PaLS: filtering common literature, biological terms and pathway information (English)
- New search for: Alibés, Andreu
- New search for: Alibés, Andreu
- New search for: Cañada, Andrés
- New search for: Díaz-Uriarte, Ramón
In:
Nucleic acids research
;
36
, 2
; W364
;
2008
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ISSN:
- Article (Journal) / Print
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Title:PaLS: filtering common literature, biological terms and pathway information
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Contributors:
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Published in:Nucleic acids research ; 36, 2 ; W364
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Publisher:
- New search for: Oxford Univ. Press
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Place of publication:Oxford
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Publication date:2008
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ISSN:
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ZDBID:
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Type of media:Article (Journal)
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Type of material:Print
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Language:English
- New search for: 35.75
- Further information on Basic classification
- New search for: 275/3820
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Keywords:
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Classification:
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Source:
Table of contents – Volume 36, Issue 2
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 353
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Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiaeHolbein, S. / Freimoser, F. M. / Werner, T. P. / Wengi, A. / Dichtl, B. et al. | 2008
- 364
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Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coliMohanty, B. K. / Kushner, S. R. et al. | 2008
- 376
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Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformationAraú / zo-Bravo, M. J. / Sarai, A. et al. | 2008
- 387
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Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyteSindelka, R. / Joná / k, J. / Hands, R. / Bustin, S. A. / Kubista, M. et al. | 2008
- 393
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The N-terminal domain of TWINKLE contributes to single-stranded DNA binding and DNA helicase activitiesFarge, G. x. / Holmlund, T. / Khvorostova, J. / Rofougaran, R. / Hofer, A. / Falkenberg, M. et al. | 2008
- 404
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DNA tape measurements of AraCRodgers, M. E. / Schleif, R. et al. | 2008
- 411
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The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficientDalal, S. / Chikova, A. / Jaeger, J. / Sweasy, J. B. et al. | 2008
- 423
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Transcription of Satellite III non-coding RNAs is a general stress response in human cellsValgardsdottir, R. / Chiodi, I. / Giordano, M. / Rossi, A. / Bazzini, S. / Ghigna, C. / Riva, S. / Biamonti, G. et al. | 2008
- 435
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Retinoic acid modulates chromatin to potentiate tumor necrosis factor alpha signaling on the DIF2 promoterWitcher, M. / Pettersson, F. / Dupé / ré / Padovani, A. / Summers-Deluca, L. / Baldwin, A. S. / Miller, W. H. et al. | 2008
- 444
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Structure of discontinuities in kinetoplast DNA-associated minicircles during S phase in Crithidia fasciculataHines, J. C. / Ray, D. S. et al. | 2008
- 451
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Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatasesSouliè / re, M. F. / Perreault, J. P. / Bisaillon, M. et al. | 2008
- 462
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Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/β-catenin signalingAmen, M. / Espinoza, H. M. / Cox, C. / Liang, X. / Wang, J. / Link, T. M. / Brennan, R. G. / Martin, J. F. / Amendt, B. A. et al. | 2008
- 477
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The formation pathway of tetramolecular G-quadruplexesBardin, C. / Leroy, J. L. et al. | 2008
- 489
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Repair of DNA double-strand breaks within the (GAA•TTC)n sequence results in frequent deletion of the triplet-repeat sequencePollard, L. M. / Bourn, R. L. / Bidichandani, S. I. et al. | 2008
- 501
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Interplay of ion binding and attraction in DNA condensed by multivalent cationsTodd, B. A. / Rau, D. C. et al. | 2008
- 511
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ATR-dependent pathways control hEXO1 stability in response to stalled forksEl-Shemerly, M. / Hess, D. / Pyakurel, A. K. / Moselhy, S. / Ferrari, S. et al. | 2008
- 520
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Mechanisms of covalent self-assembly of the Azoarcus ribozyme from four fragment oligonucleotidesDraper, W. E. / Hayden, E. J. / Lehman, N. et al. | 2008
- 532
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The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein ANolan, T. / Cecere, G. / Mancone, C. / Alonzi, T. / Tripodi, M. / Catalanotto, C. / Cogoni, C. et al. | 2008
- 539
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The dual control of TFIIB recruitment by NC2 is gene specificMasson, P. / Leimgruber, E. / Creton, S. / Collart, M. A. et al. | 2008
- 550
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Alternative splicing and protein structure evolutionBirzele, F. / Csaba, G. / Zimmer, R. et al. | 2008
- 559
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Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotidesTang, X. / Swaminathan, J. / Gewirtz, A. M. / Dmochowski, I. J. et al. | 2008
