Works matching IS 03051048 AND DT 2023 AND VI 51 AND IP W1

Results: 81

Editorial: the 21st annual Nucleic Acids Research Web Server Issue 2023.

Published in:

2023

By:

Seelow, Dominik

Publication type:

Editorial

DDMut: predicting effects of mutations on protein stability using deep learning.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W122, doi. 10.1093/nar/gkad472

By:

Zhou, Yunzhuo;
Pan, Qisheng;
Pires, Douglas E V;
Rodrigues, Carlos H M;
Ascher, David B

Publication type:

Article

sfkit: a web-based toolkit for secure and federated genomic analysis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W535, doi. 10.1093/nar/gkad464

By:

Mendelsohn, Simon;
Froelicher, David;
Loginov, Denis;
Bernick, David;
Berger, Bonnie;
Cho, Hyunghoon

Publication type:

Article

PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W451, doi. 10.1093/nar/gkad455

By:

Capriotti, Emidio;
Fariselli, Piero

Publication type:

Article

GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W237, doi. 10.1093/nar/gkad445

By:

Faessler, Erik;
Hahn, Udo;
Schäuble, Sascha

Publication type:

Article

FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W180, doi. 10.1093/nar/gkad444

By:

Zhang, Zixuan;
Zhu, Haiqi;
Dang, Pengtao;
Wang, Jia;
Chang, Wennan;
Wang, Xiao;
Alghamdi, Norah;
Lu, Alex;
Zang, Yong;
Wu, Wenzhuo;
Wang, Yijie;
Zhang, Yu;
Cao, Sha;
Zhang, Chi

Publication type:

Article

DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W154, doi. 10.1093/nar/gkad431

By:

Tastsoglou, Spyros;
Skoufos, Giorgos;
Miliotis, Marios;
Karagkouni, Dimitra;
Koutsoukos, Ioannis;
Karavangeli, Anna;
Kardaras, Filippos S;
Hatzigeorgiou, Artemis G

Publication type:

Article

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W62, doi. 10.1093/nar/gkad430

By:

Del Conte, Alessio;
Bouhraoua, Adel;
Mehdiabadi, Mahta;
Clementel, Damiano;
Monzon, Alexander Miguel;
predictors, CAID;
Tosatto, Silvio C E;
Piovesan, Damiano

Publication type:

Article

NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W372, doi. 10.1093/nar/gkad429

By:

Scheepbouwer, Chantal;
Hackenberg, Michael;
van Eijndhoven, Monique A J;
Gerber, Alan;
Pegtel, Michiel;
Gómez-Martín, Cristina

Publication type:

Article

Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W269, doi. 10.1093/nar/gkad428

By:

Ciecierski, Lukasz;
Stolarek, Ireneusz;
Figlerowicz, Marek

Publication type:

Article

SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W528, doi. 10.1093/nar/gkad427

By:

Qiu, Tianyi;
Zhang, Lu;
Chen, Zikun;
Wang, Yuan;
Mao, Tiantian;
Wang, Caicui;
Cun, Yewei;
Zheng, Genhui;
Yan, Deyu;
Zhou, Mengdi;
Tang, Kailin;
Cao, Zhiwei

Publication type:

Article

The AnnotSV webserver in 2023: updated visualization and ranking.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W39, doi. 10.1093/nar/gkad426

By:

Geoffroy, Véronique;
Lamouche, Jean-Baptiste;
Guignard, Thomas;
Nicaise, Samuel;
Kress, Arnaud;
Scheidecker, Sophie;
Le Béchec, Antony;
Muller, Jean

Publication type:

Article

CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W93, doi. 10.1093/nar/gkad425

By:

Zhou, Fengxia;
Yu, Xiaorong;
Gan, Rui;
Ren, Kuan;
Chen, Chuangeng;
Ren, Chunyan;
Cui, Meng;
Liu, Yuchen;
Gao, Yiyang;
Wang, Shouyu;
Yin, Mingyu;
Huang, Tengjin;
Huang, Zhiwei;
Zhang, Fan

Publication type:

Article

ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W478, doi. 10.1093/nar/gkad421

By:

Sharon, Moran;
Gruber, Gil;
Argov, Chanan M;
Volozhinsky, Miri;
Yeger-Lotem, Esti

Publication type:

Article

SH2db, an information system for the SH2 domain.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W542, doi. 10.1093/nar/gkad420

By:

Bajusz, Dávid;
Pándy-Szekeres, Gáspár;
Takács, Ágnes;
de Araujo, Elvin D;
Keserű, György M

Publication type:

Article

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W560, doi. 10.1093/nar/gkad419

By:

Li, Xiangshang;
Xiao, Chunfu;
Qi, Juntian;
Xue, Weizhen;
Xu, Xinwei;
Mu, Zelin;
Zhang, Jie;
Li, Chuan-Yun;
Ding, Wanqiu

Publication type:

Article

SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W520, doi. 10.1093/nar/gkad408

By:

Qian, Feng-Cui;
Zhou, Li-Wei;
Li, Yan-Yu;
Yu, Zheng-Min;
Li, Li-Dong;
Wang, Yue-Zhu;
Xu, Ming-Cong;
Wang, Qiu-Yu;
Li, Chun-Quan

Publication type:

Article

nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W365, doi. 10.1093/nar/gkad414

By:

Liu, Kai;
Lu, Xufeng;
Shi, Hang;
Xu, Xiaojun;
Kong, Ren;
Chang, Shan

Publication type:

Article

PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W411, doi. 10.1093/nar/gkad412

By:

Jiménez-Santos, María José;
Nogueira-Rodríguez, Alba;
Piñeiro-Yáñez, Elena;
López-Fernández, Hugo;
García-Martín, Santiago;
Gómez-Plana, Paula;
Reboiro-Jato, Miguel;
Gómez-López, Gonzalo;
Glez-Peña, Daniel;
Al-Shahrour, Fátima

Publication type:

Article

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W326, doi. 10.1093/nar/gkad411

By:

Chareshneu, Aliaksei;
Midlik, Adam;
Ionescu, Crina-Maria;
Rose, Alexander;
Horský, Vladimír;
Cantara, Alessio;
Svobodová, Radka;
Berka, Karel;
Sehnal, David

Publication type:

Article

GenomeFLTR: filtering reads made easy.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W232, doi. 10.1093/nar/gkad410

By:

Dotan, Edo;
Alburquerque, Michael;
Wygoda, Elya;
Huchon, Dorothée;
Pupko, Tal

Publication type:

Article

GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W251, doi. 10.1093/nar/gkad409

By:

Orzeł, Urszula;
Pasznik, Paweł;
Miszta, Przemysław;
Lorkowski, Marcin;
Niewieczerzał, Szymon;
Jakowiecki, Jakub;
Filipek, Sławomir

Publication type:

Article

SMDB: a Spatial Multimodal Data Browser.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W553, doi. 10.1093/nar/gkad413

By:

Cao, Ruifang;
Ling, Yunchao;
Meng, Jiayue;
Jiang, Ao;
Luo, Ruijin;
He, Qinwen;
Li, Anan;
Chen, Yujie;
Zhang, Zoutao;
Liu, Feng;
Li, Yixue;
Zhang, Guoqing

Publication type:

Article

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W310, doi. 10.1093/nar/gkad407

By:

Lu, Yao;
Zhou, Guangyan;
Ewald, Jessica;
Pang, Zhiqiang;
Shiri, Tanisha;
Xia, Jianguo

Publication type:

Article

WebQUAST: online evaluation of genome assemblies.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W601, doi. 10.1093/nar/gkad406

By:

Mikheenko, Alla;
Saveliev, Vladislav;
Hirsch, Pascal;
Gurevich, Alexey

Publication type:

Article

MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W305, doi. 10.1093/nar/gkad405

By:

Lopez-Ibañez, Javier;
Pazos, Florencio;
Chagoyen, Monica

Publication type:

Article

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W509, doi. 10.1093/nar/gkad404

By:

Wang, Yunxia;
Chen, Zhen;
Pan, Ziqi;
Huang, Shijie;
Liu, Jin;
Xia, Weiqi;
Zhang, Hongning;
Zheng, Mingyue;
Li, Honglin;
Hou, Tingjun;
Zhu, Feng

Publication type:

Article

Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W17, doi. 10.1093/nar/gkad400

By:

Zong, Fanjie;
Long, Chenyu;
Hu, Wanxin;
Chen, Shuang;
Dai, Wentao;
Xiao, Zhi-Xiong;
Cao, Yang

Publication type:

Article

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W213, doi. 10.1093/nar/gkad399

By:

Marino, Giacomo B;
Ngai, Michael;
Clarke, Daniel J B;
Fleishman, Reid H;
Deng, Eden Z;
Xie, Zhuorui;
Ahmed, Nasheath;
Ma'ayan, Avi

Publication type:

Article

ARMADiLLO: a web server for analyzing antibody mutation probabilities.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W51, doi. 10.1093/nar/gkad398

By:

Martin Beem, Joshua S;
Venkatayogi, Sravani;
Haynes, Barton F;
Wiehe, Kevin

Publication type:

Article

Enrichr-KG: bridging enrichment analysis across multiple libraries.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W168, doi. 10.1093/nar/gkad393

By:

Evangelista, John Erol;
Xie, Zhuorui;
Marino, Giacomo B;
Nguyen, Nhi;
Clarke, Daniel J B;
Ma'ayan, Avi

Publication type:

Article

miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W319, doi. 10.1093/nar/gkad392

By:

Aparicio-Puerta, Ernesto;
Hirsch, Pascal;
Schmartz, Georges P;
Kern, Fabian;
Fehlmann, Tobias;
Keller, Andreas

Publication type:

Article

Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W225, doi. 10.1093/nar/gkad391

By:

Cleary, Alan M;
Farmer, Andrew D

Publication type:

Article

Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W57, doi. 10.1093/nar/gkad390

By:

Potdar, Swapnil;
Ianevski, Filipp;
Ianevski, Aleksandr;
Tanoli, Ziaurrehman;
Wennerberg, Krister;
Seashore-Ludlow, Brinton;
Kallioniemi, Olli;
Östling, Päivi;
Aittokallio, Tero;
Saarela, Jani

Publication type:

Article

FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W191, doi. 10.1093/nar/gkad386

By:

Yılmaz, Turgut Mesut;
Mungan, Mehmet Direnç;
Berasategui, Aileen;
Ziemert, Nadine

Publication type:

Article

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W108, doi. 10.1093/nar/gkad385

By:

Barrett, Kristian;
Hunt, Cameron J;
Lange, Lene;
Grigoriev, Igor V;
Meyer, Anne S

Publication type:

Article

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W493, doi. 10.1093/nar/gkad384

By:

Gschwind, Rémi;
Ugarcina Perovic, Svetlana;
Weiss, Maja;
Petitjean, Marie;
Lao, Julie;
Coelho, Luis Pedro;
Ruppé, Etienne

Publication type:

Article

GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W243, doi. 10.1093/nar/gkad383

By:

Chen, Miaomiao;
Zhang, Weizhi;
Gou, Yujie;
Xu, Danyang;
Wei, Yuxiang;
Liu, Dan;
Han, Cheng;
Huang, Xinhe;
Li, Chengzhi;
Ning, Wanshan;
Peng, Di;
Xue, Yu

Publication type:

Article

PHASTEST: faster than PHASTER, better than PHAST.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W443, doi. 10.1093/nar/gkad382

By:

Wishart, David S;
Han, Scott;
Saha, Sukanta;
Oler, Eponine;
Peters, Harrison;
Grant, Jason R;
Stothard, Paul;
Gautam, Vasuk

Publication type:

Article

IRSOM2: a web server for predicting bifunctional RNAs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W281, doi. 10.1093/nar/gkad381

By:

Postic, Guillaume;
Tav, Christophe;
Platon, Ludovic;
Zehraoui, Farida;
Tahi, Fariza

Publication type:

Article

ChemMaps.com v2.0: exploring the environmental chemical universe.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W78, doi. 10.1093/nar/gkad380

By:

Borrel, Alexandre;
Conway, Mike;
Nolte, Sue Z;
Unnikrishnan, Aswani;
Schmitt, Charles P;
Kleinstreuer, Nicole C

Publication type:

Article

NBBC: a non-B DNA burden explorer in cancer.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W357, doi. 10.1093/nar/gkad379

By:

Xu, Qi;
Kowalski, Jeanne

Publication type:

Article

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W432, doi. 10.1093/nar/gkad376

By:

Rey, Julien;
Murail, Samuel;
de Vries, Sjoerd;
Derreumaux, Philippe;
Tuffery, Pierre

Publication type:

Article

OnTarget: in silico design of MiniPromoters for targeted delivery of expression.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W379, doi. 10.1093/nar/gkad375

By:

Fornes, Oriol;
Av-Shalom, Tamar V;
Korecki, Andrea J;
Farkas, Rachelle A;
Arenillas, David J;
Mathelier, Anthony;
Simpson, Elizabeth M;
Wasserman, Wyeth W

Publication type:

Article

MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W343, doi. 10.1093/nar/gkad374

By:

Jiang, Yuexu;
Jiang, Lei;
Akhil, Chopparapu Sai;
Wang, Duolin;
Zhang, Ziyang;
Zhang, Weinan;
Xu, Dong

Publication type:

Article

Pest Alert Tool—a web-based application for flagging species of concern in metabarcoding datasets.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W438, doi. 10.1093/nar/gkad364

By:

Zaiko, Anastasija;
Scheel, Maximilian;
Schattschneider, Jessica;
von Ammon, Ulla;
Scriver, Michelle;
Pochon, Xavier;
Pearman, John K

Publication type:

Article

CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W70, doi. 10.1093/nar/gkad360

By:

Mao, Zhitao;
Yuan, Qianqian;
Li, Haoran;
Zhang, Yue;
Huang, Yuanyuan;
Yang, Chunhe;
Wang, Ruoyu;
Yang, Yongfu;
Wu, Yalun;
Yang, Shihui;
Liao, Xiaoping;
Ma, Hongwu

Publication type:

Article

Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W587, doi. 10.1093/nar/gkad359

By:

Xie, Jianmin;
Chen, Yuerong;
Cai, Guanjing;
Cai, Runlin;
Hu, Zhong;
Wang, Hui

Publication type:

Article

OpenXGR: a web-server update for genomic summary data interpretation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W387, doi. 10.1093/nar/gkad357

By:

Bao, Chaohui;
Wang, Shan;
Jiang, Lulu;
Fang, Zhongcheng;
Zou, Kexin;
Lin, James;
Chen, Saijuan;
Fang, Hai

Publication type:

Article

TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W569, doi. 10.1093/nar/gkad356

By:

Yin, Rui;
Ribeiro-Filho, Helder V;
Lin, Valerie;
Gowthaman, Ragul;
Cheung, Melyssa;
Pierce, Brian G

Publication type:

Article