Volume 2014

2014

Cover image

EISSN 1758-0463

Issue navigation

< Previous Next >

Volume 2014, 2014

Original Articles

dbPPT: a comprehensive database of protein phosphorylation in plants

Han Cheng, Wankun Deng, Yongbo Wang, Jian Ren, Zexian Liu, Yu Xue

Database, Volume 2014, 2014, bau121, https://doi.org/10.1093/database/bau121

EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom

Sangita Kumari, Sachin Pundhir, Piyush Priya, Ganga Jeena, Ankita Punetha, Konika Chawla, Zohra Firdos Jafaree, Subhasish Mondal, Gitanjali Yadav

Database, Volume 2014, 2014, bau120, https://doi.org/10.1093/database/bau120

HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis

Ruchika Sahajpal, Gaurav Kandoi, Heena Dhiman, Sweety Raj, Open Source Drug Discovery Consortium, Vinod Scaria, Deeksha Bhartiya, Yasha Hasija

Database, Volume 2014, 2014, bau112, https://doi.org/10.1093/database/bau112

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants

Yi Wang, Roger Thilmony, Yunjun Zhao, Guoping Chen, Yong Q. Gu

Database, Volume 2014, 2014, bau117, https://doi.org/10.1093/database/bau117

CBMAR: a comprehensive β-lactamase molecular annotation resource

Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar

Database, Volume 2014, 2014, bau111, https://doi.org/10.1093/database/bau111

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics

Márcia Duarte, Ruy Jauregui, Ramiro Vilchez-Vargas, Howard Junca, Dietmar H. Pieper

Database, Volume 2014, 2014, bau118, https://doi.org/10.1093/database/bau118

The Halophile Protein Database

Naveen Sharma, Mohammad Samir Farooqi, Krishna Kumar Chaturvedi, Shashi Bhushan Lal, Monendra Grover, Anil Rai, Pankaj Pandey

Database, Volume 2014, 2014, bau114, https://doi.org/10.1093/database/bau114

View article

Small molecule annotation for the Protein Data Bank

Sanchayita Sen, Jasmine Young, John M. Berrisford, Minyu Chen, Matthew J. Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P. Hudson, Reiko Igarashi, Yumiko Kengaku, Yuhe Liang, Ezra Peisach, Irina Persikova, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Gaurav Sahni, Junko Sato … Marina A. Zhuravleva

Database, Volume 2014, 2014, bau116, https://doi.org/10.1093/database/bau116

View article

A robust data-driven approach for gene ontology annotation

Yanpeng Li, Hong Yu

Database, Volume 2014, 2014, bau113, https://doi.org/10.1093/database/bau113

View article

piRBase: a web resource assisting piRNA functional study

Peng Zhang, Xiaohui Si, Geir Skogerbø, Jiajia Wang, Dongya Cui, Yongxing Li, Xubin Sun, Li Liu, Baofa Sun, Runsheng Chen, Shunmin He, Da-Wei Huang

Database, Volume 2014, 2014, bau110, https://doi.org/10.1093/database/bau110

Knowledge-rich temporal relation identification and classification in clinical notes

Jennifer D’Souza, Vincent Ng

Database, Volume 2014, 2014, bau109, https://doi.org/10.1093/database/bau109

View article

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants

Aditi Kapil, Piyush Kant Rai, Asheesh Shanker

Database, Volume 2014, 2014, bau107, https://doi.org/10.1093/database/bau107

View article

VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets

Abid Qureshi, Nishant Thakur, Isha Monga, Anamika Thakur, Manoj Kumar

Database, Volume 2014, 2014, bau103, https://doi.org/10.1093/database/bau103

PolyprOnline: polyproline helix II and secondary structure assignment database

Romain Chebrek, Sylvain Leonard, Alexandre G. de Brevern, Jean-Christophe Gelly

Database, Volume 2014, 2014, bau102, https://doi.org/10.1093/database/bau102

View article

A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools

Emmanouil I. Athanasiadis, Kyriaki Antonopoulou, Foteini Chatzinasiou, Christina M. Lill, Marilena M. Bourdakou, Argiris Sakellariou, Katerina Kypreou, Irene Stefanaki, Evangelos Evangelou, John P.A. Ioannidis, Lars Bertram, Alexander J. Stratigos, George M. Spyrou

