Modeling Gene Networks to Understand Multistability in Stem Cells.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9224-9_8
Abstract: Stem cells are unique in their ability to differentiate into diverse phenotypes capable of displaying radically different, yet stable, gene expression profiles. Understanding this multistable behavior is key to rationally influencing stem cell differentiation for… read more here.
Keywords: modeling gene; gene networks; networks understand; stem ... See more keywords
Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras
Sign Up to like & getrecommendations! Published in 2017 at "Cell"
DOI: 10.1016/j.cell.2017.01.013
Abstract: The genetic dependencies of human cancers widely vary. Here, we catalog this heterogeneity and use it to identify functional gene interactions and genotype-dependent liabilities in cancer. By using genome-wide CRISPR-based screens, we generate a gene… read more here.
Keywords: gene essentiality; gene networks; oncogenic ras; gene ... See more keywords
SEGN: Inferring real-time gene networks mediating phenotypic plasticity
Sign Up to like & getrecommendations! Published in 2020 at "Computational and Structural Biotechnology Journal"
DOI: 10.1016/j.csbj.2020.08.029
Abstract: The capacity of an organism to alter its phenotype in response to environmental perturbations changes over developmental time and is a process determined by multiple genes that are co-expressed in intricate but organized networks. Characterizing… read more here.
Keywords: plasticity; gene networks; time; gene ... See more keywords
Transcriptomic analysis on the promoter regions discover gene networks involving mastitis in cattle.
Sign Up to like & getrecommendations! Published in 2019 at "Microbial pathogenesis"
DOI: 10.1016/j.micpath.2019.103801
Abstract: Mastitis is one of the costliest diseases in dairy farms caused by infection of different microorganisms such as Escherichia coli, Streptococcus uberis and Staphylococcus aureus. Promoters are significantly involved in regulating gene expression and shedding… read more here.
Keywords: mastitis; gene networks; analysis; promoter regions ... See more keywords
An improved approach for calculating energy landscape of gene networks from moment equations.
Sign Up to like & getrecommendations! Published in 2023 at "Chaos"
DOI: 10.1063/5.0128345
Abstract: The energy landscape theory has widely been applied to study the stochastic dynamics of biological systems. Different methods have been developed to quantify the energy landscape for gene networks, e.g., using Gaussian approximation (GA) approach… read more here.
Keywords: landscape gene; energy landscape; gene networks; landscape ... See more keywords
Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa014
Abstract: MOTIVATION Reconstruction of cancer gene networks from gene expression data is important for understanding the mechanisms underlying human cancer. Due to heterogeneity, the tumor tissue samples for a single cancer type can be divided into… read more here.
Keywords: cancer; tumor heterogeneity; gene networks; tumor ... See more keywords
Interactive gene networks with KNIT
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa1107
Abstract: SUMMARY KNIT is a web application that provides a hierarchical, directed graph on how a set of genes is connected to a particular gene of interest. Its primary aim is to aid researchers in discerning… read more here.
Keywords: networks knit; information; gene networks; knit ... See more keywords
GENIUS: web server to predict local gene networks and key genes for biological functions
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw702
Abstract: Summary: GENIUS is a user‐friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These… read more here.
Keywords: gene networks; biological functions; genius web; genius ... See more keywords
A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks
Sign Up to like & getrecommendations! Published in 2020 at "Human Molecular Genetics"
DOI: 10.1093/hmg/ddaa151
Abstract: Loss-of-function mutations of the X-chromosome gene UPF3B cause male neurodevelopmental disorders (NDDs) via largely unknown mechanisms. We investigated initially by interrogating a novel synonymous UPF3B variant in a male with absent speech. In-silico and functional… read more here.
Keywords: gene networks; speech; disorder; upf3b variant ... See more keywords
Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways.
Sign Up to like & getrecommendations! Published in 2019 at "Human molecular genetics"
DOI: 10.1093/hmg/ddz221
Abstract: UBE3A encodes a E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome. Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted… read more here.
Keywords: wnt signaling; gene networks; ube3a loss; ube3a deletion ... See more keywords
Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Cell Biology"
DOI: 10.1093/jmcb/mjx059
Abstract: Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been… read more here.
Keywords: tissue specific; gene networks; specific gene; gwas data ... See more keywords