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ORCIDJournal of Bioinformatics and Computational Biology, Volume 9
Volume 9, Number 1, February 2011
- Jianxiu Guo, Nini Rao:
Predicting protein Folding Rate from amino acid Sequence. 1-13 - Babak Alipanahi
, Xin Gao, Emre Karakoç, Shuai Cheng Li, Frank J. Balbach, Guangyu Feng, Logan Donaldson, Ming Li:
Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation. 15-41 - Sikander Hayat, Peter Walter, Yungki Park, Volkhard Helms:
Prediction of the Exposure Status of transmembrane beta Barrel residues from protein Sequence. 43-65 - Kanaka Durga Kedarisetti, Marcin J. Mizianty, Scott Dick, Lukasz A. Kurgan:
Improved Sequence-Based Prediction of Strand residues. 67-89 - William R. Taylor, Zoe Katsimitsoulia, Alexei Poliakov:
Simulation of Cell Movement and Interaction. 91-110 - Santitham Prom-on, Atthawut Chanthaphan, Jonathan Hoyin Chan, Asawin Meechai:
Enhancing Biological Relevance of a Weighted Gene Co-Expression Network for Functional Module Identification. 111-129 - Siling Wang, Yuhang Wang, Yang Xie, Guanghua Xiao:
A Novel Approach to DNA Copy Number Data Segmentation. 131-148 - Jiangning Song, Hao Tan, Sarah E. Boyd, Hong-Bin Shen, Khalid Mahmood, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock, Robert N. Pike:
Bioinformatic Approaches for Predicting substrates of Proteases. 149-178 - Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber:
The Janus-Faced E-Values of Hmmer2: Extreme Value Distribution or logistic Function? 179-206
Volume 9, Number 2, April 2011
- Tobias Wittkop, Sean D. Mooney:
Introduction: Advances in Computational Systems Bioinformatics. - Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions. 207-229 - Yan Liu, Alexandru Niculescu-Mizil, Aurélie C. Lozano, Yong Lu:
Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery. 231-250 - Elena A. Manilich, Z. Meral Özsoyoglu, Valeriy Trubachev, Tomas Radivoyevitch:
Classification of Large microarray Datasets Using Fast Random Forest Construction. 251-267 - Hatice Gulcin Ozer, Yi-Wen Huang, Jiejun Wu, Jeffrey D. Parvin, Tim Hui-Ming Huang, Kun Huang:
Comparing Multiple Chip-Sequencing Experiments. 269-282 - Timothy I. Shaw, Amir Manzour, Yingfeng Wang, Russell L. Malmberg, Liming Cai:
Analyzing Modular RNA Structure reveals Low Global Structural Entropy in microRNA Sequence. 283-298 - Xiongying Yuan, Yi Zhao, Changning Liu, Dongbo Bu:
Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification. 299-316 - Rujira Achawanantakun, Yanni Sun, Seyedeh Shohreh Takyar:
Ncrna Consensus Secondary Structure Derivation Using Grammar Strings. 317-337 - Wei-Bung Wang, Tao Jiang:
Inferring Haplotypes from genotypes on a Pedigree with mutations, genotyping Errors and Missing Alleles. 339-365
Volume 9, Number 3, June 2011
- Nurit Haspel, Amarda Shehu:
The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (Bionetics 2010) Special Track on Bioinformatics. - Aleksandar Poleksic:
Optimal Pairwise Alignment of Fixed protein Structures in Subquadratic Time. 367-382 - Brian S. Olson, Kevin Molloy, Amarda Shehu:
In Search of the protein Native State with a Probabilistic Sampling Approach. 383-398 - Uday Kamath, Amarda Shehu, Kenneth A. De Jong:
A Two-Stage Evolutionary Approach for Effective Classification of hypersensitive DNA Sequences. 399-413 - Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He:
Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph. 415-430 - Louis Licamele, Lise Getoor:
A Method for the Detection of Meaningful and Reproducible Group Signatures from Gene Expression Profiles. 431-451
Volume 9, Number 4, August 2011
- Limsoon Wong:
Brief Introduction to Some New Papers on Lateral Transfer Reconstruction, Drug Candidate Screening, Disease Gene Identification, and Other Results. - Marc Thuillard, Vincent Moulton:
Identifying and Reconstructing Lateral Transfers from Distance Matrices by Combining the Minimum Contradiction Method and Neighbor-Net. 453-470 - Steve Hodgkinson, Wolfgang P. Kaschka:
Patterns of Hydrophobicity Found in the First and Second transmembrane Domains of solute Transporters Suggest a Possible Role in Nascent protein Anchoring and Organization. 471-488 - Mohammad Tabrez Anwar Shamim, Hampapathalu A. Nagarajaram:
Svm-Based Method for protein Structural Class Prediction Using Secondary Structural Content and Structural Information of amino acids. 489-502 - Yun Li, Kang Tu, Siyuan Zheng, Jingfang Wang, Yixue Li, Pei Hao, Xuan Li:
Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds. 503-519 - Reiji Teramoto, Tsuyoshi Kato:
Transfer Learning for cytochrome P450 Isozyme Selectivity Prediction. 521-540 - Maria Elena Ochagavía, Jamilet Miranda, Marcelo Nazábal, Alexander Martin, Lidia Inés Novoa, Ricardo Bringas, Jorge Fernandez-de-Cossío, Hanlet Camacho:
A Methodology Based on Molecular Interactions and Pathways to Find Candidate genes Associated to Diseases: its Application to Schizophrenia and Alzheimer's Disease. 541-557 - Roberto Chignola, Alessio Del Fabbro, Marcello Farina, Edoardo Milotti:
Computational Challenges of Tumor Spheroid Modeling. 559-577 - Katarina M. Jørgensen, Pauline C. Haddow:
Visualization in Simulation Tools: Requirements and a Tool Specification to Support the Teaching of Dynamic Biological Processes. 579-595
Volume 9, Number 5, October 2011
- Xue-Wen Chen, Satoru Miyano:
INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11. - Kwangmin Choi, Sun Kim:
Sequence-Based enzyme catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content. 597-611 - Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira:
Quantitative Modeling of the Saccharomyces cerevisiae Flr1 regulatory Network Using an S-System Formalism. 613-630 - Wenlong Tang, Hongbao Cao, Junbo Duan, Yu-Ping Wang:
A Compressed Sensing Based Approach for Subtyping of Leukemia from gene Expression Data. 631-645 - Kaushal Desai, David Brott, Xiaohua Hu, Anastasia Christianson:
A Systems Biology Approach for Detecting Toxicity-Related Hotspots inside protein Interaction Networks. 647-662
Volume 9, Number 6, December 2011
- Limsoon Wong:
Introduction - Some New Results and Tools for Protein Function Prediction, RNA Target Site Prediction, Genotype Calling, Environmental Genomics, and More. - Jingyan Wang, Yongping Li:
Sequential Linear Neighborhood Propagation for Semi-Supervised protein Function Prediction. 663-679 - Marco A. Alvarez, Changhui Yan:
A Graph-Based Semantic Similarity Measure for the gene Ontology. 681-695 - Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu:
Using binding Profiles to Predict binding sites of Target RNAs. 697-713 - Bilin Fu, Jin Xu:
A New genotype calling Method for Affymetrix SNP Arrays. 715-728 - Md. Shaik Sadi, Fei-Ching Kuo, Joshua Wing Kei Ho, Michael A. Charleston, Tsong Yueh Chen:
Verification of phylogenetic Inference Programs Using Metamorphic Testing. 729-747 - Markus E. Nebel, Sebastian Wild, Michael Holzhauser, Lars Huettenberger, Raphael Reitzig, Matthias Sperber, Thorsten Stoeck:
Jaguc - a Software package for Environmental Diversity Analyses. 749-773 - Yukun Wu, Le Zhang:
Comparison of Two Academic Software packages for Analyzing Two-Dimensional gel Images. 775-794 - Ameya Deo, Jessica Carlsson, Angelica Lindlöf:
How to Choose a Normalization Strategy for miRNA Quantitative Real-Time (qPCR) Arrays. 795-812
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