Article
Multidisciplinary Sciences
Surama Biswas, Santosh Manicka, Erik Hoel, Michael Levin
Summary: Studies have shown that gene regulatory networks possess various types of memory, which is important for understanding the variability and time-dependent changes of drug action. Defining and identifying memory through a computational framework is beneficial for the biomedical field. Timed stimuli offer a powerful alternative for controlling complex in vivo dynamics.
Article
Oncology
Rika Tyebally, Angli Xue, Joseph E. Powell
Summary: Complex diseases exhibit heterogeneity in treatment response due to genetic and environmental variations. Integrating GWAS and eQTL analyses can identify cell-type specific candidate genes and pathways relevant to the disease, which can be applied to patient stratification and novel therapeutic target identification.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Review
Biochemical Research Methods
Debomita Chakraborty, Raghunathan Rengaswamy, Karthik Raman
Summary: This paper systematically organizes key works in the field of genetic circuit design using the framework of generalized morphological analysis. It maps literature based on design methodologies, modeling techniques, circuit functionalities, design characteristics, and strategies for robust design. The paper concludes with an outlook on future research areas based on the assessment of research gaps.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Ju Xiang, Jiashuai Zhang, Ruiqing Zheng, Xingyi Li, Min Li
Summary: Predicting disease-related genes is crucial for disease research, but existing methods have limitations. A network impulsive dynamics on multiplex biological network (NIDM) framework was proposed for disease-gene prediction, showing superior performance in experimental evaluations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Medicine, Research & Experimental
Jianan Xu, Yuanyuan Sun, Weineng Fu, Shuang Fu
Summary: Myc target 1 (MYCT1), located at 6q25.2, is a crucial player in cancer development with widely distributed expression in cells and variable subcellular localization across different cancer types. It is regulated by multiple transcription factors and aberrant expression of MYCT1 impacts key biological processes and tumor immune responses in cancer cells. Despite some debated functions, MYCT1 holds undeniable significance in cancer development. This review aims to comprehensively examine the relationship between MYCT1 and cancer, providing valuable insights for cancer diagnosis and treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Biochemical Research Methods
Meriem Mekedem, Patrice Ravel, Jacques Colinge
Summary: Advancements in high-throughput genomic technologies have enabled the acquisition of large perturbation data sets, allowing for the reverse engineering of gene regulatory networks in specific cell types. Modular response analysis (MRA) has proven to be a promising mathematical modeling method for such network inference tasks, showing superior performance compared to general-purpose mutual information-based algorithms on large systems. The study also introduces novel heuristics and parallelization techniques to further improve MRA's performance and scalability on extensive biological systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Ramin Hasibi, Tom Michoel
Summary: Graph neural networks are effective in representing nodes in molecular interaction networks and correlating them with gene expression data to explain gene expression variations. Using gene expression data as node features, combined with a novel graph feature auto-encoder framework, can better predict unobserved node features.
BMC BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Leah Schaffer, Trey Ideker
Summary: Biological systems are inherently multiscale, allowing for the application of diverse technologies to characterize units at different levels and create networks of proximities. By using network proximity measures to build hierarchical maps of biological systems, functionalizing them to create predictive models, and addressing challenges in multiscale modeling, a unified hierarchical approach to biological data can be achieved, spanning from the molecular to macroscopic level.
Article
Genetics & Heredity
Emily P. Y. Yu, Sofia Perin, Vishal Saxena, Marc Ekker
Summary: By studying dlx gene mutants in zebrafish, it was found that the expression of dlx genes in zebrafish is influenced by different regulatory factors, which differs from studies in mice. This may highlight evolutionary differences in gene interactions between vertebrates.
Correction
Cell Biology
Luisa Statello, Chun-Jie Guo, Ling-Ling Chen, Maite Huarte
Summary: A correction to this paper has been published at the specified link.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
Article
Medicine, General & Internal
Byung-Keun Kim, Hyun-Seung Lee, Suh-Young Lee, Heung-Woo Park
Summary: This study investigates gene regulatory networks in adult asthma patients to determine the factors influencing responsiveness to inhaled corticosteroids. The top-10 transcription factors and their associated genes were found to be significantly enriched in distinct biological pathways, providing potential targets to enhance corticosteroid sensitivity in asthma patients.
