Works matching IS 03051048 AND DT 2023 AND VI 51 AND IP 15

Results: 45

Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8293, doi. 10.1093/nar/gkad607

By:

Liu, Wenqian;
Zuo, Siqi;
Shao, Youran;
Bi, Ke;
Zhao, Jiarun;
Huang, Lei;
Xu, Zhinan;
Lian, Jiazhang

Publication type:

Article

Correction to 'COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale'.

Published in:: 2023
Publication type:: Correction Notice

Editorial: Colyn Crane-Robinson (1935–2023).

Published in:

2023

By:

Bannister, Andrew J;
Schneider, Robert;
Varga-Weisz, Patrick

Publication type:

Obituary

Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7777, doi. 10.1093/nar/gkad623

By:

Chen, Yu-Chen;
Chen, Chia-Ying;
Chiang, Tai-Wei;
Chan, Ming-Hsien;
Hsiao, Michael;
Ke, Huei-Mien;
Tsai, Isheng Jason;
Chuang, Trees-Juen

Publication type:

Article

Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N′- methylguanidine-bridged nucleic acids.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7749, doi. 10.1093/nar/gkad608

By:

Yamaguchi, Takao;
Horie, Naohiro;
Aoyama, Hiroshi;
Kumagai, Shinji;
Obika, Satoshi

Publication type:

Article

Single-worm long-read sequencing reveals genome diversity in free-living nematodes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8035, doi. 10.1093/nar/gkad647

By:

Lee, Yi-Chien;
Ke, Huei-Mien;
Liu, Yu-Ching;
Lee, Hsin-Han;
Wang, Min-Chen;
Tseng, Yung-Che;
Kikuchi, Taisei;
Tsai, Isheng Jason

Publication type:

Article

Evolution of molecular switches for regulation of transgene expression by clinically licensed gluconate.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e85, doi. 10.1093/nar/gkad600

By:

Teixeira, Ana Palma;
Xue, Shuai;
Huang, Jinbo;
Fussenegger, Martin

Publication type:

Article

YLC-assembly: large DNA assembly via yeast life cycle.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8283, doi. 10.1093/nar/gkad599

By:

He, Bo;
Ma, Yuan;
Tian, Fangfang;
Zhao, Guang-Rong;
Wu, Yi;
Yuan, Ying-Jin

Publication type:

Article

Precise and efficient C-to-U RNA base editing with SNAP-CDAR-S.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e84, doi. 10.1093/nar/gkad598

By:

Latifi, Ngadhnjim;
Mack, Aline Maria;
Tellioglu, Irem;
Di Giorgio, Salvatore;
Stafforst, Thorsten

Publication type:

Article

Characterization of an HNA aptamer suggests a non-canonical G-quadruplex motif.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7736, doi. 10.1093/nar/gkad592

By:

Schofield, Peter;
Taylor, Alexander I;
Rihon, Jérôme;
Peña Martinez, Cristian D;
Zinn, Sacha;
Mattelaer, Charles-Alexandre;
Jackson, Jennifer;
Dhaliwal, Gurpreet;
Schepers, Guy;
Herdewijn, Piet;
Lescrinier, Eveline;
Christ, Daniel;
Holliger, Philipp

Publication type:

Article

Domain acquisition by class I aminoacyl-tRNA synthetase urzymes coordinated the catalytic functions of HVGH and KMSKS motifs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8070, doi. 10.1093/nar/gkad590

By:

Tang, Guo Qing;
Elder, Jessica J H;
Douglas, Jordan;
Carter, Charles W

Publication type:

Article

Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8270, doi. 10.1093/nar/gkad583

By:

Liu, Ke;
Xiao, Yuqing;
Gan, Linyao;
Li, Weifang;
Zhang, Jin;
Min, Jinrong

Publication type:

Article

Role of DNA–DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8060, doi. 10.1093/nar/gkad582

By:

Fizari, Mounir;
Keller, Nicholas;
Jardine, Paul J;
Smith, Douglas E

Publication type:

Article

The genomic region of the 3′ untranslated region (3′UTR) of PHO84, rather than the antisense RNA, promotes gene repression.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7900, doi. 10.1093/nar/gkad579

By:

Hegazy, Youssef A;
Cloutier, Sara C;
Utturkar, Sagar M;
Das, Subhadeep;
Tran, Elizabeth J

Publication type:

Article

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e83, doi. 10.1093/nar/gkad578

By:

Tang, Xubo;
Shang, Jiayu;
Ji, Yongxin;
Sun, Yanni

Publication type:

Article

Histone divergence in trypanosomes results in unique alterations to nucleosome structure.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7882, doi. 10.1093/nar/gkad577

By:

Deák, Gauri;
Wapenaar, Hannah;
Sandoval, Gorka;
Chen, Ruofan;
Taylor, Mark R D;
Burdett, Hayden;
Watson, James A;
Tuijtel, Maarten W;
Webb, Shaun;
Wilson, Marcus D

Publication type:

Article

Predicting functional consequences of SNPs on mRNA translation via machine learning.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7868, doi. 10.1093/nar/gkad576

By:

