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Bioinformatics and Biology Insights

ISSN: 1177--9322
Publisher: Libertas Academica


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Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36

Author(s): Zineb Tarhda | Oussama Semlali | Anas Kettani | Ahmed Moussa | Nada A. Abumrad | Azeddine Ibrahimi
Volume: 2013
Issue: 7
Year: 2013
ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons

Author(s): Jun-ichi Satoh | Natsuki Kawana | Yoji Yamamoto
Volume: 2013
Issue: 7
Year: 2013
A Computational Assay to Design an Epitope-Based Peptide Vaccine Against Saint Louis Encephalitis Virus

Author(s): Md. Anayet Hasan | Mehjabeen Hossain | Md. Jibran Alam
Volume: 2013
Issue: 7
Year: 2013
Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights

Author(s): Diego Frias | Joana P. Monteiro-Cunha | Aline C. Mota-Miranda | Vagner S. Fonseca | Tulio de Oliveira | Bernardo Galvao-Castro | Luiz C. J. Alcantara
Volume: 2013
Issue: 7
Year: 2013
Automatic Identification of Algal Community from Microscopic Images

Author(s): Natchimuthu Santhi | Chinnaraj Pradeepa | Parthasarathy Subashini | Senthil Kalaiselvi
Volume: 2013
Issue: 7
Year: 2013
On Crowd-verification of Biological Networks

Author(s): The sbv IMPROVER project team (in alphabetical order): Sam Ansari | Jean Binder | Stephanie Boue | Anselmo Di Fabio | William Hayes | Julia Hoeng | Anita Iskandar | Robin Kleiman | Raquel Norel | Bruce O'Neel | Manuel C. Peitsch | Carine Poussin | Dexter Pratt | Kahn Rhrissorrakrai | Walter K. Schlage | Gustavo Stolovitzky | Marja Talikka
Volume: 2013
Issue: 7
Year: 2013
Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis

Author(s): Venkatesan Nalini | Ramya Segu | Perinkulam Ravi Deepa | Vikas Khetan | Madavan Vasudevan | Subramanian Krishnakumar
Volume: 2013
Issue: 7
Year: 2013
A Modular Cell-Type Focused Inflammatory Process Network Model for Non-Diseased Pulmonary Tissue

Author(s): Jurjen W. Westra | Walter K. Schlage | Arnd Hengstermann | Stephan Gebel | Carole Mathis | Ty Thomson | Ben Wong | Vy Hoang | Emilija Veljkovic | Michael Peck | Rosemarie B. Lichtner | Dirk Weisensee | Marja Talikka | Renee Deehan | Julia Hoeng | Manuel C. Peitsch
Volume: 2013
Issue: 7
Year: 2013
Systematic Verification of Upstream Regulators of a Computable Cellular Proliferation Network Model on Non-Diseased Lung Cells Using a Dedicated Dataset

Author(s): Vincenzo Belcastro | Carine Poussin | Stephan Gebel | Carole Mathis | Walter K. Schlage | Rosemarie B. Lichtner | Sibille Quadt-Humme | Sandra Wagner | Julia Hoeng | Manuel C. Peitsch
Volume: 2013
Issue: 7
Year: 2013
Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions

Author(s): Malini Manoharan | Kannan Sankar | Bernard Offmann | Sowdhamini Ramanathan
Volume: 2013
Issue: 7
Year: 2013
Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation

Author(s): Wangsheng Zhao | Khuram Shahzad | Mingfeng Jiang | Daniel E. Graugnard | Sandra L. Rodriguez-Zas | Jun Luo | Juan J. Loor | Walter L. Hurley
Volume: 2013
Issue: 7
Year: 2013
The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum

Author(s): Markus A. Grohme | Brahim Mali | Weronika Welnicz | Stephanie Michel | Ralph O. Schill | Marcus Frohme
Volume: 2013
Issue: 7
Year: 2013
Association Between a Multi-Locus Genetic Risk Score and Inflammatory Bowel Disease

Author(s): Pingzhao Hu | Aleixo M. Muise | Xiang Xing | John H. Brumell | Mark S. Silverberg | Wei Xu
Volume: 2013
Issue: 7
Year: 2013
miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment

Author(s): Bram Sebastian | Samuel E. Aggrey
Volume: 2013
Issue: 7
Year: 2013
Knowledge Discovery in Variant Databases Using Inductive Logic Programming

Author(s): Hoan Nguyen | Tien-Dao Luu | Olivier Poch | Julie D. Thompson
Volume: 2013
Issue: 7
Year: 2013
Computational Small RNA Prediction in Bacteria

Author(s): Jayavel Sridhar | Paramasamy Gunasekaran
Volume: 2013
Issue: 7
Year: 2013
Construction of a Computable Network Model for DNA Damage, Autophagy, Cell Death, and Senescence

Author(s): Stephan Gebel | Rosemarie B. Lichtner | Brian Frushour | Walter K. Schlage | Vy Hoang | Marja Talikka | Arnd Hengstermann | Carole Mathis | Emilija Veljkovic | Michael Peck | Manuel C. Peitsch | Renee Deehan | Julia Hoeng | Jurjen W. Westra
Volume: 2013
Issue: 7
Year: 2013
Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study

Author(s): Janneth González | Angela Gálvez | Ludis Morales | George E. Barreto | Francisco Capani | Omar Sierra | Yolima Torres
Volume: 2013
Issue: 7
Year: 2013
A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

Author(s): Riccardo Percudani
Volume: 2013
Issue: 7
Year: 2013
A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences

Author(s): Nicolas Carels | Diego Frias
Volume: 2013
Issue: 7
Year: 2013
Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers

Author(s): Madhu Beta | Nalini Venkatesan | Madavan Vasudevan | Umashankar Vetrivel | Vikas Khetan | Subramanian Krishnakumar
Volume: 2013
Issue: 7
Year: 2013
Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length

Author(s): Alexander Bolshoy | Tatiana Tatarinova
Volume: 2012
Issue: 6
Year: 2012
Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR- Supported in silico Modeling

Author(s): J. Zirkel | A. Cecil | F. Schäfer | S. Rahlfs | A. Ouedraogo | K. Xiao | S. Sawadogo | B. Coulibaly | K. Becker | T. Dandekar
Volume: 2012
Issue: 6
Year: 2012
Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium

Author(s): Baraka S. Williams | Raphael D. Isokpehi | Andreas N. Mbah | Antoinesha L. Hollman | Christina O. Bernard | Shaneka S. Simmons | Wellington K. Ayensu | Bianca L. Garner
Volume: 2012
Issue: 6
Year: 2012
Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease

Author(s): Xiaofeng Ji | Wei Wang | Yuan Zheng | Jianhua Hao | Mi Sun
Volume: 2012
Issue: 6
Year: 2012
A Fast Quad-Tree Based Two Dimensional Hierarchical Clustering

Author(s): Priscilla Rajadurai | Swamynathan Sankaranarayanan
Volume: 2012
Issue: 6
Year: 2012
Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

Author(s): Divya P. Syamaladevi | Margaret Sunitha S | S. Kalaimathy | Chandrashekar C. Reddy | Mohammed Iftekhar | Shaik N. Pasha | R. Sowdhamini
Volume: 2012
Issue: 6
Year: 2012
BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks

Author(s): Oksana Kohutyuk | Fadi Towfic | M. Heather West Greenlee | Vasant Honavar
Volume: 2012
Issue: 6
Year: 2012
The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation

Author(s): Santi Nurbaiti | Muhamad A. Martoprawiro | Akhmaloka | Rukman Hertadi
Volume: 2012
Issue: 6
Year: 2012
Integrative Structural Modelling of the Cardiac Thin Filament: Energetics at the Interface and Conservation Patterns Reveal a Spotlight on Period 2 of Tropomyosin

Author(s): Margaret Sunitha S | John A. Mercer | James A. Spudich | Ramanathan Sowdhamini
Volume: 2012
Issue: 6
Year: 2012
The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses

Author(s): John Ellis | Stephen Goodswen | Paul J Kennedy | Stephen Bush
Volume: 2012
Issue: 6
Year: 2012
Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp)

