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Castillo, Luis F.

Advances in Computational Biology

Castillo, Luis F. - Advances in Computational Biology, ebook

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ISBN: 9783319015682
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Table of contents

1. Predictive Modeling of Signaling Transduction Mediated by Tyrosine-Kinase Receptors
Ivan Mura

2. Bioinformatic Analysis of Two Proteins with Suspected Linkage to Pulmonary Atresia with Intact Ventricular Septum
Oscar Andrés Alzate Mejía, Antonio Jesús Pérez Pulido

3. Construction and Comparison of Gene Co-expression Networks Based on Immunity Microarray Data from Arabidopsis, Rice, Soybean, Tomato and Cassava
Luis Guillermo Leal, Camilo López, Liliana López-Kleine

4.
in silico Binding Free Energy Characterization of Cowpea Chlorotic Mottle Virus Coat Protein Homodimer Variants
Armando Díaz-Valle, Gabriela Chávez-Calvillo, Mauricio Carrillo-Tripp

5. Analysis of Binding Residues between PDGF-BB and Epidermal Growth Factor Receptor: A Computational Docking Study
Ricardo Cabezas, Daniel Torrente, Marco Fidel Avila, Jannet González, George Emilio Barreto

6. Software as a Service for Supporting Biodiversity Conservation Decision Making
Maria Cecilia Londoño-Murcia, Camilo Moreno, Carolina Bello, David Méndez, Mario Villamizar, Harold Castro

7. Structural and Functional Prediction of the Hypothetical Protein Pa2481 in Pseudomonas Aeruginosa Pao1

David Alberto Díaz, George Emilio Barreto, Janneth González Santos

8. Exploration of the Effect of Input Data on the Modeling of Cellular Objective in Flux Balance Analysis (FBA)
Carlos Eduardo García Sánchez, Rodrigo Gonzalo Torres Sáez

9. Prediction of Potential Kinase Inhibitors in Leishmania spp. through a Machine Learning and Molecular Docking Approach
Rodrigo Ochoa, Mark Davies, Andrés Flórez, Jairo Espinosa, Carlos Muskus

10. Functional Protein Prediction Using HMM Based Feature Representation and Relevance Analysis
Diego Fabian Collazos-Huertas, Andres Felipe Giraldo-Forero, David Cárdenas-Peña, Andres Marino Álvarez-Meza, Germán Castellanos-Domínguez

11. High Throughput Location Proteomics in Confocal Images from the Human Protein Atlas Using a Bag-of-Features Representation
Raúl Ramos-Pollán, John Arévalo, Ángel Cruz-Roa, Fabio González

12. Measuring Complexity in an Aquatic Ecosystem
Nelson Fernández, Carlos Gershenson

13. Possible Antibiofilm Effect of Peptides Derived from IcaR Repressor of Staphylococcus epidermidis Responsible for Hospital-Acquired Sepsis
Liliana Muñoz, Luz Mary Salazar, Stefany Botero, Jeannette Navarrete, Gladys Pinilla

14. “Head to Tail” Tool Analysis through ClustalW Alignment Algorithms and Construction of Distance Method Neighbor-Joining Trees Based on Genus Fusarium Genomic Distances
Juan David Henao, S. Melissa Rincón, D. Juan Jose Filgueira

15. False Positive Reduction in Automatic Segmentation System
Jheyson Vargas, Jairo Andres Velasco, Gloria Ines Alvarez, Diego Luis Linares, Enrique Bravo

16. Photosynthesis Thermodynamic Efficiency Facing Climate Change
Víctor Alonso López-Agudelo, Julián Cerón-Figueroa, Daniel Barragán

17. Thermogenesis Driven by ATP Hydrolysis in a Model with Cubic Autocatalysis
Julián Cerón-Figueroa, Víctor Alonso López-Agudelo, Daniel Barragán

18. Towards a Linked Open Data Model for Coffee Functional Relationships
Luis Bertel-Paternina, Luis F. Castillo, Gustavo Isaza, Alvaro Gaitán-Bustamente

19. Stability Analysis of Antimicrobial Peptides in Solvation Conditions by Molecular Dynamics
Daniel Osorio, Paola Rondón-Villarreal, Rodrigo Torres

