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JOURNAL

Bioinformatics and Biology Insights


An international, peer reviewed, open access journal that focusses on computational methods used in the analysis and annotation of structures, in additional to other areas of computational biology.  The journal also seeks to place computational biology within the broader context of biology.

Editor in Chief: Professor Erich Bornberg-Bauer

ISSN: 1177-9322

Processing Speed: High quality, constructive peer review and rapid editorial decision within an average of four weeks.



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2017:11

Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships
Luca Ambrosino, Maria Luisa Chiusano
Bioinformatics and Biology Insights 2017:11 1177932217690136
Original research | Published on 23 Feb 2017



Plasma MicroRNA Levels Following Resection of Metastatic Melanoma
Nicholas Latchana, Zachary B Abrams, J Harrison Howard, Kelly Regan, Naduparambil Jacob, Paolo Fadda, Alicia Terando, Joseph Markowitz, Doreen Agnese, Philip Payne, William E Carson
Bioinformatics and Biology Insights 2017:11 1177932217694837
Original research | Published on 23 Feb 2017



Current Developments in Machine Learning Techniques in Biological Data Mining
Gerard G Dumancas, Indra Adrianto, Ghalib Bello, Mikhail Dozmorov
Bioinformatics and Biology Insights 2017:11 1177932216687545
Original research | Published on 22 Mar 2017



PISMA: A Visual Representation of Motif Distribution in DNA Sequences
Rogelio Alcántara-Silva, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, Silvia Carolina Galván
Bioinformatics and Biology Insights 2017:11 1177932217700907
Original research | Published on 30 Mar 2017



An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of
Kamalakshi Devi, Lochana Patar, Mahendra K Modi, Priyabrata Sen
Bioinformatics and Biology Insights 2017:11 1177932217701735
Original research | Published on 30 Mar 2017



In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms
Jaire Alves Ferreira Filho, Lucas Soares de Brito, André Pereira Leão, Alexandre Alonso Alves, Eduardo Fernandes Formighieri, Manoel Teixeira Souza
Bioinformatics and Biology Insights 2017:11 1177932217702388
Original research | Published on 18 Apr 2017



Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows
A Agrawal, MJ Khan, DE Graugnard, M Vailati-Riboni, SL Rodriguez-Zas, JS Osorio, JJ Loor
Bioinformatics and Biology Insights 2017:11 1177932217704667
Original research | Published on 28 Apr 2017



2016:10

Nematode Sodium Calcium Exchangers: A Surprising Lack of Transport
Vishal Sharma and Damien M. O'Halloran
Bioinformatics and Biology Insights 2016:10 1-4
Original research | Published on 01 Feb 2016



Modeling Intercellular Communication as a Survival Strategy of Cancer Cells: An In Silico Approach on a Flexible Bioinformatics Framework
Maura Cárdenas-García, Pedro P. González-Pérez, Sara Montagna, Oscar Sánchez Cortés and Elena Hernández Caballero
Bioinformatics and Biology Insights 2016:10 5-18
Original research | Published on 13 Mar 2016



Use of Metatranscriptomics in Microbiome Research
Stavros Bashiardes, Gili Zilberman-Schapira and Eran Elinav
Bioinformatics and Biology Insights 2016:10 19-25
Original research | Published on 20 Apr 2016



Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
Usman Sumo Friend Tambunan, Feimmy Ruth Pratiwi Sipahutar, Arli Aditya Parikesit and Djati Kerami
Bioinformatics and Biology Insights 2016:10 27-35
Original research | Published on 28 Apr 2016



Practical Approaches for Mining Frequent Patterns in Molecular Datasets
Stefan Naulaerts, Sandy Moens, Kristof Engelen, Wim Vanden Berghe, Bart Goethals, Kris Laukens and Pieter Meysman
Bioinformatics and Biology Insights 2016:10 37-47
Original research | Published on 02 May 2016



Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets
Jelili Oyelade, Itunuoluwa Isewon, Solomon Rotimi and Ifeoluwa Okunoren
Bioinformatics and Biology Insights 2016:10 49-57
Original research | Published on 12 May 2016



Genome Data Exploration Using Correspondence Analysis
Fredj Tekaia
Bioinformatics and Biology Insights 2016:10 59-72
Original research | Published on 07 Jun 2016



PDBparam: Online Resource for Computing Structural Parameters of Proteins
R. Nagarajan, A. Archana, A. Mary Thangakani, S. Jemimah, D. Velmurugan, and M. Michael Gromiha
Bioinformatics and Biology Insights 2016:10 73-80
Original research | Published on 14 Jun 2016



S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition
Carol L. Ecale Zhou
Bioinformatics and Biology Insights 2016:10 81-95
Original research | Published on 27 Jun 2016



Molecular Shape Analysis-Guided Virtual Screening Platform for Adenosine Kinase Inhibitors
Savita Bhutoria, Ballari Das and Nanda Ghoshal
Bioinformatics and Biology Insights 2016:10 97-103
Original research | Published on 18 Jul 2016



PIMADb: A Database of Protein–Protein Interactions in Huge Macromolecular Assemblies
Oommen K. Mathew and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2016:10 105-109
Original research | Published on 19 Jul 2016



Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2)
Abdullah Alawad, Sultan Alharbi, Othman Alhazzaa, Faisal Alagrafi, Mohammed Alkhrayef, Ziyad Alhamdan, Abdullah Alenazi, Hasan Al-Johi, Ibrahim O. Alanazi and Mohamed Hammad.
Bioinformatics and Biology Insights 2016:10 111-120
Original research | Published on 26 Jul 2016



Computational Identification of Novel Genes: Current and Future Perspectives
Steffen Klasberg, Tristan Bitard-Feildel and Ludovic Mallet
Bioinformatics and Biology Insights 2016:10 121-131
Original research | Published on 01 Aug 2016



OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid
William L. Poehlman, Mats Rynge, Chris Branton, D. Balamurugan and Frank A. Feltus
Bioinformatics and Biology Insights 2016:10 133-141
Original research | Published on 02 Aug 2016



In Silico Structure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions
Arun John, Vetrivel Umashankar, A. Samdani, Manoharan Sangeetha, Subramanian Krishnakumar and Perinkulam Ravi Deepa
Bioinformatics and Biology Insights 2016:10 143-154
Original research | Published on 14 Aug 2016



Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives – An In Silico Approach
Subhomoi Borkotoky, Chetan Kumar Meena and Ayaluru Murali
Bioinformatics and Biology Insights 2016:10 155-166
Original research | Published on 29 Aug 2016



Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha
Sudeesh Karumathil, Vijaya R. Dirisala, Uthpala Srinadh, Valaboju Nikhil, N. Satya Sampath Kumar and Rahul R. Nair
Bioinformatics and Biology Insights 2016:10 167-184
Original research | Published on 22 Sep 2016



Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum
Stefan Simm, Klaus-Dieter Scharf, Sridharan Jegadeesan, Maria Luisa Chiusano, Nurit Firon and Enrico Schleiff
Bioinformatics and Biology Insights 2016:10 185-207
Original research | Published on 26 Sep 2016



Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks
Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi and Dominique Poncelet
Bioinformatics and Biology Insights 2016:10 209-224
Original research | Published on 25 Oct 2016



Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins
Ernesto J. Grasso, Adolfo E. Sottile and Carlos E. Coronel
Bioinformatics and Biology Insights 2016:10 225-236
Original research | Published on 30 Oct 2016



Clustering Algorithms: Their Application to Gene Expression Data
Jelili Oyelade, Itunuoluwa Isewon, Funke Oladipupo, Olufemi Aromolaran, Efosa Uwoghiren, Faridah Ameh, Moses Achas and Ezekiel Adebiyi
Bioinformatics and Biology Insights 2016:10 237-253
Original research | Published on 30 Nov 2016



Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets
D. D. Shrimankar and S. R. Sathe
Bioinformatics and Biology Insights 2016:10 255-265
Original research | Published on 30 Nov 2016



Integrating Epigenomics into the Understanding of Biomedical Insight
Yixing Han and Ximiao He
Bioinformatics and Biology Insights 2016:10 267-289
Original research | Published on 04 Dec 2016



Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, Camelus dromedarius
Abdullah O. Alawad, Sultan N. Alharbi, Othman A. Alhazzaa, Faisal S. Alagrafi, Mohammad N. Alkhrayef, Ziyad A. Alhamdan, Abdullah D. Alenazi, Mohamed Hammad, Sami A. Alyahya, Hasan A. AlJohi and Ibrahim O. Alanazi
Bioinformatics and Biology Insights 2016:10 291-300
Original research | Published on 21 Dec 2016



2015:9

Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum
Stefan Simm, Sotirios Fragkostefanakis, Puneet Paul, Mario Keller, Jens Einloft, Klaus-Dieter Scharf and  Enrico Schleiff
Bioinformatics and Biology Insights 2015:9 1-17
Original research | Published on 09 Feb 2015



A Systems Biology Approach Reveals the Dose- and Time-Dependent Effect of Primary Human Airway Epithelium Tissue Culture After Exposure to Cigarette Smoke In Vitro
Carole Mathis, Stephan Gebel, Carine Poussin, Vincenzo Belcastro, Alain Sewer, Dirk Weisensee, Arnd Hengstermann, Sam Ansari, Sandra Wagner, Manuel C. Peitsch and Julia Hoeng
Bioinformatics and Biology Insights 2015:9 19-35
Original research | Published on 09 Mar 2015



An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences
Nicolas Carels and Miguel Ponce de Leon
Bioinformatics and Biology Insights 2015:9 37-47
Original research | Published on 15 Apr 2015



Cross-Disciplinary Detection and Analysis of Network Motifs
Ngoc Tam L. Tran, Luke DeLuccia, Aidan F. McDonald and Chun-Hsi Huang
Bioinformatics and Biology Insights 2015:9 49-60
Original research | Published on 19 Apr 2015



Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists
Xiaoxi Dong, Anatoly Yambartsev, Stephen A. Ramsey, Lina D Thomas, Natalia Shulzhenko and Andrey Morgun
Bioinformatics and Biology Insights 2015:9 61-74
Original research | Published on 29 Apr 2015



Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis and Ioannis Iliopoulos
Bioinformatics and Biology Insights 2015:9 75-88
Original research | Published on 05 May 2015



Computational and in vitro Investigation of miRNA-Gene Regulations in Retinoblastoma Pathogenesis: miRNA Mimics Strategy
Nalini Venkatesan, Perinkulam Ravi Deepa, Vikas Khetan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2015:9 89-101
Original research | Published on 12 May 2015



Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique
Hebatallah Hassan, Amr Badr and M. B. Abdelhalim
Bioinformatics and Biology Insights 2015:9 103-109
Original research | Published on 05 Jul 2015



High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism
Monica B. Assumpção, Fabiano C. Moreira, Igor G. Hamoy, Leandro Magalhães, Amanda Vidal, Adenilson Pereira, Rommel Burbano, André Khayat, Artur Silva, Sidney Santos, Samia Demachki, Ândrea Ribeiro-dos-Santos, and Paulo Assumpção
Bioinformatics and Biology Insights 2015:9 111-117
Original research | Published on 06 Jul 2015



A Simple Rank Product Approach for Analyzing Two Classes
Tae Young Yang
Bioinformatics and Biology Insights 2015:9 119-123
Original research | Published on 16 Jul 2015



BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences
Martin Dahlö, Frédéric Haziza, Aleksi Kallio, Eija Korpelainen, Erik Bongcam-Rudloff and Ola Spjuth
Bioinformatics and Biology Insights 2015:9 125-128
Original research | Published on 10 Sep 2015



Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form
Khadija Amine, Lamia Miri, Adil Naimi, Rachid Saile, Abderrahmane El Kharrim, Afaf Mikou and Anass Kettani
Bioinformatics and Biology Insights 2015:9 129-140
Original research | Published on 13 Sep 2015



PPCheck: A Webserver for the Quantitative Analysis of Protein–Protein Interfaces and Prediction of Residue Hotspots
Anshul Sukhwal and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2015:9 141-151
Original research | Published on 21 Sep 2015



Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells
Peter R. LoVerso, Christopher M. Wachter and Feng Cui
Bioinformatics and Biology Insights 2015:9 153-164
Original research | Published on 25 Nov 2015



A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor
Peter R. LoVerso and Feng Cui
Bioinformatics and Biology Insights 2015:9 165-174
Original research | Published on 02 Dec 2015



DDA: A Novel Network-Based Scoring Method to Identify Disease–Disease Associations
Apichat Suratanee and Kitiporn Plaimas
Bioinformatics and Biology Insights 2015:9 175-186
Original research | Published on 08 Dec 2015



Sequence Analysis and Evolutionary Studies of Reelin Proteins
Malini Manoharan, Sayyed Auwn Muhammad, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2015:9 187-193
Original research | Published on 20 Dec 2015



Homology-Based Prediction of Potential Protein–Protein Interactions between Human Erythrocytes and Plasmodium falciparum
Gayatri Ramakrishnan, Narayanaswamy Srinivasan, Ponnan Padmapriya and Vasant Natarajan
Bioinformatics and Biology Insights 2015:9 195-206
Original research | Published on 20 Dec 2015



2015:Suppl. 1 Current Developments in RNA Sequence Analysis

High-Throughput Sequencing of miRNAs Reveals a Tissue Signature in Gastric Cancer and Suggests Novel Potential Biomarkers
Sylvain Darnet, Fabiano C Moreira, Igor G Hamoy, Rommel Burbano, André Khayat, Aline Cruz, Leandro Magalhães, Artur Silva, Sidney Santos, Samia Demachki, Monica Assumpção, Paulo Assumpção, and Ândrea Ribeiro-dos-Santos
Bioinformatics and Biology Insights 2015:Suppl. 1 1-8
Original research | Published on 28 Jun 2015