Author(s): Guanjie Chen | Ao Yuan | Yanxun Zhou | Amy R. Bentley | Jie Zhou | Weiping Chen | Daniel Shriner | Adebowale Adeyemo | Charles N. Rotimi
Volume: 2012
Issue: 6
Year: 2012
DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements

Author(s): Pieter Meysman | Kathleen Marchal | Kristof Engelen
Volume: 2012
Issue: 6
Year: 2012
Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies

Author(s): Guanjie Chen | Ao Yuan | Jie Zhou | Amy R. Bentley | Adebowale Adeyemo | Charles N. Rotimi
Volume: 2012
Issue: 6
Year: 2012
The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes

Author(s): André E.R. Soares | Carlos G. Schrago
Volume: 2012
Issue: 6
Year: 2012
Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems

Author(s): Beate Krueger | Torben Friedrich | Frank Förster | Jörg Bernhardt | Roy Gross | Thomas Dandekar
Volume: 2012
Issue: 6
Year: 2012
Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Author(s): Frank Förster | Daniela Beisser | Markus A. Grohme | Chunguang Liang | Brahim Mali | Alexander Matthias Siegl | Julia C. Engelmann | Alexander V. Shkumatov | Elham Schokraie | Tobias Müller | Martina Schnölzer | Ralph O. Schill | Marcus Frohme | Thomas Dandekar
Volume: 2012
Issue: 6
Year: 2012
Mining Gene Ontology Data with AGENDA

Author(s): Guvanch Ovezmyradov | Qianhao Lu | Martin C. Göpfert
Volume: 2012
Issue: 6
Year: 2012
White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection

Author(s): Casey P. Shannon | Zsuzsanna Hollander,Janet Wilson-McManus | Robert Balshaw | Raymond T. Ng | Robert McMaster | Bruce M. McManus | Paul A. Keown | Scott J. Tebbutt
Volume: 2012
Issue: 6
Year: 2012
Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. melanogaster

Author(s): K. Harini | R. Sowdhamini
Volume: 2012
Issue: 6
Year: 2012
Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1)

Author(s): Krupa S. Jani | D.S. Dalafave
Volume: 2012
Issue: 6
Year: 2012
Structural and Functional Insights on the Myosin Superfamily

Author(s): Divya P. Syamaladevi, | James A. Spudich,,* | R. Sowdhamini,*
Volume: 2012
Issue: 6
Year: 2012
A Novel Approach for the Simultaneous Analysis of Common and Rare Variants in Complex Traits

Author(s): Ao Yuan | Guanjie Chen | Yanxun Zhou | Amy Bentley | Charles Rotimi
Volume: 2012
Issue: 6
Year: 2012
Mouse Retinal Development: a Dark Horse Model for Systems Biology Research

Author(s): Xia Zhang | Jeanne M. Serb | M. Heather West Greenlee
Volume: 2011
Issue: 5
Year: 2011
Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle

Author(s): Massimo Bionaz | Juan J. Loor
Volume: 2011
Issue: 5
Year: 2011
Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution

Author(s): E. Ashrafi | A. Alemzadeh | M. Ebrahimi | E. Ebrahimie | N. Dadkhodaei | M. Ebrahimi
Volume: 2011
Issue: 5
Year: 2011
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

Author(s): Shaneka S. Simmons | Raphael D. Isokpehi | Shyretha D. Brown | Donee L. McAllister | Charnia C. Hall | Wanaki M. McDuffy | Tamara L. Medley | Udensi K. Udensi | Rajendram V. Rajnarayanan | Wellington K. Ayensu | Hari H.P. Cohly
Volume: 2011
Issue: 5
Year: 2011
Identification of Drought-Responsive Universal Stress Proteins in Viridiplantae

Author(s): Raphael D. Isokpehi | Shaneka S. Simmons | Hari H.P. Cohly | Stephen I.N. Ekunwe | Gregorio B. Begonia | Wellington K. Ayensu
Volume: 2011
Issue: 5
Year: 2011
Conceptual Aspects of Large Meta-Analyses with Publicly Available Microarray Data: A Case Study in Oncology

