default search action
Nucleic Acids Research, Volume 37
Volume 37, Number Database-Issue, January 2009
- Michael Y. Galperin
, Guy Cochrane
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. 1-4 - Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. 5-15 - Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, Yoshio Tateno:
DDBJ dealing with mass data produced by the second generation sequencer. 16-18 - Guy Cochrane
Petabyte-scale innovations at the European Nucleotide Archive. 19-25 - Dennis A. Benson, Ilene Karsch-Mizrachi
GenBank. 26-31 - Kim D. Pruitt
NCBI Reference Sequences: current status, policy and new initiatives. 32-36 - Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, Thomas Wilhelm:
DiProDB: a database for dinucleotide properties. 37-40 - Cristian Taccioli
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. 41-48 - Budrul Ahsan, Taro L. Saito, Shin-ichi Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atsushi Sasaki, Kouji Matsushima, Toshiro Aigaki, Shinichi Morishita:
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. 49-53 - Elodie Portales-Casamar
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. 54-60 - Andreas Grote, Johannes Klein, Ida Retter
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. 61-65 - Logan Everett, Antony Vo, Sridhar Hannenhalli:
PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. 66-71 - Grant H. Jacobs, Augustine Chen
Transterm: a database to aid the analysis of regulatory sequences in mRNAs. 72-76 - Daniel E. Newburger, Martha L. Bulyk:
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. 77-82 - Yurong Xin, Wilma K. Olson:
BPS: a database of RNA base-pair structures. 83-88 - Toutai Mituyama
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. 89-92 - Patricia P. Chan, Todd M. Lowe:
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. 93-97 - Qinghua Jiang, Yadong Wang, Yangyang Hao
miR2Disease: a manually curated database for microRNA deregulation in human disease. 98-104 - Feifei Xiao, Zhixiang Zuo
miRecords: an integrated resource for microRNA-target interactions. 105-110 - Daniel Gerlach
miROrtho: computational survey of microRNA genes. 111-117 - Anna Czerwoniec, Stanislaw Dunin-Horkawicz
MODOMICS: a database of RNA modification pathways, update 2008. 118-121 - Marcel E. Dinger
NRED: a database of long noncoding RNA expression. 122-126 - Michela Taufer
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. 127-135 - Paul P. Gardner
Rfam: updates to the RNA families database. 136-140 - James R. Cole, Qiong Wang, E. Cardenas, Jordan A. Fish, Benli Chai, Ryan J. Farris, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, Terry L. Marsh
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. 141-145 - Yongliang Ren, Wuming Gong, Haiyan Zhou, Yejun Wang, Feifei Xiao, Tongbin Li:
siRecords: a database of mammalian RNAi experiments and efficacies. 146-149 - Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. 150-154 - Giorgos L. Papadopoulos
The database of experimentally supported targets: a functional update of TarBase. 155-158 - Frank Jühling, Mario Mörl
tRNAdb 2009: compilation of tRNA sequences and tRNA genes. 159-162 - Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi:
tRNADB-CE: tRNA gene database curated manually by experts. 163-168 - The Universal Protein Resource (UniProt) 2009. 169-174
- Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez
CentrosomeDB: a human centrosomal proteins database. 175-180 - Yasmeen Ahmad, François-Michel Boisvert
NOPdb: Nucleolar Proteome Database - 2008 update. 181-184 - Sanguthevar Rajasekaran, Sudha Balla, Patrick Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, Martin R. Schiller
Minimotif miner 2nd release: a database and web system for motif search. 185-190 - Jason E. Donald, Eugene I. Shakhnovich:
SDR: a database of predicted specificity-determining residues in proteins. 191-194 - Raphael André Bauer, Stefan Günther, Dominic Jansen, Carolin Heeger, Paul Florian Thaben, Robert Preissner
