Article
Biochemistry & Molecular Biology
David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Geros, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R. Johnson, Hashem Koohy, Alison Simmons
Summary: This study uses single-cell RNA sequencing and spatial transcriptomics to investigate human intestinal development, identifying various cell states, developmental programs, and differentiation hierarchies. It provides insights into the formation of different cell types in the gut and offers valuable resources for further research in this field.
Article
Biochemistry & Molecular Biology
Marcio L. Acencio, Miguel Vazquez, Konika Chawla, Astrid Laegreid, Martin Kuiper
Summary: Prior knowledge of transcription factors is crucial for understanding transcriptional regulation. TFCheckpoint 2.0 is an integrated resource that provides an easy and versatile cross-referencing system for viewing and downloading collections of transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemical Research Methods
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernandez
Summary: Pathway enrichment analysis is widely used for interpreting biomedical data, but its results are influenced by various factors. Benchmark studies have evaluated these factors and identified key influences on the analysis results.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Jaydeep Sidhaye, Philipp Trepte, Natalie Sepke, Maria Novatchkova, Michael Schutzbier, Gerhard Duernberger, Karl Mechtler, Juergen A. Knoblich
Summary: By analyzing the transcriptome and epigenome during human corticogenesis, important gene regulatory networks have been identified. Through the use of human brain organoids, specific transcriptome and proteome analyses were conducted, revealing gene expression modules during cortical development. One module involving mTOR-mediated regulation of translation was investigated, showing that partial inhibition of ribosomal genes translation prevents premature translation of differentiation markers, crucial for maintaining the accuracy of cortical development.
Article
Biochemical Research Methods
Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks
Summary: Tools from graph signal processing, specifically the graph Laplacian, have been successfully used to model neural activity and investigate structure-function relationships in the human brain. The models, called graph neural fields, allow for predictions of harmonic and temporal power spectra, functional connectivity, and coherence matrices. This approach, applied directly on the human connectome graph, provides insights into the organization of brain activity and potential avenues for future research.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kenneth C. Smith, Daniel G. Chawla, Bhavjinder K. Dhillon, Zhou Ji, Randi Vita, Eva C. van der Leest, Jing Yi Jessica Weng, Ernest Tang, Amani Abid, Bjoern Peters, Robert E. W. Hancock, Aris Floratos, Steven H. Kleinstein
Summary: Advancements in high-throughput experiments and systems biology approaches have led to the identification of immune signatures. However, these signatures are often presented in a format that is not suitable for computational processing, hindering our ability to fully utilize this information. In this study, a data model and a web-enabled application were developed to facilitate the access and querying of immune signatures.
Article
Multidisciplinary Sciences
Liang Chen, Weidi Wang, Wenxiang Cai, Weichen Song, Wei Qian, Guan Ning Lin
Summary: Deletions and duplications of chromosome 7q11.23 CNVs are associated with psychiatric disorders, with specific brain regions and developmental stages playing vital roles. 7q11.23 genes converge on the DNA repair pathway, impacting brain development and contributing to the pathogenesis of psychiatric diseases.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jianguo Wang, Sidi Ma, Peijie Yu, Xionglei He
Summary: The human brain exhibits anatomical symmetry, but also possesses fine-scale structural asymmetries that contribute to distinct functional divisions. Previous studies suggested that these asymmetric structures are primate specific or unique to humans, indicating recent evolution of genes responsible for human brain asymmetry. In our study, we identified over 1,500 traits associated with human brain asymmetry and discovered approximately 200 genes that are predominantly upregulated in brain tissues. Surprisingly, these genes are evolutionarily ancient and show brain-specific upregulation in humans, indicating the role of ancient genes in shaping the structural asymmetry of the human brain over time.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Neurosciences
Jian Li, Yijun Liu, Jessica L. Wisnowski, Richard M. Leahy
Summary: The human brain exhibits dynamic fluctuations in activity across space and time. By combining a temporal synchronization process (BrainSync) and a three-way tensor decomposition method (NASCAR), we can jointly analyze rs-fMRI data from multiple subjects without imposing unnatural constraints. The resulting interacting networks represent functionally coherent activity across the brain and can be clustered into distinct functional categories, forming a representative functional network atlas for a healthy population. This atlas can be used to explore group and individual differences in neurocognitive function, as demonstrated in the context of ADHD and IQ prediction.
Article
Multidisciplinary Sciences
Neil A. Gilbert, Jennifer L. Stenglein, Jonathan N. Pauli, Benjamin Zuckerberg
Summary: Human disturbance can alter species interactions and increase co-occurrence within wildlife communities. A study in Wisconsin, USA, using camera traps, found that disturbed landscapes had shorter time intervals between species detections, indicating increased interactions. The compressed co-occurrence may intensify competition, predation, and infection, causing stress in individual animals and cascading effects in populations, communities, and ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Xueyuan Cao, Stan Pounds
Summary: GSDA is a powerful method for evaluating the association of gene sets with variables, capable of identifying complex non-monotonic gene-set associations that may be missed by other methods.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Dan Wu, Linda J. Richards, Zhiyong Zhao, Zuozhen Cao, Wanrong Luo, Wei Shao, Song-Hai Shi, Michael Miller, Susumu Mori, Seth Blackshaw, Jiangyang Zhang
Summary: The study reconstructed a four-dimensional continuum of the embryonic mouse brain from E10.5 to E15.5, revealing morphological and microscopic changes in the developing brain and correlating gene expression data with neuroanatomical changes. By identifying developmental modes and regional clusters, it demonstrates how this method can be used to analyze interactions between upstream genetic events and anatomical changes in brain development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Chen-An Tsai, James J. Chen
Summary: This study introduces a new gene set analysis framework, GSCoA, which identifies differentially expressed gene sets and highly correlated pathways by simultaneously measuring within and between gene set variation. Co-inertia analysis is applied to compare gene sets in gene expression data and measure the co-structure of expression profiles. Results demonstrate that combining co-inertia analysis and gene set enrichment analysis effectively reveals relationships between gene sets significantly associated with phenotypes.
CURRENT BIOINFORMATICS
(2021)
Article
Toxicology
Hideki Hiraoka, Ryosuke Nomura, Nobumasa Takasugi, Ryoko Akai, Takao Iwawaki, Yoshito Kumagai, Masatake Fujimura, Takashi Uehara
Summary: The study found that MeHg-induced neuronal cell death may be caused by ER stress and UPR shift, rather than just ER stress. These results suggest that UPR modulation could be a therapeutic target for treating neuropathy caused by MeHg or similar electrophiles.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Genetics & Heredity
Shur-Jen Wang, Kent C. Brodie, Jeffrey L. De Pons, Wendy M. Demos, Adam C. Gibson, G. Thomas Hayman, Morgan L. Hill, Mary L. Kaldunski, Logan Lamers, Stanley J. F. Laulederkind, Harika S. Nalabolu, Jyothi Thota, Ketaki Thorat, Marek A. Tutaj, Monika Tutaj, Mahima Vedi, Stacy Zacher, Jennifer R. Smith, Melinda R. Dwinell, Anne E. Kwitek
Summary: The COVID-19 pandemic has led to an increase in scientific literature about SARS-CoV-2 infection and its health impact. The Rat Genome Database (RGD) has created a COVID-19 Disease Portal to utilize information from this literature. Using curated data and analysis tools, the portal provides insights into the genes associated with COVID-19 and their relationship with various diseases. The portal can generate new hypotheses for potential therapies and prevention strategies for COVID-19.