Author(s): Markus Schmidberger | Sabine Lennert | Ulrich Mansmann
Volume: 2011
Issue: 5
Year: 2011
Expression of Metabolic, Tissue Remodeling, Oxidative Stress, and Inflammatory Pathways in Mammary Tissue During Involution in Lactating Dairy Cows

Author(s): Paola Piantoni | Ping Wang | James K. Drackley | Walter L. Hurley | Juan J. Loor
Volume: 2010
Issue: 4
Year: 2010
Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions

Author(s): Xiang-Ping Wang | Nigel G.F. Cooper
Volume: 2010
Issue: 4
Year: 2010
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach

Author(s): Khader Shameer | Ganesan Pugalenthi | Krishna Kumar Kandaswamy | Ponnuthurai N. Suganthan | Govindaraju Archunan | Ramanathan Sowdhamini
Volume: 2010
Issue: 4
Year: 2010
Effect of Diet Supplementation on the Expression of Bovine Genes Associated with Fatty Acid Synthesis and Metabolism

Author(s): Sandeep J. Joseph | Kelly R. Robbins | Enrique Pavan | Scott l. Pratt | Susan K. Duckett | Romdhane Rekaya
Volume: 2010
Issue: 4
Year: 2010
Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies

Author(s): R. Shyama Prasad Rao | Ole Thomsen Buus | Bernd Wollenweber
Volume: 2010
Issue: 4
Year: 2010
An Improved Approach for Mapping Quantitative Trait Loci in a Pseudo-Testcross: Revisiting a Poplar Mapping Study

Author(s): Song Wu | Jie Yang | Youjun Huang | Yao Li | Tongming Yin | Stan D. Wullschleger | Gerald A. Tuskan | Rongling Wu
Volume: 2010
Issue: 4
Year: 2010
Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors

Author(s): Marcin Kierczak | Michal Draminski | Jacek Koronacki | Jan Komorowski
Volume: 2010
Issue: 4
Year: 2010
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces

Author(s): Catherine H. Schein | Ovidiu Ivanciuc | Terumi Midoro-Horiuti | Randall M. Goldblum | Werner Braun
Volume: 2010
Issue: 4
Year: 2010
Candidate Single Nucleotide Polymorphism Markers for Arsenic Responsiveness of Protein Targets

Author(s): Raphael D. Isokpehi | Hari H.P. Cohly | Matthew N. Anyanwu | Rajendram V. Rajnarayanan | Paul B. Tchounwou | Udensi K. Udensi | Barbara E. Graham-Evans
Volume: 2010
Issue: 4
Year: 2010
Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data

Author(s): Christian Gorba | Florence Tama
Volume: 2010
Issue: 4
Year: 2010
Periodicity Detection Method for Small-Sample Time Series Datasets

Author(s): Daisuke Tominaga
Volume: 2010
Issue: 4
Year: 2010
A Plausible Role for the Presence of Internal Shine-Dalgarno Sites

Author(s): Lalit Ponnala
Volume: 2010
Issue: 4
Year: 2010
Domain Organization of Long Autotransporter Signal Sequences

Author(s): Jan A. Hiss | Gisbert Schneider
Volume: 2009
Issue: 3
Year: 2009
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences

Author(s): Ralf Aurahs | Markus Göker | Guido W. Grimm | Vera Hemleben | Christoph Hemleben | Ralf Schiebel | Michal Kučera
Volume: 2009
Issue: 3
Year: 2009
Classifying Coding DNA with Nucleotide Statistics

Author(s): Nicolas Carels | Diego Frías
Volume: 2009
Issue: 3
Year: 2009
Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data

Author(s): Haoyu Cheng | Lihua Jiang | Maoying Wu | Qi Liu
Volume: 2009
Issue: 3
Year: 2009
A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome

Author(s): Marcin Kierczak | Krzysztof Ginalski | Michał Dramiński | Jacek Koronacki | Witold Rudnicki | Jan Komorowski
Volume: 2009
Issue: 3
Year: 2009
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4

Author(s): Diamantis Sellis | Dimitrios Vlachakis | Metaxia Vlassi
Volume: 2009
Issue: 3
Year: 2009
Gene Expression Based Leukemia Sub‑Classification Using Committee Neural Networks

Author(s): Mihir S. Sewak | Narender P. Reddy | Zhong-Hui Duan
Volume: 2009
Issue: 3
Year: 2009
Graphical User Interfaces for Molecular Dynamics—Quo Vadis?