Li, Zheyu;
Chen, Liang

Publication type:

Article

Internal transcription termination widely regulates differential expression of operon-organized genes including ribosomal protein and RNA polymerase genes in an archaeon.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7851, doi. 10.1093/nar/gkad575

By:

Zhang, Wenting;
Ren, Derong;
Li, Zhihua;
Yue, Lei;
Whitman, William B;
Dong, Xiuzhu;
Li, Jie

Publication type:

Article

Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e82, doi. 10.1093/nar/gkad574

By:

Bains, Jasleen Kaur;
Qureshi, Nusrat Shahin;
Ceylan, Betül;
Wacker, Anna;
Schwalbe, Harald

Publication type:

Article

RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7832, doi. 10.1093/nar/gkad571

By:

Chen, Quanquan;
Guo, Yingmei;
Zhang, Jie;
Zheng, Nannan;
Wang, Jie;
Liu, Yan;
Lu, Jiawen;
Zhen, Sihan;
Du, Xuemei;
Li, Li;
Fu, Junjie;
Wang, Guoying;
Gu, Riliang;
Wang, Jianhua;
Liu, Yunjun

Publication type:

Article

Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e81, doi. 10.1093/nar/gkad570

By:

Wang, Ruo Han;
Wang, Jianping;
Li, Shuai Cheng

Publication type:

Article

Landscape of semi-extractable RNAs across five human cell lines.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7820, doi. 10.1093/nar/gkad567

By:

Zeng, Chao;
Chujo, Takeshi;
Hirose, Tetsuro;
Hamada, Michiaki

Publication type:

Article

Integration of gene expression and DNA methylation data across different experiments.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7762, doi. 10.1093/nar/gkad566

By:

Itai, Yonatan;
Rappoport, Nimrod;
Shamir, Ron

Publication type:

Article

Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8133, doi. 10.1093/nar/gkad564

By:

Alings, Fiona;
Scharmann, Karin;
Eggers, Cristian;
Böttcher, Bettina;
Sokołowski, Mikołaj;
Shvetsova, Ekaterina;
Sharma, Puneet;
Roth, Joël;
Rashiti, Leon;
Glatt, Sebastian;
Brunke, Sascha;
Leidel, Sebastian A

Publication type:

Article

Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. e80, doi. 10.1093/nar/gkad562

By:

Guzman, Carlos;
Duttke, Sascha;
Zhu, Yixin;
De Arruda Saldanha, Camila;
Downes, Nicholas L;
Benner, Christopher;
Heinz, Sven

Publication type:

Article

Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8048, doi. 10.1093/nar/gkad560

By:

van den Elzen, Antonia;
Helena-Bueno, Karla;
Brown, Charlotte R;
Chan, Lewis I;
Melnikov, Sergey V

Publication type:

Article

A clickable melphalan for monitoring DNA interstrand crosslink accumulation and detecting ICL repair defects in Fanconi anemia patient cells.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7988, doi. 10.1093/nar/gkad559

By:

Berrada, Sara;
Martínez-Balsalobre, Elena;
Larcher, Lise;
Azzoni, Violette;
Vasquez, Nadia;
Da Costa, Mélanie;
Abel, Sébastien;
Audoly, Gilles;
Lee, Lara;
Montersino, Camille;
Castellano, Rémy;
Combes, Sébastien;
Gelot, Camille;
Ceccaldi, Raphaël;
Guervilly, Jean-Hugues;
Soulier, Jean;
Lachaud, Christophe

Publication type:

Article

DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8255, doi. 10.1093/nar/gkad553

By:

Chojnowski, Grzegorz

Publication type:

Article

Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8237, doi. 10.1093/nar/gkad552

By:

Freda, Ida;
Exertier, Cécile;
Barile, Anna;
Chaves-Sanjuan, Antonio;
Vega, Mirella Vivoli;
Isupov, Michail N;
Harmer, Nicholas J;
Gugole, Elena;
Swuec, Paolo;
Bolognesi, Martino;
Scipioni, Anita;
Savino, Carmelinda;
Di Salvo, Martino Luigi;
Contestabile, Roberto;
Vallone, Beatrice;
Tramonti, Angela;
Montemiglio, Linda Celeste

Publication type:

Article

Extension of mRNA poly(A) tails and 3′UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8181, doi. 10.1093/nar/gkad499

By:

Kiltschewskij, Dylan J;
Harrison, Paul F;
Fitzsimmons, Chantel;
Beilharz, Traude H;
Cairns, Murray J

Publication type:

Article

DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7972, doi. 10.1093/nar/gkad549

By:

Head, PamelaSara E;
Kapoor-Vazirani, Priya;
Nagaraju, Ganji P;
Zhang, Hui;
Rath, Sandip K;
Luong, Nho C;
Haji-Seyed-Javadi, Ramona;
Sesay, Fatmata;
Wang, Shi-Ya;
Duong, Duc M;
Daddacha, Waaqo;
Minten, Elizabeth V;
Song, Boying;
Danelia, Diana;
Liu, Xu;
Li, Shuyi;
Ortlund, Eric A;
Seyfried, Nicholas T;
Smalley, David M;
Wang, Ya

