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

Author(s): Mario Flores | Tzu-Hung Hsiao | Yu-Chiao Chiu | Eric Y. Chuang | Yufei Huang | Yidong Chen
Volume: 2013
Year: 2013

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

Author(s): Amina Noor | Erchin Serpedin | Mohamed Nounou | Hazem Nounou
Volume: 2013
Year: 2013

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

Author(s): Tomas Hruz | Markus Wyss | Christoph Lucas | Oliver Laule | Peter von Rohr | Philip Zimmermann | Stefan Bleuler
Volume: 2013
Year: 2013

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

Author(s): Hassan Taghipour | Mahdi Rezaei | Heydar Ali Esmaili
Volume: 2013
Year: 2013

Computational and Statistical Approaches for Modeling of Proteomic and Genomic Networks

Author(s): Mohamed Nounou | Hazem Nounou | Erchin Serpedin | Aniruddha Datta | Yufei Huang
Volume: 2013
Year: 2013

Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs

Author(s): Ning Zhang | Shan Gao | Lei Zhang | Jishou Ruan | Tao Zhang
Volume: 2013
Year: 2013

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

Author(s): Manrique Mata-Montero | Nabil Shalaby | Bradley Sheppard
Volume: 2013
Year: 2013

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

Author(s): Amina Noor | Erchin Serpedin | Mohamed Nounou | Hazem Nounou | Nady Mohamed | Lotfi Chouchane
Volume: 2013
Year: 2013

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

Author(s): Yunyun Zhou | Douglas R. Call | Shira L. Broschat
Volume: 2013
Year: 2013

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

Author(s): Chiquito Crasto | Chandrahas Narne | Mikako Kawai | Landon Wilson | Stephen Barnes
Volume: 2013
Year: 2013

Literature Mining Solutions for Life Science Research

Author(s): Jörg Hakenberg | Goran Nenadic | Dietrich Rebholz-Schuhmann | Jin-Dong Kim
Volume: 2013
Year: 2013

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

Author(s): Kwadwo S. Agyepong | Fang-Han Hsu | Edward R. Dougherty | Erchin Serpedin
Volume: 2013
Year: 2013

Correction of Spatial Bias in Oligonucleotide Array Data

Author(s): Philippe Serhal | Sébastien Lemieux
Volume: 2013
Year: 2013

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

Author(s): Navadon Khunlertgit | Byung-Jun Yoon
Volume: 2013
Year: 2013

In Silico Docking of HNF-1a Receptor Ligands

Author(s): Gumpeny Ramachandra Sridhar | Padmanabhuni Venkata Nageswara Rao | Dowluru SVGK Kaladhar | Tatavarthi Uma Devi | Sali Veeresh Kumar
Volume: 2012
Year: 2012

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Author(s): 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
Volume: 2012
Year: 2012

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

Author(s): Salvador Eugenio C. Caoili
Volume: 2012
Year: 2012

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

Author(s): Gaston K. Mazandu | Nicola J. Mulder
Volume: 2012
Year: 2012

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

Author(s): Ian Roberts | Stephanie A. Carter | Cinzia G. Scarpini | Konstantina Karagavriilidou | Jenny C. J. Barna | Mark Calleja | Nicholas Coleman
Volume: 2012
Year: 2012

Intervention in Biological Phenomena via Feedback Linearization

Author(s): Mohamed Amine Fnaiech | Hazem Nounou | Mohamed Nounou | Aniruddha Datta
Volume: 2012
Year: 2012

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

Author(s): Mohammed Alshalalfa
Volume: 2012
Year: 2012

Sequence Complexity of Chromosome 3 in Caenorhabditis elegans

Author(s): Gaetano Pierro
Volume: 2012
Year: 2012

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

Author(s): Martin Mann | Rhodri Saunders | Cameron Smith | Rolf Backofen | Charlotte M. Deane
Volume: 2012
Year: 2012

Training Experimental Biologists in Bioinformatics

Author(s): Pedro Fernandes | Pooja Jain | Catarina Moita
Volume: 2012
Year: 2012

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

Author(s): Olga Papadodima | Allan Sirsjö | Fragiskos N. Kolisis | Aristotelis Chatziioannou
Volume: 2012
Year: 2012

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

Author(s): Hamed Bostan | Naomie Salim | Zeti Azura Hussein | Peter Klappa | Mohd Shahir Shamsir
Volume: 2012
Year: 2012

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

Author(s): Mohammed Alshalalfa | Tarek A. Bismar | Reda Alhajj
Volume: 2012
Year: 2012

Do Peers See More in a Paper Than Its Authors?

