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Sequence motif analysis

Analysis and comparison of the bacterial σ⁵⁴ regulon: Evidence of phylogenetic trends in gene regulation

Maricela Carrera-Reyna, Edna Cruz-Flores, Enrique Merino

published 01 Aug 2025

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Positional distribution of transcription factor binding sites in the human genome

Chun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen-Hsiung Li

published 30 Jul 2025

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The genetic context of bla_IMP varies among bacterial families from One Health sources

Susan Vaughn Grooters, Dixie F. Mollenkopf, Thomas E. Wittum

published 23 Jul 2025

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Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression

Nick Kinney, Dikshya Pathak, Emma Evans, Paola Arias

published 18 Jun 2025

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DeepRice6mA: A convolutional neural network approach for 6mA site prediction in the rice Genome

Hussam Alsharif

published 18 Jun 2025

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Genome-wide identification and characterization of Ethylene-Insensitive 3 (EIN3/EIL) gene family in Camellia oleifera

Shihang Huang, Fang Li, Caiqin Li, Xiaobei Li, Qiuling Pan, Yongquan Li, Wenpei Song, Juan Li

published 23 May 2025

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Evolution and classification of Ser/Thr phosphatase PP2C family in bacteria: Sequence conservation, structures, domain distribution

Hang Li, Rui Li, Haoyue Yu, Youhuan Zhang, Hong Feng

published 19 May 2025

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Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

Emily L. Bean, Janet L. Smith, Alan D. Grossman

published 16 May 2025

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Characterization and identification of extrachromosomal circular DNA in cholangiocarcinoma

Zar Zar Win, Hasaya Dokduang, Siriyakorn Kulwong, Watcharin Loilome, Nisana Namwat, Jutarop Phetcharaburanin, Thidathip Wongsurawat, Piroon Jenjaroenpun, Poramate Klanrit, Arporn Wangwiwatsin

published 05 May 2025

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Epigenetic background of lineage-specific gene expression landscapes of four Staphylococcus aureus hospital isolates

Ilya S. Korotetskiy, Sergey V. Shilov, Tatyana V. Kuznetsova, Natalya Zubenko, Lyudmila Ivanova, Oleg N. Reva

published 05 May 2025

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Coevolution in human small Heat Shock Protein 1 is promoted by interactions between the Alpha-Crystallin domain and the disordered regions

Vanesa Racigh, Luciana Rodriguez Sawicki, Facundo Nicolas Eric Bravo, Maria Silvina Fornasari

published 05 May 2025

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A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification

Loïc Omnes, Eric Angel, Pierre Bartet, François Radvanyi, Fariza Tahi

published 25 Apr 2025

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Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST

Avneesh Chopra, Jiahui Song, January Weiner 3rd, Dieter Beule, Arne S. Schaefer

published 24 Mar 2025

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