20. Application of Genome Studies of Coffee Rust
Marco Cristancho, William Giraldo, David Botero, Javier Tabima, Diana Ortiz, Alejandro Peralta, Álvaro Gaitán, Silvia Restrepo, Diego Riaño

21.
In-silico Analysis of the Active Cavity of N-Acetylgalactosamine-6-Sulfate Sulfatase in Eight Species
Sergio Olarte-Avellaneda, Alexander Rodríguez-López, Carlos Javier Alméciga-Díaz

22. Gene Predictors Ensemble for Complex Metagenomes
Nestor Díaz, Andres Felipe Ruiz Velazco, Cristian Alberto Olaya Márquez

23. Classification of Antimicrobial Peptides by Using the p-spectrum Kernel and Support Vector Machines
Paola Rondón-Villarreal, Daniel A. Sierra, Rodrigo Torres

24. Genomic Relationships among Different Timor Hybrid (Coffea L.) Accessions as Revealed by SNP Identification and RNA-Seq Analysis
Juan Carlos Herrera, Andrés Mauricio Villegas, Fernando A. Garcia, Alexis Dereeper, Marie-Christine Combes, Huver E. Posada, Philippe Lashermes

25. A Combined Sensitivity and Metabolic Flux Analysis Unravel the Importance of Amino Acid Feeding Strategies in Clavulanic Acid Biosynthesis
Claudia Sánchez, Natalia Gómez, Juan Carlos Quintero, Silvia Ochoa, Rigoberto Rios

26. Flux Balance Analysis and Strain Optimization for Ethanol Production in Saccharomyces cerevisiae

León Toro, Laura Pinilla, Juan Carlos Quintero, Rigoberto Rios

27. Domain Ontology-Based Query Expansion: Relationships Types-Centered Analysis Using Gene Ontology
Alejandra Segura, Christian Vidal-Castro, Mateus Ferreira-Satler, Salvador-Sánchez

28. FS-Tree: Sequential Association Rules and First Applications to Protein Secondary Structure Analysis
Nilson Mossos, Diego Fernando Mejia-Carmona, Irene Tischer

29. Presentation and Evaluation of ABMS (Automatic Blast for Massive Sequencing)
Nelson Enrique Vera Parra, José Nelson Pérez Castillo, Cristian Alejandro Rojas Quintero

30.
In silico Analysis of Iduronate 2 Sulfatase Mutations in Colombian Patients with Hunter Syndrome (MPSII)
Johanna Galvis, Jannet González, Daniel Torrente, Harvy Velasco, George Emilio Barreto

31. Phylogenetic Analysis of Four Dung Beetle Species of Neotropical Genus Oxyternon (Coleoptera: Scarabaeidae: Scarabaeinae) Based on 28S and COI Partial Regions
Cuadrado-Ríos Sebastián, Chacón-Vargas Katherine, Londoño-González César, García-Merchán Víctor Hugo

32. Limits to Sequencing and de novo Assembly: Classic Benchmark Sequences for Optimizing Fungal NGS Designs
José Fernando Muñoz, Elizabeth Misas, Juan Esteban Gallo, Juan Guillermo McEwen, Oliver Keatinge Clay

33. Optimal Control for a Discrete Time Influenza Model
Paula Andrea Gonzalez Parra, Martine Ceberio, Sunmi Lee, Carlos Castillo-Chavez

34. Transcriptomics of the Immune System of Hydrozoan Hydractinia symbiolongicarpus Using High Throughput Sequencing Methods
Alejandra Zárate-Potes, Luis Fernando Cadavid

35. Fuzzy Model Proposal for the Coffee Berry Borer Expansion at Colombian Coffee Fields
Nychol Bazurto Gómez, Carlos Alberto Martínez Morales, Helbert Espitia Cuchango

36. Analysis of Structure and Hemolytic Activity Relationships of Antimicrobial Peptides (AMPs)
Jennifer Ruiz, Jhon Calderon, Paola Rondón-Villarreal, Rodrigo Torres

37. Candidates for New Molecules Controlling Allorecognition in Hydractinia symbiolongicarpus

Henry J. Rodríguez, Luis Fernando Cadavid

38.
Escherichia coli’s OmpA as Biosurfactant for Cosmetic Industry: Stability Analysis and Experimental Validation Based on Molecular Simulations
Sonia Milena Aguilera Segura, Angie Paola Macías, Diana Carrero Pinto, Watson Lawrence Vargas, Martha Josefina Vives-Florez, Harold Enrique Castro Barrera, Oscar Alberto Álvarez, Andrés Fernando González Barrios

