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Database - The Journal of Biological Databases and Curation, Volume 2015

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Volume 2015, 2015

Database Tool

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Junyang Yue, Xiaojing Ma, Rongjun Ban, Qianli Huang, Wenjie Wang, Jia Liu, Yongsheng Liu:
FR database 1.0: a resource focused on fruit development and ripening.
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Bi Ma, Tian Li, Zhonghuai Xiang, Ningjia He:
MnTEdb, a collective resource for mulberry transposable elements.
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Yiyu Zheng, Xiaoman Li, Haiyan Hu:
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples.
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Zhenhua Luo, Zhiming Dai, Xiaowei Xie, Xuyang Feng, Dan Liu, Songyang Zhou, Yuanyan Xiong:
TeloPIN: a database of telomeric proteins interaction network in mammalian cells.
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Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
OntoMate: a text-mining tool aiding curation at the Rat Genome Database.
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  - journals/biodb/VillavecesJPdDD15
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Jose M. Villaveces, Rafael C. Jiménez, Pablo Porras, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Sandra E. Orchard, H. Choi, Peipei Ping, N. C. Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob:
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
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Renato H. Orsi, Teresa M. Bergholz, Martin Wiedmann, Kathryn J. Boor:
The Listeria monocytogenes strain 10403S BioCyc database.
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Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder:
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
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Tsung-Jung Wu, Lynn M. Schriml, Qingrong Chen, Maureen Colbert, Daniel J. Crichton, Richard P. Finney, Ying Hu, Warren A. Kibbe, Heather Kincaid, Daoud M. Meerzaman, Elvira Mitraka, Yang Pan, Krista Smith, Sudhir Srivastava, Sari Ward, Cheng Yan, Raja Mazumder:
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
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Eduardo Andrés León, Daniel González-Peña, Gonzalo Gómez-López, David G. Pisano:
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets.
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  - journals/biodb/PineroQBDBBSF15
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Janet Piñero González, Núria Queralt-Rosinach, Àlex Bravo, Jordi Deu-Pons, Anna Bauer-Mehren, Martin Baron, Ferran Sanz, Laura Inés Furlong:
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.
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Nadav Rappoport, Michal Linial:
ProtoBug: functional families from the complete proteomes of insects.
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Yan Wang, Mingxia Wang, Sanwen Yin, Richard Jang, Jian Wang, Zhidong Xue, Tao Xu:
NeuroPep: a comprehensive resource of neuropeptides.
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Silvia Frias, Kenneth Bryan, Fiona S. L. Brinkman, David J. Lynn:
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.
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Svenja Alter, Kai Christian Bader, Manuel Spannagl, Yu Wang, Eva Bauer, Chris-Carolin Schön, Klaus F. X. Mayer:
DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species.
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  - journals/biodb/EleftheriouBAS15
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Stergiani V. Eleftheriou, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou:
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes.
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Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen:
HCSD: the human cancer secretome database.
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Hui Zeng, Chengxiang Qiu, Qinghua Cui:
Drug-Path: a database for drug-induced pathways.
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Seyedsasan Hashemikhabir, Yaseswini Neelamraju, Sarath Chandra Janga:
Database of RNA binding protein expression and disease dynamics (READ DB).
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Anna P. Privitera, Rosario Distefano, Hugo A. Wefer, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder.
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Kang Kang, Jun Li, Boon Leong Lim, Gianni Panagiotou:
MESSI: metabolic engineering target selection and best strain identification tool.
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Dadakhalandar Doddamani, Aamir W. Khan, A. V. S. K. Mohan Katta, Gaurav Agarwal, Mahendar Thudi, Pradeep Ruperao, David Edwards, Rajeev K. Varshney:
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.
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Ksenia S. Egorova, A. N. Kondakova, Philip V. Toukach:
Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes.
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Zheng Zhao, Jing Bai, Aiwei Wu, Yuan Wang, Jinwen Zhang, Zishan Wang, Yongsheng Li, Juan Xu, Xia Li:
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.
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  - journals/biodb/ThangamG15
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Manonanthini Thangam, Ramesh Kumar Gopal:
CRCDA - Comprehensive resources for cancer NGS data analysis.
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Nathaniel J. Davies, Eran Tauber:
WaspAtlas: a Nasonia vitripennis gene database and analysis platform.
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  - journals/biodb/MeirellesGFMABP15
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Pedro Milet Meirelles, Luiz M. R. Gadelha Jr., Ronaldo Bastos Francini-Filho, Rodrigo Leão de Moura, Gilberto Menezes Amado-Filho, Alex Cardoso Bastos, Rodolfo Pinheiro da Rocha Paranhos, Carlos Eduardo Rezende, Jean Swings, Eduardo Siegle, Nils Edvin Asp Neto, Sigrid Neumann Leitão, Ricardo Coutinho, Marta Mattoso, Paulo S. Salomon, Rogério A. B. Valle, Renato Crespo Pereira, Ricardo Henrique Kruger, Cristiane Thompson, Fabiano L. Thompson:
BaMBa: towards the integrated management of Brazilian marine environmental data.
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Teresia M. Buza, Sherman W. Jack, Halid Kirunda, Margaret L. Khaitsa, Mark L. Lawrence, Stephen Pruett, Daniel G. Peterson:
ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.
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  - journals/biodb/Reyes-PrietoVLM15
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Mariana Reyes-Prieto, Carlos Vargas-Chávez, Amparo Latorre, Andrés Moya:
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships.
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Junyang Yue, Jian Liu, Rongjun Ban, Wei Tang, Lin Deng, Zhangjun Fei, Yongsheng Liu:
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics.

