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ORCIDIn Silico Biology, Volume 5
Volume 5, Number 1, 2004
- Takako Takai-Igarashi, Toshihisa Takagi, Holger Michael, Edgar Wingender:
Preface - Third "Ontology Workshop on Ontology and Genomes". 1-3 - Vivian Lee, Evelyn Camon, Emily Dimmer, Daniel Barrell, Rolf Apweiler:
GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools. 5-8 - Asako Koike, Toshihisa Takagi:
PRIME: automatically extracted PRotein Interactions and Molecular Information databas. 9-20 - Jasmin Saric, Lars Juhl Jensen, Isabel Rojas:
Large-scale extraction of gene regulation for model organisms in an ontological context. 21-32 - Jacob Köhler, Christopher J. Rawlings, Paul Verrier, Rowan A. C. Mitchell, Andre Skusa, Alexander Rüegg, Stephan Philippi:
Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures. 33-44 - Marie-Paule Lefranc, Oliver Clément, Quentin Kaas, Elodie Duprat, Patrick Chastellan, Isabelle Coelho, Kora Combres, Chantal Ginestoux, Véronique Giudicelli, Denys Chaume, Gérard Lefranc:
IMGT-Choreography for immunogenetics and immunoinformatics. 45-60 - Holger Michael, Xin Chen, Ellen Fricke, Martin Haubrock, Remko Ricanek, Edgar Wingender:
Deriving an ontology for human gene expression sources from the CYTOMER? database on human organs and cell types. 61-66 - Kenji Satou, Kaoru Yamamoto:
Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature. 67-79
Volume 5, Number 2, 2004
- Ralf Hofestädt:
Preface - Dagstuhl Seminar on Integrative Bioinformatics. 81-82 - Eberhard O. Voit, Simeone Marino, Raman Lall:
Challenges for the identification of biological systems from in vivo time series data. 83-92 - Ljudmilla Borisjuk, Mohammad-Reza Hajirezaei, Christian Klukas, Hardy Rolletschek, Falk Schreiber:
Integrating data from biological experiments into metabolic networks with the DBE information system. 93-102 - Thomas Dandekar, Steffen Schmidt:
Metabolites, pathway flexibility. 103-110 - Ming Chen, Ralf Hofestädt:
An algorithm for linear metabolic pathway alignment. 111-128 - Ina Koch, Markus Schüler, Monika Heiner:
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks. 129-137 - David S. Wishart, Robert Yang, David Arndt, Peter Tang, Joseph A. Cruz:
Dynamic cellular automata: a simple but powerful approach to cellular simulation. 139-161 - Gordon Broderick, Melania Rúaini, Eugene Chan, Michael J. Ellison:
A life-like virtual cell membrane using discrete automata. 163-178 - Manuela Pruess, Paul J. Kersey, Rolf Apweiler:
The Integr8 project - a resource for genomic and proteomic data. 179-185 - Andrei L. Turinsky, Andrew C. Ah-Seng, Paul M. K. Gordon, Julie N. Stromer, Morgan L. Taschuk, Emily W. Xu, Christoph W. Sensen:
Bioinformatics visualization and integration with open standards: the Bluejay genomic browser. 187-198 - Matteo Fattore, Patrizio Arrigo:
Knowledge Discovery and System Biology in molecular medicine: an application to neurodegenerative diseases. 199-208 - Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Julio Collado-Vides:
Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach. 209-219
Volume 5, Number 3, 2005
- Meena K. Sakharkar, Bagavathi S. Perumal, Yun Ping Lim, Lee Pern Chern, Yiting Yu, Pandjassarame Kangueane:
Alternatively Spliced Human Genes by Exon Skipping - a database. 221-225 - Michal Brylinski, Leszek Konieczny, Irena Roterman:
SPI - Structure predictability index for protein sequences. 227-237 - Angelica Lindlöf, Zelmina Lubovac:
Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks. 239-249 - Jianbin Peng, Cheng-Han Huang, Mary K. Short, Paul T. Jubinsky:
Magmas gene structure and evolution. 251-263 - Alexander N. Gorban, Tatyana G. Popova, Andrei Yu. Zinovyev:
Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. 265-282 - Alexandre G. de Brevern:
New assessment of a structural alphabet. 283-289 - Matthias Wolf, Joachim Friedrich, Thomas Dandekar, Tobias Müller:
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. 291-294 - Steffen Möller, Eilhard Mix, Martin Blüggel, Pablo Serrano-Fernández, Dirk Koczan, Vasilis Kotsikoris, Manfred Kunz, Michael Watson, Jens Pahnke, Harald Illges, Michael Kreutzer, Stefan Mikkat, Hans-Jürgen Thiesen, Michael O. Glocker, Uwe K. Zettl, Saleh M. Ibrahim:
Collection of soluble variants of membrane proteins for transcriptomics and proteomics. 295-311 - Jules J. Berman:
Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching. 313-322 - Anton Dormer, Gregory Beck:
Evolutionary analysis of human vascular endothelial growth factor, angiopoietin, and tyrosine endothelial kinase involved in angiogenesis and immunity. 323-339 - Rosario San Millán, Javier Garaizar, Joseba Bikandi:
In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA. 341-346
Volume 5, Number 4, 2005
- Meena K. Sakharkar, Bagavathi S. Perumal, Kishore R. Sakharkar, Pandjassarame Kangueane:
An analysis on gene architecture in human and mouse genomes. 347-365 - Espen Enerly, Zeng Sheng, Kuo-Bin Li:
Natural Antisense as Potential Regulator of Alternative Initiation, Splicing and Termination. 367-377 - Rana Bhadra, Narayanaswamy Srinivasan, Shashi B. Pandit:
A New Domain Family in the Superfamily of Alkaline Phosphatases. 379-387 - Robin J. Johnson, Jennifer M. Williams, Barbara M. Schreiber, Charles D. Elfe, Kelley Lennon-Hopkins, Marek S. Skrzypek, Renee D. White:
Analysis of Gene Ontology Features in Microarray Data Using the Proteome BioKnowledge® Library. 389-399 - Arun Prasad Pandurangan, Vengadesan Krishnan, Gautham Namasivayam:
MOLS - A Program to Explore the Potential Energy Surface of a Peptide and Locate Its Low Energy Conformations. 401-405 - Clark D. Jeffries, Michael Jarstfer, Diana O. Perkins:
Folded RNA from an Intron of One Gene Might Inhibit Expression of a Counteracting Gene. 407-413 - Tariq Riaz, Kuo-Bin Li, Francis Tang, Arun Krishnan:
CMDWave: Conserved Motifs Detection Using Wavelets. 415-418 - Kazuharu Arakawa, Nobuaki Kono, Yohei Yamada, Hirotada Mori, Masaru Tomita:
KEGG-Based Pathway Visualization Tool for Complex Omics Data. 419-423
Volume 5, Numbers 5-6, 2005
- Kumar Gaurav, Nitin Gupta, Ramanathan Sowdhamini:
FASSM: Enhanced Function Association in Whole Genome Analysis Using Sequence and Structural Motifs. 425-438 - Zhenlin Ju, Melissa Wells, Al Martinez, Leona Hazlewood, Ronald B. Walter:
An in silico Mining for Simple Sequence Repeats from Expressed Sequence Tags of Zebrafish, Medaka, Fundulus, and Xiphophorus. 439-463 - Francesco Piva, Giovanni Principato:
Correlation Finder. 465-468 - Francisco Prosdocimi, José Miguel Ortega:
Accessing Optimal Primer Distance from Insert. 469-477 - Roustem Miftahof:
The Wave Phenomena in Smooth Muscle Syncytia. 479-498 - Siya Ram, Rishi Shanker:
Computing TaqMan Probes for Multiplex PCR Detection of E. coli O157 Serotypes in Water. 499-504 - Quentin Kaas, Marie-Paule Lefranc:
T Cell Receptor/Peptide/MHC Molecular Characterization and Standardized pMHC Contact Sites in IMGT/3Dstructure-DB. 505-528 - Takako Takai-Igarashi:
Ontology Based Standardization of Petri Net Modeling for Signaling Pathways. 529-536 - Juan Carlos Ulloa, Adriana Matiz, Leonardo Lareo, Maria Fernanda Gutiérrez:
Molecular Analysis of A 348 Base-Pair Segment of Open Reading Frame 2 of Human Astrovirus. A Characterization of Colombian Isolates. 537-546 - Igor V. Deyneko, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer:
Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters. 547-555 - Sukanta Mondal, Ramachandran Vijayan, Kannambath Shichina, Rajasekaran Mohan Babu, Suryanarayanarao Ramakumar:
I-Superfamily Conotoxins: Sequence and Structure Analysis. 557-571 - ZhiGang Hu, Keping Chen, LinLing Wang, Qin Yao:
Identification and Characterization of Bombyx mori eIF5A Gene through Bioinformatics Approaches. 573-580 - Diego Q. Cortez, Antonio Lazcano, Arturo Becerra:
Comparative Analysis of Methodologies for the Detection of Horizontally Transferred Genes: A Reassessment of First-Order Markov Models. 581-592 - Georgina A. Ankra-Badu, Samuel E. Aggrey:
Identification of Candidate Genes at Quantitative Trait Loci on Chicken Chromosome Z Using Orthologous Comparison of Chicken, Mouse, and Human Genomes. 593-604 - P. Ajay Babu, Radha Boddepalli, V. Vasantha Lakshmi, G. Nageswara Rao:
DoD: Database of Databases - Updated Molecular Biology Databases. 605-610 - Kishore R. Sakharkar, Iti Chaturvedi, Vincent T. K. Chow, Chee Keong Kwoh, Pandjassarame Kangueane, Meena Kishore Sakharkar:
u-Genome: A Database on Genome Design in Unicellular Genomes. 611-615
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