The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology
Frank A. Feltus, Joseph R. Breen III, Juan Deng, Ryan S. Izard, Christopher A. Konger, Walter B. Ligon III, Don Preuss and Kuang-Ching Wang
Bioinformatics and Biology Insights 2015:Suppl. 1 9-19
Original research | Published on 23 Sep 2015 | Video Abstract Available



Gene Coexpression Networks in Human Brain Developmental Transcriptomes Implicate the Association of Long Noncoding RNAs with Intellectual Disability
Brian L. Gudenas and Liangjiang Wang
Bioinformatics and Biology Insights 2015:Suppl. 1 21-27
Original research | Published on 27 Oct 2015



Advanced Applications of RNA Sequencing and Challenges
Yixing Han, Shouguo Gao, Kathrin Muegge, Wei Zhang and Bing Zhou
Bioinformatics and Biology Insights 2015:Suppl. 1 29-46
Original research | Published on 15 Nov 2015



Evolutionary Character of Alternative Splicing in Plants
Chengjun Zhang, Hong Yang and Huizhao Yang
Bioinformatics and Biology Insights 2015:Suppl. 1 47-52
Original research | Published on 20 Jan 2016



RNA Sequencing in Schizophrenia
Xin Li and Shaolei Teng
Bioinformatics and Biology Insights 2015:Suppl. 1 53-60
Original research | Published on 31 Mar 2016



Introductory Editorial: Current Developments in RNA Sequence Analysis
Jianping Zhang, Shaolei Teng, Cuncong Zhong, Bo Wang, Jie Wu
Bioinformatics and Biology Insights 2015:Suppl. 1 61-63
Original research | Published on 15 May 2016



2015:Suppl. 2 Current Developments in Veterinary Bioinformatics

Antigenic Determinants of Possible Vaccine Escape by Porcine Circovirus Subtype 2b Viruses
Megan Constans, Marvin Ssemadaali, Oleksandr Kolyvushko and Sheela Ramamoorthy
Bioinformatics and Biology Insights 2015:Suppl. 2 1-12
Original research | Published on 23 Aug 2015 | Video Abstract Available



Application of Functional Genomics for Bovine Respiratory Disease Diagnostics
Aswathy N. Rai, William B. Epperson and Bindu Nanduri
Bioinformatics and Biology Insights 2015:Suppl. 2 13-23
Original research | Published on 22 Oct 2015



Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome
Laura C. Miller, Darrell O. Bayles, Eraldo L. Zanella and Kelly M. Lager
Bioinformatics and Biology Insights 2015:Suppl. 2 25-36
Original research | Published on 24 Jan 2016



Visualization of Genome Diversity in German Shepherd Dogs
Sally-Anne Mortlock, Rachel Booth, Hamutal Mazrier, Mehar S. Khatkar and Peter Williamson
Bioinformatics and Biology Insights 2015:Suppl. 2 37-42
Original research | Published on 10 Feb 2016



Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus
Devendra K. Rai, Paul Lawrence, Steve J. Pauszek, Maria E. Piccone, Nick J. Knowles and Elizabeth Rieder
Bioinformatics and Biology Insights 2015:Suppl. 2 43-58
Original research | Published on 04 Apr 2016



Cluster Analysis of Tumor Suppressor Genes in Canine Leukocytes Identifies Activation State
Julie-Anne Daly, Sally-Anne Mortlock, Rosanne M. Taylor and Peter Williamson
Bioinformatics and Biology Insights 2015:Suppl. 2 59-67
Original research | Published on 19 Jul 2016



2015:Suppl. 3 Current Developments in Machine Learning Techniques in Biological Data Mining

Development and Validation of a Clinical Risk-Assessment Tool Predictive of All-Cause Mortality
Ghalib A. Bello, Gerard G. Dumancas and Chris Gennings
Bioinformatics and Biology Insights 2015:Suppl. 3 1-10
Original research | Published on 01 Sep 2015



B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data
Mikhail G. Dozmorov, Nicolas Dominguez, Krista Bean, Susan R. Macwana, Virginia Roberts, Edmund Glass, Judith A. James and Joel M. Guthridge
Bioinformatics and Biology Insights 2015:Suppl. 3 11-19
Original research | Published on 08 Oct 2015



Machine Learning Methods for Predicting HLA–Peptide Binding Activity
Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, Donna L. Mendrick and Huixiao Hong
Bioinformatics and Biology Insights 2015:Suppl. 3 21-29
Original research | Published on 11 Oct 2015 | Video Abstract Available



Development and Application of a Genetic Algorithm for Variable Optimization and Predictive Modeling of Five-Year Mortality Using Questionnaire Data
Lucas J. Adams, Ghalib Bello and Gerard G. Dumancas
Bioinformatics and Biology Insights 2015:Suppl. 3 31-41
Original research | Published on 08 Nov 2015



Machine Learning Data Imputation and Classification in a Multicohort Hypertension Clinical Study
William Seffens, Chad Evans, Minority Health-GRID Network and Herman Taylor
Bioinformatics and Biology Insights 2015:Suppl. 3 43-54
Original research | Published on 09 May 2016



2015:Suppl. 4 Current Developments in Domestic Animal Bioinformatics

Genetics of Prion Disease in Cattle
Brenda M. Murdoch and Gordon K. Murdoch
Bioinformatics and Biology Insights 2015:Suppl. 4 1-10
Original research | Published on 24 Sep 2015



The Genetic Architecture of Domestication in Animals
Dominic Wright
Bioinformatics and Biology Insights 2015:Suppl. 4 11-20
Original research | Published on 11 Oct 2015



Transcriptome Analysis in Domesticated Species: Challenges and Strategies
Jessica P. Hekman, Jennifer L. Johnson and Anna V. Kukekova
Bioinformatics and Biology Insights 2015:Suppl. 4 21-31
Original research | Published on 16 Feb 2016



Unmasking Upstream Gene Expression Regulators with miRNA-corrected mRNA Data
Stephanie Bollmann, Dengpan Bu, Jiaqi Wang and Massimo Bionaz
Bioinformatics and Biology Insights 2015:Suppl. 4 33-48
Original research | Published on 29 May 2016



Quality Assessment of Domesticated Animal Genome Assemblies
Stefan E. Seemann, Christian Anthon, Oana Palasca and Jan Gorodkin
Bioinformatics and Biology Insights 2015:Suppl. 4 49-58
Original research | Published on 06 Jun 2016



An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters
Stephen A. Ramsey
Bioinformatics and Biology Insights 2015:Suppl. 4 59-69
Original research | Published on 25 Oct 2016



2014:8

GeneSV – an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences
Adam Zemla, Tanya Kostova, Rodion Gorchakov, Evgeniya Volkova, David W. C. Beasley, Jane Cardosa, Scott C. Weaver, Nikos Vasilakis and Pejman Naraghi-Arani
Bioinformatics and Biology Insights 2014:8 1-16
Original research | Published on 08 Jan 2014



Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated With Acute Renal Allograft Rejection
Heesun Shin, Oliver Günther, Zsuzsanna Hollander, Janet E. Wilson-McManus, Raymond T. Ng, Robert Balshaw, Paul A. Keown, Robert McMaster, Bruce M. McManus, Nicole M. Isbel, Greg Knoll and Scott J. Tebbutt; for the PROOF Centre of Excellence Team
Bioinformatics and Biology Insights 2014:8 17-33
Original research | Published on 22 Jan 2014



Probing the Unknowns in Cytokinin-Mediated Immune Defense in Arabidopsis with Systems Biology Approaches
Muhammad Naseem, Meik Kunz and Thomas Dandekar
Bioinformatics and Biology Insights 2014:8 35-44
Original research | Published on 13 Feb 2014



Postpartal Subclinical Endometritis Alters Transcriptome Profiles in Liver and Adipose Tissue of Dairy Cows
Haji Akbar, Felipe C. Cardoso, Susanne Meier, Christopher Burke, Scott McDougall, Murray Mitchell, Caroline Walker, Sandra L. Rodriguez-Zas, Robin E. Everts, Harris A. Lewin, John R. Roche and Juan J. Loor
Bioinformatics and Biology Insights 2014:8 45-63
Original research | Published on 19 Feb 2014



An In Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638)
Arafat Rahman Oany, Tahmina Pervin Jyoti and Shah Adil Ishtiyaq Ahmad
Bioinformatics and Biology Insights 2014:8 65-72
Original research | Published on 20 Mar 2014



Computational Insights of the Interaction among Sea Anemones Neurotoxins and Kv1.3 Channel
Angélica Sabogal-Arango, George E. Barreto, David Ramírez-Sánchez, Juan González-Mendoza, Viviana Barreto, Ludis Morales and Janneth González
Bioinformatics and Biology Insights 2014:8 73-81
Original research | Published on 15 Apr 2014



Promise and Reality in the Expanding Field of Network Interaction Analysis: Metabolic Networks
Susanna Bazzani
Bioinformatics and Biology Insights 2014:8 83-91
Original research | Published on 16 Apr 2014



The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins
Miguel Ponce de Leon, Antonio Basilio de Miranda, Fernando Alvarez-Valin and Nicolas Carels
Bioinformatics and Biology Insights 2014:8 93-108
Original research | Published on 20 May 2014



High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism
Joshua C. McCann, Tryon A. Wickersham and Juan J. Loor
Bioinformatics and Biology Insights 2014:8 109-125
Original research | Published on 08 Jun 2014



A Protocol for mtGenome Analysis on Large Sample Numbers
Igor G. Hamoy, André M. Ribeiro-dos-Santos, Luiz Alvarez, Silvanira Barbosa, Artur Silva, Sidney Santos, Leonor Gusmão and Ândrea Ribeiro-dos-Santos
Bioinformatics and Biology Insights 2014:8 127-134
Original research | Published on 11 Jun 2014



Identification of Chicken Pulmonary miRNAs Targeting PB1, PB1-F2, and N40 Genes of Highly Pathogenic Avian Influenza Virus H5N1 In Silico
Amod Kumar, Muhasin Asaf V.N., Ashwin Ashok Raut, Richa Sood and Anamika Mishra
Bioinformatics and Biology Insights 2014:8 135-145
Original research | Published on 12 Jun 2014



DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes
Balasubramanian Nagarathnam, Snehal D. Karpe, Krishnan Harini, Kannan Sankar, Mohammed Iftekhar, Durairaj Rajesh, Sadasivam Giji, Govidaraju Archunan, Veluchamy Balakrishnan, M. Michael Gromiha, Wataru Nemoto, Kazhuhiko Fukui and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2014:8 147-158
Original research | Published on 12 Jun 2014



In Silico Studies of Medicinal Compounds Against Hepatitis C Capsid Protein from North India
Shilu Mathew, Muhammad Faheem, Govindaraju Archunan, Muhammad Ilyas, Nargis Begum, Syed Jahangir, Ishtiaq Qadri, Mohammad Al Qahtani and Shiny Mathew
Bioinformatics and Biology Insights 2014:8 159-168
Original research | Published on 23 Jun 2014



Computational Identification of Dengue Virus MicroRNA-Like Structures and their Cellular Targets
Maicol Ospina-Bedoya, Natalia Campillo-Pedroza, Juan P. Franco-Salazar and Juan C. Gallego-Gómez
Bioinformatics and Biology Insights 2014:8 169-176
Original research | Published on 14 Aug 2014



Integrated Analysis of Dysregulated miRNA-gene Expression in HMGA2-silenced Retinoblastoma Cells
Nalini Venkatesan, PR Deepa, Madavan Vasudevan, Vikas Khetan, Ashwin M Reddy and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2014:8 177-191
Original research | Published on 04 Sep 2014



Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes
Sony Malhotra and R. Sowdhamini
Bioinformatics and Biology Insights 2014:8 193-198
Original research | Published on 10 Sep 2014



Computational Methods for CLIP-seq Data Processing
Paula H. Reyes-Herrera and Elisa Ficarra
Bioinformatics and Biology Insights 2014:8 199-207
Original research | Published on 01 Oct 2014



POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
Khader Shameer, Mahantesha BN Naika, Oommen K. Mathew, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2014:8 209-214
Original research | Published on 21 Dec 2014



2013:7

PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation
Henning Lenz and Volker Knoop
Bioinformatics and Biology Insights 2013:7 1-19
Original research | Published on 10 Jan 2013



Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers
Madhu Beta, Nalini Venkatesan, Madavan Vasudevan, Umashankar Vetrivel, Vikas Khetan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2013:7 21-34
Original research | Published on 09 Jan 2013



A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences
Nicolas Carels and Diego Frias
Bioinformatics and Biology Insights :7 35-54
Original research | Published on 23 Jan 2013



A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences
Riccardo Percudani
Bioinformatics and Biology Insights 2013:7 55-72
Original research | Published on 24 Feb 2013



Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study
Janneth González, Angela Gálvez, Ludis Morales, George E. Barreto, Francisco Capani, Omar Sierra and Yolima Torres
Bioinformatics and Biology Insights 2013:7 73-82
Original research | Published on 27 Feb 2013



Computational Small RNA Prediction in Bacteria
Jayavel Sridhar and Paramasamy Gunasekaran
Bioinformatics and Biology Insights 2013:7 83-95
Original research | Published on 07 Mar 2013



Construction of a Computable Network Model for DNA Damage, Autophagy, Cell Death, and Senescence
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 and Jurjen W. Westra
Bioinformatics and Biology Insights 2013:7 97-117
Original research | Published on 07 Mar 2013



Knowledge Discovery in Variant Databases Using Inductive Logic Programming
Hoan Nguyen, Tien-Dao Luu, Olivier Poch and Julie D. Thompson
Bioinformatics and Biology Insights 2013:7 119-131
Original research | Published on 18 Mar 2013



miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment
Bram Sebastian and Samuel E. Aggrey
Bioinformatics and Biology Insights 2013:7 133-142
Original research | Published on 02 Apr 2013



Association Between a Multi-Locus Genetic Risk Score and Inflammatory Bowel Disease
Pingzhao Hu, Aleixo M. Muise, Xiang Xing, John H. Brumell, Mark S. Silverberg and Wei Xu
Bioinformatics and Biology Insights 2013:7 143-152
Original research | Published on 19 May 2013



The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum
Markus A. Grohme, Brahim Mali, Weronika Welnicz, Stephanie Michel, Ralph O. Schill and Marcus Frohme
Bioinformatics and Biology Insights 2013:7 153-165
Original research | Published on 26 May 2013



A Modular Cell-Type Focused Inflammatory Process Network Model for Non-Diseased Pulmonary Tissue
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 and Manuel C. Peitsch
Bioinformatics and Biology Insights 2013:7 167-192
Original research | Published on 20 Jun 2013



Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation
Wangsheng Zhao, Khuram Shahzad, Mingfeng Jiang, Daniel E. Graugnard, Sandra L. Rodriguez-Zas, Jun Luo, Juan J. Loor and Walter L. Hurley
Bioinformatics and Biology Insights 2013:7 193-216
Original research | Published on 14 Jul 2013



Systematic Verification of Upstream Regulators of a Computable Cellular Proliferation Network Model on Non-Diseased Lung Cells Using a Dedicated Dataset
Vincenzo Belcastro, Carine Poussin, Stephan Gebel, Carole Mathis, Walter K. Schlage, Rosemarie B. Lichtner, Sibille Quadt-Humme, Sandra Wagner, Julia Hoeng and Manuel C. Peitsch
Bioinformatics and Biology Insights 2013:7 217-230
Original research | Published on 23 Jul 2013



Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions
Malini Manoharan, Kannan Sankar, Bernard Offmann and Sowdhamini Ramanathan
Bioinformatics and Biology Insights 2013:7 231-251
Original research | Published on 22 Jul 2013



Bioinformatics Analysis of Transcriptome Dynamics During Growth in Angus Cattle Longissimus Muscle
Sonia J. Moisá, Daniel W. Shike, Daniel E. Graugnard, Sandra L. Rodriguez-Zas, Robin E. Everts, Harris A. Lewin, Dan B. Faulkner, Larry L. Berger and Juan J. Loor
Bioinformatics and Biology Insights 2013:7 253-270
Original research | Published on 04 Aug 2013



Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1
Ajit K. Sharma, Abhilasha Mansukh, Ashok Varma, Nikhil Gadewal, and Sanjay Gupta
Bioinformatics and Biology Insights 2013:7 271-288
Original research | Published on 26 Aug 2013



Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis
Venkatesan Nalini, Ramya Segu, Perinkulam Ravi Deepa, Vikas Khetan, Madavan Vasudevan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2013:7 289-306
Original research | Published on 18 Sep 2013



On Crowd-verification of Biological Networks
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 and Marja Talikka
Bioinformatics and Biology Insights 2013:7 307-325
Original research | Published on 10 Oct 2013



Automatic Identification of Algal Community from Microscopic Images
Natchimuthu Santhi, Chinnaraj Pradeepa, Parthasarathy Subashini and Senthil Kalaiselvi
Bioinformatics and Biology Insights 2013:7 327-334
Original research | Published on 10 Oct 2013



Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights
Diego Frias, Joana P. Monteiro-Cunha, Aline C. Mota-Miranda, Vagner S. Fonseca, Tulio de Oliveira, Bernardo Galvao-Castro, and Luiz C. J. Alcantara
Bioinformatics and Biology Insights 2013:7 335-345
Original research | Published on 10 Oct 2013



A Computational Assay to Design an Epitope-Based Peptide Vaccine Against Saint Louis Encephalitis Virus
Md. Anayet Hasan, Mehjabeen Hossain and Md. Jibran Alam
Bioinformatics and Biology Insights 2013:7 347-355
Original research | Published on 24 Nov 2013



ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons
Jun-ichi Satoh, Natsuki Kawana and Yoji Yamamoto
Bioinformatics and Biology Insights 2013:7 357-368
Original research | Published on 01 Dec 2013



Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36
Zineb Tarhda, Oussama Semlali, Anas Kettani, Ahmed Moussa, Nada A. Abumrad and Azeddine Ibrahimi
Bioinformatics and Biology Insights 2013:7 369-373
Original research | Published on 02 Dec 2013



2012:6

A Novel Approach for the Simultaneous Analysis of Common and Rare Variants in Complex Traits
Ao Yuan, Guanjie Chen, Yanxun Zhou, Amy Bentley and Charles Rotimi
Bioinformatics and Biology Insights 2012:6 1-9
Original research | Published on 22 Jan 2012



Structural and Functional Insights on the Myosin Superfamily
Divya P. Syamaladevi, James A. Spudich,* and R. Sowdhamini*
Bioinformatics and Biology Insights 2012:6 11-21
Original research | Published on 01 Feb 2012 | Highly accessed (previous month)



Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1)
Krupa S. Jani and D.S. Dalafave
Bioinformatics and Biology Insights 2012:6 23-31
Original research | Published on 20 Feb 2012



Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. melanogaster
K. Harini and R. Sowdhamini
Bioinformatics and Biology Insights 2012:6 33-47
Original research | Published on 26 Mar 2012



White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection
Casey P. Shannon, Zsuzsanna Hollander,Janet Wilson-McManus, Robert Balshaw, Raymond T. Ng, Robert McMaster, Bruce M. McManus, Paul A. Keown, and Scott J. Tebbutt
Bioinformatics and Biology Insights 2012:6 49-61
Original research | Published on 10 Apr 2012



Mining Gene Ontology Data with AGENDA
Guvanch Ovezmyradov, Qianhao Lu and Martin C. Göpfert
Bioinformatics and Biology Insights 2012:6 63-67
Original research | Published on 18 Apr 2012



Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations
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 and Thomas Dandekar
Bioinformatics and Biology Insights 2012:6 69-96
Original research | Published on 23 Apr 2012



Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems
Beate Krueger, Torben Friedrich, Frank Förster, Jörg Bernhardt, Roy Gross and Thomas Dandekar
Bioinformatics and Biology Insights 2012:6 97-128
Original research | Published on 03 May 2012



The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes
André E.R. Soares and Carlos G. Schrago
Bioinformatics and Biology Insights 2012:6 129-143
Original research | Published on 31 May 2012



An Integrated Statistical Approach to Compare Transcriptomics Data Across Experiments: A Case Study on the Identification of Candidate Target Genes of the Transcription Factor PPARα
Mohammad Ohid Ullah, Michael Müller and Guido J.E.J. Hooiveld
Bioinformatics and Biology Insights 2012:6 145-154
Original research | Published on 19 Jun 2012



DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements
Pieter Meysman, Kathleen Marchal and Kristof Engelen
Bioinformatics and Biology Insights 2012:6 155-168
Original research | Published on 02 Jul 2012



Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies
Guanjie Chen, Ao Yuan, Jie Zhou, Amy R. Bentley, Adebowale Adeyemo and Charles N. Rotimi
Bioinformatics and Biology Insights 2012:6 169-176
Original research | Published on 02 Jul 2012



Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp)
Guanjie Chen, Ao Yuan, Yanxun Zhou, Amy R. Bentley, Jie Zhou, Weiping Chen, Daniel Shriner, Adebowale Adeyemo and Charles N. Rotimi
Bioinformatics and Biology Insights 2012:6 177-185
Original research | Published on 31 Jul 2012



The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses
John Ellis, Stephen Goodswen, Paul J Kennedy and Stephen Bush
Bioinformatics and Biology Insights 2012:6 187-202
Original research | Published on 03 Sep 2012



Integrative Structural Modelling of the Cardiac Thin Filament: Energetics at the Interface and Conservation Patterns Reveal a Spotlight on Period 2 of Tropomyosin
Margaret Sunitha S, John A. Mercer, James A. Spudich, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2012:6 203-223
Original research | Published on 03 Oct 2012 | Video Abstract Available



The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation
Santi Nurbaiti, Muhamad A. Martoprawiro, Akhmaloka and Rukman Hertadi
Bioinformatics and Biology Insights 2012:6 225-234
Original research | Published on 30 Oct 2012



BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks
Oksana Kohutyuk, Fadi Towfic, M. Heather West Greenlee and Vasant Honavar
Bioinformatics and Biology Insights 2012:6 235-246
Original research | Published on 08 Nov 2012



Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships
Divya P. Syamaladevi, Margaret S Sunitha, S. Kalaimathy, Chandrashekar C. Reddy, Mohammed Iftekhar, Shaik N. Pasha and R. Sowdhamini
Bioinformatics and Biology Insights 2012:6 247-254
Original research | Published on 12 Nov 2012



Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease
Xiaofeng Ji, Wei Wang, Yuan Zheng, Jianhua Hao and Mi Sun
Bioinformatics and Biology Insights 2012:6 255-263
Original research | Published on 19 Nov 2012



A Fast Quad-Tree Based Two Dimensional Hierarchical Clustering
Priscilla Rajadurai and Swamynathan Sankaranarayanan
Bioinformatics and Biology Insights 2012:6 265-274
Original research | Published on 19 Nov 2012



Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium
Baraka S. Williams, Raphael D. Isokpehi, Andreas N. Mbah, Antoinesha L. Hollman, Christina O. Bernard, Shaneka S. Simmons, Wellington K. Ayensu and Bianca L. Garner
Bioinformatics and Biology Insights 2012:6 275-286
Original research | Published on 21 Nov 2012



Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR- Supported in silico Modeling
J. Zirkel, A. Cecil, F. Schäfer, S. Rahlfs, A. Ouedraogo, K. Xiao, S. Sawadogo, B. Coulibaly, K. Becker and T. Dandekar
Bioinformatics and Biology Insights 2012:6 287-302
Original research | Published on 03 Dec 2012



Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length
Alexander Bolshoy, and Tatiana Tatarinova
Bioinformatics and Biology Insights 2012:6 317-327
Original research | Published on 10 Dec 2012



2011:5

Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites
Wei-Sheng Wu
Bioinformatics and Biology Insights 2011:5 1-11
Original research | Published on 12 Jan 2011



Conceptual Aspects of Large Meta-Analyses with Publicly Available Microarray Data: A Case Study in Oncology
Markus Schmidberger, Sabine Lennert and Ulrich Mansmann
Bioinformatics and Biology Insights 2011:5 13-39
Original research | Published on 23 Jan 2011



Identification of Drought-Responsive Universal Stress Proteins in Viridiplantae
Raphael D. Isokpehi, Shaneka S. Simmons, Hari H.P. Cohly, Stephen I.N. Ekunwe, Gregorio B. Begonia and Wellington K. Ayensu
Bioinformatics and Biology Insights 2011:5 41-58
Original research | Published on 07 Feb 2011



Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution
E. Ashrafi, A. Alemzadeh, M. Ebrahimi, E. Ebrahimie, N. Dadkhodaei and M. Ebrahimi
Bioinformatics and Biology Insights 2011:5 59-82
Original research | Published on 17 Apr 2011



Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle
Massimo Bionaz and Juan J. Loor
Bioinformatics and Biology Insights 2011:5 83-98
Original research | Published on 04 May 2011



Mouse Retinal Development: a Dark Horse Model for Systems Biology Research
Xia Zhang, Jeanne M. Serb and M. Heather West Greenlee
Bioinformatics and Biology Insights 2011:5 99-113
Original research | Published on 22 May 2011



Functional Annotation Analytics of Rhodopseudomonas palustris Genomes
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 and Hari H.P. Cohly
Bioinformatics and Biology Insights 2011:5 115-129
Original research | Published on 21 Sep 2011



2010:4

An Improved Approach for Mapping Quantitative Trait Loci in a Pseudo-Testcross: Revisiting a Poplar Mapping Study
Song Wu, Jie Yang, Youjun Huang, Yao Li, Tongming Yin, Stan D. Wullschleger, Gerald A. Tuskan and Rongling Wu
Bioinformatics and Biology Insights 2010:4 1-8
Original research | Published on 04 Feb 2010



Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies
R. Shyama Prasad Rao, Ole Thomsen Buus and Bernd Wollenweber
Bioinformatics and Biology Insights 2010:4 9-17
Original research | Published on 17 Feb 2010



Effect of Diet Supplementation on the Expression of Bovine Genes Associated with Fatty Acid Synthesis and Metabolism
Sandeep J. Joseph, Kelly R. Robbins, Enrique Pavan, Scott l. Pratt, Susan K. Duckett and Romdhane Rekaya
Bioinformatics and Biology Insights 2010:4 19-31
Original research | Published on 31 Mar 2010



Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach
Khader Shameer, Ganesan Pugalenthi, Krishna Kumar Kandaswamy, Ponnuthurai N. Suganthan, Govindaraju Archunan and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2010:4 33-42
Original research | Published on 17 Jun 2010



Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data
Christian Gorba and Florence Tama
Bioinformatics and Biology Insights 2010:4 43-54
Original research | Published on 21 Jun 2010



A Plausible Role for the Presence of Internal Shine-Dalgarno Sites
Lalit Ponnala
Bioinformatics and Biology Insights 2010:4 55-60
Original research | Published on 28 Jun 2010



Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions
Xiang-Ping Wang and Nigel G.F. Cooper
Bioinformatics and Biology Insights 2010:4 61-83
Original research | Published on 30 Aug 2010



Expression of Metabolic, Tissue Remodeling, Oxidative Stress, and Inflammatory Pathways in Mammary Tissue During Involution in Lactating Dairy Cows
Paola Piantoni, Ping Wang, James K. Drackley, Walter L. Hurley and Juan J. Loor
Bioinformatics and Biology Insights 2010:4 85-97
Original research | Published on 20 Sep 2010



Candidate Single Nucleotide Polymorphism Markers for Arsenic Responsiveness of Protein Targets
Raphael D. Isokpehi, Hari H.P. Cohly, Matthew N. Anyanwu, Rajendram V. Rajnarayanan, Paul B. Tchounwou, Udensi K. Udensi and Barbara E. Graham-Evans
Bioinformatics and Biology Insights 2010:4 99-111
Original research | Published on 11 Oct 2010



An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces
Catherine H. Schein, Ovidiu Ivanciuc, Terumi Midoro-Horiuti, Randall M. Goldblum and Werner Braun
Bioinformatics and Biology Insights 2010:4 113-125
Original research | Published on 11 Oct 2010



Periodicity Detection Method for Small-Sample Time Series Datasets
Daisuke Tominaga
Bioinformatics and Biology Insights 2010:4 127-136
Original research | Published on 22 Nov 2010



Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors
Marcin Kierczak, Michal Draminski, Jacek Koronacki and Jan Komorowski
Bioinformatics and Biology Insights 2010:4 137-146
Original research | Published on 12 Dec 2010



2009:3

Control Design for Signal Transduction Networks
Chun-Liang Lin, Yuan-Wei Liu and Chia-Hua Chuang
Bioinformatics and Biology Insights 2009:3 1-14
Original research | Published on 09 Feb 2009



Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case
Hélène San Clemente, Rafael Pont-Lezica and Elisabeth Jamet
Bioinformatics and Biology Insights 2009:3 15-28
Original research | Published on 18 Feb 2009



Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus
Xiaowu Chen and Zhiyi Shi
Bioinformatics and Biology Insights 2009:3 29-35
Original research | Published on 04 Jun 2009



Universal Features for the Classification of Coding and Non-Coding DNA Sequences
Nicolas Carels, Ramon Vidal and Diego Frías
Bioinformatics and Biology Insights 2009:3 37-49
Original research | Published on 03 Jun 2009



Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization
Junilda Spirollari, Jason T.L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park and Bruce A. Shapiro
Bioinformatics and Biology Insights 2009:3 51-69
Original research | Published on 03 Jun 2009



Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Surendra S Negi and Werner Braun
Bioinformatics and Biology Insights 2009:3 71-81
Original research | Published on 01 Jul 2009



affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data
Markus Schmidberger, Esmeralda Vicedo and Ulrich Mansmann
Bioinformatics and Biology Insights 2009:3 83-87
Original research | Published on 22 Jul 2009



Gene Expression Based Leukemia Sub‑Classification Using Committee Neural Networks
Mihir S. Sewak, Narender P. Reddy and Zhong-Hui Duan
Bioinformatics and Biology Insights 2009:3 89-98
Original research | Published on 03 Sep 2009



Gromita: A Fully Integrated Graphical User Interface to Gromacs 4
Diamantis Sellis, Dimitrios Vlachakis and Metaxia Vlassi
Bioinformatics and Biology Insights 2009:3 99-102
Original research | Published on 07 Sep 2009



Graphical User Interfaces for Molecular Dynamics—Quo Vadis?
B. Knapp and W. Schreiner
Bioinformatics and Biology Insights 2009:3 103-107
Original research | Published on 23 Sep 2009



A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome
Marcin Kierczak, Krzysztof Ginalski, Michał Dramiński, Jacek Koronacki, Witold Rudnicki and Jan Komorowski
Bioinformatics and Biology Insights 2009:3 109-127
Original research | Published on 05 Oct 2009



Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data
Haoyu Cheng, Lihua Jiang, Maoying Wu and Qi Liu
Bioinformatics and Biology Insights 2009:3 129-140
Original research | Published on 21 Oct 2009



Classifying Coding DNA with Nucleotide Statistics
Nicolas Carels and Diego Frías
Bioinformatics and Biology Insights 2009:3 141-154
Original research | Published on 28 Oct 2009



Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences
Ralf Aurahs, Markus Göker, Guido W. Grimm, Vera Hemleben, Christoph Hemleben, Ralf Schiebel and Michal Kučera
Bioinformatics and Biology Insights 2009:3 155-177
Original research | Published on 11 Nov 2009



An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments
Haiyan Hu
Bioinformatics and Biology Insights 2009:3 179-187
Original research | Published on 17 Nov 2009



Domain Organization of Long Autotransporter Signal Sequences
Jan A. Hiss and Gisbert Schneider
Bioinformatics and Biology Insights 2009:3 189-204
Original research | Published on 14 Dec 2009



2008:2

Proteomic Analysis in Diabetic Cardiomyopathy using Bioinformatics Approach
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 and Undurti N. Das
Bioinformatics and Biology Insights 2008:2 1-4
Original research | Published on 21 Jan 2008



Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain
Adam T. Zemla and Carol L. Ecale Zhou
Bioinformatic and Biology Insights 2008:2 5-13
Original research | Published on 01 Feb 2008



The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics
Wei Zhang, Mark J. Ratain and M. Eileen Dolan
Bioinformatics and Biology Insights 2008:2 15-23
Original research | Published on 01 Feb 2008



Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives
Lee-Wei Yang and Choon-Peng Chng
Bioinformatics and Biology Insights 2008:2 25-45

Original research | Published on 04 Mar 2008



Characterization of Non-Trivial Neighborhood Fold Constraints from Protein Sequences using Generalized Topohydrophobicity
Guillaume Fourty, Isabelle Callebaut and Jean-Paul Mornon
Bioinformatics and Biology Insights 2008:2 47-66
Original research | Published on 31 Jan 2008



HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction
Jing Hu and Changhui Yan
Bioinformatics and Biology Insights 2008:2 67-74
Original research | Published on 31 Jan 2008



Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes
Yurong Xin, Giulio Quarta, Hin Hark Gan and Tamar Schlick
Bioinformatics and Biology Insights 2008:2 75-94
Original research | Published on 01 Mar 2008



Effects of Feeding Periods of High Cholesterol and Saturated Fat Diet on Blood Biochemistry and Hydroxyproline Fractions in Rabbits
Mohamed A. K. Abdelhalim, N. J. Siddiqi, A. S. ALhomida and Mohammed S. Al- Ayed
Bioinformatics and Biology Insights 2008:2 95-100
Original research | Published on 22 Apr 2008



Utility of Computational Methods to Identify the Apoptosis Machinery in Unicellular Eukaryotes
Pierre Marcel Durand and Theresa Louise Coetzer
Bioinformatics and Biology Insights 2008:2 101-117
Original research | Published on 12 Mar 2008



A Unified Discussion on the Concept of Score Functions Used in the Context of Nonparametric Linkage Analysis
Lars Ängquist
Bioinformatics and Biology Insights 2008:2 119-132
Original research | Published on 14 Feb 2008



Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis
Kanaka Durga Kedarisetti, Scott Dick and Lukasz Kurgan
Bioinformatics and Biology Insights 2008:2 133-144
Original research | Published on 12 Mar 2008



A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments
Akihiro Hirakawa, Yasunori Sato, Chikuma Hamada and Isao Yoshimura
Bioinformatics and Biology Insights 2008:2 145-156
Original research | Published on 29 Feb 2008



Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis
Zhenkang Xu, Laura Gutierrez, Matthew Hitchens, Steve Scherer, Amy K. Sater and Dan E. Wells
Bioinformatics and Biology Insights 2008:2 157-169
Original research | Published on 26 Feb 2008



Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
Choon-Peng Chng and Lee-Wei Yang
Bioinformatics and Biology Insights 2008:2 171-185
Original research | Published on 05 Mar 2008



Ontologies for Bioinformatics
Nadine Schuurman and Agnieszka Leszczynski
Bioinformatics and Biology Insights 2008:2 187-200
Original research | Published on 12 Mar 2008



Borges Dilemma, Fundamental Laws, and Systems Biology
Ping Ao
Bioinformatics and Biology Insights 2008:2 201-202
Original research | Published on 10 Apr 2008



Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures
Heiko Muller and Francesco Acquati
Bioinformatics and Biology Insights 2008:2 203-213
Original research | Published on 17 Apr 2008



Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets
Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Olof Olsson and Björn Olsson
Bioinformatics and Biology Insights 2008:2 215-237
Original research | Published on 01 May 2008



Methodology for Constructing Problem Definitions in Bioinformatics
Amy M. Hauth and Gertraud Burger
Bioinformatics and Biology Insights 2008:2 239-251

Original research | Published on 24 Apr 2008



Neuroinformatics: From Bioinformatics to Databasing the Brain
Thomas M. Morse
Bioinformatics and Biology Insights 2008:2 253-264
Original research | Published on 14 May 2008



Unsupervised Meta-Analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation
Julia C. Engelmann, Roland Schwarz, Steffen Blenk, Torben Friedrich, Philipp N. Seibel, Thomas Dandekar and Tobias Müller
Bioinformatics and Biology Insights 2008:2 265-280
Original research | Published on 26 May 2008



The Use of Artificial Neural Networks in Prediction of Congenital CMV Outcome from Sequence Data
Ravit Arav-Boger, Yuval S. Boger, Charles B. Foster and Zvi Boger
Bioinformatics and Biology Insights 2008:2 281-289
Original research | Published on 29 May 2008



Normalization and Gene p-Value Estimation: Issues in Microarray Data Processing
Katrin Fundel, Robert Küffner, Thomas Aigner and Ralf Zimmer
Bioinformatics and Biology Insights 2008:2 291-305
Original research | Published on 28 May 2008



Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Jesper Lundström, Johan Björkegren and Jesper Tegnér
Bioinformatics and Biology Insights 2008:2 307-316
Original research | Published on 14 Jul 2008



Designing Toxicogenomics Studies that use DNA Array Technology
Robert R. Delongchamp, Cruz Velasco, Varsha G. Desai, Taewon Lee and James C. Fuscoe
Bioinformatics and Biology Insights 2008:2 317-328
Original research | Published on 14 Aug 2008



Association Between a Prognostic Gene Signature and Functional Gene Sets
Manuela Hummel, Klaus H. Metzeler, Christian Buske, Stefan K. Bohlander and Ulrich Mansmann
Bioinformatics and Biology Insights 2008:2 329-341
Original research | Published on 22 Sep 2008



Gene Copy Number Analysis for Family Data Using Semiparametric Copula Model
Ao Yuan, Guanjie Chen, Zhong-Cheng Zhou, George Bonney and Charles Rotimi
Bioinformatics and Biology Insights 2008:2 343-355

Original research | Published on 26 Sep 2008



IMAGE: A New Tool for the Prediction of Transcription Factor Binding Sites
R. Casilli, A. Marongiu, S. Melchionna, P. Palazzari, R. Paparcone and V. Rosato
Bioinformatics and Biology Insights 2008:2 357-367
Original research | Published on 03 Oct 2008



Identification and Investigation of Drosophila  Postsynaptic Density Homologs
Faith L.W. Liebl and David E. Featherstone
Bioinformatics and Biology Insights 2008:2 369-381
Original research | Published on 03 Nov 2008



Identification of the RGG Box Motif in Shadoo: RNA-Binding and Signaling Roles?
Susan M. Corley and Jill E. Gready
Bioinformatics and Biology Insights 2008:2 383-400
Original research | Published on 19 Nov 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
Laura A. Hecker, Timothy C. Alcon, Vasant G. Honavar and M. Heather West Greenlee
Bioinformatics and Biology Insights 2008:2 401-412
Original research | Published on 01 Feb 2008



2007:1

Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
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 and Stephen J. Meltzer
Bioinformatics and Biology Insights 2007:1 1-16
Original research | Published on 17 Sep 2007



Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines
Zhi Qun Tang, Hong Huang Lin, Hai Lei Zhang, Lian Yi Han, Xin Chen and Yu Zong Chen
Bioinformatics and Biology Insights 2007:1 19-47
Original research | Published on 15 Oct 2007



GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data
Chris Cheadle, Tonya Watkins, Jinshui Fan, Marc A. Williams, Steven Georas, John Hall, Antony Rosen and Kathleen C. Barnes
Bioinformatics and Biology Insights 2007:1 49-62
Original research | Published on 15 Oct 2007



Screening the Single Nucleotide Polymorphisms in Patients with Internal Carotid Artery Stenosis by Oligonucleotide-Based Custom DNA Array
Kenji Nakai, Mayu Oyanagi, Jiro Hitomi, Kuniaki Ogasawara, Takashi Inoue, Masakazu Kobayashi, Keiko Nakai, Akira Suwabe, Wataru Habano, Toshiaki Baba, Hiroshi Yoshida and Akira Ogawa
Bioinformatics and Biology Insights 2007:1 63-69
Original research | Published on 12 Oct 2007



Software for Quantifying and Simulating Microsatellite Genotyping Error
Paul C.D. Johnson and Daniel T. Haydon
Bioinformatics and Biology Insights 2007:1 71-75
Original research | Published on 12 Nov 2007



Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)
Antoni Hermoso, Jordi Espadaler, Enrique Querol, E, Francesc X. Aviles, Michael J.E. Sternberg, Baldomero Oliva and Narcis Fernandez-Fuentes
Bioinformatics and Biology Insights 2007:1 77-90
Original research | Published on 30 Jan 2008



The Penna Model of Biological Aging
D. Stauffer
Bioinformatics and Biology Insights 2007:1 91-100
Original research | Published on 08 Feb 2008



Peptide Vocabulary Analysis Reveals Ultra-Conservation and Homonymity in Protein Sequences
Derek Gatherer
Bioinformatics and Biology Insights 2007:1 101-126
Original research | Published on 12 Dec 2007



Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma
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 and Stephen J. Meltzer
Bioinformatics and Biology Insights 2007:1 127-136
Original research | Published on 01 Feb 2008



Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
Wei-Sheng Wu and Bor-Sen Chen
Bioinformatics and Biology Insights 2007:1 137-145
Original research | Published on 16 Oct 2007





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