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hUbiquitome: a database of experimentally verified ubiquitination cascades in humans.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar055
By:
- Yipeng Du;
- Nanfang Xu;
- Ming Lu;
- Tingting Li
Publication type:
Article
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 6, p. 1
By:
- Sirim, Demet;
- Wagner, Florian;
- Wang, Lei;
- Schmid, Rolf D;
- Pleiss, Jürgen
Publication type:
Article
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar045
By:
- Jie Zheng;
- Stoyanovich, Julia;
- Manduchi, Elisabetta;
- Junmin Liu;
- Stoeckert Jr, Christian J.
Publication type:
Article
Neisseria Base: a comparative genomics database for Neisseria meningitidis.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar035
By:
- Katz, Lee S.;
- Humphrey, Jay C.;
- Conley, Andrew B.;
- Nelakuditi, Viswateja;
- Kislyuk, Andrey O.;
- Agrawal, Sonia;
- Jayaraman, Pushkala;
- Harcourt, Brian H.;
- Olsen-Rasmussen, Melissa A.;
- Frace, Michael;
- Sharma, Nitya V.;
- Mayer, Leonard W.;
- Jordan, I. King
Publication type:
Article
A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 5, p. 1
By:
- Li, Xin;
- Wu, Fan;
- Qi, Feng;
- Beard, Daniel A.
Publication type:
Article
RAC: Repository of Antibiotic resistance Cassettes.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar054
By:
- Tsafnat, Guy;
- Copty, Joseph;
- Partridge, Sally R.
Publication type:
Article
Curation of characterized glycoside hydrolases of Fungal origin.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 20, p. 1
By:
- Murphy, Caitlin;
- Powlowski, Justin;
- Wu, Min;
- Butler, Greg;
- Tsang, Adrian
Publication type:
Article
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar050
By:
- Génova, Alex Di;
- Aravena, Andrés;
- Zapata, Luis;
- González, Mauricio;
- Maass, Alejandro;
- Iturra, Patricia
Publication type:
Article
INOH: ontology-based highly structured database of signal transduction pathways.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar052
By:
- Yamamoto, Satoko;
- Sakai, Noriko;
- Nakamura, Hiromi;
- Fukagawa, Hiroshi;
- Fukuda, Ken;
- Takagi, Toshihisa
Publication type:
Article
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar053
By:
- Hamilton, John P.;
- Neeno-Eckwall, Eric C.;
- Adhikari, Bishwo N.;
- Perna, Nicole T.;
- Tisserat, Ned;
- Leach, Jan E.;
- Lévesque, C. André;
- Buell, C. Robin
Publication type:
Article
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar051
By:
- Jung, Sook;
- Menda, Naama;
- Redmond, Seth;
- Buels, Robert M.;
- Friesen, Maren;
- Bendana, Yuri;
- Sanderson, Lacey-Anne;
- Lapp, Hilmar;
- Lee, Taein;
- MacCallum, Bob;
- Bett, Kirstin E.;
- Cain, Scott;
- Clements, Dave;
- Mueller, Lukas A.;
- Main, Dorrie
Publication type:
Article
BioMart: driving a paradigm change in biological data management.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar049
By:
- Kasprzyk, Arek
Publication type:
Article
CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar046
By:
- Hatano, Akiko;
- Chiba, Hirokazu;
- Moesa, Harry Amri;
- Taniguchi, Takeaki;
- Nagaie, Satoshi;
- Yamanegi, Koji;
- Takai-Igarashi, Takako;
- Tanaka, Hiroshi;
- Fujibuchi, Wataru
Publication type:
Article
The Histone Database: an integrated resource for histones and histone fold-containing proteins.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar048
By:
- Mariño-Ramírez, Leonardo;
- Levine, Kevin M.;
- Morales, Mario;
- Suiyuan Zhang;
- Moreland, R. Travis;
- Baxevanis, Andreas D.;
- Landsman, David
Publication type:
Article
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar047
By:
- Ndegwa, Nelson;
- Cô té, Richard G.;
- Ovelleiro, David;
- D'Eustachio, Peter;
- Hermjakob, Henning;
- Vizcaíno, Juan A.;
- Croft, David
Publication type:
Article
The Reactome BioMart.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar031
By:
- Haw, Robin A.;
- Croft, David;
- Yung, Christina K.;
- Ndegwa, Nelson;
- D'Eustachio, Peter;
- Hermjakob, Henning;
- Stein, Lincoln D.
