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Genes, Volume 16, Issue 1

2025 January - 109 articles

Cover Story: With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical elements. In this paper, we thoroughly discuss the use of cloud data warehouses to address these challenges. We propose a data management and analysis framework using Snowflake, a SaaS-based data platform. It provides convenience and effectiveness through concrete examples, such as disease variant analysis and in silico drug discovery. By introducing Snowflake, researchers can efficiently manage and analyze a wide array of biological data, enabling the discovery of new biological insights through integrated analyses. View this paper
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Articles (109)

  • Article
  • Open Access
2 Citations
2,400 Views
20 Pages
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Genome-Wide Identification and Characterization of the CDPK Family of Genes and Their Response to High-Calcium Stress in Yinshania henryi

  • Liangfeng An,
  • Huihui Fang,
  • Ximin Zhang,
  • Jing Tang,
  • Jiyi Gong,
  • Yin Yi and
  • Ming Tang
Genes2025, 16(1), 109;https://doi.org/10.3390/genes16010109

20 January 2025

Background/Objectives: Calcium-dependent protein kinases (CDPKs) are a crucial class of calcium-signal-sensing and -response proteins that significantly regulate abiotic stress. Yinshania henryi is a member of the Brassicaceae family that primarily g...

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  • Article
  • Open Access
6,276 Views
17 Pages
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Atypical Leber Hereditary Optic Neuropathy (LHON) Associated with a Novel MT-CYB:m.15309T>C(Ile188Thr) Variant

  • Sanja Petrovic Pajic,
  • Ana Fakin,
  • Martina Jarc-Vidmar,
  • Maja Sustar Habjan,
  • Lucija Malinar,
  • Kasja Pavlovic,
  • Nina Krako Jakovljevic,
  • Andjelka Isakovic,
  • Sonja Misirlic-Dencic and
  • Marko Hawlina
  • + 7 authors
Genes2025, 16(1), 108;https://doi.org/10.3390/genes16010108

20 January 2025

Background: The study presents a detailed examination and follow-up of a Slovenian patient with an Leber Hereditary Optic Neuropathy (LHON)-like phenotype and bilateral optic neuropathy in whom genetic analysis identified a novel variant MT-CYB:m.153...

Full Article
  • Review
  • Open Access
5 Citations
14,072 Views
20 Pages
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Gene Therapy and Diabetes: A Narrative Review of Recent Advances and the Role of Multidisciplinary Healthcare Teams

  • Nadia Khartabil and
  • Ani Avoundjian
Genes2025, 16(1), 107;https://doi.org/10.3390/genes16010107

20 January 2025

Introduction: Gene therapy has emerged as a promising frontier in the management of diabetes, offering innovative approaches to address both type 1 and type 2 diabetes. This narrative review examines the advancements in gene therapy applications, foc...

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  • Article
  • Open Access
4,476 Views
22 Pages
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Origin and Genealogy of Rare mtDNA Haplotypes Detected in the Serbian Population

  • Slobodan Davidović,
  • Jelena M. Aleksić,
  • Marija Tanasković,
  • Pavle Erić,
  • Milena Stevanović and
  • Nataša Kovačević-Grujičić
Genes2025, 16(1), 106;https://doi.org/10.3390/genes16010106

20 January 2025

Background: The Balkan Peninsula has served as an important migration corridor between Asia Minor and Europe throughout humankind’s history and a refugium during the Last Glacial Maximum. Past migrations such as the Neolithic expansion, Bronze...

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  • Article
  • Open Access
2 Citations
1,778 Views
17 Pages
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Transcriptome Reveals the Differential Regulation of Sugar Metabolism to Saline–Alkali Stress in Different Resistant Oats

  • Naiyu Chen,
  • Shuya Xing,
  • Jiaxin Song,
  • Shutong Lu,
  • Lei Ling and
  • Lina Qu
Genes2025, 16(1), 105;https://doi.org/10.3390/genes16010105

20 January 2025

Background: Saline–alkali stress is a major factor limiting the growth of oats. Sugar is the primary carbon and energy source in plants which regulates plant development and growth by regulating enzyme activity and gene expression. Sucrose, glu...

Full Article
  • Article
  • Open Access
1,351 Views
9 Pages
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The Epigenetic Machinery and Energy Expenditure: A Network to Be Revealed

  • Elisabetta Prada,
  • Giulia Bruna Marchetti,
  • Denise Pires Marafon,
  • Alessandra Mazzocchi,
  • Giulietta Scuvera,
  • Lidia Pezzani,
  • Carlo Agostoni and
  • Donatella Milani
Genes2025, 16(1), 104;https://doi.org/10.3390/genes16010104

19 January 2025

Mendelian disorders of the epigenetic machinery (MDEMs) include a large number of conditions caused by defective activity of a member of the epigenetic machinery. MDEMs are characterized by multiple congenital abnormalities, intellectual disability a...

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  • Feature Paper
  • Article
  • Open Access
2,533 Views
14 Pages
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Arabidopsis thaliana DNA Damage Response Mutants Challenged with Genotoxic Agents—A Different Experimental Approach to Investigate the TDP1α and TDP1β Genes

  • Anna Bertoncini,
  • Paola Pagano and
  • Anca Macovei
Genes2025, 16(1), 103;https://doi.org/10.3390/genes16010103

19 January 2025

Background/Objectives: DNA damage response (DDR) is a highly conserved and complex signal transduction network required for preserving genome integrity. DNA repair pathways downstream of DDR include the tyrosyl-DNA phosphodiesterase1 (TDP1) enzyme th...

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  • Feature Paper
  • Article
  • Open Access
1 Citations
6,723 Views
14 Pages
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Genomic Rewilding of Domestic Animals: The Role of Hybridization and Selection in Wolfdog Breeds

  • Alžběta Báčová,
  • José Ignacio Lucas Lledó,
  • Kristýna Eliášová,
  • Silvie Neradilová,
  • Astrid Vik Stronen,
  • Romolo Caniglia,
  • Marco Galaverni,
  • Elena Fabbri,
  • Frederica Mattucci and
  • Barbora Černá Bolfíková
  • + 2 authors
Genes2025, 16(1), 102;https://doi.org/10.3390/genes16010102

19 January 2025

Background/Objectives: The domestication of the grey wolf (Canis lupus) and subsequent creation of modern dog breeds have significantly shaped the genetic landscape of domestic canines. This study investigates the genomic effects of hybridization and...

Full Article
  • Article
  • Open Access
5 Citations
2,523 Views
20 Pages
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Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA

  • Prawin Rimal,
  • Shamrat Kumar Paul,
  • Shailesh Kumar Panday and
  • Emil Alexov
Genes2025, 16(1), 101;https://doi.org/10.3390/genes16010101

19 January 2025

Background/Objectives: Predicting the effects of protein and DNA mutations on the binding free energy of protein–DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions invol...

Full Article
  • Review
  • Open Access
4 Citations
4,074 Views
13 Pages
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History of Biological Databases, Their Importance, and Existence in Modern Scientific and Policy Context

  • Mikołaj Danielewski,
  • Marlena Szalata,
  • Jan Krzysztof Nowak,
  • Jarosław Walkowiak,
  • Ryszard Słomski and
  • Karolina Wielgus
Genes2025, 16(1), 100;https://doi.org/10.3390/genes16010100

18 January 2025

With the development of genome sequencing technologies, the amount of data produced has greatly increased in the last two decades. The abundance of digital sequence information (DSI) has provided research opportunities, improved our understanding of...

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Genes - ISSN 2073-4425
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