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BibGlimpse: The case for a light-weight reprint manager in distributed literature research

Author(s): Tüchler Thomas | Velez Golda | Graf Alexandra | Kreil David
From protein interactions to functional annotation: graph alignment in Herpes

Author(s): Kolář Michal | Lässig Michael | Berg Johannes
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays

Author(s): van den Berg Bart | Konieczka Jay | McCarthy Fiona | Burgess Shane
JNets: Exploring networks by integrating annotation

Author(s): MacPherson Jamie | Pinney John | Robertson David
TANGRAM for Personalized Learning Using the Semantic Web Technologies

Author(s): Jelena Jovanovic | Dragan Gašević | Vladan Devedžić
Functional Annotation of Conserved Hypothetical Proteins in Rickettsia Massiliae MTU5

Author(s): Joy Hoskeri. H | V. Krishna | C. Amruthavalli
Inferring modules from human protein interactome classes

Author(s): Marras Elisabetta | Travaglione Antonella | Chaurasia Gautam | Futschik Matthias | Capobianco Enrico
Semantic Web for Program Administration

Author(s): Qurban A Memon | Shakeel Khoja
easyDAS: Automatic creation of DAS servers

Author(s): Gel Moreno Bernat | Jenkinson Andrew | Jimenez Rafael | Messeguer Peypoch Xavier | Hermjakob Henning
Accelerating the annotation of sparse named entities by dynamic sentence selection

Author(s): Tsuruoka Yoshimasa | Tsujii Jun'ichi | Ananiadou Sophia
Prediction of evolutionarily conserved interologs in Mus musculus

Author(s): Yellaboina Sailu | Dudekula Dawood | Ko Minoru
The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes

Author(s): Vincze Veronika | Szarvas György | Farkas Richárd | Móra György | Csirik János
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

Author(s): Tsai Richard | Dai Hong-Jie | Huang Chi-Hsin | Hsu Wen-Lian
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

Author(s): Durot Maxime | Le Fèvre François | de Berardinis Véronique | Kreimeyer Annett | Vallenet David | Combe Cyril | Smidtas Serge | Salanoubat Marcel | Weissenbach Jean | Schachter Vincent
EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data

Author(s): Dondrup Michael | Albaum Stefan | Griebel Thasso | Henckel Kolja | Jünemann Sebastian | Kahlke Tim | Kleindt Christiane | Küster Helge | Linke Burkhard | Mertens Dominik | Mittard-Runte Virginie | Neuweger Heiko | Runte Kai | Tauch Andreas | Tille Felix | Pühler Alfred | Goesmann Alexander
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

Author(s): Loevenich Sandra | Brunner Erich | King Nichole | Deutsch Eric | Stein Stephen | Aebersold Ruedi | Hafen Ernst
Automated extraction of chemical structure information from digital raster images

Author(s): Park Jungkap | Rosania Gus | Shedden Kerby | Nguyen Mandee | Lyu Naesung | Saitou Kazuhiro
Protein-protein interaction as a predictor of subcellular location

Author(s): Shin Chang | Wong Simon | Davis Melissa | Ragan Mark
plantsUPS: a database of plants' Ubiquitin Proteasome System

Author(s): Du Zhou | Zhou Xin | Li Li | Su Zhen
P2CS: a two-component system resource for prokaryotic signal transduction research

Author(s): Barakat Mohamed | Ortet Philippe | Jourlin-Castelli Cécile | Ansaldi Mireille | Méjean Vincent | Whitworth David
Ab initio and homology based prediction of protein domains by recursive neural networks

Author(s): Walsh Ian | Martin Alberto | Mooney Catherine | Rubagotti Enrico | Vullo Alessandro | Pollastri Gianluca
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

Author(s): Nagel Kevin | Jimeno-Yepes Antonio | Rebholz-Schuhmann Dietrich
Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

Author(s): Shinfuku Yohei | Sorpitiporn Natee | Sono Masahiro | Furusawa Chikara | Hirasawa Takashi | Shimizu Hiroshi
Facilitating functional annotation of chicken microarray data

Author(s): Buza Teresia | Kumar Ranjit | Gresham Cathy | Burgess Shane | McCarthy Fiona
CASSIOPE: An expert system for conserved regions searches

Author(s): Rascol Virginie | Levasseur Anthony | Chabrol Olivier | Grusea Simona | Gouret Philippe | Danchin Etienne | Pontarotti Pierre
BioGateway: a semantic systems biology tool for the life sciences

Author(s): Antezana Erick | Blondé Ward | Egaña Mikel | Rutherford Alistair | Stevens Robert | De Baets Bernard | Mironov Vladimir | Kuiper Martin
Bio-jETI: a framework for semantics-based service composition