SuperSite: dictionary of metabolite and drug binding sites in proteins. 195-200 - M. Michael Gromiha, Yukimitsu Yabuki, M. Xavier Suresh
TMFunction: database for functional residues in membrane proteins. 201-204 - Aron Marchler-Bauer
CDD: specific functional annotation with the Conserved Domain Database. 205-210 - Sarah Hunter
InterPro: the integrative protein signature database. 211-215 - William Klimke, Richa Agarwala
The National Center for Biotechnology Information's Protein Clusters Database. 216-223 - Abraham O. Samson, Michael Levitt:
Protein segment finder: an online search engine for segment motifs in the PDB. 224-228 - Ivica Letunic
SMART 6: recent updates and new developments. 229-232 - Brandi L. Cantarel, Pedro M. Coutinho, Corinne Rancurel
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. 233-238 - Víctor Quesada
The Degradome database: mammalian proteases and diseases of proteolysis. 239-243 - David M. A. Martin
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. 244-250 - Chuan-Yun Li, Qing-Rong Liu
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. 251-260 - Dominique Koua, Lorenzo Cerutti, Laurent Falquet
PeroxiBase: a database with new tools for peroxidase family classification. 261-266 - Guohui Ding, Peter Lorenz
SysZNF: the C2H2 zinc finger gene database. 267-273 - Milton H. Saier Jr., Ming Ren Yen, Keith Noto, Dorjee G. Tamang, Charles Elkan:
The Transporter Classification Database: recent advances. 274-278 - Fengli Fu, Jeffry D. Sander, Morgan L. Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. 279-283 - Joel Masciocchi, Gianfranco Frau, Marco Fanton, Mattia Sturlese
MMsINC: a large-scale chemoinformatics database. 284-290 - Mathias Dunkel
SuperScent - a database of flavors and scents. 291-294 - Ulrike Schmidt, Swantje Struck, Björn A. Grüning
SuperToxic: a comprehensive database of toxic compounds. 295-299 - Amelie Stein
3did Update: domain-domain and peptide-mediated interactions of known 3D structure. 300-304 - Masafumi Shionyu
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. 305-309 - Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Oliver Redfern
The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies. 310-314 - Oliver D. Testa, Efrosini Moutevelis, Derek N. Woolfson
CC+: a relational database of coiled-coil structures. 315-322 - Ofir Goldenberg, Elana Erez, Guy Nimrod, Nir Ben-Tal
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. 323-327 - Wei-Cheng Lo
CPDB: a database of circular permutation in proteins. 328-332 - Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, Ken Nishikawa:
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. 333-337 - Stefan Günther, Joachim von Eichborn, Patrick May
JAIL: a structure-based interface library for macromolecules. 338-341 - Natalya S. Bogatyreva
KineticDB: a database of protein folding kinetics. 342-346 - Ursula Pieper
MODBASE, a database of annotated comparative protein structure models and associated resources. 347-354 - Roman A. Laskowski
PDBsum new things. 355-359 - Miho Higurashi, Takashi Ishida
PiSite: a database of protein interaction sites using multiple binding states in the PDB. 360-364 - Helen M. Berman
The protein structure initiative structural genomics knowledgebase. 365-368 - Alexandra Shulman-Peleg, Ruth Nussinov
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. 369-373 - Mathieu Lonquety, Zoé Lacroix, Nikolaos Papandreou, Jacques Chomilier
SPROUTS: a database for the evaluation of protein stability upon point mutation. 374-379 - Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus Chothia, Julian Gough:
SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny. 380-386 - Florian Kiefer, Konstantin Arnold, Michael Künzli, Lorenza Bordoli, Torsten Schwede
The SWISS-MODEL Repository and associated resources. 387-392 - Kristian Rother, Peter Werner Hildebrand, Andrean Goede
Voronoia: analyzing packing in protein structures. 393-395 - Daniel Barrell
The GOA database in 2009 - an integrated Gene Ontology Annotation resource. 396-403 - Estelle Proux-Wéra