Publication type:
Article
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar037
By:
- Smita, Shuchi;
- Lenka, Sangram Keshari;
- Katiyar, Amit;
- Jaiswal, Pankaj;
- Preece, Justin;
- Bansal, Kailash Chander
Publication type:
Article
Tripal: a construction toolkit for online genome databases.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar044
By:
- Ficklin, Stephen P.;
- Sanderson, Lacey-Anne;
- Cheng, Chun-Huai;
- Staton, Margaret E.;
- Lee, Taein;
- Cho, Il-Hyung;
- Jung, Sook;
- Bett, Kirstin E.;
- Main, Doreen
Publication type:
Article
The NIDDK Central Repository at 8 years—Ambition, Revision, Use and Impact.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar043
By:
- Turner, Charles F.;
- Pan, Huaqin;
- Silk, Gregg W.;
- Ardini, Mary-Anne;
- Bakalov, Vesselina;
- Bryant, Stephanie;
- Cantor, Susanna;
- Chang, Kung-yen;
- DeLatte, Michael;
- Eggers, Paul;
- Ganapathi, Laxminarayana;
- Lakshmikanthan, Sujatha;
- Levy, Joshua;
- Li, Sheping;
- Pratt, Joseph;
- Pugh, Norma;
- Qin, Ying;
- Rasooly, Rebekah;
- Ray, Helen;
- Richardson, Jean E.
Publication type:
Article
NetSlim: high-confidence curated signaling maps.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar032
By:
- Raju, Rajesh;
- Nanjappa, Vishalakshi;
- Balakrishnan, Lavanya;
- Radhakrishnan, Aneesha;
- Thomas, Joji Kurian;
- Sharma, Jyoti;
- Tian, Maozhen;
- Palapetta, Shyam Mohan;
- Subbannayya, Tejaswini;
- Sekhar, Nirujogi Raja;
- Muthusamy, Babylakshmi;
- Goel, Renu;
- Subbannayya, Yashwanth;
- Telikicherla, Deepthi;
- Bhattacharjee, Mitali;
- Pinto, Sneha M.;
- Syed, Nazia;
- Srikanth, Manda Srinivas;
- Sathe, Gajanan J.;
- Ahmad, Sartaj
Publication type:
Article
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar042
By:
- Shameer, Khader;
- Shingate, Prashant N.;
- Manjunath, S. C. P.;
- Karthika, M.;
- Pugalenthi, Ganesan;
- Sowdhamini, Ramanathan
Publication type:
Article
The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar034
By:
- Davis, Allan Peter;
- Wiegers, Thomas C.;
- Murphy, Cynthia G.;
- Mattingly, Carolyn J.
Publication type:
Article
International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar026
By:
- Zhang, Junjun;
- Baran, Joachim;
- Cros, A.;
- Guberman, Jonathan M.;
- Haider, Syed;
- Hsu, Jack;
- Liang, Yong;
- Rivkin, Elena;
- Wang, Jianxin;
- Whitty, Brett;
- Wong-Erasmus, Marie;
- Yao, Long;
- Kasprzyk, Arek
Publication type:
Article
BioMart: a data federation framework for large collaborative projects.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar038
By:
- Zhang, Junjun;
- Haider, Syed;
- Baran, Joachim;
- Cros, Anthony;
- Guberman, Jonathan M.;
- Hsu, Jack;
- Liang, Yong;
- Yao, Long;
- Kasprzyk, Arek
Publication type:
Article
BioMart as an integration solution for the International Knockout Mouse Consortium.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar028
By:
- Oakley, Darren J.;
- Iyer, Vivek;
- Skarnes, William C.;
- Smedley, Damian
Publication type:
Article
Sig Reannot-mart: a query environment for expression microarray probe re-annotations.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar025
By:
- Moreews, François;
- Rauffet, Gaelle;
- Dehais, Patrice;
- Klopp, Christophe
Publication type:
Article
BioMart Central Portal: an open database network for the biological community.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar041
By:
- Guberman, Jonathan M.;
- Ai, J.;
- Arnaiz, O.;
- Baran, Joachim;