Author(s): Anna Divoli | Preslav Nakov | Marti A. Hearst
Volume: 2012
Year: 2012

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

Author(s): Scott Horton | Amalie Tuerk | Daniel Cook | Jiadi Cook | Prasad Dhurjati
Volume: 2012
Year: 2012

BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

Author(s): Syed Toufeeq Ahmed | Hasan Davulcu | Sukru Tikves | Radhika Nair | Zhongming Zhao
Volume: 2012
Year: 2012

Gap Detection for Genome-Scale Constraint-Based Models

Author(s): J. Paul Brooks | William P. Burns | Stephen S. Fong | Chris M. Gowen | Seth B. Roberts
Volume: 2012
Year: 2012

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

Author(s): Amine Ghozlane | Frédéric Bringaud | Hayssam Soueidan | Isabelle Dutour | Fabien Jourdan | Patricia Thébault
Volume: 2012
Year: 2012

Applications of Natural Language Processing in Biodiversity Science

Author(s): Anne E. Thessen | Hong Cui | Dmitry Mozzherin
Volume: 2012
Year: 2012

Wavelet Packet Entropy for Heart Murmurs Classification

Author(s): Fatemeh Safara | Shyamala Doraisamy | Azreen Azman | Azrul Jantan | Sri Ranga
Volume: 2012
Year: 2012

NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

Author(s): Jens Aßmus | Armin O. Schmitt | Ralf H. Bortfeldt | Gudrun A. Brockmann
Volume: 2011
Year: 2011

Predicting Flavonoid UGT Regioselectivity

Author(s): Rhydon Jackson | Debra Knisley | Cecilia McIntosh | Phillip Pfeiffer
Volume: 2011
Year: 2011

Neutropenia Prediction Based on First-Cycle Blood Counts Using a FOS-3NN Classifier

Author(s): Elize A. Shirdel | Michael J. Korenberg | Yolanda Madarnas
Volume: 2011
Year: 2011

Prediction of Enzyme Mutant Activity Using Computational Mutagenesis and Incremental Transduction

Author(s): Nada Basit | Harry Wechsler
Volume: 2011
Year: 2011

A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

Author(s): Qihua Tan | Mads Thomassen | Jacob v. B. Hjelmborg | Anders Clemmensen | Klaus Ejner Andersen | Thomas K. Petersen | Matthew McGue | Kaare Christensen | Torben A. Kruse
Volume: 2011
Year: 2011

Polynomial Supertree Methods Revisited

Author(s): Malte Brinkmeyer | Thasso Griebel | Sebastian Böcker
Volume: 2011
Year: 2011

ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities

Author(s): Dhwani K. Desai | Soumyadeep Nandi | Prashant K. Srivastava | Andrew M. Lynn
Volume: 2011
Year: 2011

Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification

Author(s): Gaston K. Mazandu | Nicola J. Mulder
Volume: 2011
Year: 2011

Computational Design of a DNA- and Fc-Binding Fusion Protein

Author(s): Jonas Winkler | Giuliano Armano | J. Nikolaj Dybowski | Oliver Kuhn | Filippo Ledda | Dominik Heider
Volume: 2011
Year: 2011

Structural Basis for Species Selectivity in the HIV-1 gp120-CD4 Interaction: Restoring Affinity to gp120 in Murine CD4 Mimetic Peptides

Author(s): Kristin Kassler | Julia Meier | Jutta Eichler | Heinrich Sticht
Volume: 2011
Year: 2011

GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation

Author(s): Mark Gosink | Sawsan Khuri | Camilo Valdes | Zhijie Jiang | Nicholas F. Tsinoremas
Volume: 2011
Year: 2011

Data-Driven Compensation for Flow Cytometry of Solid Tissues

Author(s): Nickolaas Maria van Rodijnen | Math Pieters | Sjack Hoop | Marius Nap
Volume: 2011
Year: 2011

Cotranslational Protein Folding and Terminus Hydrophobicity

Author(s): Sheenal Srivastava | Yumi Patton | David W. Fisher | Graham R. Wood
Volume: 2011
Year: 2011

Features-Based Deisotoping Method for Tandem Mass Spectra

Author(s): Zheng Yuan | Jinhong Shi | Wenjun Lin | Bolin Chen | Fang-Xiang Wu
Volume: 2011
Year: 2011

Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case

Author(s): Dagmar Iber
Volume: 2011
Year: 2011

An Integrated Framework to Model Cellular Phenotype as a Component of Biochemical Networks

Author(s): Michael Gormley | Viswanadha U. Akella | Judy N. Quong | Andrew A. Quong
Volume: 2011
Year: 2011