Selectome: a database of positive selection. 404-407 - Mathias C. Walter
PEDANT covers all complete RefSeq genomes. 408-411 - Lars Juhl Jensen
STRING 8 - a global view on proteins and their functional interactions in 630 organisms. 412-416 - William Fu, Brigitte E. Sanders-Beer, Kenneth S. Katz, Donna R. Maglott, Kim D. Pruitt
Human immunodeficiency virus type 1, human protein interaction database at NCBI. 417-422 - In Seok Yang, Joo-Yeon Lee, Joon Seung Lee, Wayne P. Mitchell, Hee-Bok Oh, Chun Kang, Kyung Hyun Kim:
Influenza sequence and epitope database. 423-430 - Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, Andrew Rambaut
The RNA Virus Database. 431-435 - Mauricio Carrillo-Tripp
VIPERdb2: an enhanced and web API enabled relational database for structural virology. 436-442 - Bo Liu, Mihai Pop
ARDB - Antibiotic Resistance Genes Database. 443-447 - Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. 448-454 - Ren Zhang, Yan Lin
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. 455-458 - Fenglou Mao, PhuongAn Dam, Jacky Chou, Victor Olman, Ying Xu:
DOOR: a database for prokaryotic operons. 459-463 - Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides
EcoCyc: A comprehensive view of Escherichia coli biology. 464-470 - Tania Lima, Andrea H. Auchincloss
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. 471-478 - Mihaela Pertea
OperonDB: a comprehensive database of predicted operons in microbial genomes. 479-482 - Geoffrey L. Winsor
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. 483-488 - Zarraz May-Ping Lee, Carl Bussema III, Thomas M. Schmidt
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. 489-493 - Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR). 494-498 - T. B. K. Reddy, Robert Riley
TB database: an integrated platform for tuberculosis research. 499-508 - Jane E. Mabey Gilsenan, Graham Atherton
Aspergillus Genomes and the Aspergillus Cloud. 509-514 - Petra Fey
dictyBase - a Dictyostelium bioinformatics resource update. 515-519 - Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. 520-525 - Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. 526-530 - John W. Whitaker
metaTIGER: a metabolic evolution resource. 531-538 - Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant
PlasmoDB: a functional genomic database for malaria parasites. 539-543 - Alejandro A. Ackermann, Santiago J. Carmona
TcSNP: a database of genetic variation in Trypanosoma cruzi. 544-549 - David James Sherman
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. 550-554 - Susan Tweedie
FlyBase: enhancing Drosophila Gene Ontology annotations. 555-559 - Andrei Pisarev
FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. 560-566 - Doris Chen, Jürg Berger, Michaela Fellner, Takashi Suzuki
FLYSNPdb: a high-density SNP database of Drosophila melanogaster. 567-570 - John C. Martin, Sahar Abubucker, Todd Wylie, Yong Yin, Zhengyuan Wang, Makedonka Dautova Mitreva
Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. 571-578 - Adhemar Zerlotini, Mark Heiges, Haiming Wang, Romulo L. V. Moraes, Anderson J. Dominitini, Jerônimo C. Ruiz, Jessica C. Kissinger
SchistoDB: a Schistosoma mansoni genome resource. 579-582 - Daniel Lawson
VectorBase: a data resource for invertebrate vector genomics. 583-587 - Antje Chang, Maurice Scheer, Andreas Grote, Ida Schomburg, Dietmar Schomburg
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. 588-592 - Andrew G. McDonald
ExplorEnz: the primary source of the IUBMB enzyme list. 593-597 - Guillermo Carbajosa
Bionemo: molecular information on biodegradation metabolism. 598-602 - David S. Wishart
HMDB: a knowledgebase for the human metabolome. 603-610 - Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar
PMAP: databases for analyzing proteolytic events and pathways. 611-618 - Lisa Matthews
Reactome knowledgebase of human biological pathways and processes. 619-622 - Atanas Kamburov
ConsensusPathDB - a database for integrating human functional interaction networks. 623-628 - Eduardo Andrés León