Original Articles

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Leen Vandepitte, Samuel Bosch, Lennert Tyberghein, Filip Waumans, Bart Vanhoorne, Francisco Hernandez, Olivier De Clerck, Jan Mees:
Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases.
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  - journals/biodb/YangFLGZ15
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Yaohua Yang, Jie Feng, Tao Li, Feng Ge, Jindong Zhao:
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.
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  - journals/biodb/WangLHPLSNDS15
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Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama:
PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.
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  - journals/biodb/Rocca-SerraWPGZ15
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Philippe Rocca-Serra, Ramona L. Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra N. González-Beltrán:
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.
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  - journals/biodb/KimSSL15
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Hanhae Kim, Jung Eun Shim, Junha Shin, Insuk Lee:
EcoliNet: a database of cofunctional gene network for Escherichia coli.
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  - journals/biodb/HenkelWW15
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Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath:
Combining computational models, semantic annotations and simulation experiments in a graph database.
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  - journals/biodb/StrasserMNWWAMK15
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Kimchi Strasser, Erin McDonnell, Carol Nyaga, Min Wu, Sherry Wu, Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, Justin Powlowski, Gregory Butler, Adrian Tsang:
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.
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  - journals/biodb/DerbyshireGLHMW15
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Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang, Aron Marchler-Bauer:
Improving the consistency of domain annotation within the Conserved Domain Database.
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  - journals/biodb/OrchardH15
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Sandra E. Orchard, Henning Hermjakob:
Shared resources, shared costs - leveraging biocuration resources.
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  - journals/biodb/MalladiEPRCDHHL15
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Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart R. Miyasato, Greg R. Roe, Matt Simison, Cricket A. Sloan, J. Seth Strattan, Forrest Tanaka, W. James Kent, J. Michael Cherry, Eurie L. Hong:
Ontology application and use at the ENCODE DCC.
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Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi, Purshotam Sharma, Preethi S. P., Rahul Paul, Sukanya Halder, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra:
RNABP COGEST: a resource for investigating functional RNAs.
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Saurabh Loharch, Isha Bhutani, Kamal Jain, Pawan Gupta, Debendra K. Sahoo, Raman Parkesh:
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.
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Debasree Sarkar, Tanmoy Jana, Sudipto Saha:
LMPID: A manually curated database of linear motifs mediating protein-protein interactions.
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  - journals/biodb/KhareBATCHL15
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Ritu Khare, John D. Burger, John S. Aberdeen, David Tresner-Kirsch, Theodore J. Corrales, Lynette Hirschman, Zhiyong Lu:
Scaling drug indication curation through crowdsourcing.
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  - journals/biodb/YuKTSLH15
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Jingyin Yu, Tao Ke, Sadia Tehrim, Fengming Sun, Boshou Liao, Wei Hua:
PTGBase: an integrated database to study tandem duplicated genes in plants.
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  - journals/biodb/TaoSZCX15
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Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu:
Colorectal cancer drug target prediction using ontology-based inference and network analysis.
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  - journals/biodb/SmithV15
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Timothy D. Smith, Mauno Vihinen:
Standard development at the Human Variome Project.
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  - journals/biodb/WangDDYXY15
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Kun Wang, Jiao Deng, Rebecca Njeri Damaris, Mei Yang, Liming Xu, Pingfang Yang:
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study.
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  - journals/biodb/LeeYHKKPHHK15
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Ji-Hyun Lee, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byungwoo Han, Daehee Hwang, Sunghoon Kim:
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer.
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  - journals/biodb/TudorRLVWA15
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Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi:
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.
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  - journals/biodb/Ochoa-MontanoMB15
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Bernardo Ochoa-Montaño, Nishita Mohan, Tom L. Blundell:
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.
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  - journals/biodb/OliveiraASGAVAF15
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Jorge S. Oliveira, Wydemberg Araújo, Ana Isabela Lopes Sales, Alaine de Brito Guerra, Sinara Carla da Silva Araújo, Ana Tereza Ribeiro de Vasconcelos, Lucymara F. Agnez-Lima, Ana Teresa Freitas:
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.
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Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Jian Ren, Zexian Liu, Yu Xue:
dbPSP: a curated database for protein phosphorylation sites in prokaryotes.
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Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng:
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.
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Stéphanie Boué, Marja Talikka, Jurjen Willem Westra, William Hayes, Anselmo Di Fabio, Jennifer Park, Walter K. Schlage, Alain Sewer, Brett Fields, Sam Ansari, Florian Martin, Emilija Veljkovic, Renée Kenney, Manuel C. Peitsch, Julia Hoeng:
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.
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Payman Nickchi, Mohieddin Jafari, Shiva Kalantari:
PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.
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Juan Hua, Bo Xu, Yifan Yang, Rongjun Ban, Furhan Iqbal, Howard J. Cooke, Yuanwei Zhang, Qinghua Shi:
Follicle Online: an integrated database of follicle assembly, development and ovulation.
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Shradha Khater, Debasisa Mohanty:
novPTMenzy: a database for enzymes involved in novel post-translational modifications.
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Markus Oppermann, Stephan Weise, Claudia Dittmann, Helmut Knüpffer:
GBIS: the information system of the German Genebank.
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Hongdong Li, Gilbert S. Omenn, Yuanfang Guan:
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.
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Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle G. Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra E. Orchard, Sylvain Poux, Nives Skunca, Marc Robinson-Rechavi:
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
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Wasila M. Dahdul, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula M. Mabee:
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.
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Chia-Hung Chien, Yi-Fan Chiang-Hsieh, Yi-An Chen, Chi-Nga Chow, Nai-Yun Wu, Ping-Fu Hou, Wen-Chi Chang:
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs.
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Alfred Chun-Shui Luk, Huayan Gao, Sizhe Xiao, Jinyue Liao, Daxi Wang, Jiajie Tu, Owen M. Rennert, Wai-Yee Chan, Tin-Lap Lee:
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development.
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Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su:
GraP: platform for functional genomics analysis of Gossypium raimondii.
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Maulik R. Kamdar, Michel Dumontier:
An Ebola virus-centered knowledge base.
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Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz:
A general concept for consistent documentation of computational analyses.
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Jaeyoung Choi, Ki-Tae Kim, Aram Huh, Seomun Kwon, Changyoung Hong, Fred O. Asiegbu, Junhyun Jeon, Yong-Hwan Lee:
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes.
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Ismael Navas-Delgado, María Jesús García-Godoy, Esteban López-Camacho, Maciej Rybinski, Armando Reyes-Palomares, Miguel Angel Medina, José Francisco Aldana Montes:
kpath: integration of metabolic pathway linked data.
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Edward Baker, Ben W. Price, Simon D. Rycroft, Jon Hill, Vincent S. Smith:
BioAcoustica: a free and open repository and analysis platform for bioacoustics.
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Tamás Hegedüs, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi:
Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications.
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Justyna Szostak, Sam Ansari, Sumit Madan, Juliane Fluck, Marja Talikka, Anita Iskandar, Hector De Leon, Martin Hofmann-Apitius, Manuel C. Peitsch, Julia Hoeng:
Construction of biological networks from unstructured information based on a semi-automated curation workflow.
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Rian Pierneef, Louis Cronje, Oliver Bezuidt, Oleg N. Reva:
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.
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Jean-Michel Garant, Mikael J. Luce, Michelle S. Scott, Jean-Pierre Perreault:
G4RNA: an RNA G-quadruplex database.
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Karambir Kaur, Himani Tandon, Amit Kumar Gupta, Manoj Kumar:
CrisprGE: a central hub of CRISPR/Cas-based genome editing.
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Simon Jon McIlroy, Aaron Marc Saunders, Mads Albertsen, Marta Nierychlo, Bianca McIlroy, Aviaja Anna Hansen, Søren Michael Karst, Jeppe Lund Nielsen, Per Halkjær Nielsen:
MiDAS: the field guide to the microbes of activated sludge.
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Xiaobao Dong, Xiaotian Lu, Ziding Zhang:
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors.
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Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan:
SInCRe - structural interactome computational resource for Mycobacterium tuberculosis.
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David B. Rhee, Matthew McKnight Croken, Kevin R. Shieh, Julie M. Sullivan, Gos Micklem, Kami Kim, Aaron Golden:
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.
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Andrew Ndhlovu, Pierre M. Durand, Scott Hazelhurst:
EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.
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  - journals/biodb/MedvedevaLEKVPK15
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Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, Finn Drabløs:
EpiFactors: a comprehensive database of human epigenetic factors and complexes.
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  - journals/biodb/BabbittBBBCCCFG15
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Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend:
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
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Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen:
Human metabolic atlas: an online resource for human metabolism.
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  - journals/biodb/ShenSKC15
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Jun Shen, Déborah I. Scheffer, Kelvin Y. Kwan, David P. Corey:
SHIELD: an integrative gene expression database for inner ear research.
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  - journals/biodb/KumarCSKTB15
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Anil Kumar, Hasnahana Chetia, Swagata Sharma, Debajyoti Kabiraj, Narayan Chandra Talukdar, Utpal Bora:
Curcumin Resource Database.
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Matyas F. Cserhati, Sanjit Pandey, James J. Beaudoin, Lorena Baccaglini, Chittibabu Guda, Howard S. Fox:
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.
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  - journals/biodb/PathaniaRB15
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Shivalika Pathania, Sai Mukund Ramakrishnan, Ganesh Bagler:
Phytochemica: a platform to explore phytochemicals of medicinal plants.
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  - journals/biodb/MeinkenWCM15
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John Meinken, Gary Walker, Chester R. Cooper, Xiang Jia Min:
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase.
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  - journals/biodb/BoeufABCJ15
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Dominique Boeuf, Stéphane Audic, Loraine Brillet-Guéguen, Christophe Caron, Christian Jeanthon:
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.
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  - journals/biodb/WangJCHBC15
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Fei Wang, Lichun Jiang, Yong Chen, Nele A. Haelterman, Hugo J. Bellen, Rui Chen:
FlyVar: a database for genetic variation in Drosophila melanogaster.
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  - journals/biodb/AshoorKRB15
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Haitham Ashoor, Dimitrios Kleftogiannis, Aleksandar Radovanovic, Vladimir B. Bajic:
DENdb: database of integrated human enhancers.
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  - journals/biodb/ZhouSKL15
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Zhong Zhou, Yi Shen, Muhammad Riaz Khan, Ao Li:
LncReg: a reference resource for lncRNA-associated regulatory networks.
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  - journals/biodb/GobeillGPVGBR15
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Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch:
Deep Question Answering for protein annotation.
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  - journals/biodb/KorlaCHTLKHCN15
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Praveen Kumar Korla, Jack Cheng, Chien-Hung Huang, Jeffrey J. P. Tsai, Yu-Hsuan Liu, Nilubon Kurubanjerdjit, Wen-Tsong Hsieh, Huey-Yi Chen, Ka-Lok Ng:
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events.
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  - journals/biodb/NicolaBHG15
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George Nicola, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson:
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.
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Chao Pang, Annet Sollie, Anna Sijtsma, Dennis Hendriksen, Bart Charbon, Mark de Haan, Tommy de Boer, Fleur D. L. Kelpin, Jonathan Jetten, K. Joeri van der Velde, Nynke Smidt, Rolf Sijmons, Hans L. Hillege, Morris A. Swertz:
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.
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  - journals/biodb/WilmingBH15
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Laurens G. Wilming, Veronika Boychenko, Jennifer L. Harrow:
Comprehensive comparative homeobox gene annotation in human and mouse.
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  - journals/biodb/KilianHPMGSMBB15
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Norbert Kilian, Tilo Henning, Patrick Plitzner, Andreas Müller, Anton Güntsch, Ben C. Stöver, Kai F. Müller, Walter G. Berendsohn, Thomas Borsch:
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.
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  - journals/biodb/LiuWMW15
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Zhi-Ping Liu, Canglin Wu, Hongyu Miao, Hulin Wu:
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse.
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  - journals/biodb/ZhangZZZX15
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Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng, Junfeng Xia:
MGDB: a comprehensive database of genes involved in melanoma.
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  - journals/biodb/WangZZLZGGNL15
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Peng Wang, Hui Zhi, Yunpeng Zhang, Yue Liu, Jizhou Zhang, Yue Gao, Maoni Guo, Shangwei Ning, Xia Li:
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.
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  - journals/biodb/PetrilloAHBPK15
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Mauro Petrillo, Alexandre Angers-Loustau, Peter Henriksson, Laura Bonfini, Alexandre Patak, Joachim Kreysa:
JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.
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  - journals/biodb/JuhaszHM15
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Angéla Juhász, Réka Haraszi, Csaba Maulis:
ProPepper: a curated database for identification and analysis of peptide and immune-responsive epitope composition of cereal grain protein families.
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  - journals/biodb/BagewadiADIENPH15
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Shweta Bagewadi Kawalia, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger:
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.
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  - journals/biodb/GuoXYLYZ15
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Zhi-Wei Guo, Chen Xie, Jian-Rong Yang, Jun-Hao Li, Jian-Hua Yang, Limin Zheng:
MtiBase: a database for decoding microRNA target sites located within CDS and 5′UTR regions from CLIP-Seq and expression profile datasets.
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  - journals/biodb/RichardsonGMBRA15
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Lorna J. Richardson, Liz Graham, Julie Moss, Nick Burton, Yogmatee Roochun, Chris Armit, Richard A. Baldock:
Developing the eHistology Atlas.
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  - journals/biodb/RajuGGGASPG15
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Rajesh Raju, Sachin Gadakh, Priyanka Gopal, Bijesh George, Jayshree Advani, Sowmya Soman, T. S. Keshava Prasad, Reshmi Girijadevi:
Differential ligand-signaling network of CCL19/CCL21-CCR7 system.
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  - journals/biodb/CollierGSROR15
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Nigel Collier, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann:
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases.
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  - journals/biodb/ZhouYMZ15
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Yuan Zhou, Shiping Yang, Tonglin Mao, Ziding Zhang:
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
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  - journals/biodb/NanduriBSMPG15
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Ravikanth Nanduri, Isha Bhutani, Arun Kumar Somavarapu, Sahil Mahajan, Raman Parkesh, Pawan Gupta:
ONRLDB - manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery.
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Mir Asif Iquebal, Sarika Jaiswal, Ulavappa B. Angadi, Gaurav Sablok, Vasu Arora, Sunil Kumar, Anil Rai, Dinesh Kumar:
SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
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  - journals/biodb/Rodriguez-Esteban15
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Raul Rodriguez-Esteban:
Biocuration with insufficient resources and fixed timelines.
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  - journals/biodb/NegiPSMG15
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Simarjeet Negi, Sanjit Pandey, Satish Mahadevan Srinivasan, Akram Mohammed, Chittibabu Guda:
LocSigDB: a database of protein localization signals.
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  - journals/biodb/GrozaKDCOSCBZR15
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Tudor Groza, Sebastian Köhler, Sandra C. Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M. Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson:
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora.
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  - journals/biodb/BelinkyNSZSSL15
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Frida Belinky, Noam Nativ, Gil Stelzer, Shahar Zimmerman, Tsippi Iny Stein, Marilyn Safran, Doron Lancet:
PathCards: multi-source consolidation of human biological pathways.
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  - journals/biodb/PalmaVHRT15
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Guillermo Palma, Maria-Esther Vidal, Eric Haag, Louiqa Raschid, Andreas Thor:
Determining similarity of scientific entities in annotation datasets.