Author(s): Lamprecht Anna-Lena | Margaria Tiziana | Steffen Bernhard
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

Author(s): Tsafnat Guy | Coiera Enrico | Partridge Sally | Schaeffer Jaron | Iredell Jon
A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

Author(s): Marques M Carmen | Alonso-Cantabrana Hugo | Forment Javier | Arribas Raquel | Alamar Santiago | Conejero Vicente | Perez-Amador Miguel
Ultra-Structure database design methodology for managing systems biology data and analyses

Author(s): Maier Christopher | Long Jeffrey | Hemminger Bradley | Giddings Morgan
Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

Author(s): South Brett | Shen Shuying | Jones Makoto | Garvin Jennifer | Samore Matthew | Chapman Wendy | Gundlapalli Adi
ASKGene, a system for automate DNA processing - DOI: 10.3395/reciis.v1i2.Sup.100en

Author(s): Eden Cardim | Wallace Reis | Nicolas Carels | Diego Frias
Computational annotation of genes differentially expressed along olive fruit development

Author(s): Galla Giulio | Barcaccia Gianni | Ramina Angelo | Collani Silvio | Alagna Fiammetta | Baldoni Luciana | Cultrera Nicolò | Martinelli Federico | Sebastiani Luca | Tonutti Pietro
KAIKObase: An integrated silkworm genome database and data mining tool

Author(s): Shimomura Michihiko | Minami Hiroshi | Suetsugu Yoshitaka | Ohyanagi Hajime | Satoh Chikatada | Antonio Baltazar | Nagamura Yoshiaki | Kadono-Okuda Keiko | Kajiwara Hideyuki | Sezutsu Hideki | Nagaraju Javaregowda | Goldsmith Marian | Xia Qingyou | Yamamoto Kimiko | Mita Kazuei
An editor for pathway drawing and data visualization in the Biopathways Workbench

Author(s): Byrnes Robert | Cotter Dawn | Maer Andreia | Li Joshua | Nadeau David | Subramaniam Shankar
An informatics supported web-based data annotation and query tool to expedite translational research for head and neck malignancies

Author(s): Amin Waqas | Kang Hyunseok | Egloff Ann | Singh Harpreet | Trent Kerry | Ridge-Hetrick Jennifer | Seethala Raja | Grandis Jennifer | Parwani Anil
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach

Author(s): Lin Hsin-Nan | Chen Ching-Tai | Sung Ting-Yi | Ho Shinn-Ying | Hsu Wen-Lian
Investigating heterogeneous protein annotations toward cross-corpora utilization

Author(s): Wang Yue | Kim Jin-Dong | Sætre Rune | Pyysalo Sampo | Tsujii Jun'ichi
The proteolytic system of lactic acid bacteria revisited: a genomic comparison

Author(s): Liu Mengjin | Bayjanov Jumamurat | Renckens Bernadet | Nauta Arjen | Siezen Roland
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Author(s): Roberts Seth | Gowen Christopher | Brooks J Paul | Fong Stephen
Lists2Networks: Integrated analysis of gene/protein lists

Author(s): Lachmann Alexander | Ma'ayan Avi
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models

Author(s): Hoffgaard Franziska | Weil Philipp | Hamacher Kay
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Author(s): Salmon-Divon Mali | Dvinge Heidi | Tammoja Kairi | Bertone Paul
A high-throughput cloning system for reverse genetics in Trypanosoma cruzi

Author(s): Batista Michel | Marchini Fabricio | Celedon Paola | Fragoso Stenio | Probst Christian | Preti Henrique | Ozaki Luiz | Buck Gregory | Goldenberg Samuel | Krieger Marco
Network analysis of human protein location

Author(s): Kumar Gaurav | Ranganathan Shoba
Next generation models for storage and representation of microbial biological annotation

Author(s): Quest Daniel | Land Miriam | Brettin Thomas | Cottingham Robert
Genotator: A disease-agnostic tool for genetic annotation of disease

Author(s): Wall Dennis | Pivovarov Rimma | Tong Mark | Jung Jae-Yoon | Fusaro Vincent | DeLuca Todd | Tonellato Peter
Hierarchical graphs for rule-based modeling of biochemical systems

Author(s): Lemons Nathan | Hu Bin | Hlavacek William
Initial characterization of the human central proteome

