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Advances in Bioinformatics

ISSN Print: 1687-8027

ISSN Online:

Website: http://www.hindawi.com/journals/abi/

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Prediction of B-Cell Epitopes in Listeriolysin O, a Cholesterol Dependent Cytolysin Secreted by Listeria monocytogenes

Morris S. Jones,J. Mark Carter

Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram

Yunyun Zhou,Douglas R. Call,Shira L. Broschat

An Overview of the Statistical Methods Used for Inferring Gene Regulatory Networks and Protein-Protein Interaction Networks

Amina Noor,Erchin Serpedin,Mohamed Nounou,Hazem Nounou

Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis

Mario Flores,Tzu-Hung Hsiao,Yu-Chiao Chiu,Eric Y. Chuang

Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

Hassan Taghipour,Mahdi Rezaei,Heydar Ali Esmaili

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

Chiquito Crasto,Chandrahas Narne,Mikako Kawai,Landon Wilson

Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference

Navadon Khunlertgit,Byung-Jun Yoon

Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach

Kwadwo S. Agyepong,Fang-Han Hsu,Edward R. Dougherty,Erchin Serpedin

Correction of Spatial Bias in Oligonucleotide Array Data

Philippe Serhal,Sébastien Lemieux

Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs

Ning Zhang,Shan Gao,Lei Zhang,Jishou Ruan

Literature Mining Solutions for Life Science Research

Jörg Hakenberg,Goran Nenadic,Dietrich Rebholz-Schuhmann,Jin-Dong Kim

Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach

Kwadwo S. Agyepong,Fang-Han Hsu,Edward R. Dougherty,Erchin Serpedin

Gene Regulation, Modulation, and Their Applications in Gene Expression Data Analysis

Mario Flores,Tzu-Hung Hsiao,Yu-Chiao Chiu,Eric Y. Chuang,Yufei Huang,Yidong Chen

Correction of Spatial Bias in Oligonucleotide Array Data

Philippe Serhal,Sébastien Lemieux

Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases

Manrique Mata-Montero,Nabil Shalaby,Bradley Sheppard

Reverse Engineering Sparse Gene Regulatory Networks Using Cubature Kalman Filter and Compressed Sensing

Amina Noor,Erchin Serpedin,Mohamed Nounou,Hazem Nounou

Computational and Statistical Approaches for Modeling of Proteomic and Genomic Networks

Mohamed Nounou,Hazem Nounou,Erchin Serpedin,Aniruddha Datta,Yufei Huang

A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

Tomas Hruz,Markus Wyss,Christoph Lucas,Oliver Laule,Peter von Rohr,Philip Zimmermann,Stefan Bleuler

Comparing Imputation Procedures for Affymetrix Gene Expression Datasets Using MAQC Datasets

Sreevidya Sadananda Sadasiva Rao,Lori A. Shepherd,Andrew E. Bruno,Song Liu,Jeffrey C. Miecznikowski

Literature Mining Solutions for Life Science Research

J？rg Hakenberg,Goran Nenadic,Dietrich Rebholz-Schuhmann,Jin-Dong Kim

Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs

Ning Zhang,Shan Gao,Lei Zhang,Jishou Ruan,Tao Zhang

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

Chiquito Crasto,Chandrahas Narne,Mikako Kawai,Landon Wilson,Stephen Barnes

Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

Hassan Taghipour,Mahdi Rezaei,Heydar Ali Esmaili

Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram

Yunyun Zhou,Douglas R. Call,Shira L. Broschat

An Overview of the Statistical Methods Used for Inferring Gene Regulatory Networks and Protein-Protein Interaction Networks

Amina Noor,Erchin Serpedin,Mohamed Nounou,Hazem Nounou,Nady Mohamed,Lotfi Chouchane

Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference

Navadon Khunlertgit,Byung-Jun Yoon

Applications of Natural Language Processing in Biodiversity Science

Anne E. Thessen,Hong Cui,Dmitry Mozzherin

BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

Syed Toufeeq Ahmed,Hasan Davulcu,Sukru Tikves,Radhika Nair,Zhongming Zhao

Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

Sofie Van Landeghem,Kai Hakala,Samuel R？nnqvist,Tapio Salakoski,Yves Van de Peer,Filip Ginter

Detecting Cancer Outlier Genes with Potential Rearrangement Using Gene Expression Data and Biological Networks

Mohammed Alshalalfa,Tarek A. Bismar,Reda Alhajj

CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

Hamed Bostan,Naomie Salim,Zeti Azura Hussein,Peter Klappa,Mohd Shahir Shamsir

Sequence Complexity of Chromosome 3 in Caenorhabditis elegans

Gaetano Pierro

Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges

Andrea Manconi,Eloisa Vargiu,Giuliano Armano,Luciano Milanesi

A Topology-Based Metric for Measuring Term Similarity in the Gene Ontology

Gaston K. Mazandu,Nicola J. Mulder

Maximum Recommended Dosage of Lithium for Pregnant Women Based on a PBPK Model for Lithium Absorption

Scott Horton,Amalie Tuerk,Daniel Cook,Jiadi Cook,Prasad Dhurjati

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Julien Allali,Cédric Saule,Cédric Chauve,Yves d’Aubenton-Carafa,Alain Denise,Christine Drevet,Pascal Ferraro,Daniel Gautheret,Claire Herrbach,Fabrice Leclerc,Antoine de Monte,Aida Ouangraoua,Marie-France Sagot,Michel Termier,Claude Thermes,Hélène Touzet

On the Meaning of Affinity Limits in B-Cell Epitope Prediction for Antipeptide Antibody-Mediated Immunity

Salvador Eugenio C. Caoili

Do Peers See More in a Paper Than Its Authors?

Anna Divoli,Preslav Nakov,Marti A. Hearst

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains

Martin Mann,Rhodri Saunders,Cameron Smith,Rolf Backofen,Charlotte M. Deane

Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach

Amine Ghozlane,Frédéric Bringaud,Hayssam Soueidan,Isabelle Dutour,Fabien Jourdan,Patricia Thébault

Gap Detection for Genome-Scale Constraint-Based Models

J. Paul Brooks,William P. Burns,Stephen S. Fong,Chris M. Gowen,Seth B. Roberts

A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data

Ian Roberts,Stephanie A. Carter,Cinzia G. Scarpini,Konstantina Karagavriilidou,Jenny C. J. Barna,Mark Calleja,Nicholas Coleman

Training Experimental Biologists in Bioinformatics

Pedro Fernandes,Pooja Jain,Catarina Moita

Wavelet Packet Entropy for Heart Murmurs Classification

Fatemeh Safara,Shyamala Doraisamy,Azreen Azman,Azrul Jantan,Sri Ranga

Application of an Integrative Computational Framework in Trancriptomic Data of Atherosclerotic Mice Suggests Numerous Molecular Players

Olga Papadodima,Allan Sirsj？,Fragiskos N. Kolisis,Aristotelis Chatziioannou

MicroRNA Response Elements-Mediated miRNA-miRNA Interactions in Prostate Cancer

Mohammed Alshalalfa

Intervention in Biological Phenomena via Feedback Linearization

Mohamed Amine Fnaiech,Hazem Nounou,Mohamed Nounou,Aniruddha Datta

In Silico Docking of HNF-1a Receptor Ligands

Gumpeny Ramachandra Sridhar,Padmanabhuni Venkata Nageswara Rao,Dowluru SVGK Kaladhar,Tatavarthi Uma Devi

In Silico Docking of HNF-1a Receptor Ligands

Gumpeny Ramachandra Sridhar,Padmanabhuni Venkata Nageswara Rao,Dowluru SVGK Kaladhar,Tatavarthi Uma Devi,Sali Veeresh Kumar

Prediction of Enzyme Mutant Activity Using Computational Mutagenesis and Incremental Transduction

Nada Basit,Harry Wechsler

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