Database, Volume 2014, 2014, bau101, https://doi.org/10.1093/database/bau101

View article

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

Julien Rey, Patrick Deschavanne, Pierre Tuffery

Database, Volume 2014, 2014, bau106, https://doi.org/10.1093/database/bau106

View article

DEOP: a database on osmoprotectants and associated pathways

Salim Bougouffa, Aleksandar Radovanovic, Magbubah Essack, Vladimir B. Bajic

Database, Volume 2014, 2014, bau100, https://doi.org/10.1093/database/bau100

MetaProx: the database of metagenomic proximons

Gregory Vey, Trevor C. Charles

Database, Volume 2014, 2014, bau097, https://doi.org/10.1093/database/bau097

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

Adam Ameur, Ignas Bunikis, Stefan Enroth, Ulf Gyllensten

Database, Volume 2014, 2014, bau098, https://doi.org/10.1093/database/bau098

CarrotDB: a genomic and transcriptomic database for carrot

Zhi-Sheng Xu, Hua-Wei Tan, Feng Wang, Xi-Lin Hou, Ai-Sheng Xiong

Database, Volume 2014, 2014, bau096, https://doi.org/10.1093/database/bau096

View article

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

Christopher Wilks, Melissa S. Cline, Erich Weiler, Mark Diehkans, Brian Craft, Christy Martin, Daniel Murphy, Howdy Pierce, John Black, Donavan Nelson, Brian Litzinger, Thomas Hatton, Lori Maltbie, Michael Ainsworth, Patrick Allen, Linda Rosewood, Elizabeth Mitchell, Bradley Smith, Jim Warner … Daniel Maltbie

Database, Volume 2014, 2014, bau093, https://doi.org/10.1093/database/bau093

An online system for metabolic network analysis

Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Ozsoyoglu, Gultekin Ozsoyoglu

Database, Volume 2014, 2014, bau091, https://doi.org/10.1093/database/bau091

View article

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

Qingzhou Zhang, Bo Yang, Xujiao Chen, Jing Xu, Changlin Mei, Zhiguo Mao

Database, Volume 2014, 2014, bau092, https://doi.org/10.1093/database/bau092

View article

Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman

Database, Volume 2014, 2014, bau094, https://doi.org/10.1093/database/bau094

RADB: a database of rheumatoid arthritis-related polymorphisms

Ruijie Zhang, Meiwei Luan, Zhenwei Shang, Lian Duan, Guoping Tang, Miao Shi, Wenhua Lv, Hongjie Zhu, Jin Li, Hongchao Lv, Mingming Zhang, Guiyou Liu, He Chen, Yongshuai Jiang

Database, Volume 2014, 2014, bau090, https://doi.org/10.1093/database/bau090

View article

A semi-automated methodology for finding lipid-related GO terms

Mengyuan Fan, Hong Sang Low, Markus R. Wenk, Limsoon Wong

Database, Volume 2014, 2014, bau089, https://doi.org/10.1093/database/bau089

Unsupervised gene function extraction using semantic vectors

Ehsan Emadzadeh, Azadeh Nikfarjam, Rachel E. Ginn, Graciela Gonzalez

Database, Volume 2014, 2014, bau084, https://doi.org/10.1093/database/bau084

View article

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification

Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch

Database, Volume 2014, 2014, bau088, https://doi.org/10.1093/database/bau088

View article

Integrating information retrieval with distant supervision for Gene Ontology annotation

Dongqing Zhu, Dingcheng Li, Ben Carterette, Hongfang Liu

Database, Volume 2014, 2014, bau087, https://doi.org/10.1093/database/bau087

View article

LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations

Hong-Jie Dai, Johnny Chi-Yang Wu, Wei-San Lin, Aaron James F. Reyes, Mira Anne C. dela Rosa, Shabbir Syed-Abdul, Richard Tzong-Han Tsai, Wen-Lian Hsu

