Article
Biochemistry & Molecular Biology
Adam H. Freedman, Michele Clamp, Timothy B. Sackton
Summary: De novo transcriptome assembly is a powerful tool for evolutionary inferences, but it often faces bias and noise issues in data analysis, leading to underestimation of diversity and gene expression estimates. Researchers should look for ways to minimize the impact of bias in transcriptome assemblies.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Devon A. DeRaad, Marlon E. Cobos, Abdelghafar Alkishe, Uzma Ashraf, Koffi Mensah Ahadji-Dabla, Claudia Nunez-Penichet, A. Townsend Peterson
Summary: The concept of fundamental ecological niche is crucial for various ecological questions. This study examined the potential role of genome environment association (GEA) testing in understanding genetic basis of ecological niche using genomic data from Anopheles gambiae 1000 Genomes Consortium. The results indicated that while commonly implemented GEA methods can account for confounding patterns of genetic variation, challenges remain in discerning true signals of genome environment adaptation.
Article
Biology
Paul Anderson, Richa Gadgil, William A. Johnson, Ella Schwab, Jean M. Davidson
Summary: Deep learning neural networks have shown improved performance in breast cancer subtype classification, but face issues of parameter diversity and distribution mismatch. Embedding prior knowledge from literature can enhance predictive models, particularly in breast cancer research which offers abundant knowledge on subtype biomarkers and genetic signatures.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Editorial Material
Multidisciplinary Sciences
Amber Dance
Summary: Methods that combine imaging with sequencing are revealing the organizational principles of the genome and its impact on cell fates.
Article
Oncology
Christopher P. Wardell, Emilie Darrigues, Annick De Loose, Madison P. Lee, Murat Gokden, Issam Makhoul, Alan J. Tackett, Analiz Rodriguez
Summary: Brain metastases are the most common brain tumors in adults, with most mutations occurring before metastasis and a specific copy number event identified. Melanoma BMs show distinct characteristics compared to other subtypes, and poor survival is associated with race and treatment options.
Article
Genetics & Heredity
Musu Yuan, Liang Chen, Minghua Deng
Summary: Single-cell multiomics sequencing techniques, such as CITE-seq, provide a powerful tool for simultaneous quantification of gene expression and surface proteins. However, clustering analysis of CITE-seq data is challenging due to noise, high dimensionality, and sparsity. To address these challenges, researchers proposed scCTClust, a method that utilizes omics-specific neural networks to extract cluster information, finds maximally correlated representations of two omics, and applies decentralized clustering to the combined representations. Extensive experiments demonstrated the effectiveness of scCTClust and its potential for generalization to different data sets.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Editorial Material
Biochemistry & Molecular Biology
Sarah J. Salisbury, M. Lisette Delgado, Anne C. Dalziel
Summary: The research highlights the importance of alternative splicing as a potential mechanism underlying local adaptation, showing that different regulatory mechanisms may affect different cellular traits to complementarily alter organismal phenotype. Genetic basis may play a role in the regulatory divergence, with DE and DS genes more likely to be hub genes and have a variety of phenotypic effects, suggesting a complex interplay of gene expression and splicing in adaptive divergence.
Article
Biochemistry & Molecular Biology
Kathrin A. Otte
Summary: This article presents a new approach to genotype-environment association (GEA) studies called genomic window analysis, which combines the information of neighboring single-nucleotide polymorphisms (SNPs) to enhance the detection of genomic signals of environmental adaptation. The method is proven to be superior to several established GEA approaches, especially in cases with small sample sizes, through simulations and real data analysis.
MOLECULAR ECOLOGY RESOURCES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Lars Opgenoorth, Christian Rellstab
Summary: The study of drought resistance in white spruce utilized multiple data sources and analytical approaches to identify candidate genes involved in growth and resistance to extreme drought events, showcasing how diverse datasets can provide complementary evidence to overcome challenges in the research field.
Article
Oncology
Chie Kikutake, Mikita Suyama
Summary: This study investigates the association between mutations in open chromatin regions and their possible functions. The findings suggest that highly mutated open chromatin regions play an important role in cancer pathogenesis and are associated with patient prognosis.
Article
Biochemistry & Molecular Biology
Tania Chavarria-Pizarro, Philipp Resl, Aleksandar Janjic, Silke Werth
Summary: Anthropogenic climate change has caused unprecedented temperature shifts in many ecosystems, leading organisms to adjust gene expression to cope with novel thermal conditions. Lobaria pulmonaria lichens demonstrate the ability to acclimate to new habitats through transcriptomic convergence, although their long-term survival may be impacted negatively by rising temperatures and decreasing precipitation levels associated with global climate change.
Review
Biochemistry & Molecular Biology
Edson Ishengoma
Summary: Africa is the birthplace of humankind and home to the most diverse wildlife and flora. Understanding genetic variation and adaptation is crucial for the sustainable utilization of Africa's biodiversity. Despite a lag in genomics research, African scientists are increasingly interested in using omics technology to study native African species. This overview on vertebrate biodiversity in Africa aims to provide insights from prior genomics research and guide future studies.
Article
Biotechnology & Applied Microbiology
Ravi S. Pandey, Kevin P. Kotredes, Michael Sasner, Gareth R. Howell, Gregory W. Carter
Summary: By analyzing gene splicing patterns in aging mouse models carrying humanized APOE4 and/or Trem2*R47H variant, it is found that differentially expressed genes are enriched in AD-related pathways, while differentially spliced genes are enriched in neuronal functions. Significant overlap is observed between differentially spliced genes in Trem2*R47H mice and human AD subjects, suggesting a link between Trem2*R47H and molecular signatures of LOAD.
Article
Biochemistry & Molecular Biology
William Hemstrom, Melissa Jones
Summary: Genomic data analysis can be intimidating, especially for researchers without programming experience. snpR is a user-friendly R package that automates data subsetting and analysis based on categorical metadata, integrating methods from multiple packages to streamline repeated analyses.
MOLECULAR ECOLOGY RESOURCES
(2023)
