Works matching IS 0305-1048 AND VI 41 AND DT 2013

Results: 1390

DigSee: disease gene search engine with evidence sentences (version cancer).

Published in:

Nucleic Acids Research, 2013, v. 41, p. W510, doi. 10.1093/nar/gkt531

By:

Jeongkyun Kim;
Seongeun So;
Hee-Jin Lee;
Park, Jong C.;
Jung-jae Kim;
Hyunju Lee

Publication type:

Article

PGMRA: a web server for (phenotype x genotype) many-to-many relation analysis in GWAS.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W142, doi. 10.1093/nar/gkt496

By:

Arnedo, Javier;
del Val, Coral;
de Erausquin, Gabriel Alejandro;
Romero-Zaliz, Rocío;
Svrakic, Dragan;
Cloninger, Claude Robert;
Zwir, Igor

Publication type:

Article

VLDP web server: a powerful geometric tool for analysing protein structures in their environment.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W373, doi. 10.1093/nar/gkt509

By:

Esque, Jérémy;
Léonard, Sylvain;
de Brevern, Alexandre G.;
Oguey, Christophe

Publication type:

Article

PosMed: ranking genes and bioresources based on Semantic Web Association Study.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W109, doi. 10.1093/nar/gkt474

By:

Yuko Makita;
Norio Kobayashi;
Yuko Yoshida;
Koji Doi;
Yoshiki Mochizuki;
Koro Nishikata;
Akihiro Matsushima;
Satoshi Takahashi;
Manabu Ishii;
Terue Takatsuki;
Rinki Bhatia;
Zolzaya Khadbaatar;
Hajime Watabe;
Hiroshi Masuya;
Tetsuro Toyoda

Publication type:

Article

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W492, doi. 10.1093/nar/gkt501

By:

Hanjoo Kim;
Cordero, Pablo;
Das, Rhiju;
Sungroh Yoon

Publication type:

Article

ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes—now with human data.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W198, doi. 10.1093/nar/gkt532

By:

Basha, Omer;
Tirman, Shoval;
Eluk, Amir;
Yeger-Lotem, Esti

Publication type:

Article

TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W562, doi. 10.1093/nar/gkt529

By:

Lubbock, Alexander L. R.;
Katz, Elad;
Harrison, David J.;
Overton, Ian M.

Publication type:

Article

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W180, doi. 10.1093/nar/gkt463

By:

Kazan, Hilal;
Morris, Quaid

Publication type:

Article

FIDEA: a server for the functional interpretation of differential expression analysis.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W84, doi. 10.1093/nar/gkt516

By:

D’Andrea, Daniel;
Grassi, Luigi;
Mazzapioda, Mariagiovanna;
Tramontano, Anna

Publication type:

Article

Inferring the functional effect of gene expression changes in signaling pathways.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W213, doi. 10.1093/nar/gkt451

By:

Sebastián-León, Patricia;
Carbonell, José;
Salavert, Francisco;
Sanchez, Rubén;
Medina, Ignacio;
Dopazo, Joaquín

Publication type:

Article

HIV N-linked glycosylation site analyzer and its further usage in anchored alignment.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W454, doi. 10.1093/nar/gkt472

By:

Shaw, Timothy I.;
Ming Zhang

Publication type:

Article

The UCSC Interaction Browser: multidimensional data views in pathway context.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W218, doi. 10.1093/nar/gkt473

By:

Wong, Christopher K.;
Vaske, Charles J.;
Ng, Sam;
Sanborn, J. Zachary;
Benz, Stephen C.;
Haussler, David;
Stuart, Joshua M.

Publication type:

Article

Genome Maps, a new generation genome browser.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W41, doi. 10.1093/nar/gkt530

By:

Medina, Ignacio;
Salavert, Francisco;
Sanchez, Rubén;
de Maria, Alejandro;
Alonso, Roberto;
Escobar, Pablo;
Bleda, Marta;
Dopazo, Joaquín

Publication type:

Article

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W480, doi. 10.1093/nar/gkt461

By:

Yang Zhang;
Ponty, Yann;
Blanchette, Mathieu;
Lécuyer, Eric;
Waldispühl, Jérôme

Publication type:

Article

GeneMANIA Prediction Server 2013 Update.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W115, doi. 10.1093/nar/gkt533

By:

Zuberi, Khalid;
Franz, Max;
Rodriguez, Harold;
Montojo, Jason;
Lopes, Christian Tannus;
Bader, Gary D.;
Morris, Quaid

Publication type:

Article

CoPAP: Coevolution of Presence–Absence Patterns.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W232, doi. 10.1093/nar/gkt471

By:

Cohen, Ofir;
Ashkenazy, Haim;
Karin, Eli Levy;
Burstein, David;
Pupko, Tal

Publication type:

Article

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W544, doi. 10.1093/nar/gkt519

By:

Fletez-Brant, Christopher;
Lee, Dongwon;
McCallion, Andrew S.;
Beer, Michael A.