Author(s): B. Knapp | W. Schreiner
Volume: 2009
Issue: 3
Year: 2009
affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data

Author(s): Markus Schmidberger | Esmeralda Vicedo | Ulrich Mansmann
Volume: 2009
Issue: 3
Year: 2009
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences

Author(s): Surendra S Negi | Werner Braun
Volume: 2009
Issue: 3
Year: 2009
Universal Features for the Classification of Coding and Non-Coding DNA Sequences

Author(s): Nicolas Carels | Ramon Vidal | Diego Frías
Volume: 2009
Issue: 3
Year: 2009
Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Author(s): Junilda Spirollari | Jason T.L. Wang | Kaizhong Zhang | Vivian Bellofatto | Yongkyu Park | Bruce A. Shapiro
Volume: 2009
Issue: 3
Year: 2009
Control Design for Signal Transduction Networks

Author(s): Chun-Liang Lin | Yuan-Wei Liu | Chia-Hua Chuang
Volume: 2009
Issue: 3
Year: 2009
Identification of the RGG Box Motif in Shadoo: RNA-Binding and Signaling Roles?

Author(s): Susan M. Corley | Jill E. Gready
Volume: 2008
Issue: 2
Year: 2008
Identification and Investigation of Drosophila  Postsynaptic Density Homologs

Author(s): Faith L.W. Liebl | David E. Featherstone
Volume: 2008
Issue: 2
Year: 2008
Gene Copy Number Analysis for Family Data Using Semiparametric Copula Model

Author(s): Ao Yuan | Guanjie Chen | Zhong-Cheng Zhou | George Bonney | Charles Rotimi
Volume: 2008
Issue: 2
Year: 2008
Association Between a Prognostic Gene Signature and Functional Gene Sets

Author(s): Manuela Hummel | Klaus H. Metzeler | Christian Buske | Stefan K. Bohlander | Ulrich Mansmann
Volume: 2008
Issue: 2
Year: 2008
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae

Author(s): Jesper Lundström | Johan Björkegren | Jesper Tegnér
Volume: 2008
Issue: 2
Year: 2008
The Use of Artificial Neural Networks in Prediction of Congenital CMV Outcome from Sequence Data

Author(s): Ravit Arav-Boger | Yuval S. Boger | Charles B. Foster | Zvi Boger
Volume: 2008
Issue: 2
Year: 2008
Normalization and Gene p-Value Estimation: Issues in Microarray Data Processing

Author(s): Katrin Fundel | Robert Küffner | Thomas Aigner | Ralf Zimmer
Volume: 2008
Issue: 2
Year: 2008
Unsupervised Meta-Analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation

Author(s): Julia C. Engelmann | Rol | Schwarz | Steffen Blenk | Torben Friedrich | Philipp N. Seibel | Thomas Dandekar | Tobias Müller
Volume: 2008
Issue: 2
Year: 2008
Neuroinformatics: From Bioinformatics to Databasing the Brain

Author(s): Thomas M. Morse
Volume: 2008
Issue: 2
Year: 2008
Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets

Author(s): Angelica Lindlöf | Marcus Bräutigam | Aakash Chawade | Olof Olsson | Björn Olsson
Volume: 2008
Issue: 2
Year: 2008
Methodology for Constructing Problem Definitions in Bioinformatics

Author(s): Amy M. Hauth | Gertraud Burger
Volume: 2008
Issue: 2
Year: 2008
Effects of Feeding Periods of High Cholesterol and Saturated Fat Diet on Blood Biochemistry and Hydroxyproline Fractions in Rabbits

Author(s): Mohamed A. K. Abdelhalim | N. J. Siddiqi | A. S. ALhomida | Mohammed S. Al- Ayed
Volume: 2008
Issue: 2
Year: 2008
Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures

Author(s): Heiko Muller | Francesco Acquati
Volume: 2008
Issue: 2
Year: 2008
Utility of Computational Methods to Identify the Apoptosis Machinery in Unicellular Eukaryotes

Author(s): Pierre Marcel Dur | Theresa Louise Coetzer
Volume: 2008
Issue: 2
Year: 2008
Ontologies for Bioinformatics

Author(s): Nadine Schuurman | Agnieszka Leszczynski
Volume: 2008
Issue: 2
Year: 2008
Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis

Author(s): Kanaka Durga Kedarisetti | Scott Dick | Lukasz Kurgan
Volume: 2008
Issue: 2
Year: 2008
Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes

Author(s): Yurong Xin | Giulio Quarta | Hin Hark Gan | Tamar Schlick
Volume: 2008
Issue: 2
Year: 2008
A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments

Author(s): Akihiro Hirakawa | Yasunori Sato | Chikuma Hamada | Isao Yoshimura
Volume: 2008
Issue: 2
Year: 2008
Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis

Author(s): Zhenkang Xu | Laura Gutierrez | Matthew Hitchens | Steve Scherer | Amy K. Sater | Dan E. Wells
Volume: 2008
Issue: 2
Year: 2008
Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain

Author(s): Adam T. Zemla | Carol L. Ecale Zhou
Volume: 2008
Issue: 2
Year: 2008
Using a Seed-Network to Query Multiple Large-Scale Gene Expression Datasets from the Developing Retina in Order to Identify and Prioritize Experimental Targets

Author(s): Laura A. Hecker | Timothy C. Alcon | Vasant G. Honavar | M. Heather West Greenlee
Volume: 2008
Issue: 2
Year: 2008
The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics

Author(s): Wei Zhang | Mark J. Ratain | M. Eileen Dolan
Volume: 2008
Issue: 2
Year: 2008
HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction

Author(s): Jing Hu | Changhui Yan
Volume: 2008
Issue: 2
Year: 2008
Characterization of Non-Trivial Neighborhood Fold Constraints from Protein Sequences using Generalized Topohydrophobicity

Author(s): Guillaume Fourty | Isabelle Callebaut | Jean-Paul Mornon
Volume: 2008
Issue: 2
Year: 2008
Proteomic Analysis in Diabetic Cardiomyopathy using Bioinformatics Approach

Author(s): Allam Appa Rao | Hanuman Thota | Ramamurthy Adapala | Suresh Babu Changalasetty | Ramachandra Sridhar Gumpeny | Annapurna Akula | Lalitha Saroja Thota | Siva Reddy Challa | M.R. Narasinga Rao | Undurti N. Das
Volume: 2008
Issue: 2
Year: 2008
Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma

Author(s): Florin M. Selaru | Suna Wang | Jing Yin | Karsten Schulmann | Yan Xu | Yuriko Mori | Alexandru V. Olaru | Fumiaki Sato | James P. Hamilton | John M. Abraham | Paul Schneider | Bruce D. Greenwald | Jan Brabender | Stephen J. Meltzer
Volume: 2007
Issue: 1
Year: 2008
Peptide Vocabulary Analysis Reveals Ultra-Conservation and Homonymity in Protein Sequences

Author(s): Derek Gatherer
Volume: 2007
Issue: 1
Year: 2007
Software for Quantifying and Simulating Microsatellite Genotyping Error

Author(s): Paul C.D. Johnson | Daniel T. Haydon
Volume: 2007
Issue: 1
Year: 2007
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data

Author(s): Wei-Sheng Wu | Bor-Sen Chen
Volume: 2007
Issue: 1
Year: 2007
Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines

Author(s): Zhi Qun Tang | Hong Huang Lin | Hai Lei Zhang | Lian Yi Han | Xin Chen | Yu Zong Chen
Volume: 2007
Issue: 1
Year: 2007
The Use of Artificial Neural Networks in Prediction of Congenital CMV Outcome from Sequence Data

Author(s): Ravit Arav-Boger | Yuval S. Boger | Charles B. Foster | Zvi Boger
Volume: 2
Year: 2008
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae

Author(s): Jesper Lundström | Johan Björkegren | Jesper Tegnér
Volume: 2
Year: 2008
Normalization and Gene p-Value Estimation: Issues in Microarray Data Processing

