Works matching IS 03051048 AND DT 2024 AND VI 52 AND IP 9

Results: 46

SifiNet: a robust and accurate method to identify feature gene sets and annotate cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. e46, doi. 10.1093/nar/gkae307

By:

Gao, Qi;
Ji, Zhicheng;
Wang, Liuyang;
Owzar, Kouros;
Li, Qi-Jing;
Chan, Cliburn;
Xie, Jichun

Publication type:

Article

Genome-wide screening and functional validation of methylation barriers near promoters.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4857, doi. 10.1093/nar/gkae302

By:

Shu, Jingmin;
Jelinek, Jaroslav;
Chen, Hai;
Zhang, Yan;
Qin, Taichun;
Li, Ming;
Liu, Li;
Issa, Jean-Pierre J

Publication type:

Article

Correction to 'STIM1 translocation to the nucleus protects cells from DNA damage'.

Published in:: 2024
Publication type:: Correction Notice

High-density generation of spatial transcriptomics with STAGE.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4843, doi. 10.1093/nar/gkae294

By:

Li, Shang;
Gai, Kuo;
Dong, Kangning;
Zhang, Yiyang;
Zhang, Shihua

Publication type:

Article

Comprehensive genomic features indicative for Notch responsiveness.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5179, doi. 10.1093/nar/gkae292

By:

Giaimo, Benedetto Daniele;
Friedrich, Tobias;
Ferrante, Francesca;
Bartkuhn, Marek;
Borggrefe, Tilman

Publication type:

Article

SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5257, doi. 10.1093/nar/gkae290

By:

Wang, Xionglue;
Zhu, Bin

Publication type:

Article

Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m<sup>6</sup>A detection efficiency and calling bias correcting pipeline.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. e45, doi. 10.1093/nar/gkae288

By:

Dennis, Allison F;
Xu, Zhuwei;
Clark, David J

Publication type:

Article

Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5241, doi. 10.1093/nar/gkae283

By:

Olivi, Lorenzo;
Bagchus, Cleo;
Pool, Victor;
Bekkering, Ezra;
Speckner, Konstantin;
Offerhaus, Hidde;
Wu, Wen Y;
Depken, Martin;
Martens, Koen J A;
Staals, Raymond H J;
Hohlbein, Johannes

Publication type:

Article

m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4830, doi. 10.1093/nar/gkae280

By:

Ye, Haokai;
Li, Tenglong;
Rigden, Daniel J;
Wei, Zhen

Publication type:

Article

Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase β.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5392, doi. 10.1093/nar/gkae277

By:

Gao, Shijun;
Oden, Peyton N;
Ryan, Benjamin J;
Yang, Haozhe;
Freudenthal, Bret D;
Greenberg, Marc M

Publication type:

Article

CRISPR-Cas tools for simultaneous transcription & translation control in bacteria.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5406, doi. 10.1093/nar/gkae275

By:

Cardiff, Ryan A L;
Faulkner, Ian D;
Beall, Juliana G;
Carothers, James M;
Zalatan, Jesse G

Publication type:

Article

Comprehensive profiling of L1 retrotransposons in mouse.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5166, doi. 10.1093/nar/gkae273

By:

Zhang, Xuanming;
Celic, Ivana;
Mitchell, Hannah;
Stuckert, Sam;
Vedula, Lalitha;
Han, Jeffrey S

Publication type:

Article

Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4761, doi. 10.1093/nar/gkae267

By:

Nguyen, Hung;
Nguyen, Ha;
Tran, Duc;
Draghici, Sorin;
Nguyen, Tin

Publication type:

Article

Activity reconstitution of Kre33 and Tan1 reveals a molecular ruler mechanism in eukaryotic tRNA acetylation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5226, doi. 10.1093/nar/gkae262

By:

Ma, Chun-Rui;
Liu, Na;
Li, Hong;
Xu, Hong;
Zhou, Xiao-Long

Publication type:

Article

Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4799, doi. 10.1093/nar/gkae260

By:

Sarli, Samantha L;
Fakih, Hassan H;
Kelly, Karen;
Devi, Gitali;
Rembetsy-Brown, Julia M;
McEachern, Holly R;
Ferguson, Chantal M;
Echeverria, Dimas;
Lee, Jonathan;
Sousa, Jacquelyn;
Sleiman, Hanadi F;
Khvorova, Anastasia;
Watts, Jonathan K

Publication type:

Article

The discovery of novel noncoding RNAs in 50 bacterial genomes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5152, doi. 10.1093/nar/gkae248

By:

Narunsky, Aya;
Higgs, Gadareth A;
Torres, Blake M;
Yu, Diane;
de Andrade, Gabriel Belem;
Kavita, Kumari;
Breaker, Ronald R

Publication type:

Article

Caspase-mediated processing of TRBP regulates apoptosis during viral infection.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5209, doi. 10.1093/nar/gkae246

By:

Shibata, Keiko;
Moriizumi, Harune;
Onomoto, Koji;
Kaneko, Yuka;
Miyakawa, Takuya;
Zenno, Shuhei;
Tanokura, Masaru;
Yoneyama, Mitsutoshi;
Takahashi, Tomoko;
Ui-Tei, Kumiko

Publication type:

Article

A novel transient receptor potential C3/C6 selective activator induces the cellular uptake of antisense oligonucleotides.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4784, doi. 10.1093/nar/gkae245

By:

Kohashi, Hiroto;
Nagata, Ryu;
Tamenori, Yusuke;
Amatani, Tomorrow;
Ueda, Yoshifumi;
Mori, Yasuo;
Kasahara, Yuuya;
Obika, Satoshi;
Shimojo, Masahito

Publication type:

Article

RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5195, doi. 10.1093/nar/gkae243

By:

Skutel, Mikhail;
Yanovskaya, Daria;
Demkina, Alina;
Shenfeld, Aleksandr;
Musharova, Olga;
Severinov, Konstantin;
Isaev, Artem

Publication type:

Article

Retraction of 'Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR'.

Published in:: 2024
Publication type:: Correction Notice

Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4818, doi. 10.1093/nar/gkae215

By:

Lipps, Georg

Publication type:

Article

Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5138, doi. 10.1093/nar/gkae205

By:

Karri, Srinivasu;
Yang, Yi;
Zhou, Jiaqi;
Dickinson, Quinn;
Jia, Jing;
Huang, Yuxin;
Wang, Zhiquan;
Gan, Haiyun;
Yu, Chuanhe

Publication type:

Article

NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. e44, doi. 10.1093/nar/gkae197

By:

Ruiz-Arenas, Carlos;
Marín-Goñi, Irene;
Wang, Liewei;
Ochoa, Idoia;
Pérez-Jurado, Luis A;
Hernaez, Mikel

Publication type:

Article

S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5121, doi. 10.1093/nar/gkae192

By:

Bugallo, Alberto;
Sánchez, Mar;
Fernández-García, María;
Segurado, Mónica

Publication type:

Article

SIRT2 promotes base excision repair by transcriptionally activating OGG1 in an ATM/ATR-dependent manner.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5107, doi. 10.1093/nar/gkae190

By:

Geng, Anke;
Sun, Jiahui;
Tang, Huanyin;
Yu, Yang;
Wang, Xiyue;
Zhang, Jingyuan;
Wang, Xiaona;
Sun, Xiaoxiang;
Zhou, Xiaofang;
Gao, Neng;
Tan, Rong;
Xu, Zhu;
Jiang, Ying;
Mao, Zhiyong

Publication type:

Article

HBO1 determines SMAD action in pluripotency and mesendoderm specification.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4935, doi. 10.1093/nar/gkae158

By:

Zhang, Cong;
Shan, Yongli;
Lin, Huaisong;
Zhang, Yanqi;
Xing, Qi;
Zhu, Jinmin;
Zhou, Tiancheng;
Lin, Aiping;
Chen, Qianyu;
Wang, Junwei;
Pan, Guangjin