EcID. A database for the inference of functional interactions in E. coli. 629-635 - Pankaj Kumar, Bu-Cong Han, Z. Shi, Jia Jia, Yupeng Wang
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. 636-641 - V. Glenn Tarcea, Terry E. Weymouth, Alexander S. Ade, Aaron V. Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür
Michigan molecular interactions r2: from interacting proteins to pathways. 642-646 - Tim Driscoll
PIG - the pathogen interaction gateway. 647-650 - Mark D. McDowall
PIPs: human protein-protein interaction prediction database. 651-656 - Gautam Chaurasia, Soniya Malhotra, Jenny Russ
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. 657-660 - Vincent Navratil
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. 661-668 - Andrew Chatr-aryamontri, Arnaud Céol
VirusMINT: a viral protein interaction database. 669-673 - Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, Kenneth H. Buetow:
PID: the Pathway Interaction Database. 674-679 - Anthony J. Harmar
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. 680-685 - Byungwook Lee, Gwangsik Shin:
CleanEST: a database of cleansed EST libraries. 686-689 - Tim J. P. Hubbard, Bronwen L. Aken
Ensembl 2009. 690-697 - Dae-Soo Kim, Chi-Young Cho, Jae-Won Huh, Heui-Soo Kim
EVOG: a database for evolutionary analysis of overlapping genes. 698-702 - Ashwini Bhasi, Philge Philip, Vinu Manikandan, Periannan Senapathy:
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. 703-711 - Judith A. Blake
The Mouse Genome Database genotypes: : phenotypes. 712-719 - Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult, Molly A. Bogue:
Mouse Phenome Database. 720-730 - Tim Hulsen
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. 731-737 - Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein:
Pseudofam: the pseudogene families database. 738-743 - Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor
The Rat Genome Database 2009: variation, ontologies and pathways. 744-749 - R. Andrew Cameron
SpBase: the sea urchin genome database and web site. 750-754 - Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Ting Wang, Kayla E. Smith, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Belinda Giardine, Pauline A. Fujita, Mark Diekhans
The UCSC Genome Browser Database: update 2009. 755-761 - Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, Nobuo Nomura:
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. 762-766 - T. S. Keshava Prasad
Human Protein Reference Database - 2009 update. 767-772 - Kumaran Kandasamy, Shivakumar Keerthikumar
Human Proteinpedia: a unified discovery resource for proteomics research. 773-781 - Nobutaka Mitsuhashi
BodyParts3D: 3D structure database for anatomical concepts. 782-785 - Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. 786-792 - Joanna S. Amberger, Carol A. Bocchini, Alan F. Scott, Ada Hamosh:
McKusick's Online Mendelian Inheritance in Man (OMIM®). 793-796 - Gudmundur A. Thorisson
HGVbaseG2P: a central genetic association database. 797-802 - Alexander R. Pico
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. 803-809 - Makoto K. Shimada
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. 810-815 - Luiz Gonzaga Almeida, Noboru J. Sakabe, Alice R. de Oliveira, Maria Cristina C. Silva, Alex S. Mundstein, Tzeela Cohen, Yao-Tseng Chen, Ramon Chua, Sita Gurung, Sacha Gnjatic
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. 816-819 - Mandeep Kaur
Database for exploration of functional context of genes implicated in ovarian cancer. 820-823 - Christopher J. Richardson, Qiong Gao
MoKCa database - mutations of kinases in cancer. 824-831 - Saumyendra N. Basu, Ravi Kollu, Sharmila Banerjee-Basu:
AutDB: a gene reference resource for autism research. 832-836 - Sue Cotterill, Stephen E. Kearsey:
DNAReplication: a database of information and resources for the eukaryotic DNA replication community. 837-839 - An-Yuan Guo, Bradley Todd Webb
ERGR: An ethanol-related gene resource. 840-845 - Michael D. R. Croning, Michael C. Marshall, Peter McLaren, J. Douglas Armstrong
