Software Tools and Algorithms for Biological Systems

1. A Technical Platform for Generating Reproducible Expression Data from Streptomyces coelicolor Batch Cultivations
F. Battke, A. Herbig, A. Wentzel, Ø. M. Jakobsen, M. Bonin, D. A. Hodgson, W. Wohlleben, T. E. Ellingsen, K. Nieselt

2. MiRNA Recognition with the yasMiR System: The Quest for Further Improvements
Daniel Pasailă, Andrei Sucilă, Irina Mohorianu, Ştefan Panţiru, Liviu Ciortuz

3. Top Scoring Pair Decision Tree for Gene Expression Data Analysis
Marcin Czajkowski, Marek Krȩtowski

4. Predictive Minimum Description Length Principle Approach to Inferring Gene Regulatory Networks
Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Ping Gong, Edward J. Perkins, Youping Deng

5. Parsimonious Selection of Useful Genes in Microarray Gene Expression Data
Félix F. González-Navarro, Lluís A. Belanche-Muñoz

6. Hierarchical Signature Clustering for Time Series Microarray Data
Lars Koenig, Eunseog Youn

7. Microarray Database Mining and Cell Differentiation Defects in Schizophrenia
Aurelian Radu, Gabriela Hristescu, Pavel Katsel, Vahram Haroutunian, Kenneth L. Davis

8. miRNA Prediction Using Computational Approach
A. K. Mishra, D. K. Lobiyal

9. Improving the Accuracy of Gene Expression Profile Classification with Lorenz Curves and Gini Ratios
Quoc-Nam Tran

10. Feature Selection in Gene Expression Data Using Principal Component Analysis and Rough Set Theory
Debahuti Mishra, Rajashree Dash, Amiya Kumar Rath, Milu Acharya

11. Dramatically Reduced Precision in Microarray Analysis Retains Quantitative Properties and Provides Additional Benefits
William C. Ray

12. Algebraic Model Checking for Boolean Gene Regulatory Networks
Quoc-Nam Tran

13. Comparative Advantages of Novel Algorithms Using MSR Threshold and MSR Difference Threshold for Biclustering Gene Expression Data
Shyama Das, Sumam Mary Idicula

14. Performance Comparison of SLFN Training Algorithms for DNA Microarray Classification
Hieu Trung Huynh, Jung-Ja Kim, Yonggwan Won

15. Clustering Microarray Data to Determine Normalization Method
Marie Vendettuoli, Erin Doyle, Heike Hofmann

16. Estimation, Modeling, and Simulation of Patterned Growth in Extreme Environments
B. Strader, K. E. Schubert, M. Quintana, E. Gomez, J. Curnutt, P. Boston

17. Performance of Univariate Forecasting on Seasonal Diseases: The Case of Tuberculosis
Adhistya Erna Permanasari, Dayang Rohaya Awang Rambli, P. Dhanapal Durai Dominic

18. Predicting Individual Affect of Health Interventions to Reduce HPV Prevalence
Courtney D. Corley, Rada Mihalcea, Armin R. Mikler, Antonio P. Sanfilippo

19. Decision Tree and Ensemble Learning Algorithms with Their Applications in Bioinformatics
Dongsheng Che, Qi Liu, Khaled Rasheed, Xiuping Tao

20. Pattern Recognition of Surface EMG Biological Signals by Means of Hilbert Spectrum and Fuzzy Clustering
Ruben-Dario Pinzon-Morales, Katherine-Andrea Baquero-Duarte, Alvaro-Angel Orozco-Gutierrez, Victor-Hugo Grisales-Palacio

21. Rotation of Random Forests for Genomic and Proteomic Classification Problems
Gregor Stiglic, Juan J. Rodriguez, Peter Kokol

22. Improved Prediction of MHC Class I Binders/Non-Binders Peptides Through Artificial Neural Network Using Variable Learning Rate: SARS Corona Virus, a Case Study
Sudhir Singh Soam, Bharat Bhasker, Bhartendu Nath Mishra

23. Fast Three-Dimensional Noise Reduction for Real-Time Electron Tomography
José Antonio Martínez, José Jesús Fernández

24. Prediction of Chemical-Protein Binding Activity Using Contrast Graph Patterns
Andrzej Dominik, Zbigniew Walczak, Jacek Wojciechowski

25. Topological Constraint in High-Density Cells’ Tracking of Image Sequences
Chunming Tang, Ling Ma, Dongbin Xu

26. STRIKE: A Protein–Protein Interaction Classification Approach
Nazar Zaki, Wassim El-Hajj, Hesham M. Kamel, Fadi Sibai

