Transcriptomics for clinical and experimental biology research: hang on a seq

T Stokes, HH Cen, P Kapranov, IJ Gallagher… - Advanced …, 2023 - Wiley Online Library
Sequencing the human genome empowers translational medicine, facilitating transcriptome‐
wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are …

SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding

Z Yang, C Luo, X Pei, S Wang, Y Huang… - Nucleic Acids …, 2024 - academic.oup.com
Advanced multi-omics technologies offer much information that can uncover the regulatory
mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases …

Cross-ancestry atlas of gene, isoform, and splicing regulation in the develo** human brain

C Wen, M Margolis, R Dai, P Zhang, PF Przytycki… - Science, 2024 - science.org
Neuropsychiatric genome-wide association studies (GWASs), including those for autism
spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the …

COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations

T Obayashi, S Kodate, H Hibara, Y Kagaya… - Nucleic Acids …, 2023 - academic.oup.com
Gene coexpression is synchronization of gene expression across many cellular and
environmental conditions and is widely used to infer the biological function of genes. Gene …

Accurately modeling biased random walks on weighted networks using node2vec+

R Liu, M Hirn, A Krishnan - Bioinformatics, 2023 - academic.oup.com
Motivation Accurately representing biological networks in a low-dimensional space, also
known as network embedding, is a critical step in network-based machine learning and is …

[HTML][HTML] Importance of transcript variants in transcriptome analyses

K Vo, Y Sharma, A Paul, R Mohamadi, A Mohamadi… - Cells, 2024 - mdpi.com
RNA sequencing (RNA-Seq) has become a widely adopted technique for studying gene
expression. However, conventional RNA-Seq analyses rely on gene expression (GE) values …

Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New …

A Bullones, AJ Castro, E Lima-Cabello… - Plants, 2023 - mdpi.com
The pollen tube is a key innovation of land plants that is essential for successful fertilisation.
Its development and growth have been profusely studied in model organisms, but in spite of …

[HTML][HTML] Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the develo** human brain

C Wen, M Margolis, R Dai, P Zhang, PF Przytycki… - medRxiv, 2023 - ncbi.nlm.nih.gov
Genomic regulatory elements active in the develo** human brain are notably enriched in
genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD) …

Network-based drug repurposing for schizophrenia

TTT Truong, ZSJ Liu, B Panizzutti, JH Kim… - …, 2024 - nature.com
Despite recent progress, the challenges in drug discovery for schizophrenia persist.
However, computational drug repurposing has gained popularity as it leverages the wealth …

From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology

JM Acién, E Cañizares, H Candela… - International Journal of …, 2023 - mdpi.com
The selection of plant genotypes with improved productivity and tolerance to environmental
constraints has always been a major concern in plant breeding. Classical approaches …