Publication type:

Article

CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8115, doi. 10.1093/nar/gkad546

By:

Domgaard, Hannah;
Cahoon, Christian;
Armbrust, Matthew J;
Redman, Olivine;
Jolley, Alivia;
Thomas, Aaron;
Jackson, Ryan N

Publication type:

Article

Alteration of replication protein A binding mode on single-stranded DNA by NSMF potentiates RPA phosphorylation by ATR kinase.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7936, doi. 10.1093/nar/gkad543

By:

Kang, Yujin;
Han, Ye Gi;
Khim, Keon Woo;
Choi, Woo Gyun;
Ju, Min Kyung;
Park, Kibeom;
Shin, Kyeong Jin;
Chae, Young Chan;
Choi, Jang Hyun;
Kim, Hongtae;
Lee, Ja Yil

Publication type:

Article

Dna2 removes toxic ssDNA-RPA filaments generated from meiotic recombination-associated DNA synthesis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7914, doi. 10.1093/nar/gkad537

By:

Zhai, Binyuan;
Zhang, Shuxian;
Li, Bo;
Zhang, Jiaming;
Yang, Xuan;
Tan, Yingjin;
Wang, Ying;
Tan, Taicong;
Yang, Xiao;
Chen, Beiyi;
Tian, Zhongyu;
Cao, Yanding;
Huang, Qilai;
Gao, Jinmin;
Wang, Shunxin;
Zhang, Liangran

Publication type:

Article

Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8020, doi. 10.1093/nar/gkad532

By:

Xie, Haoling;
Li, Wen;
Guo, Yuqing;
Su, Xinjie;
Chen, Kexuan;
Wen, Lu;
Tang, Fuchou

Publication type:

Article

MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7951, doi. 10.1093/nar/gkad548

By:

Jin, Bangming;
Zhu, Jiamei;
Pan, Ting;
Yang, Yunqiao;
Liang, Li;
Zhou, Yuxia;
Zhang, Tuo;
Teng, Yin;
Wang, Ziming;
Wang, Xuyan;
Tian, Qianting;
Guo, Bing;
Li, Haiyang;
Chen, Tengxiang

Publication type:

Article

N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7714, doi. 10.1093/nar/gkad528

By:

Buscà, Roser;
Onesto, Cercina;
Egensperger, Mylène;
Pouysségur, Jacques;
Pagès, Gilles;
Lenormand, Philippe

Publication type:

Article

RIG-I recognizes metabolite-capped RNAs as signaling ligands.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8102, doi. 10.1093/nar/gkad518

By:

Schweibenz, Brandon D;
Solotchi, Mihai;
Hanpude, Pranita;
Devarkar, Swapnil C;
Patel, Smita S

Publication type:

Article

Updated protein domain annotation of the PARP protein family sheds new light on biological function.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8217, doi. 10.1093/nar/gkad514

By:

Suskiewicz, Marcin J;
Munnur, Deeksha;
Strømland, Øyvind;
Yang, Ji-Chun;
Easton, Laura E;
Chatrin, Chatrin;
Zhu, Kang;
Baretić, Domagoj;
Goffinont, Stéphane;
Schuller, Marion;
Wu, Wing-Fung;
Elkins, Jonathan M;
Ahel, Dragana;
Sanyal, Sumana;
Neuhaus, David;
Ahel, Ivan

Publication type:

Article

RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8085, doi. 10.1093/nar/gkad511

By:

Fan, Jun;
El Sayyed, Hafez;
Pambos, Oliver J;
Stracy, Mathew;
Kyropoulos, Jingwen;
Kapanidis, Achillefs N

Publication type:

Article

Alu RNA fold links splicing with signal recognition particle proteins.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8199, doi. 10.1093/nar/gkad500

By:

Borovská, Ivana;
Vořechovský, Igor;
Královičová, Jana

Publication type:

Article

Spatially resolved transcriptomic analysis of the germinating barley grain.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 7798, doi. 10.1093/nar/gkad521

By:

Peirats-Llobet, Marta;
Yi, Changyu;
Liew, Lim Chee;
Berkowitz, Oliver;
Narsai, Reena;
Lewsey, Mathew G;
Whelan, James

Publication type:

Article

Global transmission of broad-host-range plasmids derived from the human gut microbiome.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8005, doi. 10.1093/nar/gkad498

By:

Yang, Lili;
Mai, Guoqin;
Hu, Zheng;
Zhou, Haokui;
Dai, Lei;
Deng, Ziqing;
Ma, Yingfei

Publication type:

Article

Translation initiation with exotic amino acids using EF-P-responsive artificial initiator tRNA.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8169, doi. 10.1093/nar/gkad496

By:

Katoh, Takayuki;
Suga, Hiroaki

Publication type:

Article

Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8150, doi. 10.1093/nar/gkad495

By:

Shmakov, Sergey A;
Barth, Zachary K;
Makarova, Kira S;
Wolf, Yuri I;
Brover, Vyacheslav;
Peters, Joseph E;
Koonin, Eugene V

Publication type:

Article