Author(s): Burkard Thomas | Planyavsky Melanie | Kaupe Ines | Breitwieser Florian | Bürckstümmer Tilmann | Bennett Keiryn | Superti-Furga Giulio | Colinge Jacques
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Author(s): Thiele Ines | Hyduke Daniel | Steeb Benjamin | Fankam Guy | Allen Douglas | Bazzani Susanna | Charusanti Pep | Chen Feng-Chi | Fleming Ronan | Hsiung Chao | De Keersmaecker Sigrid | Liao Yu-Chieh | Marchal Kathleen | Mo Monica | Özdemir Emre | Raghunathan Anu | Reed Jennifer | Shin Sook-Il | Sigurbjörnsdóttir Sara | Steinmann Jonas | Sudarsan Suresh | Swainston Neil | Thijs Inge | Zengler Karsten | Palsson Bernhard | Adkins Joshua | Bumann Dirk
HaloWeb: the haloarchaeal genomes database

Author(s): DasSarma Satyajit | Capes Melinda | DasSarma Priya | DasSarma Shiladitya
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

Author(s): Otero José | Vongsangnak Wanwipa | Asadollahi Mohammad | Olivares-Hernandes Roberto | Maury Jérôme | Farinelli Laurent | Barlocher Loïc | Østerås Magne | Schalk Michel | Clark Anthony | Nielsen Jens
Proteome of the phytopathogen Xanthomonas citri subsp. citri: a global expression profile

Author(s): Soares Márcia | Facincani Agda | Ferreira Rafael | Moreira Leandro | de Oliveira Julio | Ferro Jesus | Ferro Maria | Meneghini Rogério | Gozzo Fábio
A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder

Author(s): McEachin Richard | Chen Haiming | Sartor Maureen | Saccone Scott | Keller Benjamin | Prossin Alan | Cavalcoli James | McInnis Melvin
Establishment of cDNA Microarray Analysis at the Genomic Medicine Research Core Laboratory (GMRCL) of Chang Gung Memorial Hospital .

Author(s): Tzu-Hao Wang | Yun-Shien Lee | En-Shih Chen | Wei-Hsiang Kong | Lung-Kun Chen | Ding-Wei Hsueh | Min-Li Wei | Hsing-Shih Wang | Ying-Shiung Lee
Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata

Author(s): Gomulski Ludvik | Dimopoulos George | Xi Zhiyong | Soares Marcelo | Bonaldo Maria | Malacrida Anna | Gasperi Giuliano
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

Author(s): Dräger Andreas | Hassis Nadine | Supper Jochen | Schröder Adrian | Zell Andreas
Can single knockouts accurately single out gene functions?

Author(s): Deutscher David | Meilijson Isaac | Schuster Stefan | Ruppin Eytan
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses

Author(s): Zvi Anat | Ariel Naomi | Fulkerson John | Sadoff Jerald | Shafferman Avigdor
Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

Author(s): Botton Alessandro | Galla Giulio | Conesa Ana | Bachem Christian | Ramina Angelo | Barcaccia Gianni
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

Author(s): Huan Tianxiao | Sivachenko Andrey | Harrison Scott | Chen Jake
The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)

Author(s): Lukas A. Mueller | Steven D. Tanksley | Jim J. Giovannoni | Joyce van Eck | Stephen Stack | Doil Choi | Byung Dong Kim | Mingsheng Chen | Zhukuan Cheng | Chuanyou Li | Hongqing Ling | Yongbiao Xue | Graham Seymour | Gerard Bishop | Glenn Bryan | Rameshwar Sharma | Jiten Khurana | Akhilesh Tyagi | Debasis Chattopadhyay | Nagendra K. Singh | Willem Stiekema | P. Lindhout | Taco Jesse | Rene Klein Lankhorst | Mondher Bouzayen | Daisuke Shibata | Satoshi Tabata | Antonio Granell | Miguel A. Botella | Giovanni Giuliano | Luigi Frusciante | Mathilde Causse | Dani Zamir
Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

Author(s): Letizia Da Sacco | Antonella Baldassarre | Andrea Masotti
FROM 3D MODEL DATA TO SEMANTICS

Author(s): My Abdellah Kassimi | Omar El beqqali
Using Hausdorff Distance for New Medical Image Annotation

Author(s): Riadh BOUSLIMI | Jalel AKAICHI
Semantic Based Image Annotation Using Descriptive Features and Retagging approach

Author(s): P.Nagarani | R.VenkataRamanaChary | D.Rajya Lakshmi
Investigating heterogeneous protein annotations toward cross-corpora utilization

Author(s): Wang Yue | Kim Jin-Dong | Rune Sætre | Pyysalo Sampo | Tsujii Jun'ichi
Tag Recommendation System for Social Annotation System

Author(s): Ali Kohi | Mehrdad Jalali | Seyed Javad Ebrahimi
Paraconsistent Algorithm Extractor of Contradiction Effects - Paraextrctrctr

