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ORCIDJournal of Bioinformatics and Computational Biology, Volume 10
Volume 10, Number 1, February 2012
- Sun Kim, Wei Wang:
Introduction. - Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci:
Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring. - Omar Odibat, Chandan K. Reddy
:
Ranking differential Hubs in gene Co-Expression Networks. - Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu:
A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. - A. Ercüment Çiçek, Gultekin Özsoyoglu:
Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis. - Yixuan Chen, Jing Li:
Generation of Synthetic Data and Experimental Designs in Evaluating Interactions for Association Studies. - Yin Tang, Fei Wang:
Neural System Modeling and Simulation Using Hybrid Functional Petri Net. - Chengcheng Shen, Ying Liu:
A tripartite Clustering Analysis on microRNA, gene and Disease Model. - Sylvia C. Boyd, Maryam Haghighi:
A Fast Method for Large-Scale Multichromosomal Breakpoint Median Problems. - Ameet Soni, Jude W. Shavlik:
Probabilistic Ensembles for Improved Inference in protein-Structure Determination.
Volume 10, Number 2, April 2012
- Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot:
Identification of Shortened 3′ untranslated Regions from Expression Arrays. - Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov, Ilya A. Vakser:
Structure fluctuations and conformational Changes in protein binding. - Evgeniy Aksianov, Andrei Alexeevski:
Sheep: a Tool for Description of β-Sheets in protein 3D Structures. - Alexander A. Osypov, Gleb G. Krutinin, Eugenia A. Krutinina, Svetlana G. Kamzolova:
Deppdb - DNA electrostatic Potential Properties Database: electrostatic Properties of genome DNA Elements. - Irina I. Abnizova, Steven Leonard, Tom Skelly, Andy Brown, David K. Jackson, Marina Gourtovaia, Guoying Qi, Rene te Boekhorst, Nadeem Faruque, Kevin Lewis, Tony Cox:
Analysis of Context-Dependent Errors for Illumina sequencing. - Slavica Dimitrieva, Philipp Bucher:
Practicality and Time Complexity of a Sparsified RNA Folding Algorithm. - Olga Y. Gorlova, Jun Ying, Christopher I. Amos, Margaret R. Spitz, Bo Peng, Ivan P. Gorlov:
Derived SNP Alleles are Used More Frequently than Ancestral Alleles as Risk-associated Variants in Common Human Diseases. - Irina Volokhina, Yury Gusev, Svyatoslav Mazilov, Mikhail Chumakov:
Vire2-Dependent Pores for ssDNA Transfer across Artificial and Cell Membranes. - Adelene Y. L. Sim, Olivier Schwander, Michael Levitt, Julie Bernauer:
Evaluating Mixture Models for Building RNA Knowledge-Based Potentials. - Sergei Vakulenko, Ovidiu Radulescu:
Flexible and Robust Networks. - Alexander A. Terentiev, Nurbubu T. Moldogazieva, Olga V. Levtsova, Dmitry M. Maximenko, Denis A. Borozdenko, Konstantin V. Shaitan:
Modeling of Three Dimensional Structure of Human alpha-Fetoprotein complexed with Diethylstilbestrol: docking and molecular Dynamics Simulation Study. - Ivan P. Gorlov, Jinyoung Byun, Hongya Zhao, Christopher J. Logothetis, Olga Y. Gorlova:
Beyond Comparing Means: the Usefulness of Analyzing Interindividual Variation in gene Expression for Identifying genes associated with Cancer Development.
Volume 10, Number 3, June 2012
- Alberto Casagrande, Francesco Fabris:
Family Fingerprints: a Global Approach to Structural Classification. - Bahar Akbal-Delibas, Irina Hashmi, Amarda Shehu, Nurit Haspel:
An Evolutionary conservation-Based Method for Refining and Reranking protein Complex Structures. - Jianlin Cheng, Jesse Eickholt, Zheng Wang, Xin Deng:
Recursive protein Modeling: a Divide and Conquer Strategy for protein Structure Prediction and its Case Study in CASP9. - Brian Yuan Chen, Soutir Bandyopadhyay:
A Regionalizable Statistical Model of Intersecting Regions in protein-ligand binding Cavities. - Brian S. Olson, Kevin Molloy, S. Farid Hendi, Amarda Shehu:
Guiding Probabilistic Search of the protein conformational Space with Structural Profiles. - Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He:
Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. - Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu:
P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics. - Irina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, Amarda Shehu:
Guiding protein docking with Geometric and Evolutionary Information. - Antonio Mucherino, Carlile Lavor, Leo Liberti:
Exploiting Symmetry Properties of the Discretizable molecular Distance Geometry Problem. - Filip Jagodzinski, Jeanne Hardy, Ileana Streinu:
Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins.