Author(s): Katrin Fundel | Robert Küffner | Thomas Aigner | Ralf Zimmer
Volume: 2
Year: 2008
Unsupervised Meta-Analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation

Author(s): Julia C. Engelmann | Roland Schwarz | Steffen Blenk | Torben Friedrich | Philipp N. Seibel | Thomas Dandekar | Tobias Müller
Volume: 2
Year: 2008
Neuroinformatics: From Bioinformatics to Databasing the Brain

Author(s): Thomas M . Morse
Volume: 2
Year: 2008
Effects of Feeding Periods of High Cholesterol and Saturated Fat Diet on Blood Biochemistry and Hydroxyproline Fractions in Rabbits

Author(s): Mohamed A. K. Abdelhalim | N. J. Siddiqi | A. S. ALhomida | Mohammed S. Al- Ayed
Volume: 2
Year: 2008
Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing

Author(s): Takatsugu Kan | Bogdan C. Paun | Yuriko Mori | Fumiaki Sato | Zhe Jin | James P. Hamilton | Tetsuo Ito | Yulan Cheng | Stefan David | Alexandru V. Olaru | Jian Yang | Rachana Agarwal | John M. Abraham | Stephen J. Meltzer
Volume: 1
Year: 2007
Screening the Single Nucleotide Polymorphisms in Patients with Internal Carotid Artery Stenosis by Oligonucleotide-Based Custom DNA Array

Author(s): Kenji Nakai | Mayu Oyanagi | Jiro Hitomi | Kuniaki Ogasawara | Takashi Inoue | Masakazu Kobayashi | Keiko Nakai | Akira Suwabe | Wataru Habano | Toshiaki Baba | Hiroshi Yoshida | Akira Ogawa
Volume: 1
Year: 2007
GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data

Author(s): Chris Cheadle | Tonya Watkins | Jinshui Fan | Marc A. Williams | Steven Georas | John Hall | Antony Rosen | Kathleen C. Barnes
Volume: 1
Year: 2007
Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines

Author(s): Zhi Qun Tang | Hong Huang Lin | Hai Lei Zhang | Lian Yi Han | Xin Chen | Yu Zong Chen
Volume: 1
Year: 2007
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data

Author(s): Wei-Sheng Wu | Bor-Sen Chen
Volume: 1
Year: 2007
Software for Quantifying and Simulating Microsatellite Genotyping Error

Author(s): Paul C.D. Johnson | Daniel T. Haydon
Volume: 1
Year: 2007
Proteomic Analysis in Diabetic Cardiomyopathy using Bioinformatics Approach

Author(s): Allam Appa Rao | Hanuman Thota | Ramamurthy Adapala | Suresh Babu Changalasetty | Ramachandra Sridhar Gumpeny | Annapurna Akula | Lalitha Saroja Thota | Siva Reddy Challa | M.R. Narasinga Rao | Undurti N. Das
Volume: 2
Year: 2008
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)

Author(s): Antoni Hermoso | Jordi Espadaler | Enrique Querol, E | Francesc X. Aviles | Michael J.E. Sternberg | Baldomero Oliva | Narcis Fernandez-Fuentes
Volume: 1
Year: 2007
Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma

Author(s): Florin M. Selaru | Suna Wang | Jing Yin | Karsten Schulmann | Yan Xu | Yuriko Mori | Alexandru V. Olaru | Fumiaki Sato | James P. Hamilton | John M. Abraham | Paul Schneider | Bruce D. Greenwald | Jan Brabender | Stephen J. Meltzer
Volume: 1
Year: 2007
Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets

Author(s): Angelica Lindlöf | Marcus Bräutigam | Aakash Chawade | Olof Olsson | Björn Olsson
Volume: 2
Year: 2008
Characterization of Non-Trivial Neighborhood Fold Constraints from Protein Sequences using Generalized Topohydrophobicity

Author(s): Guillaume Fourty | Isabelle Callebaut | Jean-Paul Mornon
Volume: 2
Year: 2008
Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain

Author(s): Adam T. Zemla | Carol L. Ecale Zhou
Volume: 2
Year: 2008
Using a Seed-Network to Query Multiple Large-Scale Gene Expression Datasets from the Developing Retina in Order to Identify and Prioritize Experimental Targets

Author(s): Laura A. Hecker | Timothy A. Alcon | Vasant G. Honavar | M. Heather West Greenlee
Volume: 2
Year: 2008
Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis

Author(s): Zhenkang Xu | Laura Gutierrez | Matthew Hitchens | Steve Scherer | Amy K. Sater | Dan E. Wells
Volume: 2
Year: 2008
A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments

Author(s): Akihiro Hirakawa | Yasunori Sato | Chikuma Hamada | Isao Yoshimura
Volume: 2
Year: 2008
Ontologies for Bioinformatics

Author(s): Nadine Schuurman | Agnieszka Leszczynski
Volume: 2
Year: 2008
Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis

Author(s): Kanaka Durga Kedarisetti | Scott Dick | Lukasz Kurgan
Volume: 2
Year: 2008
Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures

Author(s): Heiko Muller | Francesco Acquati
Volume: 2
Year: 2008
affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data

Author(s): Markus Schmidberger | Esmeralda Vicedo | Ulrich Mansmann
Volume: 3
Year: 2009
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences

Author(s): Surendra S Negi | Werner Braun
Volume: 3
Year: 2009
Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Author(s): Junilda Spirollari | Jason T.L. Wang | Kaizhong Zhang | Vivian Bellofatto | Yongkyu Park | Bruce A. Shapiro
Volume: 3
Year: 2009
Association Between a Prognostic Gene Signature and Functional Gene Sets

Author(s): Manuela Hummel | Klaus H. Metzeler | Christian Buske | Stefan K. Bohlander | Ulrich Mansmann
Volume: 2
Year: 2008
Universal Features for the Classification of Coding and Non-Coding DNA Sequences

Author(s): Nicolas Carels | Ramon Vida | Diego Frías
Volume: 3
Year: 2009
Control Design for Signal Transduction Networks

Author(s): Chun-Liang Lin | Yuan-Wei Liu | Chia-Hua Chuang
Volume: 3
Year: 2009
Identification of the RGG Box Motif in Shadoo: RNA-Binding and Signaling Roles?

Author(s): Susan M. Corley | Jill E. Gready
Volume: 2
Year: 2008
IMAGE: A New Tool for the Prediction of Transcription Factor Binding Sites

Author(s): R. Casilli | A. Marongiu | S. Melchionna | P. Palazzari | R. Paparcone | V. Rosato
Volume: 2
Year: 2008
Gene Copy Number Analysis for Family Data Using Semiparametric Copula Model

Author(s): Ao Yuan | Guanjie Chen | Zhong-Cheng Zhou | George Bonney | Charles Rotimi
Volume: 2
Year: 2008
Methodology for Constructing Problem Definitions in Bioinformatics

Author(s): Amy M. Hauth | Gertraud Burger
Volume: 2
Year: 2008
The Penna Model of Biological Aging

Author(s): D. Stauffer
Volume: 1
Year: 2007
Designing Toxicogenomics Studies that use DNA Array Technology

Author(s): Robert R. Delongchamp | Cruz Velasco | Varsha G. Desai | Taewon Lee | James C. Fuscoe
Volume: 2
Year: 2008
The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics

Author(s): Wei Zhang | Mark J. Ratain | M. Eileen Dolan
Volume: 2
Year: 2008
Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes

Author(s): Yurong Xin | Giulio Quarta | Hin Hark Gan | Tamar Schlick
Volume: 2
Year: 2008
Utility of Computational Methods to Identify the Apoptosis Machinery in Unicellular Eukaryotes

Author(s): Pierre Marcel Durand | Theresa Louise Coetzer
Volume: 2
Year: 2008
Identification and Investigation of Drosophila Postsynaptic Density Homologs

Author(s): Faith L.W. Liebl | David E. Featherstone
Volume: 2
Year: 2008
Borges Dilemma, Fundamental Laws, and Systems Biology

Author(s): Ping Ao
Volume: 2
Year: 2008
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