- 570
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Nε-Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin functionWiś / niewski, J. R. / Zougman, A. / Mann, M. et al. | 2008
- 578
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Identifying foldable regions in protein sequence from the hydrophobic signalPang, C. N. / Lin, K. / Wouters, M. A. / Heringa, J. / George, R. A. et al. | 2008
- 589
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The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mtHaque, M. E. / Grasso, D. / Spremulli, L. L. et al. | 2008
- 598
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Overlapping activator sequences determined for two oppositely oriented promoters in halophilic ArchaeaBauer, M. / Marschaus, L. / Reuff, M. / Besche, V. / Sartorius-Neef, S. / Pfeifer, F. et al. | 2008
- 607
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Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParRHoischen, C. / Bussiek, M. / Langowski, J. / Diekmann, S. et al. | 2008
- 616
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Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPsKatahira, J. / Miki, T. / Takano, K. / Maruhashi, M. / Uchikawa, M. / Tachibana, T. / Yoneda, Y. et al. | 2008
- 629
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The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferasesLeulliot, N. / Bohnsack, M. T. / Graille, M. / Tollervey, D. / Van Tilbeurgh, H. et al. | 2008
- 640
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Efficient siRNA selection using hybridization thermodynamicsLu, Z. J. / Mathews, D. H. et al. | 2008
- 648
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Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cellsKirilyuk, A. / Tolstonog, G. V. / Damert, A. / Held, U. / Hahn, S. / Lö / wer, R. / Buschmann, C. / Horn, A. V. / Traub, P. et al. | 2008
- 666
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Epstein–Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5Barth, S. / Pfuhl, T. / Mamiani, A. / Ehses, C. / Roemer, K. / Kremmer, E. / Jä / ker, C. / Hö / ck, J. et al. | 2008
- 676
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Structure–function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacementNaji, S. / Bertero, M. G. / Spitalny, P. / Cramer, P. / Thomm, M. et al. | 2008
- 688
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DNA polymerase kappa produces interrupted mutations and displays polar pausing within mononucleotide microsatellite sequencesHile, S. E. / Eckert, K. A. et al. | 2008
- 697
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Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivativesKawamoto, S. A. / Sudhahar, C. G. / Hatfield, C. L. / Sun, J. / Behrman, E. J. / Gopalan, V. et al. | 2008
- e10
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Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assaysPetersen, J. / Poulsen, L. / Petronis, S. / Birgens, H. / Dufva, M. et al. | 2008
- e11
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Model-based variance-stabilizing transformation for Illumina microarray dataLin, S. M. / Du, P. / Huber, W. / Kibbe, W. A. et al. | 2008
- e12
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Gene Ontology annotation quality analysis in model eukaryotesBuza, T. J. / McCarthy, F. M. / Wang, N. / Bridges, S. M. / Burgess, S. C. et al. | 2008
- e13
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Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH dataKlijn, C. / Holstege, H. / de Ridder, J. / Liu, X. / Reinders, M. / Jonkers, J. / Wessels, L. et al. | 2008
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RAPIDO: a web server for the alignment of protein structures in the presence of conformational changesMosca, Roberto et al. | 2008
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QUMA: quantification tool for methylation analysisKumaki, Yuichi et al. | 2008
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The RosettaDock server for local protein-protein dockingLyskov, Sergey et al. | 2008
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FFPred: an integrated feature-based function prediction server for vertebrate proteomesLobley, A.E. et al. | 2008
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GEPAS, a web-based tool for microarray data analysis and interpretationTárraga, Joaquín et al. | 2008
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MAGNOLIA: multiple alignment of protein-coding and structural RNA sequencesFontaine, Arnaud et al. | 2008
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FireDock: a web server for fast interaction refinement in molecular dockingMashiach, Efrat et al. | 2008
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DAhunter: a web-based server that identifies homologous proteins by comparing domain architectureLee, Byungwook et al. | 2008
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HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structuresFukuhara, Naoshi et al. | 2008
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Immune epitope database analysis resource (IEDB-AR)Zhang, Qing et al. | 2008
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SerbGO: searching for the best GO toolMosquera, J.L. et al. | 2008
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Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organismsOehm, Sebastian et al. | 2008
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The Vienna RNA WebsuiteGruber, Andreas R. et al. | 2008
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SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browserWalsh, Thomas P. et al. | 2008
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WAR: Webserver for aligning structural RNAsTorarinsson, Elfar et al. | 2008
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AMIC@: All MIcroarray Clusterings @ onceGeraci, Filippo et al. | 2008
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E1DS: catalytic site prediction based on 1D signatures of concurrent conservationChien, Ting-Ying et al. | 2008
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IMGT-V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysisBrochet, Xavier et al. | 2008
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PharmaGist: a webserver for ligand-based pharmacophore detectionSchneidman-Duhovny, Dina et al. | 2008
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bioNMF: a web-based tool for nonnegative matrix factorization in biologyMejía-Roa, E. et al. | 2008
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PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discoveryGarcia-Boronat, Maria et al. | 2008
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Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sitesEgea, Raquel et al. | 2008
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NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathwaysBrohée, Sylvain et al. | 2008
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GraphWeb: mining heterogeneous biological networks for gene modules with functional significanceReimand, Jüri et al. | 2008
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The CGView Server: a comparative genomics tool for circular genomesGrant, Jason R. et al. | 2008
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AsiDesigner: exon-based siRNA design server considering alternative splicingPark, Young-Kyu et al. | 2008
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TargetRNA: a tool for predicting targets of small RNA action in bacteriaTjaden, Brian et al. | 2008
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PIE: an online prediction system for protein-protein interactions from textKim, Sun et al. | 2008
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OligoWalk: an online siRNA design tool utilizing hybridization thermodynamicsLu, Zhi John et al. | 2008
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DiRE: identifying distant regulatory elements of co-expressed genesGotea, Valer et al. | 2008
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PROMALS3D web server for accurate multiple protein sequence and structure alignmentsPei, Jimin et al. | 2008
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KFC Server: interactive forecasting of protein interaction hot spotsDarnell, Steven J. et al. | 2008
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MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactionsShulman-Peleg, Alexandra et al. | 2008
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ISPIDER Central: an integrated database web-server for proteomicsSiepen, Jennifer A. et al. | 2008
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The Jpred 3 secondary structure prediction serverCole, Christian et al. | 2008
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Superimpose: a 3D structural superposition serverBauer, Raphael A. et al. | 2008
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ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across speciesHooghe, Bart et al. | 2008
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SARSA: a web tool for structural alignment of RNA using a structural alphabetChang, Yen-Fu et al. | 2008
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LocalMove: computing on-lattice fits for biopolymersPonty, Y. et al. | 2008
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BioLit: integrating biological literature with databasesFink, J.Lynn et al. | 2008
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The University of Minnesota pathway prediction system: predicting metabolic logicEllis, Lynda B.M. et al. | 2008
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NCBI BLAST: a better web interfaceJohnson, Mark et al. | 2008
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GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized librariesFirth, Andrew E. et al. | 2008
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RSAT: regulatory sequence analysis toolsThomas-Chollier, Morgane et al. | 2008
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The Predikin webserver: improved prediction of protein kinase peptide specificity using structural informationSaunders, Neil F.W. et al. | 2008
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OGtree: a tool for creating genome trees of prokaryotes based on overlapping genesJiang, Li-Wei et al. | 2008
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NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11Lundegaard, Claus et al. | 2008
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SEQATOMS: a web tool for identifying missing regions in PDB in sequence contextBrandt, Bernd W. et al. | 2008
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MolAxis: a server for identification of channels in macromoleculesYaffe, Eitan et al. | 2008
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Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray dataIvliev, Alexander E. et al. | 2008
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The Ontology Lookup Service: more data and better tools for controlled vocabulary queriesCôté, Richard G. et al. | 2008
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GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathwaysMartinez-Guerrero, C.E. et al. | 2008
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Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and designSullivan, Robert T. et al. | 2008
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Software.ncrna.org: web servers for analyses of RNA sequencesAsai, Kiyoshi et al. | 2008
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RNALogo: a new approach to display structural RNA alignmentChang, Tzu-Hao et al. | 2008
