Works matching IS 03051048 AND DT 2022 AND VI 50 AND IP W1

Results: 102

Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022.

Published in:: 2022
Publication type:: Editorial

REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W639, doi. 10.1093/nar/gkac508

By:

Weiss, Zoe;
DasGupta, Saurja

Publication type:

Article

Identification of genome edited cells using CRISPRnano.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W199, doi. 10.1093/nar/gkac440

By:

Nguyen, Thach;
Ramachandran, Haribaskar;
Martins, Soraia;
Krutmann, Jean;
Rossi, Andrea

Publication type:

Article

HemI 2.0: an online service for heatmap illustration.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W405, doi. 10.1093/nar/gkac480

By:

Ning, Wanshan;
Wei, Yuxiang;
Gao, Letian;
Han, Cheng;
Gou, Yujie;
Fu, Shanshan;
Liu, Dan;
Zhang, Chi;
Huang, Xinhe;
Wu, Sicheng;
Peng, Di;
Wang, Chenwei;
Xue, Yu

Publication type:

Article

CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W191, doi. 10.1093/nar/gkac466

By:

Konstantakos, Vasileios;
Nentidis, Anastasios;
Krithara, Anastasia;
Paliouras, Georgios

Publication type:

Article

AllerCatPro 2.0: a web server for predicting protein allergenicity potential.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W36, doi. 10.1093/nar/gkac446

By:

Nguyen, Minh N;
Krutz, Nora L;
Limviphuvadh, Vachiranee;
Lopata, Andreas L;
Gerberick, G Frank;
Maurer-Stroh, Sebastian

Publication type:

Article

FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W330, doi. 10.1093/nar/gkac441

By:

de Jong, Anne;
Kuipers, Oscar P;
Kok, Jan

Publication type:

Article

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W412, doi. 10.1093/nar/gkac481

By:

Oteri, Francesco;
Sarti, Edoardo;
Nadalin, Francesca;
Carbone, Alessandra

Publication type:

Article

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W510, doi. 10.1093/nar/gkac439

By:

Høie, Magnus Haraldson;
Kiehl, Erik Nicolas;
Petersen, Bent;
Nielsen, Morten;
Winther, Ole;
Nielsen, Henrik;
Hallgren, Jeppe;
Marcatili, Paolo

Publication type:

Article

5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W21, doi. 10.1093/nar/gkac423

By:

Chen, Chih-Chieh;
Liu, Yen-Yi;
Yang, Ya-Chu;
Hsu, Chu-Yi

Publication type:

Article

Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W690, doi. 10.1093/nar/gkac427

By:

Emelianova, Mariia;
Gainullina, Anastasiia;
Poperechnyi, Nikolay;
Loboda, Alexander;
Artyomov, Maxim;
Sergushichev, Alexey

Publication type:

Article

PRECOGx: exploring GPCR signaling mechanisms with deep protein representations.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W598, doi. 10.1093/nar/gkac426

By:

Matic, Marin;
Singh, Gurdeep;
Carli, Francesco;
Oliveira Rosa, Natalia De;
Miglionico, Pasquale;
Magni, Lorenzo;
Gutkind, J Silvio;
Russell, Robert B;
Inoue, Asuka;
Raimondi, Francesco

Publication type:

Article

PCGA: a comprehensive web server for phenotype-cell-gene association analysis.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W568, doi. 10.1093/nar/gkac425

By:

Xue, Chao;
Jiang, Lin;
Zhou, Miao;
Long, Qihan;
Chen, Ying;
Li, Xiangyi;
Peng, Wenjie;
Yang, Qi;
Li, Miaoxin

Publication type:

Article

Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W66, doi. 10.1093/nar/gkac424

By:

Zeng, Qifan;
Zhao, Baojun;
Wang, Hao;
Wang, Mengqiu;
Teng, Mingxuan;
Hu, Jingjie;
Bao, Zhenmin;
Wang, Yangfan

Publication type:

Article

Web-based platform for analysis of RNA folding from high throughput chemical probing data.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W266, doi. 10.1093/nar/gkac435

By:

Jurich, Christopher P;
Brivanlou, Amir;
Rouskin, Silvi;
Yesselman, Joseph D

Publication type:

Article

Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W516, doi. 10.1093/nar/gkac420

By:

Vernette, Caroline;
Lecubin, Julien;
Sánchez, Pablo;
Coordinators, Tara Oceans;
Sunagawa, Shinichi;
Delmont, Tom O;
Acinas, Silvia G;
Pelletier, Eric;
Hingamp, Pascal;
Lescot, Magali

Publication type:

Article

CircadiOmics: circadian omic web portal.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W183, doi. 10.1093/nar/gkac419

By:

Samad, Muntaha;
Agostinelli, Forest;
Sato, Tomoki;
Shimaji, Kohei;
Baldi, Pierre

Publication type:

Article

Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W57, doi. 10.1093/nar/gkac418

By:

Liu, Zhu;
Mushayahama, Tremayne;
Queme, Bryan;
Ebert, Dustin;
Muruganujan, Anushya;
Mills, Caitlin;
Thomas, Paul D;
Mi, Huaiyu

Publication type:

Article

MDsrv: visual sharing and analysis of molecular dynamics simulations.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W483, doi. 10.1093/nar/gkac398

By:

Kampfrath, Michelle;
Staritzbichler, René;
Hernández, Guillermo Pérez;
Rose, Alexander S;
Tiemann, Johanna K S;
Scheuermann, Gerik;
Wiegreffe, Daniel;
Hildebrand, Peter W

Publication type:

Article

RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W633, doi. 10.1093/nar/gkac415

By:

Zheng, Lei;
Liu, Dongyang;
Li, Yuan Alex;
Yang, Siqi;
Liang, Yuchao;
Xing, Yongqiang;
Zuo, Yongchun

Publication type:

Article

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W375, doi. 10.1093/nar/gkac402

By:

Ghani, Nur Syatila Ab;
Emrizal, Reeki;
Moffit, Sabrina Mohamed;
Hamdani, Hazrina Yusof;
Ramlan, Effirul Ikhwan;
Firdaus-Raih, Mohd

Publication type:

Article

PADLOC: a web server for the identification of antiviral defence systems in microbial genomes.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W541, doi. 10.1093/nar/gkac400

By:

Payne, Leighton J;
Meaden, Sean;
Mestre, Mario R;
Palmer, Chris;
Toro, Nicolás;
Fineran, Peter C;
Jackson, Simon A

Publication type:

Article

ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W312, doi. 10.1093/nar/gkac399

By:

Liu, Xian;
Xu, Kaikun;
Tao, Xin;
Yin, Ronghua;
Ren, Guangming;
Yu, Miao;
Li, Changyan;
Chen, Hui;
Zhao, Ke;
Xiang, Shensi;
Gao, Huiying;
Bo, Xiaochen;
Chang, Cheng;
Yang, Xiaoming

Publication type:

Article

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W75, doi. 10.1093/nar/gkac417

By:

Yang, Yi;
Mao, Yufeng;
Wang, Ruoyu;
Li, Haoran;
Liu, Ye;
Cheng, Haijiao;
Shi, Zhenkun;
Wang, Yu;
Wang, Meng;
Zheng, Ping;
Liao, Xiaoping;
Ma, Hongwu

Publication type:

Article

EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W290, doi. 10.1093/nar/gkac397

By:

Tang, Li;
Zhong, Zhizhou;
Lin, Yisheng;
Yang, Yifei;
Wang, Jun;
Martin, James F;
Li, Min

Publication type:

Article

3DGenBench: a web-server to benchmark computational models for 3D Genomics.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W4, doi. 10.1093/nar/gkac396

By:

Consortium, International Nucleome

Publication type:

Article

enrichMiR predicts functionally relevant microRNAs based on target collections.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W280, doi. 10.1093/nar/gkac395

By:

Soutschek, Michael;
Germade, Tomás;
Germain, Pierre-Luc;
Schratt, Gerhard

Publication type:

Article

CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W159, doi. 10.1093/nar/gkac394

By:

Liu, Yang;
Yang, Xiaocong;
Gan, Jianhong;
Chen, Shuang;
Xiao, Zhi-Xiong;
Cao, Yang

Publication type:

Article

FABIAN-variant: predicting the effects of DNA variants on transcription factor binding.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W322, doi. 10.1093/nar/gkac393

By:

Steinhaus, Robin;
Robinson, Peter N;
Seelow, Dominik

Publication type:

Article

WebCSEA: web-based cell-type-specific enrichment analysis of genes.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W782, doi. 10.1093/nar/gkac392

By:

Dai, Yulin;
Hu, Ruifeng;
Liu, Andi;
Cho, Kyung Serk;
Manuel, Astrid Marilyn;
Li, Xiaoyang;
Dong, Xianjun;
Jia, Peilin;
Zhao, Zhongming

Publication type:

Article

AlignMe: an update of the web server for alignment of membrane protein sequences.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W29, doi. 10.1093/nar/gkac391

By:

Staritzbichler, René;
Yaklich, Emily;
Sarti, Edoardo;
Ristic, Nikola;
Hildebrand, Peter W;
Forrest, Lucy R

Publication type:

Article

PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W593, doi. 10.1093/nar/gkac389

By:

Jakubec, David;
Skoda, Petr;
Krivak, Radoslav;
Novotny, Marian;
Hoksza, David

Publication type:

Article

AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W44, doi. 10.1093/nar/gkac388

By:

Niemyska, Wanda;
Rubach, Pawel;
Gren, Bartosz A;
Nguyen, Mai Lan;
Garstka, Wojciech;
Bruno da Silva, Fernando;
Rawdon, Eric J;
Sulkowska, Joanna I

Publication type:

Article

FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W337, doi. 10.1093/nar/gkac386

By:

Hatos, Andras;
Tosatto, Silvio C E;
Vendruscolo, Michele;
Fuxreiter, Monika

Publication type:

Article

Dali server: structural unification of protein families.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W210, doi. 10.1093/nar/gkac387

By:

Holm, Liisa

Publication type:

Article

OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W534, doi. 10.1093/nar/gkac385

By:

Ilnitskiy, Ivan S;
Zharikova, Anastasia A;
Mironov, Andrey A

Publication type:

Article

Cancer driver drug interaction explorer.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W138, doi. 10.1093/nar/gkac384

By:

Hartung, Michael;
Anastasi, Elisa;
Mamdouh, Zeinab M;
Nogales, Cristian;
Schmidt, Harald H H W;
Baumbach, Jan;
Zolotareva, Olga;
List, Markus

Publication type:

Article

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W165, doi. 10.1093/nar/gkac383

By:

Wang, Fei;
Allen, Dana;
Tian, Siyang;
Oler, Eponine;
Gautam, Vasuk;
Greiner, Russell;
Metz, Thomas O;
Wishart, David S

Publication type:

Article

SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W739, doi. 10.1093/nar/gkac382

By:

Ianevski, Aleksandr;
Giri, Anil K;
Aittokallio, Tero

Publication type:

Article

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W204, doi. 10.1093/nar/gkac381

By:

Rodrigues, Carlos H M;
Ascher, David B

Publication type:

Article

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W99, doi. 10.1093/nar/gkac380

By:

Bayarri, Genís;
Andrio, Pau;
Hospital, Adam;
Orozco, Modesto;
Gelpí, Josep Lluís

Publication type:

Article

Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W682, doi. 10.1093/nar/gkac371

By:

Mungan, Mehmet Direnç;
Harbig, Theresa Anisja;
Perez, Naybel Hernandez;
Edenhart, Simone;
Stegmann, Evi;
Nieselt, Kay;
Ziemert, Nadine

Publication type:

Article

PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W583, doi. 10.1093/nar/gkac379

By:

Fang, Hai

Publication type:

Article

SWORD2: hierarchical analysis of protein 3D structures.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W732, doi. 10.1093/nar/gkac370

By:

Cretin, Gabriel;
Galochkina, Tatiana;
Vander Meersche, Yann;
de Brevern, Alexandre G;
Postic, Guillaume;
Gelly, Jean-Christophe

Publication type:

Article

DLEB: a web application for building deep learning models in biological research.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W254, doi. 10.1093/nar/gkac369

By:

Wy, Suyeon;
Kwon, Daehong;
Kwon, Kisang;
Kim, Jaebum

Publication type:

Article

CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W145, doi. 10.1093/nar/gkac378

By:

Kunka, Antonin;
Lacko, David;
Stourac, Jan;
Damborsky, Jiri;
Prokop, Zbynek;
Mazurenko, Stanislav

Publication type:

Article

TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W761, doi. 10.1093/nar/gkac374

By:

Chen, Li;
Chen, Tianjian;
Zhang, Ya;
Lin, Haichen;
Wang, Ruihan;
Wang, Yihang;
Li, Hongyu;
Zuo, Zhixiang;
Ren, Jian;
Xie, Yubin

Publication type:

Article

GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W398, doi. 10.1093/nar/gkac377

By:

Seçilmiş, Deniz;
Hillerton, Thomas;
Sonnhammer, Erik L L

Publication type:

Article

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W527, doi. 10.1093/nar/gkac376

By:

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

Publication type:

Article

rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W657, doi. 10.1093/nar/gkac372

By:

Magnus, Marcin

Publication type:

Article