florida International University, USA) and Giri Narasimhan (Florida International University, USA)
3.
Infer Species Phylogenies Using Self-Organizing Maps (pages 29-49)
Xiaoxu Han (Eastern Michigan University, USA)
4.
Wave-SOM: A Novel Wavelet-Based Clustering Algorithm for Analysis of Gene Expression Patterns (pages 50-73)
Andrew Blanchard (University of Arkansas, USA), Christopher Wolter (University of Arkansas & University of Minnesota, USA), David S. McNabb (University of Arkansas, USA) and Eitan Gross (University of Arkansas, USA)
Issue 3
1.
Incorporating Network Topology Improves Prediction of Protein Interaction Networks from Transcriptomic Data (pages 1-19)
Peter E. Larsen (Argonne National Laboratory, USA), Frank Collart (Argonne National Laboratory, USA) and Yang Dai (University of Illinois at Chicago, USA)
2.
Mining Protein Interactome Networks to Measure Interaction Reliability and Select Hub Proteins (pages 20-35)
Young-Rae Cho (Baylor University, USA) and Aidong Zhang (State University of New York, Buffalo, USA)
3.
Discriminative Subgraph Mining for Protein Classification (pages 36-52)
Ning Jin (University of North Carolina, Chapel Hill, USA), Calvin Young (University of North Carolina, Chapel Hill, USA) and Wei Wang (University of North Carolina, Chapel Hill, USA)
4.
Identification of Distinguishing Motifs (pages 53-67)
Wangsen Feng (Peking University, China) and Lusheng Wang (City University of Hong Kong, China)
5.
Mining Frequent Boolean Expressions: Application to Gene Expression and Regulatory Modeling (pages 68-96)
Mohammed J. Zaki (Rensselaer Polytechnic Institute, USA), Naren Ramakrishnan (Virginia Tech., USA) and Lizhuang Zhao (Microsoft Corp., USA)
6.
Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression (pages 97-112)
Richipal Singh Bindra (New Jersey Institute of Technology, USA), Jason T. L. Wang (New Jersey Institute of Technology, USA) and Paramjeet Singh Bagga (Ramapo College of New Jersey, USA)
Issue 4
1.
Hierarchical Density-Based Clustering of White Matter Tracts in the Human Brain (pages 1-25)
Junming Shao (University of Munich, Germany), Klaus Hahn (HMGU Helmholtz Center Munich, Germany), Qinli Yang (University of Edinburgh, UK), Afra Wohlschläeger (Technical University of Munich, Germany), Christian Boehm (University of Munich, Germany), Nicholas Myers (Technical University of Munich, Germany) and Claudia Plant (Florida State University, USA)
2.
Revealing the Origin and Nature of Drug Resistance of Dynamic Tumour Systems (pages 26-53)
Ricardo Santiago-Mozos (National University of Ireland Galway, Ireland), Imtiaz A. Khan (Cardiff University, UK) and Michael G. Madden (National University of Ireland Galway, Ireland)
4.
Efficient Mining Frequent Closed Discriminative Biclusters by Sample-Growth: The FDCluster Approach (pages 69-88)
Miao Wang (Northwestern Polytechnical University, China), Xuequn Shang (Northwestern Polytechnical University, China), Shaohua Zhang (Northwestern Polytechnical University, China) and Zhanhuai Li (Northwestern Polytechnical University, China)