Works matching IS 03051048 AND DT 2025 AND VI 53 AND IP 2

Results: 67

Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf006

By:

Zhegalova, Irina V;
Ulianov, Sergey V;
Galitsyna, Aleksandra A;
Pletenev, Ilya A;
Tsoy, Olga V;
Luzhin, Artem V;
Vasiluev, Petr A;
Bulavko, Egor S;
Ivankov, Dmitry N;
Gavrilov, Alexey A;
Khrameeva, Ekaterina E;
Gelfand, Mikhail S;
Razin, Sergey V

Publication type:

Article

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.

Published in:

2025

By:

Chen, Yunshun;
Chen, Lizhong;
Lun, Aaron T L;
Baldoni, Pedro L;
Smyth, Gordon K

Publication type:

Literature Review

Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf004

By:

Guo, Fangfei;
Tromp, Alisha;
Wang, Haitao;
Hall, Thomas E;
Giacomotto, Jean

Publication type:

Article

An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf011

By:

Gleason, Charles;
Terry, Sandra N;
Hernandez, Matthew M;
Jacob, Samson;
Fenyo, David;
Johnson, Jeffrey R;
Deikus, Gintaras;
Francoeur, Nancy;
Hahn, Aana;
Sebra, Robert;
Zamarin, Dmitriy;
Molina, Henrik;
Simon, Viviana;
Mulder, Lubbertus C F

Publication type:

Article

The SARS-CoV-2 nucleocapsid protein interferes with the full enzymatic activation of UPF1 and its interaction with UPF2.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf010

By:

Nuccetelli, Veronica;
Mghezzi-Habellah, Makram;
Deymier, Séverine;
Roisin, Armelle;
Gérard-Baraggia, Francine;
Rocchi, Cecilia;
Coureux, Pierre-Damien;
Gouet, Patrice;
Cimarelli, Andrea;
Mocquet, Vincent;
Fiorini, Francesca

Publication type:

Article

A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf005

By:

Jonsdottir, Thorey K;
Paoletta, Martina S;
Ishizaki, Takahiro;
Hernandez, Sophia;
Ivanova, Maria;
Herrera Curbelo, Alicia;
Saiki, Paulina A;
Selinger, Martin;
Das, Debojyoti;
Henriksson, Johan;
Bushell, Ellen S C

Publication type:

Article

Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf016

By:

Garcia-Guerra, Antonio;
Sathyaprakash, Chaitra;
de Jong, Olivier G;
Lim, Wooi F;
Vader, Pieter;
El Andaloussi, Samir;
Bath, Jonathan;
Reine, Jesus;
Aoki, Yoshitsugu;
Turberfield, Andrew J;
Wood, Matthew J A;
Rinaldi, Carlo

Publication type:

Article

Alkylated DNA repair by a novel HhH-GPD family protein from Crenarchaea.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf012

By:

Zhang, Likui;
Gao, Tian;
Li, Zheng;
Chen, Cai;
Jiang, Donghao;
Yin, Youcheng;
Zheng, Yaqi;
Cao, Peng;
Gong, Yong;
Yang, Zhihui

Publication type:

Article

Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf003

By:

Helmling, Christina;
Chan, Alix I;
Cunningham, Christian N

Publication type:

Article

'Splice-at-will' Cas12a crRNA engineering enabled direct quantification of ultrashort RNAs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkaf002

By:

Fei, Xinrui;
Lei, Chao;
Ren, Wei;
Liu, Chenghui

Publication type:

Article

Novel archaeal ribosome dimerization factor facilitating unique 30S–30S dimerization.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1324

By:

Hassan, Ahmed H;
Pinkas, Matyas;
Yaeshima, Chiaki;
Ishino, Sonoko;
Uchiumi, Toshio;
Ito, Kosuke;
Demo, Gabriel

Publication type:

Article

Modular organization of enhancer network provides transcriptional robustness in mammalian development.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1323

By:

Lin, Hongli;
Ye, Xinyun;
Chen, Wenyan;
Hong, Danni;
Liu, Lifang;
Chen, Feng;
Sun, Ning;
Ye, Keying;
Hong, Jizhou;
Zhang, Yalin;
Lu, Falong;
Li, Lei;
Huang, Jialiang

Publication type:

Article

Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1322

By:

Djordjevic, Magdalena;
Zivkovic, Lidija;
Ou, Hong-Yu;
Djordjevic, Marko

Publication type:

Article

Transcription factors induce differential splicing of duplicated ribosomal protein genes during meiosis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1321

By:

Petibon, Cyrielle;
Catala, Mathieu;
Morales, Danna;
Panchapakesan, Shanker Shyam;
Unrau, Peter J;
Abou Elela, Sherif

Publication type:

Article

Single-nucleotide-resolution genomic maps of O<sup>6</sup>-methylguanine from the glioblastoma drug temozolomide.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1320

By:

Kubitschek, Jasmina;
Takhaveev, Vakil;
Mingard, Cécile;
Rochlitz, Martha I;
Reinert, Patricia B;
Keller, Giulia;
Kloter, Tom;
Fernández Cereijo, Raúl;
Huber, Sabrina M;
McKeague, Maureen;
Sturla, Shana J