- Blake, Andrew;
- Baldock, Richard;
- Chelala, Claude;
- Croft, David;
- Cros, Anthony;
- Cutts, Rosalind J.;
- Di Génova, A.;
- Forbes, Simon;
- Fujisawa, T.;
- Gadaleta, E.;
- Goodstein, D. M.;
- Gundem, Gunes;
- Haggarty, Bernard;
- Haider, Syed;
- Hall, Matthew;
- Harris, Todd
Publication type:
Article
The BioMart interface to the eMouseAtlas gene expression database EMAGE.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar029
By:
- Stevenson, Peter;
- Richardson, Lorna;
- Venkataraman, Shanmugasundaram;
- Yiya Yang;
- Baldock, Richard
Publication type:
Article
The InterPro BioMart: federated query and web service access to the InterPro Resource.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar033
By:
- Jones, Philip;
- Binns, David;
- McMenamin, Conor;
- McAnulla, Craig;
- Hunter, Sarah
Publication type:
Article
Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar030
By:
- Kinsella, Rhoda J.;
- Kähäri, Andreas;
- Haider, Syed;
- Zamora, Jorge;
- Proctor, Glenn;
- Spudich, Giulietta;
- Almeida-King, Jeff;
- Staines, Daniel;
- Derwent, Paul;
- Kerhornou, Arnaud;
- Kersey, Paul;
- Flicek, Paul
Publication type:
Article
The strategies WDK: a graphical search interface and web development kit for functional genomics databases.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar027
By:
- Fischer, Steve;
- Aurrecoechea, Cristina;
- Brunk, Brian P.;
- Xin Gao;
- Harb, Omar S.;
- Kraemer, Eileen T.;
- Pennington, Cary;
- Treatman, Charles;
- Kissinger, Jessica C.;
- Roos, David S.;
- Stoeckert, Christian J.
Publication type:
Article
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar004
By:
- Costanzo, Maria C.;
- Park, Julie;
- Balakrishnan, Rama;
- Cherry, J. Michael;
- Hong, Eurie L.
Publication type:
Article
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar003
By:
- Bluhm, Wolfgang F.;
- Beran, Bojan;
- Bi, Chunxiao;
- Dimitropoulos, Dimitris;
- Prlić, Andreas;
- Quinn, Gregory B.;
- Rose, Peter W.;
- Shah, Chaitali;
- Young, Jasmine;
- Yukich, Benjamin;
- Berman, Helen M.;
- Bourne, Philip E.
Publication type:
Article
The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. 1, doi. 10.1093/database/bar002
By:
- Laulederkind, Stanley J. F.;
- Shimoyama, Mary;
- Hayman, G. Thomas;
- Lowry, Timothy F.;
- Nigam, Rajni;
- Petri, Victoria;
- Smith, Jennifer R.;
- Shur-Jen Wang;
- de Pons, Jeff;
- Kowalski, George;
- Liu, Weisong;
- Rood, Wes;
- Munzenmaier, Diane H.;
- Dwinell, Melinda R.;
- Twigger, Simon N.;
- Jacob, Howard J.
Publication type:
Article
FunSecKB: the Fungal Secretome KnowledgeBase.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, p. N.PAG, doi. 10.1093/database/bar001
By:
- Lum, Gengkon;
- Min, Xiang Jia
Publication type:
Article
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 40, p. 1
By:
- Gubelmann, Carine;
- Gattiker, Alexandre;
- Massouras, Andreas;
- Hens, Korneel;
- David, Fabrice;
- Decouttere, Frederik;
- Rougemont, Jacques;
- Deplancke, Bart
Publication type:
Article
Integrative Cancer Genomics (IntOGen) in Biomart.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 39, p. 1
By:
- Perez-Llamas, Christian;
- Gundem, Gunes;
- Lopez-Bigas, Nuria
Publication type:
Article
Methods and strategies for gene structure curation in WormBase.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 39, p. 1
By:
- Williams, G.W.;
- Davis, P.A.;
- Rogers, A.S.;
- Bieri, T.;
- Ozersky, P.;
- Spieth, J.
Publication type:
Article
ppiTrim: constructing non-redundant and up-to-date interactomes.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 36, p. 1
By:
- Stojmirović, Aleksandar;
- Yu, Yi-Kuo
Publication type:
Article
Using BioMart as a framework to manage and query pancreatic cancer data.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 24, p. 1
By:
- Cutts, Rosalind J.;
- Gadaleta, Emanuela;
- Lemoine, Nicholas R.;
- Chelala, Claude
Publication type:
Article
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 23, p. 1
By:
- Washington, Nicole L.;
- Stinson, E. O.;
- Perry, Marc D.;
- Ruzanov, Peter;
- Contrino, Sergio;
- Smith, Richard;
- Zha, Zheng;
- Lyne, Rachel;
- Carr, Adrian;
- Lloyd, Paul;
- Kephart, Ellen;
- McKay, Sheldon J.;
- Micklem, Gos;
- Stein, Lincoln D.;
- Lewis, Suzanna E.
Publication type:
Article
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 21, p. 1
By:
- Raju, Rajesh;
- Balakrishnan, Lavanya;
- Nanjappa, Vishalakshi;
- Bhattacharjee, Mitali;
- Getnet, Derese;
- Muthusamy, Babylakshmi;
- Kurian Thomas, Joji;
- Sharma, Jyoti;
- Rahiman, B. Abdul;
- Harsha, H.C.;
- Shankar, Subramanian;
- Prasad, T.S. Keshava;
- Mohan, S. Sujatha;
- Bader, Gary D.;
- Wani, Mohan R.;
- Pandey, Akhilesh
Publication type:
Article
MaizeGDB: curation and outreach go hand-in-hand.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 22, p. 1
By:
- Schaeffer, Mary L.;
- Harper, Lisa C.;
- Gardiner, Jack M.;
- Andorf, Carson M.;
- Campbell, Darwin A.;
- Cannon, Ethalinda K.S.;
- Sen, Taner Z.;
- Lawrence, Carolyn J.
Publication type:
Article
ParkDB: a Parkinson’s disease gene expression database.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 7, p. 1
By:
- Taccioli, Cristian;
- Maselli, Vincenza;
- Tegnér, Jesper;
- Gomez-Cabrero, David;
- Altobelli, Gioia;
- Emmett, Warren;
- Lescai, Francesco;
- Gustincich, Stefano;
- Stupka, Elia
Publication type:
Article
ParkDB: a Parkinson’s disease gene expression database.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 7, p. 1
By:
- Taccioli, Cristian;
- Tegnér, Jesper;
- Maselli, Vincenza;
- Gomez-Cabrero, David;
- Altobelli, Gioia;
- Emmett, Warren;
- Lescai, Francesco;
- Gustincich, Stefano;
- Stupka, Elia
Publication type:
Article
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 19, p. 1
By:
- Sridhara, Viswanadham;
- Marchler-Bauer, Aron;
- Bryant, Stephen H.;
- Geer, Lewis Y.
Publication type:
Article
A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 18, p. 1, doi. 10.1093/database/baq038
By:
- Milc, Justyna;
- Sala, Antonio;
- Bergamaschi, Sonia;
- Pecchioni, Nicola
Publication type:
Article
PubMed and beyond: a survey of web tools for searching biomedical literature.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 18, p. 1, doi. 10.1093/database/baq036
By:
- Zhiyong Lu
Publication type:
Article
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 18, p. 1
By:
- Shepherd, Rebecca;
- Forbes, Simon A.;
- Beare, David;
- Bamford, S.;
- Cole, Charlotte G.;
- Ward, Sari;
- Bindal, Nidhi;
- Gunasekaran, Prasad;
- Jia, Mingming;
- Kok, Chai Yin;
- Leung, Kenric;
- Menzies, Andrew;
- Butler, Adam P.;
- Teague, Jon W.;
- Campbell, Peter J.;
- Stratton, Michael R.;
- Futreal, P. Andrew
Publication type:
Article
The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.
Published in:
Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 16, p. 1
By:
- Harper, Lisa C.;
- Schaeffer, Mary L.;
- Thistle, Jordan;
- Gardiner, Jack M.;
- Andorf, Carson M.;
- Campbell, Darwin A.;
- Cannon, Ethalinda K.S.;
- Braun, Bremen L.;
- Birkett, Scott M.;
- Lawrence, Carolyn J.;
- Sen, Taner Z.
Publication type:
Article

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