Database, Volume 2014, 2014, bau085, https://doi.org/10.1093/database/bau085

View article

Overview of the gene ontology task at BioCreative IV

Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu … Zhiyong Lu

Database, Volume 2014, 2014, bau086, https://doi.org/10.1093/database/bau086

View article

miRBase Tracker: keeping track of microRNA annotation changes

Gert Van Peer, Steve Lefever, Jasper Anckaert, Anneleen Beckers, Ali Rihani, Alan Van Goethem, Pieter-Jan Volders, Fjoralba Zeka, Maté Ongenaert, Pieter Mestdagh, Jo Vandesompele

Database, Volume 2014, 2014, bau080, https://doi.org/10.1093/database/bau080

FusoBase: an online Fusobacterium comparative genomic analysis platform

Mia Yang Ang, Hamed Heydari, Nick S. Jakubovics, Mahafizul Imran Mahmud, Avirup Dutta, Wei Yee Wee, Guat Jah Wong, Naresh V.R. Mutha, Shi Yang Tan, Siew Woh Choo

Database, Volume 2014, 2014, bau082, https://doi.org/10.1093/database/bau082

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain

Michaela Matthes, Martin Preusse, Jingzhong Zhang, Julia Schechter, Daniela Mayer, Bernd Lentes, Fabian Theis, Nilima Prakash, Wolfgang Wurst, Dietrich Trümbach

Database, Volume 2014, 2014, bau083, https://doi.org/10.1093/database/bau083

LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes

Manas R. Dikhit, Kanhu C. Moharana, Bikash R. Sahoo, Ganesh C. Sahoo, Pradeep Das

Database, Volume 2014, 2014, bau078, https://doi.org/10.1093/database/bau078

View article

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu

Database, Volume 2014, 2014, bau081, https://doi.org/10.1093/database/bau081

BC4GO: a full-text corpus for the BioCreative IV GO task

Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu

Database, Volume 2014, 2014, bau074, https://doi.org/10.1093/database/bau074

View article

tmBioC: improving interoperability of text-mining tools with BioC

Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu

Database, Volume 2014, 2014, bau073, https://doi.org/10.1093/database/bau073

APADB: a database for alternative polyadenylation and microRNA regulation events

Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter

Database, Volume 2014, 2014, bau076, https://doi.org/10.1093/database/bau076

Standardized description of scientific evidence using the Evidence Ontology (ECO)

Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna E. Lewis, Michelle Giglio

Database, Volume 2014, 2014, bau075, https://doi.org/10.1093/database/bau075

View article

Assisting manual literature curation for protein–protein interactions using BioQRator

Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur

Database, Volume 2014, 2014, bau067, https://doi.org/10.1093/database/bau067

View article

Text-mining-assisted biocuration workflows in Argo

Rafal Rak, Riza Theresa Batista-Navarro, Andrew Rowley, Jacob Carter, Sophia Ananiadou

Database, Volume 2014, 2014, bau070, https://doi.org/10.1093/database/bau070

RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses

Baoshan Ma, Jinyan Huang, Liming Liang

Database, Volume 2014, 2014, bau066, https://doi.org/10.1093/database/bau066

View article

OMICtools: an informative directory for multi-omic data analysis

Vincent J. Henry, Anita E. Bandrowski, Anne-Sophie Pepin, Bruno J. Gonzalez, Arnaud Desfeux

Database, Volume 2014, 2014, bau069, https://doi.org/10.1093/database/bau069

View article

yStreX: yeast stress expression database

Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranovic

Database, Volume 2014, 2014, bau068, https://doi.org/10.1093/database/bau068

Processing biological literature with customizable Web services supporting interoperable formats

Rafal Rak, Riza Theresa Batista-Navarro, Jacob Carter, Andrew Rowley, Sophia Ananiadou

Database, Volume 2014, 2014, bau064, https://doi.org/10.1093/database/bau064

View article

BioC interoperability track overview

Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Doğan, Antonio Jimeno Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur

Database, Volume 2014, 2014, bau053, https://doi.org/10.1093/database/bau053

View article

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Conrad L. Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, Laszlo Irinyi, Wieland Meyer, R. Henrik Nilsson, Karen Hughes, Andrew N. Miller, Paul M. Kirk, Kessy Abarenkov, M. Catherine Aime, Hiran A. Ariyawansa, Martin Bidartondo, Teun Boekhout, Bart Buyck, Qing Cai, Jie Chen … Scott Federhen

Database, Volume 2014, 2014, bau061, https://doi.org/10.1093/database/bau061

BioC implementations in Go, Perl, Python and Ruby

Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau

Database, Volume 2014, 2014, bau059, https://doi.org/10.1093/database/bau059

View article

A controlled vocabulary for pathway entities and events

Steve Jupe, Bijay Jassal, Mark Williams, Guanming Wu

Database, Volume 2014, 2014, bau060, https://doi.org/10.1093/database/bau060

View article

A novel multi-alignment pipeline for high-throughput sequencing data

Shunping Huang, James Holt, Chia-Yu Kao, Leonard McMillan, Wei Wang

Database, Volume 2014, 2014, bau057, https://doi.org/10.1093/database/bau057

View article

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

Donald C. Comeau, Haibin Liu, Rezarta Islamaj Doğan, W. John Wilbur

Database, Volume 2014, 2014, bau056, https://doi.org/10.1093/database/bau056

View article

Curation accuracy of model organism databases

Ingrid M. Keseler, Marek Skrzypek, Deepika Weerasinghe, Albert Y. Chen, Carol Fulcher, Gene-Wei Li, Kimberly C. Lemmer, Katherine M. Mladinich, Edmond D. Chow, Gavin Sherlock, Peter D. Karp

Database, Volume 2014, 2014, bau058, https://doi.org/10.1093/database/bau058

IFIM: a database of integrated fitness information for microbial genes

Wen Wei, Yuan-Nong Ye, Sen Luo, Yan-Yan Deng, Dan Lin, Feng-Biao Guo

Database, Volume 2014, 2014, bau052, https://doi.org/10.1093/database/bau052

View article

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

Thomas C. Wiegers, Allan Peter Davis, Carolyn J. Mattingly

Database, Volume 2014, 2014, bau050, https://doi.org/10.1093/database/bau050

View article

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora

Rezarta Islamaj Doğan, Donald C. Comeau, Lana Yeganova, W. John Wilbur

Database, Volume 2014, 2014, bau044, https://doi.org/10.1093/database/bau044

View article

miRror-Suite: decoding coordinated regulation by microRNAs

Yitzhak Friedman, Solange Karsenty, Michal Linial

Database, Volume 2014, 2014, bau043, https://doi.org/10.1093/database/bau043

View article

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, Julio Collado-Vides

Database, Volume 2014, 2014, bau049, https://doi.org/10.1093/database/bau049

View article

Automated semantic annotation of rare disease cases: a case study

Maria Taboada, Hadriana Rodríguez, Diego Martínez, María Pardo, María Jesús Sobrido

Database, Volume 2014, 2014, bau045, https://doi.org/10.1093/database/bau045

View article

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation

Kathrin Poos, Jan Smida, Michaela Nathrath, Doris Maugg, Daniel Baumhoer, Anna Neumann, Eberhard Korsching

Database, Volume 2014, 2014, bau042, https://doi.org/10.1093/database/bau042

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins

Pierrick Craveur, Joseph Rebehmed, Alexandre G. de Brevern

Database, Volume 2014, 2014, bau041, https://doi.org/10.1093/database/bau041

View article

HeteroGenome: database of genome periodicity

Maria Chaley, Vladimir Kutyrkin, Gayane Tulbasheva, Elena Teplukhina, Nafisa Nazipova

Database, Volume 2014, 2014, bau040, https://doi.org/10.1093/database/bau040

View article

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system

Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker

Database, Volume 2014, 2014, bau038, https://doi.org/10.1093/database/bau038

View article

dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors

Yong-Min Kim, Jaeyoung Choi, Hye-Young Lee, Gir-Won Lee, Yong-Hwan Lee, Doil Choi

