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In Silico Biology, Volume 6
Volume 6, Numbers 1-2, 2006
- Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano:
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. 1-13 - Leszek Konieczny, Michal Brylinski, Irena Roterman:
Gauss-Function-Based Model of Hydrophobicity Density in Proteins. 15-22 - Imtiaz A. Khan, Matthew E. Mort, Paul R. Buckland, Michael C. O'Donovan, David N. Cooper, Nadia A. Chuzhanova:
In Silico Discrimination of Single Nucleotide Polymorphisms and Pathological Mutations in Human Gene Promoter Regions by Means of Local DNA Sequence Context and Regularity. 23-34 - Daniel R. Matute, Emiliano Barreto-Hernandez, Laurent Falquet:
Hunting for Insect-Specific Protein Domains. 35-42 - Anirban Dutta, Shashi Singh, Payel Ghosh, Runni Mukherjee, Sayak Mitter, Debashis Bandyopadhyay:
In Silico Identification of Potential Therapeutic Targets in the Human Pathogen Helicobacter Pylori. 43-47 - Kazuharu Arakawa, Yoichi Nakayama, Masaru Tomita:
GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness. 49-60 - Ralf Wessel, Volker Foos, Allan Aspelmeier, Martin Jürgens, Adolf Graessmann, Andreas Klein:
CorrXpression - Identification of Significant Groups of Genes and Experiments by Means of Correspondence Analysis and Ratio Analysis. 61-70 - Lokesh Kumar, Matthias E. Futschik, Hanspeter Herzel:
DNA Motifs and Sequence Periodicities. 71-78 - Daisuke Komura, Kunihiro Nishimura, Shumpei Ishikawa, Binaya Panda, Jing Huang, Hiroshi Nakamura, Sigeo Ihara, Michitaka Hirose, Keith W. Jones, Hiroyuki Aburatani:
Noise Reduction from Genotyping Microarrays Using Probe Level Information. 79-92 - Anna Gambin, Slawomir Lasota, Michai Rutkowski:
Analyzing Stationary States of Gene Regulatory Network Using Petri Nets. 93-109 - Harpreet Kaur, Gajendra P. S. Raghava:
Prediction of Cα-H·O and Cα-H·π Interactions in Proteins Using Recurrent Neural Network. 111-125 - Aswin Sai Narain Seshasayee:
Social Behavior of The Yeast Protein-Protein Interaction Network. 127-130 - Christoph Bock, Jürgen Hesser:
Analysis and Prediction of Helix Shift Errors in Homology Modeling. 131-145 - Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Ichitaro Oya, Kenji Oosawa, Toshio Shimizu:
Analysis of Tandem Repeats Found in 44 Prokaryotic Genomes. 147-159
Volume 6, Number 3, 2006
- Tamanna Anwar, Sunil K. Lal, Asad U. Khan:
In silico Analysis of Genes Nucleoprotein, Neuraminidase and Hemagglutinin: A Comparative Study on Different Strains of Influenza A (Bird Flu) Virus Sub-Type H5N1. 161-168 - Patnala Kiranmayi, Pamarthi Maruthi Mohan:
Metal Transportome of Neurospora crassa. 169-180 - Armand Bankhead, Nancy S. Magnuson, Robert B. Heckendorn:
Gene Knockout Experiments to Quantify a G2/M Genetic Network Simulation for Mammary Cancer Susceptibility. 181-192 - Peter Gennemark, Bodil Nordlander, Stefan Hohmann, Dag Wedelin:
A Simple Mathematical Model of Adaptation to High Osmolarity in Yeast. 193-214 - Achuthsankar S. Nair, T. Mahalakshmi:
Are Categorical Periodograms and Indicator Sequences of Genomes Spectrally Equivalent? 215-222 - Michael Bose, Robert Barber:
Prophage Finder: A Prophage Loci Prediction Tool for Prokaryotic Genome Sequences. 223-227 - Bhagavathimuthu Balamurugan, M. N. A. Mohd. Roshan, Daliah Michael, Majumder Ambaree, Subramanyam Divya, Hanumanthagowda Keerthana, Mahadev Seemanthini, Kanagaraj Sekar:
SMS: Sequence, Motif and Structure - A Database on the Structural Rigidity of Peptide Fragments in Non-Redundant Proteins. 229-235 - Krishna R. Kalari, Melanie Casavant, Thomas B. Bair, Henry L. Keen, Josep M. Comeron, Thomas L. Casavant, Todd E. Scheetz:
First Exons and Introns - A Survey of GC Content and Gene Structure in the Human Genome. 237-242 - Lorenz Bülow, Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Reinhard Hehl:
AthaMap: From in silico Data to Real Transcription Factor Binding Sites. 243-252 - Francesco Piva, Giovanni Principato:
RANDNA: A Random DNA Sequence Generator. 253-258
Volume 6, Number 4, 2006
- Steven E. Massey:
Basic Faced α-Helices are Widespread in the Peptide Extensions of the Eukaryotic Aminoacyl-tRNA Synthetases. 259-273 - Meena Kishore Sakharkar, Pandjassarame Kangueane, Kishore R. Sakharkar, Zhaowei Zhong:
Huge Proteins in The Human Proteome and Their Participation in Hereditary Diseases. 275-279 - Rainer Merkl:
AMIGOS: A Method for the Inspection of Genomic Organisation or Structure and its Application to Characterise Conserved Gene Arrangements. 281-306 - Gang Su, Binchen Mao, Jin Wang:
MACO: A Gapped-Alignment Scoring Tool for Comparing Transcription Factor Binding Sites. 307-310 - Saikat Chakrabarti, Gowri Manohari, Ganesan Pugalenthi, Ramanathan Sowdhamini:
SSToSS - Sequence-Structural Templates of Single-Member Superfamilies. 311-319 - Gordon Blackshields, Iain M. Wallace, Mark A. Larkin, Desmond G. Higgins:
Analysis and Comparison of Benchmarks for Multiple Sequence Alignment. 321-339 - Chan-Eng Chong, Boon-San Lim, Sheila Nathan, Rahmah Mohamed:
In Silico Analysis of Burkholderia pseudomallei Genome Sequence for Potential Drug Targets. 341-346 - Andres Julian Gutierrez, Aylan Farid Arenas, Jorge E. Gomez-Marin:
Molecular Evolution of Serine/Arginine Splicing Factors Family (SR) by Positive Selection. 347-350
Volume 6, Number 5, 2006
- Chandrashekar Reddy, Arunachalam Manonmani, Meenakshi Babu, Ramanathan Sowdhamini:
Enhanced Structure Prediction of Gene Products Containing Class III Adenylyl Cyclase Domains. 351-362 - Alessandra C. Faria-Campos, Sérgio Vale Aguiar Campos, Francisco Prosdocimi, Glaura C. Franco, Glória R. Franco, José Miguel Ortega:
Efficient Secondary Database Driven Annotation Using Model Organism Sequences. 363-372 - Pratip Shil, Niraj Dudani, Pandit B. Vidyasagar:
ISHAN: Sequence Homology Analysis Package. 373-377 - Mamoun Ahram, Zoi I. Litou, Ruihua Fang, Ghaith Al-Tawallbeh:
Estimation of Membrane Proteins in the Human Proteome. 379-386 - Melissa J. Davis, Fasheng Zhang, Zheng Yuan, Rohan D. Teasdale:
MemO: A Consensus Approach to the Annotation of a Protein's Membrane Organization. 387-399 - Paras Chopra, Akhil Kamma:
Engineering Life through Synthetic Biology. 401-410 - Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita, Akio Kanai:
SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level. 411-418 - Mark Doderer, Kihoon Yoon, John Salinas, Stephen Kwek:
Protein Subcellular Localization Prediction Using a Hybrid of Similarity Search and Error-Correcting Output Code Techniques That Produces Interpretable Results. 419-433 - Pagadala Nataraj Sekhar, Polavarapu B. Kavi Kishor, Lakkireddy Ananda Reddy, Prosenjit Mondal, Ardhendu K. Dash, Manoranjan Kar, Satya Mohanty, Surendra C. Sabat:
In Silico Modeling and Hydrogen Peroxide Binding Study of Rice Catalase. 435-447 - Vito Librando, Danilo Gullotto, Zelica Minniti:
Automated Molecular Library Generation of Proteic Fragments by Virtual Proteolysis for Molecular Modelling Studies. 449-457 - Abdelouahab Chikhi, Abderrahmane Bensegueni, Abderrahmane Boulahrouf, Mustapha Bencharif:
Theoretical Study of Escherichia Coli Peptide Deformylase Inhibition by Several Drugs. 459-466
Volume 6, Number 6, 2006
- Alfonso Benítez-Páez:
Sequence Analysis of the Receptor Activity-Modifying Proteins Family, New Putative Peptides and Structural Conformation Inferenc. 467-483 - Nitesh Kumar Singh, S. Mahalaxmi Selvam, Paulsharma Chakravarthy:
T-iDT: Tool for Identification of Drug Target in Bacteria and Validation by Mycobacterium Tuberculosis. 485-493 - Jorge Andrade, Lisa Berglund, Mathias Uhlen, Jacob Odeberg:
Using Grid Technology for Computationally Intensive Applied Bioinformatics Analyses. 495-504 - Adrian E. H. Png, Keng Wah Choo, Cheryl I. P. Lee, Siew Hong Leong, Oi Lian Kon:
Primer Design for Whole Genome Amplification Using Genetic Algorithms. 505-514 - Shinsuke Dohkan, Asako Koike, Toshihisa Takagi:
Improving the Performance of an SVM-Based Method for Predicting Protein-Protein Interactions. 515-529 - Tae-Min Kim, Myeong Ho Jung:
Identification of Transcriptional Regulators Using Binding Site Enrichment Analysis. 531-544 - Najl V. Valeyev, A. Kristina Downing, Andrei Skorinkin, Iain D. Campbell, Nikolai V. Kotov:
A Calcium Dependent De-Adhesion Mechanism Regulates the Direction and Rate of Cell Migration: A Mathematical Model. 545-572 - Kevin Bleakley, Véronique Giudicelli, Yan Wu, Marie-Paule Lefranc, Gérard Biau:
IMGT Standardization for Statistical Analyses of T Cell Receptor Junctions: The TRAV-TRAJ Example. 573-588 - Michal Brylinski, Marek Kochanczyk, Leszek Konieczny, Irena Roterman:
Sequence-Structure-Function Relation Characterized in silico. 589-600 - Saju Joy, Parvathy S. Nair, Ramkumar Hariharan, Radhakrishna M. Pillai:
Detailed Comparison of the Protein-Ligand Docking Efficiencies of GOLD, a Commercial Package and ArgusLab, a Licensable Freeware. 601-605 - B. Jayashree, Ramu Punna, P. Prasad, Kassahun Bantte, C. Tom Hash, Subhash Chandra, David A. Hoisington, Rajeev K. Varshney:
A Database of Simple Sequence Repeats from Cereal and Legume Expressed Sequence Tags Mined in silico: Survey and Evaluation. 607-620 - Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita:
MEGU: Pathway Mapping Web-Service Based on KEGG and SVG. 621-625
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