27. Cooperativity of Protein Binding to Vesicles
Francisco Torrens, Gloria Castellano

28. The Role of Independent Test Set in Modeling of Protein Folding Kinetics
Nikola Štambuk, Paško Konjevoda

29. Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees
Jean-Philippe Doyon, Cedric Chauve

30. Sequence-Specific Sequence Comparison Using Pairwise Statistical Significance
Ankit Agrawal, Alok Choudhary, Xiaoqiu Huang

31. Modelling Short Time Series in Metabolomics: A Functional Data Analysis Approach
Giovanni Montana, Maurice Berk, Tim Ebbels

32. Modeling of Gene Therapy for Regenerative Cells Using Intelligent Agents
Aya Sedky Adly, Amal Elsayed Aboutabl, M. Shaarawy Ibrahim

33. Biomarkers Discovery in Medical Genomics Data
A. Benis, M. Courtine

34. Computer Simulation on Disease Vector Population Replacement Driven by the Maternal Effect Dominant Embryonic Arrest
Mauricio Guevara-Souza, Edgar E. Vallejo

35. Leukocytes Segmentation Using Markov Random Fields
C. Reta, J. A. Gonzalez, R. Diaz, J. S. Guichard

36. Ontology-Based Knowledge Discovery in Pharmacogenomics
Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes

37. Enabling Heterogeneous Data Integration and Biomedical Event Prediction Through ICT: The Test Case of Cancer Reoccurrence
Marco Picone, Sebastian Steger, Konstantinos Exarchos, Marco Fazio, Yorgos Goletsis, Dimitrios I. Fotiadis, Elena Martinelli, Diego Ardigò

38. Complexity and High-End Computing in Biology and Medicine
Dimitri Perrin

39. Molecular Modeling Study of Interaction of Anthracenedione Class of Drug Mitoxantrone and Its Analogs with DNA Tetrameric Sequences
Pamita Awasthi, Shilpa Dogra, Lalit K. Awasthi, Ritu Barthwal

40. A Monte Carlo Analysis of Peritoneal Antimicrobial Pharmacokinetics
Sanjukta Hota, Philip Crooke, John Hotchkiss

41. Histopathology Tissue Segmentation by Combining Fuzzy Clustering with Multiphase Vector Level Sets
Filiz Bunyak, Adel Hafiane, Kannappan Palaniappan

42. A Dynamically Masked Gaussian Can Efficiently Approximate a Distance Calculation for Image Segmentation
Shareef M. Dabdoub, Sheryl S. Justice, William C. Ray

43. Automatic and Robust System for Correcting Microarray Images’ Rotations and Isolating Spots
Anlei Wang, Naima Kaabouch, Wen-Chen Hu

44. Multimodality Medical Image Registration and Fusion Techniques Using Mutual Information and Genetic Algorithm-Based Approaches
Mahua Bhattacharya, Arpita Das

45. Microcalcifications Detection Using Fisher’s Linear Discriminant and Breast Density
G. A. Rodriguez, J. A. Gonzalez, L. Altamirano, J. S. Guichard, R. Diaz

46. Enhanced Optical Flow Field of Left Ventricular Motion Using Quasi-Gaussian DCT Filter
Slamet Riyadi, Mohd. Marzuki Mustafa, Aini Hussain, Oteh Maskon, Ika Faizura Mohd. Nor

47. An Efficient Algorithm for Denoising MR and CT Images Using Digital Curvelet Transform
S. Ali Hyder, R. Sukanesh

48. On the Use of Collinear and Triangle Equation for Automatic Segmentation and Boundary Detection of Cardiac Cavity Images
Riyanto Sigit, Mohd. Marzuki Mustafa, Aini Hussain, Oteh Maskon, Ika Faizura Mohd. Nor

49. The Electromagnetic-Trait Imaging Computation of Traveling Wave Method in Breast Tumor Microwave Sensor System
Zhi-fu Tao, Zhong-ling Han, Meng Yao

50. Medical Image Processing Using Novel Wavelet Filters Based on Atomic Functions: Optimal Medical Image Compression
Cristina Juarez Landin, Magally Martinez Reyes, Anabelem Soberanes Martin, Rosa Maria Valdovinos Rosas, Jose Luis Sanchez Ramirez, Volodymyr Ponomaryov, Maria Dolores Torres Soto

51. Cancellation of Artifacts in ECG Signals Using Block Adaptive Filtering Techniques
Mohammad Zia Ur Rahman, Rafi Ahamed Shaik, D. V. Rama Koti Reddy

