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Genes, Volume 14, Issue 1

January 2023 - 237 articles

Cover Story: The genome-wide association study (GWAS) has been in use for 15 years. It has made immense progress in multiple fields from medicine to crop breeding. Although the methodology under the hood of GWAS has been improving, there is a substantial lack of easy-to-use tools for GWAS utilization. One such improved GWAS is the synthetic phenotype to causative mutation strategy (SP2CM) that enables causative mutation (CM) identification through accuracy calculation. AccuCalc is a Python package for convenient SP2CM strategy utilization for every species. AccuCalc has three inputs: genotype (vcf or hmp), binary phenotype (synthetic or observed) and GWAS result (p-values). Conclusion, AccuCalc creates synthetic phenotypes, calculates accuracy and draws Manhattan plots accentuated by accuracy. AccuCalc is especially beneficial for CM identification of rare phenotypes where GWAS would be underpowered. View this paper
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Articles (237)

  • Article
  • Open Access
7 Citations
2,719 Views
16 Pages

Pathogenicity of PKCγ Genetic Variants—Possible Function as a Non-Invasive Diagnostic Biomarker in Ovarian Cancer

  • Kanza Shahid,
  • Khushbukhat Khan,
  • Yasmin Badshah,
  • Naeem Mahmood Ashraf,
  • Arslan Hamid,
  • Janeen H. Trembley,
  • Maria Shabbir,
  • Tayyaba Afsar,
  • Ali Almajwal and
  • Ali Abusharha
  • + 1 author

16 January 2023

Ovarian cancer has the highest mortality rate among gynecologic malignancies, owing to its misdiagnosis or late diagnosis. Identification of its genetic determinants could improve disease outcomes. Conventional Protein Kinase C-γ (PKCγ) d...

  • Article
  • Open Access
5 Citations
3,355 Views
16 Pages

Development of Toehold Switches as a Novel Ribodiagnostic Method for West Nile Virus

  • Antonis Giakountis,
  • Zoe Stylianidou,
  • Anxhela Zaka,
  • Styliani Pappa,
  • Anna Papa,
  • Christos Hadjichristodoulou and
  • Kostas D. Mathiopoulos

16 January 2023

West Nile virus (WNV) is an emerging neurotropic RNA virus and a member of the genus Flavivirus. Naturally, the virus is maintained in an enzootic cycle involving mosquitoes as vectors and birds that are the principal amplifying virus hosts. In human...

  • Communication
  • Open Access
4 Citations
2,828 Views
9 Pages

16 January 2023

Sperm sexing is a technique for spermatozoa sorting into populations enriched with X- or Y-chromosome-bearing cells and is widely used in the dairy industry. Investigation of the characteristics of sorted semen is of practical interest, because it co...

  • Review
  • Open Access
4 Citations
5,556 Views
16 Pages

Methodological Changes in the Field of Paleogenetics

  • Mikołaj Danielewski,
  • Joanna Żuraszek,
  • Aleksandra Zielińska,
  • Karl-Heinz Herzig,
  • Ryszard Słomski,
  • Jarosław Walkowiak and
  • Karolina Wielgus

16 January 2023

Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool c...

  • Article
  • Open Access
5 Citations
4,452 Views
10 Pages

16 January 2023

Background: Due to the extreme infectivity of SARS-CoV-2, sample-to-answer SARS-CoV-2 reverse transcription (RT) polymerase chain reaction (PCR) assays are urgently needed in order to facilitate infectious disease surveillance and control. The purpos...

  • Article
  • Open Access
10 Citations
4,767 Views
13 Pages

Genetic and Morphological Variation in Hypodontia of Maxillary Lateral Incisors

  • Bernadette Kerekes-Máthé,
  • Krisztina Mártha,
  • Claudia Bănescu,
  • Matthew Brook O’Donnell and
  • Alan H. Brook

16 January 2023

(1) Background: Hypodontia has a multifactorial aetiology, in which genetic factors are a major component. Associated with this congenital absence, the formed teeth may show differences in size and shape, which may vary with the specific genetic vari...

  • Communication
  • Open Access
1 Citations
2,385 Views
9 Pages

16 January 2023

Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidr...

  • Article
  • Open Access
5 Citations
3,000 Views
9 Pages

Transcriptome Profiling of Developing Testes and First Wave of Spermatogenesis in the Rat

  • Yan Zhang,
  • Zaixia Liu,
  • Xia Yun,
  • Baiyin Batu,
  • Zheng Yang,
  • Xinlai Zhang,
  • Wenguang Zhang and
  • Taodi Liu

16 January 2023

Spermatogenesis is a complicated course of several rigorous restrained steps that spermatogonial stem cells undergo to develop into highly specialized spermatozoa; however, specific genes and signal pathways, which regulate the amplification, differe...

  • Article
  • Open Access
11 Citations
4,642 Views
14 Pages

Metatranscriptomic Analyses Reveal Important Roles of the Gut Microbiome in Primate Dietary Adaptation

  • Mingyi Zhang,
  • Xiaochen Wang,
  • Ziming Wang,
  • Shuxin Mao,
  • Jiali Zhang,
  • Ming Li and
  • Huijuan Pan

15 January 2023

The gut microbiome plays a vital role in host ecological adaptation, especially dietary adaptations. Primates have evolved a variety of dietary and gut physiological structures that are useful to explore the role of the gut microbiome in host dietary...

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Genes - ISSN 2073-4425