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ORCIDJournal of Bioinformatics and Computational Biology, Volume 8
Volume 8, Number 1, February 2010
- Manja Marz, Nathalie Vanzo, Peter F. Stadler
:
Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. 1-17 - Ziying Liu, Sieu Phan, Fazel Famili, Youlian Pan, Anne E. G. Lenferink, Christiane Cantin, Catherine Collins, Maureen D. McCourt O'Connor:
A Multi-Strategy Approach to Informative Gene Identification from Gene Expression Data. 19-38 - Rezwan Ahmed, Huzefa Rangwala, George Karypis:
Toptmh: Topology Predictor for transmembrane alpha-helices. 39-57 - Hongwei Huo, Vojislav Stojkovic, Qiao-Luan Xie:
A Quantum-Inspired Genetic Algorithm Based on Probabilistic Coding for Multiple Sequence Alignment. 59-75 - Guozhu Dong, Lei Duan, Changjie Tang:
Mining Disease State converters for Medical Intervention of Diseases. 77-97 - Jiyuan An, Kwok Pui Choi, Christine A. Wells, Yi-Ping Phoebe Chen:
Identifying Co-Regulating microRNA Groups. 99-115 - Vachiranee Limviphuvadh, Ling Ling Chua, Frank Eisenhaber, Sharmila Adhikari, Sebastian Maurer-Stroh:
Is Lgi2 the Candidate Gene for Partial Epilepsy with Pericentral Spikes? 117-127 - Dietrich Rebholz-Schuhmann, Nigel Collier, Jong C. Park, Limsoon Wong:
Wrestling with Biomedical Research Results: Language Resources and Literature Analysis. 129-130 - Makoto Miwa, Rune Sætre, Jin-Dong Kim, Jun'ichi Tsujii:
Event Extraction with Complex Event Classification Using Rich Features. 131-146 - Yutaka Sasaki, John McNaught, Sophia Ananiadou:
The Value of an in-Domain Lexicon in genomics QA. 147-161 - Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Erik M. van Mulligen, Ning Kang, Jan A. Kors, David Milward, Peter T. Corbett, Ekaterina Buyko, Elena Beisswanger, Udo Hahn:
Calbc Silver Standard Corpus. 163-179
Volume 8, Number 2, April 2010
- Ying Xu, Peter W. Markstein:
Foreword: Advances in Computational Systems Bioinformatics. - Rajib Sengupta, Dhundy Bastola, Hesham H. Ali:
Classification and Identification of fungal Sequences Using Characteristic restriction endonuclease Cut Order. 181-198 - Misael Mongiovì, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro, Roded Sharan:
Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm. 199-218 - Arvind Rao, David J. States, Alfred O. Hero III, James Douglas Engel:
Understanding Distal transcriptional Regulation from Sequence, Expression and interactome Perspectives. 219-246 - Ali Cakmak, Gultekin Özsoyoglu, Richard W. Hanson:
Querying metabolism under Different Physiological Constraints. 247-293 - Xiaolin Yin, Jing Li:
Detecting Copy Number Variations from Array CGH Data Based on a Conditional Random Field Model. 295-314 - Paritosh A. Kavathekar, Bruce A. Craig, Alan M. Friedman, Chris Bailey-Kellogg, Devin J. Balkcom:
Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data. 315-335 - Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Art Chaovalitwongse, Chun-An Chou, Bhaskar DasGupta:
Combinatorial Reconstruction of Half-Sibling Groups from Microsatellite Data. 337-356 - Artem Sokolov, Asa Ben-Hur:
Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method. 357-376
Volume 8, Number 3, June 2010
- Tatyana B. Mamonova, Anna V. Glyakina, Maria G. Kurnikova, Oxana V. Galzitskaya:
Flexibility and Mobility in Mesophilic and Thermophilic homologous proteins from Molecular Dynamics and Foldunfold Method. 377-394 - Anna V. Glyakina, Oxana V. Galzitskaya:
A Comparative Analysis of Folding Pathways of Thermophilic and Mesophilic proteins by Monte Carlo Simulations. 395-411 - Alexander A. Osypov, Gleb G. Krutinin, Svetlana G. Kamzolova:
Deppdb - DNA electrostatic Potential Properties Database: electrostatic Properties of genome DNA. 413-425 - Sergei Rahmanov, Ivan V. Kulakovskiy, Leonid Uroshlev, Vsevolod J. Makeev:
Empirical Potentials for ion Binding in proteins. 427-435 - Daniil G. Naumoff:
Gh101 Family of Glycoside hydrolases: subfamily Structure and Evolutionary Connections with Other Families. 437-451 - Alexander Grishin, Ines Fonfara, Andrei Alexeevski, Sergei A. Spirin, Olga Zanegina, Anna S. Karyagina, Daniil Alexeyevsky, Wolfgang Wende:
Identification of conserved Features of Laglidadg Homing endonucleases. 453-469 - Vladimir Arzhanik, Darja Svistunova, Oleg V. Koliasnikov, Alexey M. Egorov:
Interaction of antibodies with Aromatic ligands: the Role of pi-Stacking. 471-483 - Solenne Carat, Rémi Houlgatte, Jérémie Bourdon:
A Parallel Scheme for Comparing transcription Factor Binding Sites Matrices. 485-502 - Boris Burkov, Boris Nagaev, Sergei A. Spirin, Andrei Alexeevski:
Malakite: an Automatic Tool for Characterisation of Structure of Reliable Blocks in Multiple alignments of protein Sequences. 503-517 - Sergey I. Mitrofanov, Alexander Y. Panchin, Sergei A. Spirin, Andrei Alexeevski, Yuri V. Panchin:
Exclusive Sequences of Different genomes. 519-534 - Ivan Antonov, Mark Borodovsky:
Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm. 535-551 - Anna S. Karyagina, Michail O. Vassiliev, Anna S. Ershova, Ramil N. Nurtdinov, Ilya S. Lossev:
Probe-Level Universal Search (Plus) Algorithm for Gender Differentiation in Affymetrix Datasets. 553-577 - Irina I. Abnizova, Tom Skelly, Fedor Naumenko, Nava Whiteford, Clive Brown, Tony Cox:
Statistical Comparison of Methods to Estimate the Error Probability in Short-Read Illumina Sequencing. 579-591 - Ekaterina Kotelnikova, Anton Yuryev, Ilya Mazo, Nikolai Daraselia:
Computational Approaches for Drug Repositioning and Combination Therapy Design. 593-606 - Valentin V. Suslov, Petr M. Ponomarenko, Vadim M. Efimov, Ludmila K. Savinkova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov:
Snps in the HIV-1 TATA Box and the Aids pandemic. 607-625 - Sergey A. Lashin, Valentin V. Suslov, Yuri G. Matushkin:
Comparative Modeling of Coevolution in Communities of Unicellular Organisms: Adaptability and Biodiversity. 627-643
Volume 8, Number 4, August 2010
- Limsoon Wong:
Brief Introduction to Some New Results in Gene Expression Analysis, Systems Biology Modeling, Motif Identification, and (noncoding) RNA Analysis. - Yichuan Zhao, Guoshen Wang:
Additive Risk Analysis of microarray Gene Expression Data via Correlation Principal Component Regression. 645-659 - Shuhei Kimura, Yuichi Shiraishi, Mariko Okada:
Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations. 661-677 - André Fujita, João Ricardo Sato, Kaname Kojima, Luciana Rodrigues Gomes, Masao Nagasaki, Mari Cleide Sogayar, Satoru Miyano:
Identification of Granger Causality between Gene Sets. 679-701 - Miroslava Cuperlovic-Culf:
The Importance of inhibitors for the Simulation of metabolic Processes: in silico Zn2+ Inhibition of M-Aconitase from Analysis of glycolysis and Krebs Cycle Kinetic Models. 703-715 - Abhilash Mohan, Sharmila Anishetty, Pennathur Gautam:
Global metal-ion Binding protein Fingerprint: a Method to Identify Motif-Less metal-ion Binding proteins. 717-726 - Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. 727-742 - Fei Xia, Yong Dou, Guo-Qing Lei:
Fpqrna: Hardware-Accelerated Qrna Package for noncoding RNA Gene Detecting on FPGA. 743-761 - Yun Zheng, Weixiong Zhang:
Animal microRNA Target Prediction Using Diverse Sequence-Specific determinants. 763-788
Volume 8, Number 5, October 2010
- Winnie W. M. Lam, Keith C. C. Chan, David K. Y. Chiu, Andrew K. C. Wong:
A Graph-Based Algorithm for Mining Multi-Level Patterns in genomic Data. 789-807 - Fredrik Johansson, Hiroyuki Toh:
Relative von Neumann Entropy for Evaluating amino acid conservation. 809-823 - Ulavappa B. Angadi, M. Venkatesulu:
Fuzzyart Neural Network for protein Classification. 825-841 - Tsutomu Matsunaga, Shuhei Kuwata, Masaaki Muramatsu:
Computational Gene knockout reveals Transdisease-Transgene Association Structure. 843-866 - Yuzhong Zhao, Babak Alipanahi, Shuai Cheng Li, Ming Li:
Protein Secondary Structure Prediction Using NMR Chemical Shift Data. 867-884 - Rune Thomsen, Christina Ane Elisabeth Sølvsten, Toke Elbek Linnet, Jenny Blechingberg, Anders Lade Nielsen:
Analysis of Qpcr Data by Converting Exponentially Related CT Values into Linearly Related X0 Values. 885-900 - Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
Improving the Inter-Corpora Compatibility for protein Annotations. 901-916 - Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii:
A Re-Evaluation of Biomedical Named Entity-Term Relations. 917-928
Volume 8, Number 6, December 2010
- Nassim Sohaee, Christian V. Forst:
Identification of Functional Modules in a PPI Network by Bounded Diameter Clustering. 929-943 - Mizanur R. Khondoker, Till T. Bachmann, Muriel Mewissen, Paul Dickinson, Bartosz Dobrzelecki, Colin J. Campbell, Andrew R. Mount, Anthony J. Walton, Jason Crain, Holger Schulze, Gerard Giraud, Alan J. Ross, Ilenia Ciani, Stuart W. J. Ember, Chaker Tlili, Jonathan G. Terry, Eilidh Grant, Nicola McDonnell, Peter Ghazal:
Multi-Factorial Analysis of Class Prediction Error: Estimating Optimal Number of Biomarkers for Various Classification Rules. 945-965 - Vandanaben Patel, Jason T. L. Wang, Shefali Setia, Anurag Verma, Charles D. Warden, Kaizhong Zhang:
On Comparing Two Structured RNA Multiple alignments. 967-980 - Lin He, Bin Ma:
Adepts: Advanced peptide de novo Sequencing with a Pair of Tandem Mass Spectra. 981-994 - Hao Zheng, Hongwei Wu:
Short prokaryotic DNA Fragment Binning Using a Hierarchical Classifier Based on Linear Discriminant Analysis and Principal Component Analysis. 995-1011 - Alexander Churkin, Moriah Cohen, Yonat Shemer-Avni, Danny Barash:
Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements across genotypes reveals Evidence for Direct Evolution of Genetic Robustness in HCV. 1013-1026 - Petr Sulc, Andreas Wagner, Olivier C. Martin:
Quantifying Slow Evolutionary Dynamics in RNA Fitness Landscapes. 1027-1040 - John O'Quigley:
Dynamic Equilibrium of reconstituting Hematopoietic Stem Cell Populations. 1041-1051
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