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Genes and Gene Networks Regulating Mineralization
The chapter addresses current understanding of gene regulation and defines hierarchical gene regulatory circuits mediating vertebrate mineral...
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Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the...
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Genome-Wide Prediction of Disease Resistance Gene Analogs in Flax
Flax (Linum usitatissimum L.) is an important crop as the sources of fiber and seed oil. Annually, various pathogens cause significant loss to flax...
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Multiple sclerosis patient-derived spontaneous B cells have distinct EBV and host gene expression profiles in active disease
Epstein–Barr virus (EBV) is an aetiologic risk factor for the development of multiple sclerosis (MS). However, the role of EBV-infected B cells in...
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Context-specific regulation of extracellular vesicle biogenesis and cargo selection
To coordinate, adapt and respond to biological signals, cells convey specific messages to other cells. An important aspect of cell–cell communication...
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Scale-dependent habitat selection is shaped by landscape context in dispersing white-tailed deer
ContextIdentifying how animals select habitat while navigating landscapes is important for understanding behavioral ecology and guiding management...
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Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach
This chapter describes the usage of homologizer to phase gene copies into polyploid subgenomes. Allopolyploids contain multiple copies of each...
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Context-dependent antioxidant defense system (ADS)-based stress memory in response to recurrent environmental challenges in congeneric invasive species
Marine ecosystems are facing escalating environmental fluctuations owing to climate change and human activities, imposing pressures on marine...
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Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements...
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Comparative genomics and gene finding in fungi
In the spring of 2005, we had access to 18 fully sequenced fungal genomes, and more are coming rapidly. New approaches and methods are being...
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Gene regulation on extrachromosomal DNA
Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer and is associated with poor outcomes. Clonal, megabase-sized...
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Context dependency of nucleotide probabilities and variants in human DNA
BackgroundGenomic DNA has been shaped by mutational processes through evolution. The cellular machinery for error correction and repair has left its...
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Integration of protein context improves protein-based COVID-19 patient stratification
BackgroundClassification of disease severity is crucial for the management of COVID-19. Several studies have shown that individual proteins can be...
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Gene-edited cells: novel allogeneic gene/cell therapy for epidermolysis bullosa
Epidermolysis bullosa (EB) is a group of rare genetic skin fragility disorders, which are hereditary. These disorders are associated with mutations...
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Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model
BackgroundThe growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of...
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Modelling jaguar gene flow in fragmented landscapes offers insights into functional population connectivity
ContextPreserving functional connectivity is a conservation priority to secure the long-term viability of geographically dispersed subpopulations,...
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The role of non-additive gene action on gene expression variation in plant domestication
BackgroundPlant domestication is a remarkable example of rapid phenotypic transformation of polygenic traits, such as organ size. Evidence from a...
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Predicting Gene Regulatory Interactions Using Natural Genetic Variation
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype–phenotype map. Although GWAS are usually used to assess simple...
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MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for...
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Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects
CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a number of biases and artifacts that can confound the results....