Database, Volume 2014, 2014, bau037, https://doi.org/10.1093/database/bau037

TuberQ: a Mycobacterium tuberculosis protein druggability database

Leandro Radusky, Lucas A. Defelipe, Esteban Lanzarotti, Javier Luque, Xavier Barril, Marcelo A. Marti, Adrián G. Turjanski

Database, Volume 2014, 2014, bau035, https://doi.org/10.1093/database/bau035

PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

Faouzi Jaziri, Nicolas Parisot, Anis Abid, Jérémie Denonfoux, Céline Ribière, Cyrielle Gasc, Delphine Boucher, Jean-François Brugère, Antoine Mahul, David R.C. Hill, Eric Peyretaillade, Pierre Peyret

Database, Volume 2014, 2014, bau036, https://doi.org/10.1093/database/bau036

View article

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

Juan Miguel Cejuela, Peter McQuilton, Laura Ponting, Steven J. Marygold, Raymund Stefancsik, Gillian H. Millburn, Burkhard Rost, the FlyBase Consortium

Database, Volume 2014, 2014, bau033, https://doi.org/10.1093/database/bau033

View article

FixPred: a resource for correction of erroneous protein sequences

Alinda Nagy, László Patthy

Database, Volume 2014, 2014, bau032, https://doi.org/10.1093/database/bau032

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences

Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom

Database, Volume 2014, 2014, bau027, https://doi.org/10.1093/database/bau027

EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications

Enyu Dai, Xuexin Yu, Yan Zhang, Fanlin Meng, Shuyuan Wang, Xinyi Liu, Dianming Liu, Jing Wang, Xia Li, Wei Jiang

Database, Volume 2014, 2014, bau023, https://doi.org/10.1093/database/bau023

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder

Database, Volume 2014, 2014, bau022, https://doi.org/10.1093/database/bau022

DBatVir: the database of bat-associated viruses

Lihong Chen, Bo Liu, Jian Yang, Qi Jin

Database, Volume 2014, 2014, bau021, https://doi.org/10.1093/database/bau021

View article

Linking tissues to phenotypes using gene expression profiles

Anika Oellrich, Sanger Mouse Genetics Project, Damian Smedley

Database, Volume 2014, 2014, bau017, https://doi.org/10.1093/database/bau017

View article

GigaDB: promoting data dissemination and reproducibility

Tam P. Sneddon, Xiao Si Zhe, Scott C. Edmunds, Peter Li, Laurie Goodman, Christopher I. Hunter

Database, Volume 2014, 2014, bau018, https://doi.org/10.1093/database/bau018

View article

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

Sylvain Poux, Michele Magrane, Cecilia N. Arighi, Alan Bridge, Claire O’Donovan, Kati Laiho, The UniProt Consortium

Database, Volume 2014, 2014, bau016, https://doi.org/10.1093/database/bau016

View article

YTRP: a repository for yeast transcriptional regulatory pathways

Tzu-Hsien Yang, Chung-Ching Wang, Yu-Chao Wang, Wei-Sheng Wu

Database, Volume 2014, 2014, bau014, https://doi.org/10.1093/database/bau014

View article

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses

Filip Claes, Dmitry Kuznetsov, Robin Liechti, Sophie Von Dobschuetz, Bao Dinh Truong, Anne Gleizes, Daniele Conversa, Alessandro Colonna, Ettore Demaio, Sabina Ramazzotto, Fairouz Larfaoui, Julio Pinto, Philippe Le Mercier, Ioannis Xenarios, Gwenaelle Dauphin

Database, Volume 2014, 2014, bau008, https://doi.org/10.1093/database/bau008

View article

BambooGDB: a bamboo genome database with functional annotation and an analysis platform

Hansheng Zhao, Zhenhua Peng, Benhua Fei, Lubin Li, Tao Hu, Zhimin Gao, Zehui Jiang

Database, Volume 2014, 2014, bau006, https://doi.org/10.1093/database/bau006

View article

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

Janos X. Binder, Sune Pletscher-Frankild, Kalliopi Tsafou, Christian Stolte, Seán I. O’Donoghue, Reinhard Schneider, Lars Juhl Jensen

Database, Volume 2014, 2014, bau012, https://doi.org/10.1093/database/bau012

View article

AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource

Margherita Scarpato, Roberta Esposito, Daniela Evangelista, Marianna Aprile, Maria Rosaria Ambrosio, Claudia Angelini, Alfredo Ciccodicola, Valerio Costa

Database, Volume 2014, 2014, bau009, https://doi.org/10.1093/database/bau009

TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling

Jun Zhong, Jyoti Sharma, Rajesh Raju, Shyam Mohan Palapetta, T. S. Keshava Prasad, Tai-Chung Huang, Akinori Yoda, Jeffrey W. Tyner, Diederik van Bodegom, David M. Weinstock, Steven F. Ziegler, Akhilesh Pandey

Database, Volume 2014, 2014, bau007, https://doi.org/10.1093/database/bau007

View article

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

Paulo R. Pagliosa, João G. Doria, Dairana Misturini, Mariana B. P. Otegui, Mariana S. Oortman, Wilson A. Weis, Larisse Faroni-Perez, Alexandre P. Alves, Maurício G. Camargo, A. Cecília Z. Amaral, Antonio C. Marques, Paulo C. Lana

Database, Volume 2014, 2014, bau002, https://doi.org/10.1093/database/bau002

View article

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Antonio Jimeno Yepes, Karin Verspoor

Database, Volume 2014, 2014, bau003, https://doi.org/10.1093/database/bau003

View article

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

Justen Manasa, Richard Lessells, Theresa Rossouw, Kevindra Naidu, Cloete Van Vuuren, Dominique Goedhals, Gert van Zyl, Armand Bester, Andrew Skingsley, Katharine Stott, Siva Danaviah, Terusha Chetty, Lavanya Singh, Pravi Moodley, Collins Iwuji, Nuala McGrath, Christopher J. Seebregts, Tulio de Oliveira

Database, Volume 2014, 2014, bat082, https://doi.org/10.1093/database/bat082

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

Michele Tinti, Fábio Madeira, Gavuthami Murugesan, Gerta Hoxhaj, Rachel Toth, Carol MacKintosh

Database, Volume 2014, 2014, bat085, https://doi.org/10.1093/database/bat085

Rule-based deduplication of article records from bibliographic databases

Yu Jiang, Can Lin, Weiyi Meng, Clement Yu, Aaron M. Cohen, Neil R. Smalheiser

Database, Volume 2014, 2014, bat086, https://doi.org/10.1093/database/bat086

tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis

Kandarp Rakeshkumar Joshi, Heena Dhiman, Vinod Scaria

Database, Volume 2014, 2014, bat083, https://doi.org/10.1093/database/bat083

DevMouse, the mouse developmental methylome database and analysis tools

Hongbo Liu, Rangfei Zhu, Jie Lv, Hongjuan He, Lin Yang, Zhijun Huang, Jianzhong Su, Yan Zhang, Shihuan Yu, Qiong Wu

Database, Volume 2014, 2014, bat084, https://doi.org/10.1093/database/bat084

View article

Database Tool

Kin-Driver: a database of driver mutations in protein kinases

Franco L. Simonetti, Cristian Tornador, Nuria Nabau-Moretó, Miguel A. Molina-Vila, Cristina Marino-Buslje

Database, Volume 2014, 2014, bau104, https://doi.org/10.1093/database/bau104

View article

iPathCons and iPathDB: an improved insect pathway construction tool and the database

Zan Zhang, Chuanlin Yin, Ying Liu, Wencai Jie, Wenjie Lei, Fei Li

Database, Volume 2014, 2014, bau105, https://doi.org/10.1093/database/bau105

miRIAD—integrating microRNA inter- and intragenic data

Ludwig Christian Hinske, Gustavo S. França, Hugo A. M. Torres, Daniel T. Ohara, Camila M. Lopes-Ramos, Jens Heyn, Luiz F. L. Reis, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante

Database, Volume 2014, 2014, bau099, https://doi.org/10.1093/database/bau099

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

Jonathan R. Karr, Nolan C. Phillips, Markus W. Covert

Database, Volume 2014, 2014, bau095, https://doi.org/10.1093/database/bau095

View article

‘Isotopo’ a database application for facile analysis and management of mass isotopomer data

Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Eva Eylert, Wolfgang Eisenreich, Thomas Dandekar

Database, Volume 2014, 2014, bau077, https://doi.org/10.1093/database/bau077

PlantCAZyme: a database for plant carbohydrate-active enzymes

Alexander Ekstrom, Rahil Taujale, Nathan McGinn, Yanbin Yin

Database, Volume 2014, 2014, bau079, https://doi.org/10.1093/database/bau079

ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis

Chuanlin Yin, Ying Liu, Jinding Liu, Huamei Xiao, Shuiqing Huang, Yongjun Lin, Zhaojun Han, Fei Li

Database, Volume 2014, 2014, bau065, https://doi.org/10.1093/database/bau065

‘RetinoGenetics’: a comprehensive mutation database for genes related to inherited retinal degeneration

Xia Ran, Wei-Jun Cai, Xiu-Feng Huang, Qi Liu, Fan Lu, Jia Qu, Jinyu Wu, Zi-Bing Jin

Database, Volume 2014, 2014, bau047, https://doi.org/10.1093/database/bau047

View article

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

Chun-Wei Tung, Ying-Chi Lin, Hsun-Shuo Chang, Chia-Chi Wang, Ih-Sheng Chen, Jhao-Liang Jheng, Jih-Heng Li

Database, Volume 2014, 2014, bau055, https://doi.org/10.1093/database/bau055

View article

ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures

Divya Mehta, Priya Anand, Vineet Kumar, Anshika Joshi, Deepika Mathur, Sandeep Singh, Abhishek Tuknait, Kumardeep Chaudhary, Shailendra K. Gautam, Ankur Gautam, Grish C. Varshney, Gajendra P.S. Raghava

Database, Volume 2014, 2014, bau051, https://doi.org/10.1093/database/bau051

View article

MorusDB: a resource for mulberry genomics and genome biology

Tian Li, Xiwu Qi, Qiwei Zeng, Zhonghuai Xiang, Ningjia He

Database, Volume 2014, 2014, bau054, https://doi.org/10.1093/database/bau054

View article

Egas: a collaborative and interactive document curation platform

David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira

Database, Volume 2014, 2014, bau048, https://doi.org/10.1093/database/bau048

View article

agl genes, a curated and searchable database of archaeal N-glycosylation pathway components

Noa Godin, Jerry Eichler

Database, Volume 2014, 2014, bau046, https://doi.org/10.1093/database/bau046

View article

PLIC: protein–ligand interaction clusters

Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma Chandra

Database, Volume 2014, 2014, bau029, https://doi.org/10.1093/database/bau029

‘ In silico expression analysis’, a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis -regulatory sequences

Julio C. Bolívar, Fabian Machens, Yuri Brill, Artyom Romanov, Lorenz Bülow, Reinhard Hehl

Database, Volume 2014, 2014, bau030, https://doi.org/10.1093/database/bau030

View article

The quail anatomy portal

Avnika A. Ruparelia, Johanna E. Simkin, David Salgado, Donald F. Newgreen, Gabriel G. Martins, Robert J. Bryson-Richardson

Database, Volume 2014, 2014, bau028, https://doi.org/10.1093/database/bau028

View article

CancerEST: a web-based tool for automatic meta-analysis of public EST data

Julia Feichtinger, Ramsay J. McFarlane, Lee D. Larcombe

Database, Volume 2014, 2014, bau024, https://doi.org/10.1093/database/bau024

HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology

Guang Lan Zhang, Angelika B. Riemer, Derin B. Keskin, Lou Chitkushev, Ellis L. Reinherz, Vladimir Brusic

Database, Volume 2014, 2014, bau031, https://doi.org/10.1093/database/bau031

View article

Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes

Cao Nguyen, Abdul Baten, Grant Morahan

Database, Volume 2014, 2014, bau020, https://doi.org/10.1093/database/bau020

SoyFN: a knowledge database of soybean functional networks

Yungang Xu, Maozu Guo, Xiaoyan Liu, Chunyu Wang, Yang Liu

Database, Volume 2014, 2014, bau019, https://doi.org/10.1093/database/bau019

BCL2DB: database of BCL-2 family members and BH3-only proteins

Valentine Rech de Laval, Gilbert Deléage, Abdel Aouacheria, Christophe Combet

Database, Volume 2014, 2014, bau013, https://doi.org/10.1093/database/bau013

View article

The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation

Meghna Singh, Deeksha Bhartiya, Jayant Maini, Meenakshi Sharma, Angom Ramcharan Singh, Subburaj Kadarkaraisamy, Rajiv Rana, Ankit Sabharwal, Srishti Nanda, Aravindhakshan Ramachandran, Ashish Mittal, Shruti Kapoor, Paras Sehgal, Zainab Asad, Kriti Kaushik, Shamsudheen Karuthedath Vellarikkal, Divya Jagga, Muthulakshmi Muthuswami, Rajendra K. Chauhan … Sridhar Sivasubbu

Database, Volume 2014, 2014, bau011, https://doi.org/10.1093/database/bau011

StaphyloBase: a specialized genomic resource for the staphylococcal research community

Hamed Heydari, Naresh V.R. Mutha, Mahafizul Imran Mahmud, Cheuk Chuen Siow, Wei Yee Wee, Guat Jah Wong, Amir Hessam Yazdi, Mia Yang Ang, Siew Woh Choo

Database, Volume 2014, 2014, bau010, https://doi.org/10.1093/database/bau010

DBM-DB: the diamondback moth genome database

Weiqi Tang, Liying Yu, Weiyi He, Guang Yang, Fushi Ke, Simon W. Baxter, Shijun You, Carl J. Douglas, Minsheng You

Database, Volume 2014, 2014, bat087, https://doi.org/10.1093/database/bat087

View article

Database Update

DCDB 2.0: a major update of the drug combination database

Yanbin Liu, Qiang Wei, Guisheng Yu, Wanxia Gai, Yongquan Li, Xin Chen

Database, Volume 2014, 2014, bau124, https://doi.org/10.1093/database/bau124

View article

microPIR2: a comprehensive database for human–mouse comparative study of microRNA–promoter interactions

Jittima Piriyapongsa, Chaiwat Bootchai, Chumpol Ngamphiw, Sissades Tongsima

Database, Volume 2014, 2014, bau115, https://doi.org/10.1093/database/bau115

View article

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud

Kamran Karimi, Peter D. Vize

Database, Volume 2014, 2014, bau108, https://doi.org/10.1093/database/bau108

View article

Plant rDNA database: update and new features

Sònia Garcia, Francisco Gálvez, Airy Gras, Aleš Kovařík, Teresa Garnatje

Database, Volume 2014, 2014, bau063, https://doi.org/10.1093/database/bau063

View article

UCbase 2.0: ultraconserved sequences database (2014 update)

Vincenzo Lomonaco, Riccardo Martoglia, Federica Mandreoli, Laura Anderlucci, Warren Emmett, Silvio Bicciato, Cristian Taccioli

Database, Volume 2014, 2014, bau062, https://doi.org/10.1093/database/bau062

View article

RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

Kai-Yao Huang, Hsin-Yi Wu, Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Yun-Chung Hsieh, Chih-Ming Tsai, Kuo-I Lin, Hsien-Da Huang, Tzong-Yi Lee, Yu-Ju Chen

Database, Volume 2014, 2014, bau034, https://doi.org/10.1093/database/bau034

SysPTM 2.0: an updated systematic resource for post-translational modification

Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yang, Michael O. Glocker, Liangxiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li, Lu Xie

Database, Volume 2014, 2014, bau025, https://doi.org/10.1093/database/bau025