Volume 10, Number 4, August 2012
- Limsoon Wong:
A Short Introduction to Some Recent Progress in phylogenetic Network Reconstruction, genome Mapping, gene Expression Analysis, molecular Dynamic Simulation, and Other Problems in Bioinformatics. - Lei Hua, Jason T. L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro, Kaizhong Zhang:
A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection. - Kouichi Kimura, Asako Koike, Kenta Nakai:
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. - Rukshan Batuwita, Vasile Palade:
Adjusted Geometric-mean: a Novel Performance Measure for Imbalanced Bioinformatics Datasets Learning. - Philippe Gambette, Vincent Berry, Christophe Paul:
Quartets and Unrooted phylogenetic Networks. - Qian Han, Guozhu Dong:
Using Attribute Behavior Diversity to Build Accurate Decision Tree Committees for microarray Data. - Bhakti Limaye, Ruma Banerjee, Avik Datta, Harshal Inamdar, Pankaj Vats, Sonal Dahale, Alok Bhandari, E. P. Ramakrishnan, Rajnikanth Tupakula, Sandeep Malviya, Avinash Bayaskar, Renu Gadhari, Sankalp Jain, Vivek Gavane, Rashmi Mahajan, K. Sunitha, Rajendra Joshi:
Anvaya: a Workflows Environment for Automated genome Analysis. - Jin Xu:
A New Method for Nonhomogeneous Time Course Expression Analysis. - Noah C. Benson, Valerie Daggett:
A Chemical Group Graph Representation for Efficient High-Throughput Analysis of atomistic protein Simulations. - Bing Liu, P. S. Thiagarajan:
Modeling and Analysis of biopathways Dynamics.
Volume 10, Number 5, October 2012
- William Krivan, Nick Arnold, Cecile Morales, Darrick Carter:
Flexgrepps - Flexible Greedy peptide Pool Search: Computation of Near-Optimal Sets of degenerate polypeptides for antigenic Screening. - Alok Sharma, Seiya Imoto, Satoru Miyano:
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis. - Natalia Novoselova, Igor Tom:
Entropy-Based Cluster Validation and Estimation of the Number of Clusters in gene Expression Data. - Sherine Awad, Nicholas Panchy, See-Kiong Ng, Jin Chen:
Inferring the Regulatory Interaction Models of transcription Factors in transcriptional Regulatory Networks. - Michel Habib, Thu-Hien To:
Constructing a Minimum phylogenetic Network from a Dense triplet Set. - Zeehasham Rasheed, Huzefa Rangwala:
Metagenomic Taxonomic Classification Using Extreme Learning Machines. - Frank Eisenhaber:
A Decade after the First Full Human genome sequencing: when will We Understand our Own genome?
Volume 10, Number 6, December 2012
- Madhavi Ganapathiraju, Asia D. Mitchell, Mohamed Thahir, Kamiya Motwani, Seshan Ananthasubramanian:
Suite of Tools for Statistical n-Gram Language Modeling for Pattern Mining in whole genome Sequences. - Ruogu Sheng, Sergey Bereg:
Approximating Metrics with Planar boundary-Labeled Phylogenetic Networks. - Biswa Ranjan Meher, Mattaparthi Venkata Satish Kumar, Smriti Sharma, Pradipta Bandyopadhyay:
Conformational Dynamics of HIV-1 protease: a Comparative molecular Dynamics Simulation Study with Multiple AMBER Force Fields. - Rajat K. De, Namrata Tomar:
Modeling the Optimal Central carbon metabolic pathways under Feedback Inhibition using flux Balance Analysis. - Fernanda L. Sirota, Arsen O. Batagov, Georg Schneider, Birgit Eisenhaber, Frank Eisenhaber, Sebastian Maurer-Stroh:
Beware of Moving targets: Reference proteome Content Fluctuates substantially over the Years. - Ket Fah Chong, Hon Wai Leong:
Tutorial on de novo peptide sequencing using MS/MS Mass spectrometry. - Wentian Li:
Volcano Plots in Analyzing differential Expressions with mRNA microarrays. - Yuhua Jiao, Bruce A. Rosa, Sookyung Oh, Beronda L. Montgomery, Wensheng Qin, Jin Chen:
Detection and Decomposition: Treatment-induced Cyclic gene Expression Disruption in High-Throughput Time-Series Datasets.
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