52. Segmentation of Medical Image Sequence by Parallel Active Contour
Abdelkader Fekir, Nacéra Benamrane

53. Computerized Decision Support System for Mass Identification in Breast Using Digital Mammogram: A Study on GA-Based Neuro-Fuzzy Approaches
Arpita Das, Mahua Bhattacharya

54. Optimization-Based Technique for Separation and Detection of Saccadic Movements and Eye-Blinking in Electrooculography Biosignals
Robert Krupiński, Przemysław Mazurek

55. A Framework for Lipoprotein Ontology
Meifania Chen, Maja Hadzic

56. Verbal Decision Analysis Applied on the Optimization of Alzheimer’s Disease Diagnosis: A Case Study Based on Neuroimaging
Isabelle Tamanini, Ana Karoline Castro, Plácido Rogério Pinheiro, Mirian Calíope Dantas Pinheiro

57. Asynchronous Brain Machine Interface-Based Control of a Wheelchair
C. R. Hema, M. P. Paulraj, Sazali Yaacob, Abdul Hamid Adom, R. Nagarajan

58. Toward an Application to Psychological Disorders Diagnosis
Luciano Comin Nunes, Plácido Rogério Pinheiro, Tarcı́sio Cavalcante Pequeno, Mirian Calíope Dantas Pinheiro

59. Enhancing Medical Research Efficiency by Using Concept Maps
Varadraj P. Gurupur, Amit S. Kamdi, Tolga Tuncer, Murat M. Tanik, Murat N. Tanju

60. Analysis of Neural Sources of P300 Event-Related Potential in Normal and Schizophrenic Participants
Malihe Sabeti, Ehsan Moradi, Serajeddin Katebi

61. Design and Development of a Tele-Healthcare Information System Based on Web Services and HL7 Standards
Ean-Wen Huang, Rui-Suan Hung, Shwu-Fen Chiou, Fei-Ying Liu, Der-Ming Liou

62. Fuzzy Logic Based Expert System for the Treatment of Mobile Tooth
Vijay Kumar Mago, Anjali Mago, Poonam Sharma, Jagmohan Mago

63. A Microcomputer FES System for Wrist Moving Control
Li Cao, Jin-Sheng Yang, Zhi-Long Geng, Gang Cao

64. Computer-Aided Decision System for the Clubfeet Deformities
Tien Tuan Dao, Frédéric Marin, Henri Bensahel, Marie Christine Ho Ba Tho

65. A Framework for Specifying Safe Behavior of the CIIP Medical System
Seyed Morteza Babamir

66. Lotka–Volterra System with Volterra Multiplier
Klaus Gürlebeck, Xinhua Ji

67. A Biological Compression Model and Its Applications
Minh Duc Cao, Trevor I. Dix, Lloyd Allison

68. Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research
Paolo Locatelli, Emanuele Baj, Nicola Restifo, Gianni Origgi, Silvia Bragagia

69. Analysis and Clustering of MicroRNA Array: A New Efficient and Reliable Computational Method
Luca Sterpone, Federica Collino, Giovanni Camussi, Claudio Loconsole

70. Stochastic Simulations of Mixed-Lipid Compartments: From Self-Assembling Vesicles to Self-Producing Protocells
Kepa Ruiz-Mirazo, Gabriel Piedrafita, Fulvio Ciriaco, Fabio Mavelli

71. A New Genetic Algorithm for Polygonal Approximation
Cecilia Di Ruberto, Andrea Morgera

72. Challenges When Using Real-World Bio-data to Calibrate Simulation Systems
Elaine M. Blount, Stacie I. Ringleb, Andreas Tolk

73. Credibility of Digital Content in a Healthcare Collaborative Community
Wail M. Omar, Dinesh K. Saini, Mustafa Hasan

74. Using Standardized Numerical Scores for the Display and Interpretation of Biomedical Data
Robert A. Warner

75. ImagCell: A Computer Tool for Cell Culture Image Processing Applications in Bioimpedance Measurements
Alberto Yúfera, Estefanía Gallego, Javier Molina

76. From Ontology Selection and Semantic Web to an Integrated Information System for Food-borne Diseases and Food Safety
Xianghe Yan, Yun Peng, Jianghong Meng, Juliana Ruzante, Pina M. Fratamico, Lihan Huang, Vijay Juneja, David S. Needleman

77. Algebraic Analysis of Social Networks for Bio-surveillance: The Cases of SARS-Beijing-2003 and AH1N1 Influenza-México-2009
Doracelly Hincapié, Juan Ospina

Keywords: Life Sciences, Bioinformatics, Computational Biology/Bioinformatics, Systems Biology