39. Molecular Cloning, Modelling and Docking with Curcumin of the Dengue Virus 2 NS5 Polymerase Domain
Leidy Lorena García Ariza, Germán Alberto Téllez Ramirez, Héctor Fabio Cortes Hernández, Leonardo Padilla Sanabria, Jhon Carlos Castaño Osorio

40.
In Silico Analysis for Biomass Synthesis under Different CO2 Levels for Chlamydomonas reinhardtii Utilizing a Flux Balance Analysis Approach
David Orlando Páez Melo, Rossmary Jay-Pang Moncada, Flavia Vischi Winck, Andrés Fernando González Barrios

41. Analysis of Metabolic Functionality and Thermodynamic Feasibility of a Metagenomic Sample from “El Coquito” Hot Spring
Maria A. Zamora, Andres Pinzón, Maria M. Zambrano, Silvia Restrepo, Linda J. Broadbelt, Matthew Moura, Andrés Fernando González Barrios

42. Identification of Small Non-coding RNAs in Bacterial Genome Annotation Using Databases and Computational Approaches
Mauricio Corredor, Oscar Murillo

43. Structural Modeling of Toxoplasma gondii TGME49_289620 Proteinase
Mateo Murillo León, Diego Mauricio Moncada Giraldo, Diego Alejandro Molina, Aylan Farid Arenas, Jorge Enrique Gómez

44. Diversification of the Major Histocompatibility Complex (MHC) -G and -B Loci in New World Primates
Juan Sebastian Lugo-Ramos, Luis Fernando Cadavid

45. A Methodology for Optimizing the E-value Threshold in Alignment-Based Gene Ontology Prediction Using the ROC Curve
Ricardo Andrés Burgos-Ocampo, Andrés Felipe Giraldo-Forero, Jorge Alberto Jaramillo-Garzón, C. German Castellanos-Dominguez

46. Hydrolytic Activity of OXA and CTX-M beta-Lactamases against beta-Lactamic Antibiotics
Ana Rosa Rodríguez Blanco, María Teresa Reguero Reza, Emiliano Barreto

47. Analysis in Silico of 5’-Terminal Secondary Structures of Hepatitis C Virus Sequences Genotype 1 from Colombia
Luisa Fernanda Restrepo, Johanna Carolina Arroyave, Fabian Mauricio Cortés-Mancera

48.
In Silico Hybridization System for Mapping Functional Genes of Soil Microorganism Using Next Generation Sequencing
Guillermo G. Torres-Estupiñan, Emiliano Barreto-Hernández

49. Identification of Differently Expresed Proteins Related to Drillings Fluids Exposure in Hydractinia Symbiolongicarpus by Mass Spectrometry
Iván Aurelio Páez-Gutiérrez, Luis Fernando Cadavid

50.
In silico Modificiton of Cathelicidins Generates Analogous Peptides with Improved Antimycobacterial Activity
Sandra Chingaté, Carlos Yesid Soto, Luz Mary Salazar

51. Harmonizing Protection and Publication of Research Findings in Biosciences and Bioinformatics
Oscar Lizarazo Cortés, Natalia Lamprea, Gabriel Nemogá Soto

52. Mathematical Modeling of Lignocellulolytic Enzyme Production from Three Species of White Rot Fungi by Solid-State Fermentation
Sandra Montoya, Óscar Julián Sánchez, Laura Levin

53. Bioinformatics Tools and Data Mining for Therapeutic Drug Analysis
Juan Manuel Pérez Agudelo, Néstor Jaime Castaño Pérez, Jhon Fredy Betancur Pérez

54. iTRAQ, The High Throughput Data Analysis of Proteins to Understand Immunologic Expression in Insect
Amalia Muñoz-Gómez, Mauricio Corredor, Alfonso Benítez-Páez, Carlos Peláez

Keywords: Engineering, Computational Intelligence, Artificial Intelligence (incl. Robotics), Computational Biology/Bioinformatics

Author(s)
 
 
 
 
Publisher
Springer
Publication year
2014
Language
en
Edition
2014
Series
Advances in Intelligent Systems and Computing
Category
Technology, Energy, Traffic
Format
Ebook
eISBN (PDF)
9783319015682

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