FRONTIERS IN MEDICINE
(2021)
Review
Oncology
Yang Zhao, Marisela Sheldon, Yutong Sun, Li Ma
Summary: The Hippo pathway plays a crucial role in regulating cell growth, tumor spread, and resistance to cancer treatments. Dysregulation of this pathway can contribute to tumor growth, metastasis, and therapy resistance. This review focuses on the involvement of the Hippo pathway in cancer, discussing the role of YAP/TAZ-TEAD-mediated gene regulation, mechanisms contributing to metastasis and therapy resistance, and advances in therapeutic strategies targeting this pathway. It also addresses ongoing controversies and provides perspectives on specific debated topics in this field.
Article
Chemistry, Multidisciplinary
Roser Montagud-Martinez, Rosa Marquez-Costa, Guillermo Rodrigo
Summary: In this study, a novel framework for regulating translation using the CRISPR-Cas13 immune system is developed. The engineered CRISPR-dCas13a ribonucleoproteins can be programmed to repress or activate translation. The system shows potential applications and complements the ability to regulate transcription with other CRISPR-Cas systems.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Chris Gaiteri, David R. Connell, Faraz A. Sultan, Artemis Iatrou, Bernard Ng, Boleslaw K. Szymanski, Ada Zhang, Shinya Tasaki
Summary: Clustering molecular data into informative groups is essential for extracting robust conclusions from big data. This study compares popular clustering algorithms on synthetic and real biological datasets, finding that no single method is universally optimal. The SpeakEasy2 algorithm generally provides robust, scalable, and informative clusters for various applications.
Article
Biology
Erika Fox, Bree Cummins, William Duncan, Tomas Gedeon
Summary: A gene regulatory network is a summary of interactions between genes and regulatory gene products, including transcriptional regulation, protein activity regulation, and regulation of protein transport between compartments. DSGRN is a network modeling approach based on discrete-time Boolean models and continuous-time switching system models. This paper presents an extension of the DSGRN approach to modeling transport regulation across compartments such as cellular membranes, demonstrated through the search for potential stable periodic cycles in a model of the p53-Mdm2 network.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Correction
Evolutionary Biology
J. Roman Arguello, Stefan Laurent, Andrew G. Clark
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Nutrition & Dietetics
Wanhui Kang, Alexa Barad, Andrew G. Clark, Yiqin Wang, Xu Lin, Zhenglong Gu, Kimberly O. O'Brien
Summary: Iron is unique among minerals because humans lack a regulatable pathway to eliminate excess iron after absorption. Iron deficiency leads to anemia, while iron overload can result in deposition in key organs. Accumulation of iron in the body increases the risk of chronic diseases. Only about 30% of variability in iron absorption can be captured by biomarkers or hormones.
ADVANCES IN NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Iskander Said, Michael P. McGurk, Andrew G. Clark, Daniel A. Barbash
Summary: Competition between transposable elements (TEs) may lead to the emergence of new variants, with hosts preferentially producing antisense piRNAs to silence these emerging variants.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Manisha Munasinghe, Benjamin C. Haller, Andrew G. Clark
Summary: In this study, the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population were investigated using computer simulations. Disrupting these interactions resulted in less-fit males, but the strength of these interactions was not enough to drive population isolation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Matthew Metzloff, Emily Yang, Sumit Dhole, Andrew G. Clark, Philipp W. Messer, Jackson Champer
Summary: Our study demonstrates the construction of a tethered drive system in Drosophila, utilizing a locally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency).
Article
Evolutionary Biology
Tram N. Nguyen, Nancy Chen, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Andrew G. Clark
Summary: Understanding the genomic consequences of population decline is crucial for predicting species' vulnerability to global change. This study compared the genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations of Florida scrub jays that have experienced different demographic trajectories. The results showed that the population decline led to decreased heterozygosity and increased inbreeding in the declining population, while the stable population did not show significant changes. This study highlights the divergence in genetic characteristics caused by local population decline despite ongoing gene flow.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Neurosciences
You Chen, Andrew G. Clark, Haiyuan Yu
Summary: This article presents a fine-mapping approach called RefMap, which integrates functional genomics with GWAS summary statistics to prioritize causal variants for amyotrophic lateral sclerosis.