G2Cdb: the Genes to Cognition database. 846-851 - Shamith A. Samarajiwa
INTERFEROME: the database of interferon regulated genes. 852-857 - Suisheng Tang, Zhuo Zhang, Kavitha Gopalakrishnan, Eng-King Tan, See-Kiong Ng:
MDPD: an integrated genetic information resource for Parkinson's disease. 858-862 - Shivakumar Keerthikumar
RAPID: Resource of Asian Primary Immunodeficiency Diseases. 863-867 - Helen E. Parkinson
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. 868-872 - Diego Miranda-Saavedra, Subhajyoti De, Matthew W. B. Trotter
BloodExpress: a database of gene expression in mouse haematopoiesis. 873-879 - Viviane Praz, Philipp Bucher:
CleanEx: new data extraction and merging tools based on MeSH term annotation. 880-884 - Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Rolf N. Muertter, Ron Edgar
NCBI GEO: archive for high-throughput functional genomic data. 885-890 - Tin-Lap Lee
GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development. 891-897 - Jeremy Hubble, Janos Demeter
Implementation of GenePattern within the Stanford Microarray Database. 898-901 - Florian Gnad
MAPU 2.0: high-accuracy proteomes mapped to genomes. 902-906 - Su-Jun Li, Mao Peng
Sys-BodyFluid: a systematical database for human body fluid proteome research. 907-912 - Hong Xi, Jongsun Park
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. 913-920 - Mounir Errami, Zhaohui Sun, Tara C. Long, Angela C. George, Harold R. Garner:
Déjà vu: a database of highly similar citations in the scientific literature. 921-924 - Paolo Romano
Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines. 925-932 - Guangshun Wang, Xia Li, Zhe Wang:
APD2: the updated antimicrobial peptide database and its application in peptide design. 933-937 - Jean-Marie Rouillard, Erdogan Gulari:
OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. 938-941 - Steve Lefever, Jo Vandesompele
RTPrimerDB: the portal for real-time PCR primers and probes. 942-945 - Emmet A. O'Brien, Yue Zhang, Eric Wang, Veronique Marie, Wole Badejoko, B. Franz Lang, Gertraud Burger:
GOBASE: an organelle genome database. 946-950 - Chris Duran, Nikki Appleby, Terry Clark, David Wood, Michael Imelfort, Jacqueline Batley
AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. 951-953 - Diego Mauricio Riaño-Pachón
GabiPD: the GABI primary database - a plant integrative 'omics' database. 954-959 - Jianjiong Gao
P3DB: a plant protein phosphorylation database. 960-962 - Riadh Hammami
PhytAMP: a database dedicated to antimicrobial plant peptides. 963-968 - Qi Sun, Boris L. Zybailov
PPDB, the Plant Proteomics Database at Cornell. 969-974 - Zhiyu Peng
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. 975-982 - Lorenz Bülow, Stefan Engelmann, Martin Schindler, Reinhard Hehl
AthaMap, integrating transcriptional and post-transcriptional data. 983-986 - Takeshi Obayashi, Shinpei Hayashi
ATTED-II provides coexpressed gene networks for Arabidopsis. 987-991 - Gaëtan Droc
OryGenesDB 2008 update: database interoperability for functional genomics of rice. 992-995 - Supat Thongjuea
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. 996-1000 - Uma Maheswari
Update of the Diatom EST Database: a new tool for digital transcriptomics. 1001-1005 - Marie-Paule Lefranc
IMGT®, the international ImMunoGeneTics information system®. 1006-1012 - James Robinson
The IMGT/HLA database. 1013-1017 - Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert Strausberg, Marvin Frazier, J. Craig Venter, Saul Kravitz, Samuel Levy:
The HuRef Browser: a web resource for individual human genomics. 1018-1024 - Guoqing Li, Lijia Ma, Chao Song, Zhentao Yang
The YH database: the first Asian diploid genome database. 1025-1028
Volume 37, Number Web-Server-Issue, July 2009
- Gary Benson:
Nucleic Acids Research annual Web Server Issue in 2009. 1-2
- Michelle D. Brazas
Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory. 3-5 - Hamish McWilliam
Web services at the European Bioinformatics Institute-2009. 6-10 - Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara:
