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In Silico Biology, Volume 7
Volume 7, Number 1, 2007
- Rajaiah Paramasivan, Ramamoorthy Sivaperumal, Kutty Jegadeeswaran Dhananjeyan, Velayutham Thenmozhi, Brij Kishore Tyagi:
Prediction of 3-Dimensional Structure of Salivary Odorant-Binding Protein-2 of the Mosquito Culex Quinquefasciatus, the Vector of Human Lymphatic Filariasis. 1-6 - Dipnarayan Saha, Anand M. Prasad, Thankeswaran P. Sujatha, Vajinder Kumar, Pradeep K. Jain, Sripad R. Bhat, Ramamurthy Srinivasan:
In Silico Analysis of the Lateral Organ Junction (LOJ) Gene and Promoter of Arabidopsis Thaliana. 7-19 - Kagan Tuncay, Lisa Ensman, Jingjun Sun, Alaa Abi-Haidar, Frank Stanley, Michael Trelinski, Peter J. Ortoleva:
Transcriptional Regulatory Networks via Gene Ontology and Expression Data. 21-34 - Diederik W. J. Bosman, Evert-Jan Blom, Patrick J. Ogao, Oscar P. Kuipers, Jos B. T. M. Roerdink:
MOVE: A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks. 35-59 - Yuchen Yang, Erwin Tantoso, Gek Huey Chua, Zhen Xuan Yeo, Felicia Soo Lee Ng, Sum Thai Wong, Cheuk Wang Chung, Kuo-Bin Li:
In Silico Analysis of P53 Using the P53 Knowledgebase: Mutations, Polymorphisms, MicroRNAs and Pathways. 61-75 - Waiming Kong, Tsu Soo Tan, Lawrence Tham, Keng Wah Choo:
Improved Prediction of Allergenicity by Combination of Multiple Sequence Motifs. 77-86 - Paras Chopra, Andreas Bender:
Evolved Cellular Automata for Protein Secondary Structure Prediction Imitate the Determinants for Folding Observed in Nature. 87-93 - Pradeep Kota:
GUIMACS - A Java Based Front End for GROMACS. 95-99 - Tarcísio de Souza Peres, Fernando Ferreira Costa, Fernando Lopes Alberto:
LyM: A Tool to Reach the Best Factor in Gene Expression Comparison. 101-104 - Lambros V. Skarlas, Panos Ioannidis, Spiridon D. Likothanassis:
Coding Potential Prediction in Wolbachia Using Artificial Neural Networks. 105-113 - King-Hwa Ling, Shu-San Loo, Rozita Rosli, Mariana Nor Shamsudin, Rahmah Mohamed, Kiew-Lian Wan:
In Silico Identification and Characterization of a Putative Phosphatidylinositol 4-Phosphate 5-Kinase (PIP5K) Gene in Eimeria Tenella. 115-121
Volume 7, Number 2, 2007
- Kalyan Gayen, Manish Gupta, Kareenhalli V. Venkatesh:
Elementary Mode Analysis to Study the Preculturing Effect on the Metabolic State of Lactobacillus rhamnosus During Growth on Mixed Substrates. 123-139 - Yoshiteru Negishi, Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita:
eXpanda: An Integrated Platform for Network Analysis and Visualization. 141-144 - J. Lynn Fink, Nicholas A. Hamilton:
DomainDraw: A Macromolecular Feature Drawing Program. 145-150 - Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann:
Deep Metazoan Phylogeny. 151-154 - Ahmed Ahmed, Gabriel Frey, Christian J. Michel:
Frameshift Signals in Genes Associated with the Circular Code. 155-168 - Aruna Ranganath, K. C. Shet, Nagardone Vidyavathi:
Efficient Shape Descriptors for Feature Extraction in 3D Protein Structures. 169-174 - Sukanta Mondal, Rajasekaran Mohan Babu, Rajasekaran Bhavna, S. Ramakumar:
In Silico Detection of Binding Mode of J-Superfamily Conotoxin pl14a with Kv1.6 Channel. 175-186 - Bharath Srinivasan, Hemalatha Balaram:
ISN1 Nucleotidases and HAD Superfamily Protein Fold: In silico Sequence and Structure Analysis. 187-193 - Jiqiang Yao, Hong Lin, Harsha Doddapaneni, Edwin L. Civerolo:
nWayComp: A Genome-Wide Sequence Comparison Tool for Multiple Strains/Species of Phylogenetically Related Microorganisms. 195-200 - Atul Grover, Prakash C. Sharma:
Microsatellite Motifs with Moderate GC Content Are Clustered Around Genes on Arabidopsis thaliana Chromosome 2. 201-213 - Rozana Othman, Habibah A. Wahab, Rohana Yusof, Noorsaadah Abdul Rahman:
Analysis of Secondary Structure Predictions of Dengue Virus Type 2 NS2B/NS3 Against Crystal Structure to Evaluate the Predictive Power of theIn Silico Methods. 215-224 - Susan Idicula-Thomas, Petety V. Balaji:
Correlation Between the Structural Stability and Aggregation Propensity of Proteins. 225-237
Volume 7, Number 3, 2007
- Sergei N. Rodin, Nikolay A. Kolchanov:
Fifth International Conference on Bioinformatics of Genome Regulation and Structure-BGRS'2006. 239-240 - Yuriy L. Orlov, Jiangtao Zhou, Leonard Lipovich, Atif Shahab, Vladimir A. Kuznetsov:
Quality Assessment of the Affymetrix U133A&B Probesets by Target Sequence Mapping and Expression Data Analysis. 241-260 - Sergey A. Lashin, Valentin V. Suslov, Nikolay A. Kolchanov, Yuri G. Matushkin:
Simulation of Coevolution in Community by Using the "Evolutionary Constructor" Program. 261-275 - Jury Sergeevich Bukin, Tatyana Anatoljevna Pudovkina, Dmitry Jurjevich Sherbakov, Tatyana Jakovlevna Sitnikova:
Genetic Flows in a Structured One-Dimensional Population: Simulation and Real Data on Baikalian Polychaetes M. Godlewskii. 277-284 - Lev I. Rubanov, Vassily A. Lyubetsky:
RNAmodel Web Server: Modeling Classic Attenuation in Bacteria. 285-308 - Andrei S. Rodin, Sergei N. Rodin:
Translation of Both Complementary Strands Might Govern Early Evolution of the Genetic Code. 309-318 - Sergey S. Pintus, Eduard S. Fomin, Ivan S. Oshurkov, Vladimir A. Ivanisenko:
Phylogenetic Analysis of the p53 and p63/p73 Gene Families. 319-332 - Konstantin V. Gunbin, Dmitry A. Afonnikov, Nikolay A. Kolchanov:
The Evolution of the Hh-Signaling Pathway Genes: A Computer-Assisted Study. 333-354
Volume 7, Numbers 4-5, 2007
- Abinash Padhi, Bindhu Verghese, Subhendu K. Otta, Binu Varghese, Karri Ramu:
Positive Darwinian Selection on Crustacean Hyperglycemic Hormone (CHH) of the Green Shore Crab, Carcinus maenas. 355-367 - Sudipto Saha, Gajendra P. S. Raghava:
Prediction of Neurotoxins Based on Their Function and Source. 369-387 - Boon-San Lim, Chan-Eng Chong, Zulkeflie Zamrod, Sheila Nathan, Rahmah Mohamed:
Genome-wide Prediction and Annotation of Burkholderia Pseudomallei AraC/XylS Family Transcription Regulator. 389-397 - Anjali Bajpai, Settu Sridhar, Hemakumar M. Reddy, Rachel A. Jesudasan:
BRM-Parser: A Tool for Comprehensive Analysis of BLAST and RepeatMasker Results. 399-403 - Sudipto Saha, Gajendra P. S. Raghava:
BTXpred: Prediction of Bacterial Toxins. 405-412 - Rengaraj Rajesh, Kasinathan Gunasekaran, Subramanian Muthukumaravel, Kothandapani Balaraman, Purusothaman Jambulingam:
In Silico Analysis of Voltage-gated Sodium Channel in Relation to DDT Resistance in Vector Mosquitoes. 413-421 - Ashutosh Ranjan, Ambarish Sharan Vidyarthi, Raju Poddar:
Evaluation of Codon Bias Perspectives in Phage Therapy of Mycobacterium tuberculosis by Multivariate Analysis. 423-431 - Bangaly Kaba, Nicolas Pinet, Gaëlle Lelandais, Alain Sigayret, Anne Berry:
Clustering Gene Expression Data Using Graph Separators. 433-452 - Deepak Perumal, Chu Sing Lim, Kishore R. Sakharkar, Meena K. Sakharkar:
Differential Genome Analyses of Metabolic Enzymes in Pseudomonas aeruginosa for Drug Target Identification. 453-465 - Sylvain Blachon, Ruggero G. Pensa, Jérémy Besson, Céline Robardet, Jean-François Boulicaut, Olivier Gandrillon:
Clustering Formal Concepts to Discover Biologically Relevant Knowledge from Gene Expression Data. 467-483 - Jiayu Wen, Brian J. Parker, Georg F. Weiller:
In Silico Identification and Characterization of mRNA-Like Noncoding Transcripts in Medicago truncatula. 485-505 - Matteo Ramazzotti, Matteo Brilli, Renato Fani, Giampaolo Manao, Donatella Degl'Innocenti:
The CAI Analyser Package: Inferring Gene Expressivity from Raw Genomic Data. 507-526 - Li Liao, Zhongwei Li:
Correlation Between Gene Silencing Activity and Structural Features of Antisense Oligodeoxynucleotides and Target RNA. 527-534 - Olav Zimmermann, Longhui Wang, Ulrich H. E. Hansmann:
BETTY: Prediction of beta;-Strand Type from Sequence. 535-542 - Soma S. Marla, Vinay Kumar Singh:
PGV - Prokaryotic Genome Viewer. 543-545 - Gargi Sen, Saubashya Sur, Debadin Bose, Uttam Kr. Mondal, Teal Furnholm, Asim Bothra, Louis Tisa, Arnab Sen:
Analysis of Codon Usage Patterns and Predicted Highly Expressed Genes for Six Phytopathogenic Xanthomonas Genomes Shows a High Degree of Conservation. 547-558
Volume 7, Number 6, 2007
- Kunal Jaiswal:
Prediction of Ubiquitin Proteins using Artificial Neural Networks, Hidden Markov Model and Support Vector Machines. 559-568 - Shu Chen, Arunkumar Chinnaswamy, Subhra K. Biswas, Andrew B. Goryachev, Choon-Kong Yap, Koi-Yau Lam, Cheng-Pei Tay, Hong Sang Low, Alexandra V. Pokhilko, Da-Jun Toh, Santosh K. Mishra:
Cell Interaction Knowledgebase: An Online Database for Innate Immune Cells, Cytokines and Chemokines. 569-574 - Yiannis Kourmpetis, Ate van der Burgt, Marco C. A. M. Bink, Cajo J. F. ter Braak, Roeland C. H. J. van Ham:
The Use of Multiple Hierarchically Independent Gene Ontology Terms in Gene Function Prediction and Genome Annotation. 575-582 - Sangeeta Kundu, Debjani Roy:
Structural Considerations for Designing Adenosine Analogs as Selective Inhibitors of Trichomonas sp. Glyceraldehyde-3- Phosphate Dehydrogenase. 583-593 - Jochen Farwer, Martin J. Packer, Christopher A. Hunter:
PREDICTOR: A Web-Based Tool for the Prediction of Atomic Structure from Sequence for Double Helical DNA with up to 150 Base Pairs. 595-600 - Jayavel Sridhar, Ziauddin Ahamed Rafi:
Identification of Novel Genomic Islands Associated with Small RNAs. 601-611 - Martin Stephan, Friedrich Möller, Thomas Wiehe, Jürgen Kleffe:
Self-Alignments to Detect Mutually Exclusive Exon Usage. 613-621 - Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano:
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. 623-638 - Amitava Karmaker, Stephen Kwek:
CGHsweep: An Algorithm for Analyzing Chromosomal Aberrations in Genome Using aCGH Profiles. 639-649 - Abhishek Tiwari, Sunil K. Panigrahi:
HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. 651-661
Volume 7, Supplement 2, 2007
- Isabel Rojas, Ulrike Wittig:
Workshop on "Storage and Annotation of Reaction Kinetics Data", Villa Bosch in Heidelberg, May 21-23, 2007. 1-2 - Manuel Cánovas, Vicente Bernal, Ángel Sevilla, José Iborra:
Role of Wet Experiment Design in Data Generation: From in Vivo to in Silico and Back. 3-16 - Edgar Wingender, Jennifer Hogan, Frank Schacherer, Anatolij Potapov, Olga V. Kel-Margoulis:
Integrating Pathway Data for Systems Pathology. 17-25 - Carel van Gend, Riaan Conradie, Franco B. du Preez, Jacky L. Snoep:
Data and Model Integration Using JWS Online. 27-35 - Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig:
Storing and Annotating of Kinetic Data. 37-44 - Kirill Degtyarenko, Marcus Ennis, John S. Garavelli:
"Good Annotation Practice" for Chemical Data in Biology. 45-56 - Carsten Kettner:
Good Publication Practice As A Prerequisite for Comparable Enzyme Data? 57-64 - Ursula Kummer:
Usage of Reaction Kinetics Data Stored in Databases - A Modeler's Point of View. 65-71 - Simon Borger, Jannis Uhlendorf, Anselm Helbig, Wolfram Liebermeister:
Integration of Enzyme Kinetic Data from Various Sources. 73-79 - Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Hiroaki Kitano:
Integration of CellDesigner and SABIO-RK. 81-90
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