Publication type:

Article

A trigger-inducible split-Csy4 architecture for programmable RNA modulation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1319

By:

Zhang, Lihang;
Qiu, Xinyuan;
Zhou, Yuting;
Luo, Zhengyang;
Zhu, Lingyun;
Shao, Jiawei;
Xie, Mingqi;
Wang, Hui

Publication type:

Article

A mobile genetic element-derived primase-polymerase harbors multiple activities implicated in DNA replication and repair.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1318

By:

Fu, Pan;
Wang, Yuwei;
Liu, Yanqiu;
Han, Zhenhao;
Peng, Zhangzhong;
Liu, Linfeng;
Han, Wenyuan

Publication type:

Article

A tunable and reversible thermo-inducible bio-switch for streptomycetes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1236

By:

Lv, Lanxin;
Liu, Shuo;
Fu, Yudie;
Zhang, Yuxin;
Wang, Meiyan;
Sun, Jiahe;
Wang, Yi;
Lu, Yinhua;
Niu, Guoqing

Publication type:

Article

Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1317

By:

Sen, Sagnik;
Estève, Pierre-Olivier;
Raman, Karthikeyan;
Beaulieu, Julie;
Chin, Hang Gyeong;
Feehery, George R;
Vishnu, Udayakumar S;
Xu, Shuang-yong;
Samuelson, James C;
Pradhan, Sriharsa

Publication type:

Article

Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1290

By:

Baral, Saroj;
Chakraborty, Sagnik;
Steinbach, Peter J;
Paul, Debamita;
Min, Jung-Hyun;
Ansari, Anjum

Publication type:

Article

Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1277

By:

Jungfer, Kenny;
Moravčík, Štefan;
Garcia-Doval, Carmela;
Knörlein, Anna;
Hall, Jonathan;
Jinek, Martin

Publication type:

Article

Generative design-enabled exploration of wireframe DNA origami nanostructures.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1268

By:

Vetturini, Anthony J;
Cagan, Jonathan;
Taylor, Rebecca E

Publication type:

Article

Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1240

By:

Kopczyńska, Magda;
Saha, Upasana;
Romanenko, Anastasiia;
Nojima, Takayuki;
Gdula, Michał R;
Kamieniarz-Gdula, Kinga

Publication type:

Article

A cross-species inducible system for enhanced protein expression and multiplexed metabolic pathway fine-tuning in bacteria.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1315

By:

Li, Yang;
Wu, Yaokang;
Xu, Xianhao;
Liu, Yanfeng;
Li, Jianghua;
Du, Guocheng;
Lv, Xueqin;
Li, Yangyang;
Liu, Long

Publication type:

Article

Cryo-EM structure of human TUT1:U6 snRNA complex.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1314

By:

Yamashita, Seisuke;
Tomita, Kozo

Publication type:

Article

Synthetic rational design of live-attenuated Zika viruses based on a computational model.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1313

By:

Roopin, Modi;
Zafrir, Zohar;
Siridechadilok, Bunpote;
Suphatrakul, Amporn;
Julander, Justin;
Tuller, Tamir

Publication type:

Article

inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1312

By:

Juzenas, Simonas;
Goda, Karolis;
Kiseliovas, Vaidotas;
Zvirblyte, Justina;
Quintinal-Villalonga, Alvaro;
Siurkus, Juozas;
Nainys, Juozas;
Mazutis, Linas

Publication type:

Article

GENA-LM: a family of open-source foundational DNA language models for long sequences.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1310

By:

Fishman, Veniamin;
Kuratov, Yuri;
Shmelev, Aleksei;
Petrov, Maxim;
Penzar, Dmitry;
Shepelin, Denis;
Chekanov, Nikolay;
Kardymon, Olga;
Burtsev, Mikhail

Publication type:

Article

DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1306

By:

Wirecki, Tomasz K;
Lach, Grzegorz;
Badepally, Nagendar Goud;
Moafinejad, S Naeim;
Jaryani, Farhang;
Klaudel, Gaja;
Nec, Kalina;
Baulin, Eugene F;
Bujnicki, Janusz M

Publication type:

Article

The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1305

By:

Ruggiero, Emanuela;
Marušič, Maja;
Zanin, Irene;
Peña Martinez, Cristian David;
Christ, Daniel;
Plavec, Janez;
Richter, Sara N

Publication type:

Article

Extensive homologous recombination safeguards oocyte genome integrity in mammals.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1304

By:

Cao, Huiwen;
Qiu, Cheng;
Fang, Anxuan;
Shang, Jianzhou;
Xu, Wei;
He, Lugeng;
Duan, Xing;
Zhang, Qianting;
Yu, Chao

Publication type:

Article

Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1301

By:

D'Halluin, Alexandre;
Gilet, Laetitia;
Lablaine, Armand;
Pellegrini, Olivier;
Serrano, Mónica;
Tolcan, Anastasia;
Ventroux, Magali;
Durand, Sylvain;
Hamon, Marion;
Henriques, Adriano O;
Carballido-López, Rut;
Condon, Ciarán

Publication type:

Article

The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1300

By:

Fournes, Florian;
Campos, Manuel;
Cury, Jean;
Schiavon, Caroline;
Pagès, Carine;
Touchon, Marie;
Rocha, Eduardo P C;
Rousseau, Philippe;
Cornet, François

Publication type:

Article

Mapping the spatial atlas of the human bone tissue integrating spatial and single-cell transcriptomics.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1298

By:

Lin, Weiqiang;
Li, Yisu;
Qiu, Chuan;
Zou, Binghao;
Gong, Yun;
Zhang, Xiao;
Tian, Di;
Sherman, William;
Sanchez, Fernando;
Wu, Di;
Su, Kuan-Jui;
Xiao, Xinyi;
Luo, Zhe;
Tian, Qing;
Chen, Yiping;
Shen, Hui;
Deng, Hongwen

Publication type:

Article

GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1295

By:

Ryu, Hyunwoo;
Han, Hyunho;
Kim, Chuna;
Kim, Jun

Publication type:

Article

Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1291

By:

Kasho, Kazutoshi;
Miyoshi, Kenya;
Yoshida, Mizuki;
Sakai, Ryuji;
Nakagawa, Sho;
Katayama, Tsutomu

Publication type:

Article

Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1224

By:

Szokoli, Deni;
Mutschler, Hannes

Publication type:

Article

Lig3-dependent rescue of mouse viability and DNA double-strand break repair by catalytically inactive Lig4.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1216

By:

Medina-Suárez, David;
Han, Li;
O'Reilly, Sandra;
Liu, Jiali;
Wei, Chao;
Brenière, Manon;
Goff, Noah J;
Chen, Chen;
Modesti, Mauro;
Meek, Katheryn;
Harrington, Bonnie;
Yu, Kefei

Publication type:

Article

Precision genome editing using combinatorial viral vector delivery of CRISPR-Cas9 nucleases and donor DNA constructs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1213

By:

Li, Zhen;
Wang, Xiaoling;
Janssen, Josephine M;
Liu, Jin;
Tasca, Francesca;
Hoeben, Rob C;
Gonçalves, Manuel A F V

Publication type:

Article

Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1209

By:

Zheng, Haifeng;
Liu, Xiyu;
Liu, Luhui;
Hu, Jiarui;
Chen, Xianjun

Publication type:

Article

Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1208

By:

Seth, Paul;
Xing, Eric;
Hendrickson, Andrew D;
Li, Kevin;
Monsen, Robert;
Chaires, Jonathan B;
Neidle, Stephen;
Yatsunyk, Liliya A

Publication type:

Article

Novel BRCA1–PLK1–CIP2A axis orchestrates homologous recombination-mediated DNA repair to maintain chromosome integrity during oocyte meiosis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1207

By:

Lee, Crystal;
Oh, Jeong Su

Publication type:

Article

Kinetoplast DNA: a polymer physicist's topological Olympic dream.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1206

By:

Michieletto, Davide

Publication type:

Article

Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1202

By:

Van Deynze, Kinsey;
Mumm, Camille;
Maltby, Connor J;
Switzenberg, Jessica A;
Todd, Peter K;
Boyle, Alan P

Publication type:

Article

BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1201

By:

Xu, Moping;
Liu, Xiaoyang;
Wang, Miao;
Luo, Tingting;
Gao, Yawei;
Liu, Jun;
Shi, Jiejun

Publication type:

Article

DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1188

By:

Ranjan, Venkatesh V;
Leighton, Gage O;
Yan, Chenbo;
Arango, Maria;
Lustig, Janna;
Corona, Rosario I;
Guo, Jun-Tao;
Nesmelov, Yuri E;
Ivics, Zoltán;
Nesmelova, Irina V

Publication type:

Article

The phage protein paratox is a multifunctional metabolic regulator of Streptococcus.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1200

By:

Muna, Tasneem Hassan;
Rutbeek, Nicole R;
Horne, Julia;
Lao, Ying W;
Krokhin, Oleg V;
Prehna, Gerd

Publication type:

Article

Structural plasticity of the coiled–coil interactions in human SFPQ.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1198

By:

Koning, Heidar J;
Lai, Jia Y;
Marshall, Andrew C;
Stroeher, Elke;
Monahan, Gavin;
Pullakhandam, Anuradha;
Knott, Gavin J;
Ryan, Timothy M;
Fox, Archa H;
Whitten, Andrew;
Lee, Mihwa;
Bond, Charles S

Publication type:

Article

The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1197

By:

Arpin, Dominic;
Palacios, Armando;
Basu, Kaustuv;
Ortega, Joaquin

Publication type:

Article

Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 2, p. 1, doi. 10.1093/nar/gkae1196

By:

Hasenauer, Flavia C;
Barreto, Hugo C;
Lotton, Chantal;
Matic, Ivan

Publication type:

Article