Web API for biology with a workflow navigation system. 11-16 - Tadashi Imanishi
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. 17-22 - Syed Haider, Benoît Ballester
BioMart Central Portal - unified access to biological data. 23-27 - Jeff Elhai, Arnaud Taton, J. P. Massar, John K. Myers, Michael Travers, Johnny Casey, Mark Slupesky, Jeff Shrager:
BioBIKE: A Web-based, programmable, integrated biological knowledge base. 28-32 - Xiao-Qiao Liu, Jianmin Wu
WebLab: a data-centric, knowledge-sharing bioinformatic platform. 33-39 - Michael J. Czar, Yizhi Cai
Writing DNA with GenoCADTM. 40-47 - Bernd W. Brandt
webPRC: the Profile Comparer for alignment-based searching of public domain databases. 48-52 - Marianne M. Lee, Michael K. Chan
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches. 53-56 - Akihiro Matsushima, Norio Kobayashi, Yoshiki Mochizuki, Manabu Ishii, Shuji Kawaguchi, Takaho A. Endo, Ryo Umetsu, Yuko Makita
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. 57-62 - Fiona Achcar
AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology. 63-67 - Michael Hackenberg
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. 68-76 - Chun Liang, Lin Liu, Guoli Ji:
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. 77-83 - Ruchira S. Datta
Berkeley PHOG: PhyloFacts orthology group prediction web server. 84-89 - Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. 90-94 - Bruno Contreras-Moreira
primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. 95-100 - Katharina Jasmin Hoff
Orphelia: predicting genes in metagenomic sequencing reads. 101-105 - Sharon Bruckner, Falk Hüffner
Torque: topology-free querying of protein interaction networks. 106-108 - Pablo Minguez
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. 109-114 - Zhenjun Hu, Jui-Hung Hung
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. 115-121 - Hagen Blankenburg
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. 122-128 - Chih-Hung Chou
FMM: a web server for metabolic pathway reconstruction and comparative analysis. 129-134 - Matthias Frisch, Bernward Klocke, Manuela Haltmeier, Kornelie Frech:
LitInspector: literature and signal transduction pathway mining in PubMed abstracts. 135-140 - Jean-Fred Fontaine, Adriano Barbosa-Silva
MedlineRanker: flexible ranking of biomedical literature. 141-146 - Yuko Yoshida, Yuko Makita
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. 147-152 - Miguel Vázquez
SENT: semantic features in text. 153-159 - Martin Krallinger
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. 160-165 - Takeru Nakazato
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. 166-169 - Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Daniel L. Rubin, Margaret-Anne D. Storey, Christopher G. Chute, Mark A. Musen
BioPortal: ontologies and integrated data resources at the click of a mouse. 170-173 - Zhao Xu, Bailin Hao:
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. 174-178 - Jorn Bruggeman
PhyloPars: estimation of missing parameter values using phylogeny. 179-184 - Fabian Schreiber
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences. 185-188 - Schraga Schwartz
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. 189-192 - Deepak Sharma, Debasisa Mohanty
RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. 193-201 - Timothy L. Bailey, Mikael Bodén
MEME SUITE: tools for motif discovery and searching. 202-208 - Robin Boutros, Nicola Stokes, Michaël Bekaert
UniPrime2: a web service providing easier Universal Primer design. 209-213 - Marcus Bode, Samuel Khor, Hongye Ye, Mo-Huang Li, Jackie Y. Ying
TmPrime: fast, flexible oligonucleotide design software for gene synthesis. 214-221 - Richard D. Boyce, Parmit K. Chilana, Timothy M. Rose:
iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. 222-228 - Adam M. Phillippy
Insignia: a DNA signature search web server for diagnostic assay development. 229-234 - Marc van Dijk
3D-DART: a DNA structure modelling server. 235-239 - Guohui Zheng, Xiang-Jun Lu
Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. 240-246 - Federico Zambelli
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. 247-252 - Jeffrey P. Mower
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. 253-259 - Emidio Capriotti
SARA: a server for function annotation of RNA structures. 260-265 - Jean Hausser
MirZ: an integrated microRNA expression atlas and target prediction resource. 266-272 - Manolis Maragkakis
DIANA-microT web server: elucidating microRNA functions through target prediction. 273-276 - Kengo Sato
CENTROIDFOLD: a web server for RNA secondary structure prediction. 277-280 - Jérôme Waldispühl
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. 281-286 - Chin-En Lai, Ming-Yuan Tsai, Yun-Chen Liu, Chih-Wei Wang, Kun-Tze Chen, Chin Lung Lu:
FASTR3D: a fast and accurate search tool for similar RNA 3D structures. 287-295 - Alexandre Gattiker, Christophe Dessimoz
The Microbe browser for comparative genomics. 296-299 - Conrad Plake, Loïc Royer
GoGene: gene annotation in the fast lane. 300-304 - Jing Chen
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. 305-311 - Gabriele Beate Schweikert, Jonas Behr, Alexander Zien, Georg Zeller
mGene.web: a web service for accurate computational gene finding. 312-316 - Rubén Nogales-Cadenas, Pedro Carmona-Saez
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. 317-322 - Alexey V. Antonov, Sabine Dietmann
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists. 323-328 - Daniel Glez-Peña
WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis. 329-334 - Nicolas Goffard, Tancred Frickey, Georg Weiller:
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. 335-339 - Ignacio Medina
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. 340-344 - Zhidian Du, Lin Li, Chin-Fu Chen, Philip S. Yu, James Z. Wang:
G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. 345-349 - Choong-Hyun Sun, Min-Sung Kim, Youngwoong Han, Gwan-Su Yi:
COFECO: composite function annotation enriched by protein complex data. 350-355 - Seungyoon Nam
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. 356-362 - Guy Naamati
ClanTox: a classifier of short animal toxins. 363-368 - Chun-Chen Chen, Chun-Yu Lin
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. 369-375 - Antonín Pavelka, Eva Chovancová, Jirí Damborský
HotSpot Wizard: a web server for identification of hot spots in protein engineering. 376-383 - Yan Yuan Tseng, Craig Dupree, Z. Jeffrey Chen, Wen-Hsiung Li
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. 384-389 - Sriram Sankararaman, Bryan Kolaczkowski, Kimmen Sjölander:
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. 390-395 - Wen-Yi Chu, Yu-Feng Huang
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. 396-401 - Wijnand T. M. Mooij, Eirini Mitsiki, Anastassis Perrakis
ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments. 402-405 - Lun Yang, Heng Luo
SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome. 406-412 - Marylens Hernandez, Dario Ghersi, Roberto Sanchez:
SITEHOUND-web: a server for ligand binding site identification in protein structures. 413-416 - Duangdao Wichadakul
d-Omix: a mixer of generic protein domain analysis tools. 417-421 - Alexander A. Kantardjiev, Boris P. Atanasov:
PHEMTO: protein pH-dependent electric moment tools. 422-427 - Arnold Kuzniar
ProGMap: an integrated annotation resource for protein orthology. 428-434 - Hong Sain Ooi, Chia Yee Kwoh, Michael Wildpaner, Fernanda L. Sirota
ANNIE: integrated de novo protein sequence annotation. 435-440 - Regina Z. Cer, Uma Mudunuri, Robert M. Stephens, Frank J. Lebeda:
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. 441-445 - Michael Remmert, Dirk Linke
HHomp - prediction and classification of outer membrane proteins. 446-451 - Smriti Shridhar, Debasis Chattopadhyay, Gitanjali Yadav
PLecDom: a program for identification and analysis of plant lectin domains. 452-458 - Gaëlle Debret, Arnaud Martel, Philippe Cuniasse:
RASMOT-3D PRO: a 3D motif search webserver. 459-464 - Andreas Bernsel, Håkan Viklund, Aron Hennerdal, Arne Elofsson