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Signature, a web server for taxonomic characterization of sequence samples using signature genesDutilh, Bas E. et al. | 2008
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SuperPred: drug classification and target predictionDunkel, Mathias et al. | 2008
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Keeping pace with the data: 2008 update on the Bioinformatics Links DirectoryBrazas, Michelle D. et al. | 2008
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BIOSMILE web search: a web application for annotating biomedical entities and relationsDai, Hong-Jie et al. | 2008
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OREST: the online resource for EST analysisWaegele, Brigitte et al. | 2008
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soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alertsLesburg, Charles A. et al. | 2008
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ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networksKlein, Johannes et al. | 2008
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PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotationMontgomerie, Scott et al. | 2008
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ENDEAVOUR update: a web resource for gene prioritization in multiple speciesTranchevent, Léon-Charles et al. | 2008
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Onto-CC: a web server for identifying Gene Ontology conceptual clustersRomero-Zaliz, R. et al. | 2008
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GOEAST: a web-based software toolkit for Gene Ontology enrichment analysisZheng, Qi et al. | 2008
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PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolitesCheng, Dean et al. | 2008
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ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput dataAntonov, Alexey V. et al. | 2008
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GeneCAT--novel webtools that combine BLAST and co-expression analysesMutwil, Marek et al. | 2008
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PBEQ-Solver for online visualization of electrostatic potential of biomoleculesJo, Sunhwan et al. | 2008
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3D-Fun: predicting enzyme function from structurevon Grotthuss, Marcin et al. | 2008
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MassTRIX: mass translator into pathwaysSuhre, Karsten et al. | 2008
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Phylogeny.fr: robust phylogenetic analysis for the non-specialistDereeper, A. et al. | 2008
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xREI: a phylo-grammar visualization webserverBarquist, Lars et al. | 2008
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Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experimentsAl-Shahrour, Fátima et al. | 2008
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PaLS: filtering common literature, biological terms and pathway informationAlibés, Andreu et al. | 2008
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CoPub: a literature-based keyword enrichment tool for microarray data analysisFrijters, Raoul et al. | 2008
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GenoWatch: a disease gene mining browser for association studyChen, Yan-Hau et al. | 2008
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IDT SciTools: a suite for analysis and design of nucleic acid oligomersOwczarzy, Richard et al. | 2008
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Hubba: hub objects analyzer--a framework of interactome hubs identification for network biologyLin, Chung-Yen et al. | 2008
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pFlexAna: detecting conformational changes in remotely related proteinsNigham, Anshul et al. | 2008
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KEGG Atlas mapping for global analysis of metabolic pathwaysOkuda, Shujiro et al. | 2008
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MassNet: a functional annotation service for protein mass spectrometry dataPark, Daeui et al. | 2008
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pssRNAMiner: a plant short small RNA regulatory cascade analysis serverDai, Xinbin et al. | 2008
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E3Miner: a text mining tool for ubiquitin-protein ligasesLee, Hodong et al. | 2008
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CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeatsGrissa, Ibtissem et al. | 2008
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Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structureKoczyk, Grzegorz et al. | 2008
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TarO: a target optimisation system for structural biologyOverton, Ian M. et al. | 2008
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MADNet: microarray database network web serverSegota, Igor et al. | 2008
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R-Coffee: a web server for accurately aligning noncoding RNA sequencesMoretti, Sébastien et al. | 2008
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NOBAI: a web server for character coding of geometrical and statistical features in RNA structureKnudsen, Vegeir et al. | 2008
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webPIPSA: a web server for the comparison of protein interaction propertiesRichter, Stefan et al. | 2008
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CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence dataWishart, David S. et al. | 2008
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EditorialBenson, Gary et al. | 2008
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OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequencesCroce, Olivier et al. | 2008
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EpiToolKit--a web server for computational immunomicsFeldhahn, Magdalena et al. | 2008