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ORCIDIn Silico Biology, Volume 4
Volume 4, Number 1, 2003
- Takako Takai-Igarashi, Toshihisa Takagi, Edgar Wingender:
Preface: The Second Workshop on Ontology and Genome. 1-3 - Evelyn Camon, Daniel Barrell, Vivian Lee, Emily Dimmer, Rolf Apweiler:
The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase. 5-6 - Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda:
MaXML: mouse annotation XML. 7-15 - Marie-Paule Lefranc, Véronique Giudicelli, Chantal Ginestoux, Nathalie Bosc, Géraldine Folch, Delphine Guiraudou, Joumana Jabado-Michaloud, Séverine Magris, Dominique Scaviner, Valérie Thouvenin, Kora Combres, David Girod, Stéphanie Jeanjean, Céline Protat, Mehdi Yousfi Monod, Elodie Duprat, Quentin Kaas, Christelle Pommié, Denys Chaume, Gérard Lefranc:
IMGT-ONTOLOGY for immunogenetics and immunoinformatics. 17-29 - Teruyoshi Hishiki, Osamu Ogasawara, Yoshimasa Tsuruoka, Kousaku Okubo:
Indexing anatomical concepts to OMIM Clinical Synopsis using UMLS Metathesaurus. 31-54 - Edgar Wingender:
TRANSPATH, TRANSFAC and CYTOMER as starting points for an ontology of regulatory networks. 55-61 - Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi:
FREX: A query interface for biological processes with hierarchical and recursive structures. 63-79 - Takako Takai-Igarashi, Riichiro Mizoguchi:
Cell Signaling Networks Ontology. 81-87 - Isabel Rojas, Esther Ratsch, Jasmin Saric, Ulrike Wittig:
Notes on the use of ontologies in the biochemical domain. 89-96
Volume 4, Number 2, 2004
- Julio Vera, Néstor V. Torres:
MetMAP: An integrated Matlab TM package for analysis and optimization of metabolic systems. 97-108 - Vladimir B. Bajic, Vidhu Choudhary, Chuan Koh Hock:
Content analysis of the core promoter region of human genes. 109-125 - Evanthia E. Pashou, Zoi I. Litou, Theodore Liakopoulos, Stavros J. Hamodrakas:
waveTM: Wavelet-based transmembrane segment prediction. 127-131 - Arun Krishnan, Kuo-Bin Li, Praveen Issac:
Rapid detection of conserved regions in protein sequences using wavelets. 133-148 - Chintalapati Janaki, Rajendra R. Joshi:
Motif detection in Arabidopsis: Correlation with gene expression data. 149-161 - Daniel V. Guebel:
Canonical sensitivities: A useful tool to deal with large perturbations in metabolic network modeling. 163-182 - Lance W. Hahn, Jason H. Moore:
Ideal discrimination of discrete clinical endpoints using multilocus genotypes. 183-194 - Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer, Johann Christoph Freytag:
Efficient prediction of alternative splice forms using protein domain homology. 195-208 - Hans B. Sieburg, Christa E. Müller-Sieburg:
Classification of short kinetics by shape. 209-217 - Kishore R. Sakharkar, Vincent T. K. Chow:
PPD - Proteome Profile Database. 219-223 - Adam Ameur, Erik Aurell, Mats Carlsson, Jakub Orzechowski Westholm:
Global gene expression analysis by combinatorial optimization. 225-241
Volume 4, Number 3, 2004
- Katja Wegner, Stephan Jansen, Stefan Wuchty, Ralph Gauges, Ursula Kummer:
combAlign: A protein sequence comparison algorithm considering recombinations. 243-254 - Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong:
Using amino acid patterns to accurately predict translation initiation sites. 255-269 - Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano:
Constructing biological pathway models with hybrid functional Petri net. 271-291 - Tan Chee Meng, Sandeep Somani, Pawan Dhar:
Modeling and simulation of biological systems with stochasticity. 293-309 - Haïtham Sghaier, Thuy Le Huyen Ai, Tokumasa Horiike, Takao Shinozawa:
Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database. 311-322 - Mi Zhou, Yan Cui:
GeneInfoViz: Constructing and visualizing gene relation networks. 323-333 - Phillip P. Le, Amit Bahl, Lyle H. Ungar:
Using prior knowledge to improve genetic network reconstruction from microarray data. 335-353 - Kishore R. Sakharkar, Meena K. Sakharkar, Vincent T. K. Chow:
A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa. 355-360 - Limor Kozobay-Avraham, Sergey Hosid, Alexander Bolshoy:
Curvature distribution in prokaryotic genomes. 361-375 - Sávio Torres de Farias, Marx G. van der Linden, Thaís Gaudencio do Rêgo, Demétrius A. M. Araújo, Maria Christina M. Bonato:
Thermo-search: lifestyle and thermostability analysis. 377-380 - Alexandre G. de Brevern, Cristina Benros, Romain Gautier, Hélène Valadié, Serge A. Hazout, Catherine Etchebest:
Local backbone structure prediction of proteins. 381-386
Volume 4, Number 4, 2004
- Meena K. Sakharkar, Vincent T. K. Chow, Pandjassarame Kangueane:
Distributions of exons and introns in the human genome. 387-393 - Fan Long, Hong Liu, Chang S. Hahn, Pavel Sumazin, Michael Q. Zhang, Asher Zilberstein:
Genome-wide prediction and analysis of function-specific transcription factor binding sites. 395-410 - Davinder K. Kohli, Chittur V. Srikanth, Anand K. Bachhawat:
A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoters. 411-415 - Steffen Möller, Dirk Koczan, Pablo Serrano-Fernández, Uwe K. Zettl, Hans-Jürgen Thiesen, Saleh M. Ibrahim:
Selecting SNPs for association studies based on population frequencies: a novel interactive tool and its application to polygenic diseases. 417-427 - Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano:
Large-scale collection and characterization of promoters of human and mouse genes. 429-444 - Seema Namboori, Narayanaswamy Srinivasan, Shashi B. Pandit:
Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures. 445-460 - Jobst Landgrebe, Frank Bretz, Edgar Brunner:
Efficient two-sample designs for microarray experiments with biological replications. 461-470 - Betsey D. Dyer, Mark D. LeBlanc, Stephen Benz, Peter Cahalan, Brian Donorfio, Patrick Sagui, Adam Villa, Gregory Williams:
A DNA motif lexicon: cataloguing, annotating sequences. 471-478 - Katja Rateitschak, Tobias Müller, Martin Vingron:
Annotating significant pairs of transcription factor binding sites in regulatory DNA. 479-487 - Hong Liu, Nanxiang Ge, Kin-Tak Yu, David Krolikowski, Asher Zilberstein, Chang S. Hahn:
Prediction of IFN-gamma regulated gene transcription. 489-505 - Nestor Sosa, Andreas Kremling, Esther Ratsch, Isabel Rojas:
Web-based visualisation of the transcriptional control network of Escherichia coli. 507-515 - Guillaume Meurice, Catherine Deborde, Daniel Jacob, Hélène Falentin, Patrick Boyaval, Diliana Dimova:
In silico exploration of the fructose-6-phosphate phosphorylation step in glycolysis: genomic evidence of the coexistence of an atypical ATP-dependent along with a PPi-dependent phosphofructokinase in Propionibacterium freudenreichii subsp. shermanii. 517-528 - Lorenz Bülow, Martin Schindler, Claudia Choi, Reinhard Hehl:
PathoPlant: a database on plant-pathogen interactions. 529-536 - Mack E. Crayton III, Carll E. Ladd, Martin Sommer, Gregory Hampikian, Linda D. Strausbaugh:
An organizational model of transcription factor binding sites for a histone promoter in D. melanogaster. 537-548 - A. V. S. K. Mohan Katta, Rajeshwari Marikkannu, Rajiv V. Basaiawmoit, Sankaran Krishnaswamy:
Consensus based validation of membrane porins. 549-561 - Shashi B. Pandit, Narayanaswamy Srinivasan:
Identification and analysis of a new family of bacterial serine proteinases. 563-572 - Tannistha Nandi, Samir K. Brahmachari, Krishnamoorthy Kannan, Srinivasan Ramachandran:
Clusters of proteins in archaeal and bacterial proteomes using compositional analysis. 573-591 - Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem:
STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes. 593-604 - Vignesh Muthuvijayan, Mark R. Marten:
In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans. 605-631
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