Author(s): Joao Inacio Da Silva Filho | Germano Lambert-Torres | Luiz Fernando Pompeo Ferrara | Maurício Conceição Mário | Marcos Rosa dos Santos | Alexandre Shozo Onuki | José de Melo Camargo | Alexandre Rocco
Immunome database for marsupials and monotremes

Author(s): Wong Emily | Papenfuss Anthony | Belov Katherine
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

Author(s): Ansong Charles | Tolić Nikola | Purvine Samuel | Porwollik Steffen | Jones Marcus | Yoon Hyunjin | Payne Samuel | Martin Jessica | Burnet Meagan | Monroe Matthew | Venepally Pratap | Smith Richard | Peterson Scott | Heffron Fred | McClelland Michael | Adkins Joshua
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Author(s): Milne Caroline | Eddy James | Raju Ravali | Ardekani Soroush | Kim Pan-Jun | Senger Ryan | Jin Yong-Su | Blaschek Hans | Price Nathan
Overview of the BioCreative III Workshop

Author(s): Arighi Cecilia | Lu Zhiyong | Krallinger Martin | Cohen Kevin | Wilbur W | Valencia Alfonso | Hirschman Lynette | Wu Cathy
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Author(s): Krallinger Martin | Vazquez Miguel | Leitner Florian | Salgado David | Chatr-aryamontri Andrew | Winter Andrew | Perfetto Livia | Briganti Leonardo | Licata Luana | Iannuccelli Marta | Castagnoli Luisa | Cesareni Gianni | Tyers Mike | Schneider Gerold | Rinaldi Fabio | Leaman Robert | Gonzalez Graciela | Matos Sergio | Kim Sun | Wilbur W | Rocha Luis | Shatkay Hagit | Tendulkar Ashish | Agarwal Shashank | Liu Feifan | Wang Xinglong | Rak Rafal | Noto Keith | Elkan Charles | Lu Zhiyong | Dogan Rezarta | Fontaine Jean-Fred | Andrade-Navarro Miguel | Valencia Alfonso
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Author(s): Chatr-aryamontri Andrew | Winter Andrew | Perfetto Livia | Briganti Leonardo | Licata Luana | Iannuccelli Marta | Castagnoli Luisa | Cesareni Gianni | Tyers Mike
Identifying Tmem59 related gene regulatory network of mouse neural stem cell from a compendium of expression profiles

Author(s): Zhang Luwen | Ju Xiangchun | Cheng Yumin | Guo Xiuyun | Wen Tieqiao
Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information

Author(s): Meinel Thomas | Schweiger Michal | Ludewig Andreas | Chenna Ramu | Krobitsch Sylvia | Herwig Ralf
Modeling the Relationship between Texture Semantics and Textile Images

Author(s): Xiaohui Wang | Jia Jia | Yongxin Wang | Lianhong Cai
A Semantics and Data-Driven Biomedical Multimedia Software System

Author(s): Shih-Hsi Liu | Yu Cao | Ming Li | Pranay Kilaru | Thell Smith | Shaen Toner
Guest Editorial

Author(s): Mei-Ling Shyu | Yu Cao | Ming Li | Jun Kong | Jie Bao
Guest Editorial

Author(s): Fei Yu | Haiwen Liu | Wenlang Luo | Huojiao He | Chin-Chen Chang
An integrative approach to inferring biologically meaningful gene modules

Author(s): Cho Ji-Hoon | Wang Kai | Galas David
Semantic annotation of requirements for automatic UML class diagram generation

Author(s): Soumaya Amdouni | Soumaya Amdouni | Wahiba Ben Abdessalem Karaa | Sondes Bouabid
PRIN: a predicted rice interactome network

Author(s): Gu Haibin | Zhu Pengcheng | Jiao Yinming | Meng Yijun | Chen Ming
Integrating multiple types of data to predict novel cell cycle-related genes

Author(s): Wang Lin | Hou Lin | Qian Minping | Li Fangting | Deng Minghua
454 sequencing of pooled BAC clones on chromosome 3H of barley

Author(s): Sato Kazuhiro | Motoi Yuka | Yamaji Nami | Yoshida Hideya
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Author(s): Fang Kechi | Zhao Hansheng | Sun Changyue | Lam Carolyn | Chang Suhua | Zhang Kunlin | Panda Gurudutta | Godinho Miguel | Martins dos Santos Vítor | Wang Jing
A Feasible Approach for Automatic Detection and Recognition of the Bengalese Finch Songnotes and Their Sequences

Author(s): Khan Md. Mahfuzus Salam | Tetsuro Nishino | Kazutoshi Sasahara | Miki Takahasi | Kazuo Okanoya
Enhanced PAPR in OFDM without Deteriorating BER Performance

Author(s): Spyridon K. Chronopoulos | Giorgos Tatsis | Vasilis Raptis | Panos Kostarakis
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