Publication type:

Article

LC3B drives transcription-associated homologous recombination via direct interaction with R-loops.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5088, doi. 10.1093/nar/gkae156

By:

Yoon, Junghyun;
Hwang, Yiseul;
Yun, Hansol;
Chung, Jee Min;
Kim, Soyeon;
Kim, Gyeongmin;
Lee, Yeji;
Lee, Byoung Dae;
Kang, Ho Chul

Publication type:

Article

CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5067, doi. 10.1093/nar/gkae154

By:

Batenburg, Nicole L;
Sowa, Dana J;
Walker, John R;
Andres, Sara N;
Zhu, Xu-Dong

Publication type:

Article

UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5376, doi. 10.1093/nar/gkae136

By:

Chapman, Joseph H;
Youle, Alice M;
Grimme, Acadia L;
Neuman, Keir C;
Hogg, J Robert

Publication type:

Article

Viral reprogramming of host transcription initiation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5016, doi. 10.1093/nar/gkae175

By:

Ungerleider, Nathan A;
Roberts, Claire;
O'Grady, Tina M;
Nguyen, Trang T;
Baddoo, Melody;
Wang, Jia;
Ishaq, Eman;
Concha, Monica;
Lam, Meggie;
Bass, Jordan;
Nguyen, Truong D;
Van Otterloo, Nick;
Wickramarachchige-Dona, Nadeeshika;
Wyczechowska, Dorota;
Morales, Maria;
Ma, Tianfang;
Dong, Yan;
Flemington, Erik K

Publication type:

Article

DNA-PKcs suppresses illegitimate chromosome rearrangements.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5048, doi. 10.1093/nar/gkae140

By:

Wang, Jinglong;
Sadeghi, Cheyenne A;
Frock, Richard L

Publication type:

Article

Defining the contribution of microRNA-specific Argonautes with slicer capability in animals.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5002, doi. 10.1093/nar/gkae173

By:

Pal, Anisha;
Vasudevan, Vaishnav;
Houle, François;
Lantin, Michael;
Maniates, Katherine A;
Huberdeau, Miguel Quévillon;
Abbott, Allison L;
Simard, Martin J

Publication type:

Article

Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4985, doi. 10.1093/nar/gkae170

By:

Kotagama, Kasuen;
Grimme, Acadia L;
Braviner, Leah;
Yang, Bing;
Sakhawala, Rima M;
Yu, Guoyun;
Benner, Lars Kristian;
Joshua-Tor, Leemor;
McJunkin, Katherine

Publication type:

Article

WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4969, doi. 10.1093/nar/gkae161

By:

Zhang, Jie;
Yu, Yuanyuan;
Zou, Xiuqun;
Du, Yaning;
Liang, Qiankun;
Gong, Mengyao;
He, Yurong;
Luo, Junqi;
Wu, Dandan;
Jiang, Xiaoli;
Sinclair, Matt;
Tajkhorshid, Emad;
Chen, Hong-Zhuan;
Hou, Zhaoyuan;
Zheng, Yuejuan;
Chen, Lin-Feng;
Yang, Xiao-Dong

Publication type:

Article

ATRX guards against aberrant differentiation in mesenchymal progenitor cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4950, doi. 10.1093/nar/gkae160

By:

Fang, Yan;
Barrows, Douglas;
Dabas, Yakshi;
Carroll, Thomas S;
Singer, Sam;
Tap, William D;
Nacev, Benjamin A

Publication type:

Article

Tracking pairwise genomic loci by the ParB–ParS and Noc-NBS systems in living cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4922, doi. 10.1093/nar/gkae134

By:

He, Xiaohui;
Tan, Yuxi;
Feng, Ying;
Sun, Yadong;
Ma, Hanhui

Publication type:

Article

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5033, doi. 10.1093/nar/gkae132