Article
Multidisciplinary Sciences
Felicia N. New, Benjamin R. Baer, Andrew G. Clark, Martin T. Wells, Ilana L. Brito
Summary: This study examines the interactions between host genetics and gut microbiome by analyzing the gut microbiomes and human variants of 250 individuals. The findings reveal associations between host genetics and microbiome-related metabolic traits, disorders, and certain cancers. The study also identifies common and rare microbial functions that are associated with host genetics.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Emily Yang, Matthew Metzloff, Anna M. Langmueller, Xuejiao Xu, Andrew G. Clark, Philipp W. Messer, Jackson Champer
Summary: Gene drives are engineered alleles that can bias inheritance and spread throughout a population. This study constructed a homing suppression drive in Drosophila melanogaster using multiplexed gRNAs to inhibit the formation of resistance alleles, reaching a moderate equilibrium frequency in cage populations but with a fitness cost preventing elimination. The results demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Yiqin Wang, Xiaoxian Guo, Xiumei Hong, Guoying Wang, Colleen Pearson, Barry Zuckerman, Andrew G. Clark, Kimberly O. O'Brien, Xiaobin Wang, Zhenglong Gu
Summary: This study investigates the role of mitochondrial genome (mtDNA) in autism spectrum disorder (ASD) risk, and finds that mutations in mtDNA are associated with increased ASD risk in children, and the heteroplasmies in parents have different effects in ASD children.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Dawn S. Chen, Andrew G. Clark, Mariana F. Wolfner
Summary: In a study on Drosophila, researchers found that inhibiting the activity of Tdc2 neurons in females resulted in a higher proportion of offspring from the first male. This suggests that octopaminergic/tyraminergic signaling plays a role in biased sperm usage in multiply-mated females, and highlights a new role for the female nervous system in postcopulatory sexual selection.
Article
Biology
Anna M. Langmueller, Jackson Champer, Sandra Lapinska, Lin Xie, Matthew Metzloff, Samuel E. Champer, Jingxian Liu, Yineng Xu, Jie Du, Andrew G. Clark, Philipp W. Messer
Summary: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a highly efficient genome editing technology with a wide range of potential applications. However, integrating CRISPR/Cas9 into an organism's genome may have harmful effects on transgenic individuals, particularly in the case of gene drives that aim to alter the genetics of entire populations. This study assesses the fitness effects of CRISPR/Cas9 expression in Drosophila melanogaster populations, and finds that a high-fidelity version of Cas9 performs well in terms of drive conversion efficiency. These findings have implications for the design of gene drives and other applications involving genomic integration of CRISPR endonucleases.
Article
Biochemistry & Molecular Biology
Wenqi Cao, Kory C. Douglas, Paul B. Samollow, John L. VandeBerg, Xu Wang, Andrew G. Clark
Summary: Genomic imprinting is a phenomenon that plays important roles in many biological processes, and is only observed in therian mammals. A study investigated the imprinting pattern in marsupials using unbiased RNA-seq studies, discovering and validating 13 imprinted genes, including nine novel imprinted genes. Differential methylation and clustering were observed at marsupial-specific imprinted genes, revealing common mechanisms in the epigenetic regulation of marsupial imprinting.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Sofie Y. N. Delbare, Sara Venkatraman, Kate Scuderi, Martin T. Wells, Mariana F. Wolfner, Sumanta Basu, Andrew G. Clark
Summary: This study used high-resolution time series RNA-sequencing data to explore the genetic architecture of female's response to SP in Drosophila melanogaster. The results showed that SP not only triggers the transcriptional switch in females after mating, but also affects metabolic gene regulatory network and neuronal gene regulatory network, especially the disruption of female's circadian rhythm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Jullien M. Flynn, Kevin B. Hu, Andrew G. Clark
Summary: This study discovered chromosome fusion and fission events in a strain of D. virilis, leading to genome instability. One substrain with an X-autosome fusion had a 20x higher nondisjunction rate and another substrain with higher satellite DNA had an overall higher DNA breakage rate. These findings suggest a potential role of satellite DNA abundance in genome instability. The establishment of a novel system with four different karyotypes provides a valuable tool for future studies on genome instability, centromere function, and sex chromosome evolution.