Reviews

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Saikat Chowdhury, Ram Rup Sarkar:
Comparison of human cell signaling pathway databases - evolution, drawbacks and challenges.

Database Update

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Wei Zhang, Eric R. Gamazon, Xu Zhang, Anuar Konkashbaev, Cong Liu, Keely L. Szilágyi, M. Eileen Dolan, Nancy J. Cox:
SCAN database: facilitating integrative analyses of cytosine modification and expression QTL.
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Jing Gong, Chun-Jie Liu, Wei Liu, Yuliang Wu, Zhaowu Ma, Hu Chen, An-Yuan Guo:
An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools.
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  - journals/biodb/SablokRMPSBYRP15
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Gaurav Sablok, G. V. Padma Raju, Suresh B. Mudunuri, Ratna Prabha, Dhananjaya P. Singh, Vesselin Baev, Galina Yahubyan, Peter J. Ralph, Nicola La Porta:
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.
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  - journals/biodb/WangWLCW15
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Xiaobo Wang, Jian Wu, Jianli Liang, Feng Cheng, Xiaowu Wang:
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.
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  - journals/biodb/LopezNP15
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Yosvany López, Kenta Nakai, Ashwini Patil:
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
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  - journals/biodb/NguyenVGAC15
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Tien Dung Nguyen, Oriol Vidal-Cortes, Óscar Gallardo, Joaquin Abian, Montserrat Carrascal:
LymPHOS 2.0: an update of a phosphosite database of primary human T cells.

Corrigendum

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Maria Taboada, Hadriana Rodríguez, Diego Martínez Hernández, María Pardo, María Jesús Sobrido:
Automated semantic annotation of rare disease cases: a case study.

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