By:

Dagva, Oyut;
Thibessard, Annabelle;
Lorenzi, Jean-Noël;
Labat, Victor;
Piotrowski, Emilie;
Rouhier, Nicolas;
Myllykallio, Hannu;
Leblond, Pierre;
Bertrand, Claire

Publication type:

Article

The jet-like chromatin structure defines active secondary metabolism in fungi.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4906, doi. 10.1093/nar/gkae131

By:

Shao, Wenyong;
Wang, Jingrui;
Zhang, Yueqi;
Zhang, Chaofan;
Chen, Jie;
Chen, Yun;
Fei, Zhangjun;
Ma, Zhonghua;
Sun, Xuepeng;
Jiao, Chen

Publication type:

Article

RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5301, doi. 10.1093/nar/gkae112

By:

Scherer, Natalie M;
Maurel, Cindy;
Graus, Matthew S;
McAlary, Luke;
Richter, Grant;
Radford, Rowan A W;
Hogan, Alison;
Don, Emily K;
Lee, Albert;
Yerbury, Justin;
Francois, Mathias;
Chung, Roger S;
Morsch, Marco

Publication type:

Article

Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5356, doi. 10.1093/nar/gkae119

By:

Angel, Mor;
Fleshler, Eden;
Atrash, Mohammad Khaled;
Kinor, Noa;
Benichou, Jennifer I C;
Shav-Tal, Yaron

Publication type:

Article

RNA–RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4872, doi. 10.1093/nar/gkae116

By:

Ressel, Sarah;
Kumar, Sujai;
Bermúdez-Barrientos, Jose Roberto;
Gordon, Katrina;
Lane, Julia;
Wu, Jin;
Abreu-Goodger, Cei;
Schwarze, Jürgen;
Buck, Amy H

Publication type:

Article

Dynamics of miRNA accumulation during C. elegans larval development.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5336, doi. 10.1093/nar/gkae115

By:

Nahar, Smita;
Morales Moya, Lucas J;
Brunner, Jana;
Hendriks, Gert-Jan;
Towbin, Benjamin;
Hauser, Yannick P;
Brancati, Giovanna;
Gaidatzis, Dimos;
Großhans, Helge

Publication type:

Article

A Fur family protein BosR is a novel RNA-binding protein that controls rpoS RNA stability in the Lyme disease pathogen.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5320, doi. 10.1093/nar/gkae114

By:

Raghunandanan, Sajith;
Priya, Raj;
Alanazi, Fuad;
Lybecker, Meghan C;
Schlax, Paula Jean;
Yang, X Frank

Publication type:

Article

Processivity and specificity of histone acetylation by the male-specific lethal complex.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 4889, doi. 10.1093/nar/gkae123

By:

Kiss, Anna E;
Venkatasubramani, Anuroop V;
Pathirana, Dilan;
Krause, Silke;
Sparr, Aline Campos;
Hasenauer, Jan;
Imhof, Axel;
Müller, Marisa;
Becker, Peter B

Publication type:

Article

Cryo-EM structure of SRP68/72 reveals an extended dimerization domain with RNA-binding activity.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5285, doi. 10.1093/nar/gkae107

By:

Zhong, Yichen;
Feng, Junjie;
Koh, Adrian F;
Kotecha, Abhay;
Greber, Basil J;
Ataide, Sandro F

Publication type:

Article

A combinatorial approach for achieving CNS-selective RNAi.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5273, doi. 10.1093/nar/gkae100

By:

Ferguson, Chantal M;
Godinho, Bruno M D C;
Echeverria, Dimas;
Hassler, Matthew;
Vangjeli, Lorenc;
Sousa, Jacquelyn;
McHugh, Nicholas;
Alterman, Julia;
Hariharan, Vignesh;
Krishnamurthy, Pranathi Meda;
Watts, Jonathan;
Rogaev, Eveny;
Khvorova, Anastasia

Publication type:

Article