Publication type:

Article

CABS-fold: server for the de novo and consensus-based prediction of protein structure.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W406, doi. 10.1093/nar/gkt462

By:

Blaszczyk, Maciej;
Jamroz, Michal;
Kmiecik, Sebastian;
Kolinski, Andrzej

Publication type:

Article

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W535, doi. 10.1093/nar/gkt448

By:

Zambelli, Federico;
Pesole, Graziano;
Pavesi, Giulio

Publication type:

Article

INMEX—a web-based tool for integrative meta-analysis of expression data.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W63, doi. 10.1093/nar/gkt338

By:

Xia, Jianguo;
Fjell, Christopher D.;
Mayer, Matthew L.;
Pena, Olga M.;
Wishart, David S.;
Hancock, Robert E. W.

Publication type:

Article

SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W187, doi. 10.1093/nar/gkt459

By:

Nim, Tri Hieu;
White, Jacob K.;
Tucker-Kellogg, Lisa

Publication type:

Article

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W249, doi. 10.1093/nar/gkt284

By:

Kaya, Cihan;
Armutlulu, Andac;
Ekesan, Solen;
Haliloglu, Turkan

Publication type:

Article

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W314, doi. 10.1093/nar/gkt503

By:

Tan, Kuan Pern;
Nguyen, Thanh Binh;
Patel, Siddharth;
Varadarajan, Raghavan;
Madhusudhan, M. S.

Publication type:

Article

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W204, doi. 10.1093/nar/gkt449

By:

Blin, Kai;
Medema, Marnix H.;
Kazempour, Daniyal;
Fischbach, Michael A.;
Breitling, Rainer;
Takano, Eriko;
Weber, Tilmann

Publication type:

Article

RNAtips: analysis of temperature-induced changes of RNA secondary structure.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W486, doi. 10.1093/nar/gkt486

By:

Chursov, Andrey;
Kopetzky, Sebastian J.;
Bocharov, Gennady;
Frishman, Dmitrij;
Shneider, Alexander

Publication type:

Article

GalaxyRefine: protein structure refinement driven by side-chain repacking.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W384, doi. 10.1093/nar/gkt458

By:

Lim Heo;
Hahnbeom Park;
Chaok Seok

Publication type:

Article

SPACER: server for predicting allosteric communication and effects of regulation.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W266, doi. 10.1093/nar/gkt460

By:

Goncearenco, Alexander;
Mitternacht, Simon;
Taipang Yong;
Eisenhaber, Birgit;
Eisenhaber, Frank;
Berezovsky, Igor N.

Publication type:

Article

PromoterCAD: data-driven design of plant regulatory DNA.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W569, doi. 10.1093/nar/gkt518

By:

Cox III, Robert Sidney;
Koro Nishikata;
Sayoko Shimoyama;
Yuko Yoshida;
Minami Matsui;
Yuko Makita;
Tetsuro Toyoda

Publication type:

Article

BeEP Server: using evolutionary information for quality assessment of protein structure models.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W398, doi. 10.1093/nar/gkt453

By:

Palopoli, Nicolas;
Lanzarotti, Esteban;
Parisi, Gustavo

Publication type:

Article

PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W441, doi. 10.1093/nar/gkt428

By:

Shengnan Tang;
Tonghua Li;
Peisheng Cong;
Wenwei Xiong;
Zhiheng Wang;
Jiangming Sun

Publication type:

Article

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W286, doi. 10.1093/nar/gkt497

By:

Jessen, Leon Eyrich;
Hoof, Ilka;
Lund, Ole;
Nielsen, Morten

Publication type:

Article

PELE web server: atomistic study of biomolecular systems at your fingertips.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W322, doi. 10.1093/nar/gkt454

By:

Madadkar-Sobhani, Armin;
Guallar, Victor

Publication type:

Article

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W150, doi. 10.1093/nar/gkt456

By:

Mulin Jun Li;
Lily Yan Wang;
Zhengyuan Xia;
Pak Chung Sham;
Junwen Wang

Publication type:

Article

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W333, doi. 10.1093/nar/gkt450

By:

Dehouck, Yves;
Kwasigroch, Jean Marc;
Rooman, Marianne;
Gilis, Dimitri

Publication type:

Article

IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W432, doi. 10.1093/nar/gkt431

By:

Nadzirin, Nurul;
Willett, Peter;
Artymiuk, Peter J.;
Firdaus-Raih, Mohd

Publication type:

Article

BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W582, doi. 10.1093/nar/gkt420

By:

Paraskevopoulou, Maria D.;
Vlachos, Ioannis S.;
Athanasiadis, Emmanouil;
Spyrou, George

Publication type:

Article

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W15, doi. 10.1093/nar/gkt417

By:

Rahrig, Ryan R.;
Petrov, Anton I.;
Leontis, Neocles B.;
Zirbel, Craig L.

Publication type:

Article

T-RMSD: a web server for automated fine-grained protein structural classification.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W358, doi. 10.1093/nar/gkt383

By:

Magis, Cedrik;
Di Tommaso, Paolo;
Notredame, Cedric

Publication type:

Article

MISTIC: mutual information server to infer coevolution.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W8, doi. 10.1093/nar/gkt427

By:

Simonetti, Franco L.;
Teppa, Elin;
Chernomoretz, Ariel;
Nielsen, Morten;
Buslje, Cristina Marino

Publication type:

Article

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W225, doi. 10.1093/nar/gkt401

By:

Zhenjun Hu;
Yi-Chien Chang;
Yan Wang;
Chia-Ling Huang;
Yang Liu;
Feng Tian;
Granger, Brian;
DeLisi, Charles

Publication type:

Article

miRmap web: comprehensive microRNA target prediction online.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W165, doi. 10.1093/nar/gkt430

By:

Vejnar, Charles E.;
Blum, Matthias;
Zdobnov, Evgeny M.

Publication type:

Article

PiDNA: predicting protein–DNA interactions with structural models.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W523, doi. 10.1093/nar/gkt388

By:

Chih-Kang Lin;
Chien-Yu Chen

Publication type:

Article

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W56, doi. 10.1093/nar/gkt437

By:

Tianyin Zhou;
Lin Yang;
Yan Lu;
Dror, Iris;
Dantas Machado, Ana Carolina;
Ghane, Tahereh;
Di Felice, Rosa;
Rohs, Remo

Publication type:

Article

ComiR: combinatorial microRNA target prediction tool.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W159, doi. 10.1093/nar/gkt379

By:

Coronnello, Claudia;
Benos, Panayiotis V.

Publication type:

Article

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W281, doi. 10.1093/nar/gkt390

By:

Parca, Luca;
Ferré, Fabrizio;
Ausiello, Gabriele;
Helmer-Citterich, Manuela

Publication type:

Article

PubTator: a web-based text mining tool for assisting biocuration.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W518, doi. 10.1093/nar/gkt441

By:

Chih-Hsuan Wei;
Hung-Yu Kao;
Zhiyong Lu

Publication type:

Article

MetaRanker 2.0: a web server for prioritization of genetic variation data.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W104, doi. 10.1093/nar/gkt387

By:

Pers, Tune H.;
Dworzyński, Piotr;
Thomas, Cecilia Engel;
Lage, Kasper;
Brunak, Søren

Publication type:

Article

RNAiFold: a web server for RNA inverse folding and molecular design.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W465, doi. 10.1093/nar/gkt280

By:

Garcia-Martin, Juan Antonio;
Clote, Peter;
Dotu, Ivan

Publication type:

Article

QA-RecombineIt: a server for quality assessment and recombination of protein models.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W389, doi. 10.1093/nar/gkt408

By:

Pawlowski, Marcin;
Bogdanowicz, Albert;
Bujnicki, Janusz M.

Publication type:

Article

WebAUGUSTUS—a web service for training AUGUSTUS and predicting genes in eukaryotes.

Published in:

Nucleic Acids Research, 2013, v. 41, p. W123, doi. 10.1093/nar/gkt418

By:

Hoff, Katharina J.;
Stanke, Mario

Publication type:

Article