Results 300-350 of 791 for Bioinformatics

A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 43-68
Original Research | Published on 26 Feb 2013

A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Tradeoff on Phenotype Robustness in Biological Networks Part II: Ecological Networks
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 69-85
Original Research | Published on 26 Feb 2013

A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 87-109
Original Research | Published on 26 Feb 2013

Decomposing Phenotype Descriptions for the Human Skeletal Phenome
Tudor Groza, Jane Hunter and Andreas Zankl
Biomedical Informatics Insights 2013:6 1-14
Original Research | Published on 04 Feb 2013

Application of a Bioinformatics-Based Approach to Identify Novel Putative in vivo BACE 1 Substrates
Joseph L. Johnson, Emily Chambers and Keerthi Jayasundera
Biomedical Engineering and Computational Biology 2013:5 1-15
Original Research | Published on 03 Feb 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

The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway
Minghui Wang, Qishan Wang, Zhen Wang, Qingping Wang, Xiangzhe Zhang and Yuchun Pan
Evolutionary Bioinformatics 2013:9 1-16
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

Prediction of Breast Cancer Metastasis by Gene Expression Profiles: A Comparison of Metagenes and Single Genes
Mark Burton, Mads Thomassen, Qihua Tan and Torben A. Kruse
Cancer Informatics 2012:11 193-217
Original Research | Published on 10 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

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

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

Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Ence Yang, Amanda M. Hulse and James J. Cai
Evolutionary Bioinformatics 2012:8 623-644
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

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 Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence
Eli Reuveni and Alessandro Giuliani
Evolutionary Bioinformatics 2012:8 611-622
Methodology | Published on 14 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

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
Software or database review | Published on 08 Nov 2012

Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes
Payal Singh and Supratim Sengupta
Evolutionary Bioinformatics 2012:8 589-609
Original Research | Published on 06 Nov 2012

What’s In a Note: Construction of a Suicide Note Corpus
John P. Pestian, Pawel Matykiewicz and Michelle Linn-Gust
Biomedical Informatics Insights 2012:5 1-6
Original Research | Published on 05 Nov 2012

Newton, Laplace, and The Epistemology of Systems Biology
Michael L. Bittner and Edward R. Dougherty
Cancer Informatics 2012:11 185-190
Perspective | Published on 30 Oct 2012

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

Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants
Li-yu Daisy Liu and Yuh-Chyang Charng
Evolutionary Bioinformatics 2012:8 575-587
Original Research | Published on 08 Oct 2012 | Video abstract

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

Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana
Wanjun Gu, Chuanying Zhai, Xiaofei Wang, Xueying Xie, Gurunadh Parinandi, and Tong Zhou,
Evolutionary Bioinformatics 2012:8 565-574
Original Research | Published on 25 Sep 2012

Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses
Namrata Misra, Prasanna Kumar Panda, Bikram Kumar Parida and Barada Kanta Mishra
Evolutionary Bioinformatics 2012:8 545-564
Original Research | Published on 20 Sep 2012

Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection
Ulf Sorhannus
Evolutionary Bioinformatics 2012:8 535-544
Original Research | Published on 17 Sep 2012

Significance Analysis of Microarrays (SAM) Offers Clues to Differences Between the Genomes of Adult Philadelphia Positive ALL and the Lymphoid Blast Transformation of CML
Colin Grace and Elisabeth P. Nacheva
Cancer Informatics 2012:11 173-183
Original Research | Published on 12 Sep 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

Cloud Computing for Comparative Genomics with Windows Azure Platform
Insik Kim, Jae-Yoon Jung, Todd F. DeLuca, Tristan H. Nelson and Dennis P. Wall
Evolutionary Bioinformatics 2012:8 527-534
Technical Advance | Published on 30 Aug 2012

Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach
Mayakannan Manikandan, Ganesh Raksha and Arasambattu Kannan Munirajan
Cancer Informatics 2012:11 157-171
Perspective | Published on 29 Aug 2012

Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling
Thomas Meinel and Antje Krause
Evolutionary Bioinformatics 2012:8 489-525
Original Research | Published on 07 Aug 2012

Inference of Self-Regulated Transcriptional Networks by Comparative Genomics
Joseph P. Cornish, Fialelei Matthews, Julien R. Thomas and Ivan Erill
Evolutionary Bioinformatics 2012:8 449-461
Original Research | Published on 06 Aug 2012

TreeCmp: Comparison of Trees in Polynomial Time
Damian Bogdanowicz, Krzysztof Giaro and Borys Wróbel,
Evolutionary Bioinformatics 2012:8 475-487
Software review | Published on 06 Aug 2012

Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups
Julia Lambret-Frotté, Fernando Araújo Perini and Claudia Augusta de Moraes Russo
Evolutionary Bioinformatics 2012:8 463-473
Original Research | Published on 06 Aug 2012

The Chordate Proteome History Database
Anthony Levasseur, Julien Paganini, Jacques Dainat, Julie D. Thompson, Olivier Poch, Pierre Pontarotti and Philippe Gouret
Evolutionary Bioinformatics 2012:8 437-447
Original Research | Published on 01 Aug 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
Methodology | Published on 31 Jul 2012

TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer
Xi Chen, Jiang Li, William H. Gray, Brian D. Lehmann, Joshua A. Bauer, Yu Shyr, and Jennifer A. Pietenpol
Cancer Informatics 2012:11 147-156
Case report | Published on 24 Jul 2012

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny
Runhua Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, Mindy L. Wood, Mary C. Christman, George H. Perry, Edward E. Louis Jr and Guoqing Lu
Evolutionary Bioinformatics 2012:8 423-435
Software review | Published on 23 Jul 2012

Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX
Julien Paganini and Philippe Gouret
Evolutionary Bioinformatics 2012:8 417-421
Rapid Communication | Published on 05 Jul 2012

Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species
Gideon C.-T. Wu, and Feng-Chi Chen
Evolutionary Bioinformatics 2012:8 389-415
Original Research | Published on 04 Jul 2012

Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species
Shu-Hsi Lin, Miwa Yoshimoto, Ping-Chiang Lyu, Chuan-Yi Tang and Masanori Arita
Evolutionary Bioinformatics 2012:8 373-387
Original Research | Published on 04 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
Short Report | Published on 02 Jul 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
Review | Published on 02 Jul 2012

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity
Sohta A. Ishikawa, Yuji Inagaki, and Tetsuo Hashimoto
Evolutionary Bioinformatics 2012:8 357-371
Original Research | Published on 25 Jun 2012

AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots
Muhammad Rashid, He Guangyuan, Yang Guangxiao, Javeed Hussain and Yan Xu
Evolutionary Bioinformatics 2012:8 321-355
Original Research | Published on 21 Jun 2012

Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors
Balasubramanian Nagarathnam, Singaravelu Kalaimathy, Veluchamy Balakrishnan and Ramanathan Sowdhamini
Evolutionary Bioinformatics 2012:8 229-259
Original Research | Published on 19 Jun 2012

Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion
Dapeng Wang, Yao Su, Xumin Wang, Hongxing Lei and Jun Yu
Evolutionary Bioinformatics 2012:8 301-319
Original Research | Published on 19 Jun 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
Methodology | Published on 19 Jun 2012

MiIP: The Monomer Identification and Isolation Program
Christopher Bun, William Ziccardi, Jeffrey Doering and Catherine Putonti
Evolutionary Bioinformatics 2012:8 293-300
Software or database review | Published on 14 Jun 2012