TOPCONS: consensus prediction of membrane protein topology. 465-468 - Changsik Kim, Jiwon Choi, Seong Joon Lee, William J. Welsh, Sukjoon Yoon:
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation. 469-473 - Aroop Sircar, Eric T. Kim, Jeffrey J. Gray
RosettaAntibody: antibody variable region homology modeling server. 474-479 - Thomas Margraf, Gundolf Schenk, Andrew E. Torda:
The SALAMI protein structure search server. 480-484 - Jean-Luc Pons, Gilles Labesse
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes. 485-491 - Kevin Karplus:
SAM-T08, HMM-based protein structure prediction. 492-497 - Julien Maupetit
PEP-FOLD: an online resource for de novo peptide structure prediction. 498-503 - Olivier Sperandio
wwLigCSRre: a 3D ligand-based server for hit identification and optimization. 504-509 - Pascal Benkert
QMEAN server for protein model quality estimation. 510-514 - Allison N. Tegge, Zheng Wang, Jesse Eickholt, Jianlin Cheng
NNcon: improved protein contact map prediction using 2D-recursive neural networks. 515-518 - Weerayuth Kittichotirat
Protinfo PPC: A web server for atomic level prediction of protein complexes. 519-525 - Shuoyong Shi, Bhadrachalam Chitturi, Nick V. Grishin:
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. 526-531 - Bong-Hyun Kim, Hua Cheng, Nick V. Grishin:
HorA web server to infer homology between proteins using sequence and structural similarity. 532-538 - Stefan J. Suhrer, Markus Wiederstein
COPS - a novel workbench for explorations in fold space. 539-544 - Wei-Cheng Lo
iSARST: an integrated SARST web server for rapid protein structural similarity searches. 545-551 - Darby Tien-Hao Chang, Ting-Ying Chien, Chien-Yu Chen
seeMotif: exploring and visualizing sequence motifs in 3D structures. 552-558 - Po-Hsien Lee, Kuei-Ling Kuo, Pei-Ying Chu, Eric Minwei Liu
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters. 559-564 - Stefano Angaran, Mary Ellen Bock, Claudio Garutti, Concettina Guerra:
MolLoc: a web tool for the local structural alignment of molecular surfaces. 565-570 - Peter Werner Hildebrand, Andrean Goede
SuperLooper - a prediction server for the modeling of loops in globular and membrane proteins. 571-574 - Alexander S. Rose
RHYTHM - a server to predict the orientation of transmembrane helices in channels and membrane-coils. 575-580 - Edward R. Morrissey
Pomelo II: finding differentially expressed genes. 581-586 - Darya Krushevskaya, Hedi Peterson
VisHiC - hierarchical functional enrichment analysis of microarray data. 587-592 - Dominik Seelow
HomozygosityMapper - an interactive approach to homozygosity mapping. 593-599 - Zongli Xu
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. 600-605 - Lee S. Katz
Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data. 606-611 - Jing Sun, Di Wu, Tianlei Xu, Xiaojing Wang, Xiaolian Xu, Lin Tao
SEPPA: a computational server for spatial epitope prediction of protein antigens. 612-616 - Nora C. Toussaint
OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines. 617-622 - Yanli Wang, Jewen Xiao, Tugba O. Suzek
PubChem: a public information system for analyzing bioactivities of small molecules. 623-633 - Luiz Carlos Júnior Alcântara, Sharon Cassol, Pieter Libin
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. 634-642 - Yu-Chieh Liao
ATIVS: analytical tool for influenza virus surveillance. 643-646 - Anne-Kathrin Schultz
jpHMM: Improving the reliability of recombination prediction in HIV-1. 647-651 - Jianguo Xia
MetaboAnalyst: a web server for metabolomic data analysis and interpretation. 652-660 - Chih-Chiang Tsou
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS. 661-669 - Mark V. Berjanskii, Peter Tang, Jack Liang, Joseph A. Cruz, Jianjun Zhou, You Zhou, Edward Bassett, Cam Macdonell, Paul Lu, Guohui Lin, David S. Wishart
GeNMR: a web server for rapid NMR-based protein structure determination. 670-677
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-12-31 21:34 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by: