Browsing Genetics by Title
Now showing items 72-91 of 146
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Learning from Large-scale Mutagenesis Data
Mutations can have profound effects on protein function. For example, mutations can increase or decrease enzymatic activity, influence aggregation propensity, or lead to novel protein functions. Mastery of the rules governing ... -
Learning from the past: Searching for novel TRIM, CypA, and TRIMCyp antiviral factors in primates
(2013-07-23)The evolutionary history and genetic composition of mammals has been strongly influenced by viruses. This is reflected by evolved mechanisms of host defense mediated by restriction factors that are in an arms race to win ... -
Leveraging natural isolates and experimental evolution to characterize biofilm-related phenotypes in Saccharomyces cerevisiae
Biofilm formation is a protective community building behavior in which microbes participate to respond to external stress or colonize new ecological niches. It is a primary mechanism used by pathogenic yeast to persist on ... -
Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. One way in which cis-regulatory elements can be delineated is by their characteristic ... -
Maps and mechanisms of three-dimensional genome organization
The three-dimensional organization of the genome inside the nucleus both impacts and is influenced by its functions, including transcription and DNA replication. Recent technological advances, particularly the high-throughput ... -
Massively parallel analysis of nucleic acid strucure
A goal amongst modern biologists is to “compute” cellular and organismal function. This “computation” necessitates a holistic understanding of the biochemical mechanisms underlying different cellular states. Methods that ... -
Massively parallel analysis of the functional effects of mutations
Massively parallel assays can dramatically advance our understanding of biological processes. Coupling them with modern mutagenesis techniques allows for fine mapping of the link between genotype and phenotype. In this ... -
Massively parallel characterization of enhancers in evolution and disease
On average, protein-coding sequence is over 99.9% identical between humans, yet some individuals develop disease while others do not. Similarly, protein-coding sequences are over 99% identical between human and chimpanzees ... -
Massively parallel functional dissection of regulatory elements
(2013-02-25)Massively parallel sequencing has accelerated the cataloging of cis-regulatory elements in mammalian genomes. However, it remains challenging to estimate the functional effects of variation in cis-regulatory elements. The ... -
Mechanisms of buffering of phenotypic variation in A. thaliana: Features of HSP90 and characterization of AGO1 as a new regulator of robustness
Biological systems have molecular mechanisms that allow them to maintain a constant phenotype despite environmental and genetic perturbations. These mechanisms can take the form of master regulator of robustness, gene ... -
Mechanistic consequences of splicing factor mutations and their use for targeted cancer therapy
In 2011 Yoshida et al. identified mutations in RNA splicing factors as some of the most common mutations in patients with myelodysplastic syndrome (MDS). Mutations in splicing machinery result in the dysregulation of ... -
Metabolic modeling-based tools for integrative microbiome data analysis
Complex communities of microbes reside in and on humans, where they closely interact with their hosts by performing a massively diverse array of metabolic reactions. Genomic and metabolomic technologies can now describe ... -
Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome
Though invisible to the naked eye, microbes are crucial to life as we know it. These tiny single-celled organisms are found in almost every known environment, helping to maintain balance across a vast array of ecological ... -
Methods for harmonizing and calibrating quantitative mass spectrometry experiments
The field of mass spectrometry proteomics has made great technological progress, and these techniques are now being used to address essential questions in basic biology and are increasingly being used on samples of clinical ... -
Model-based computational methods to aid the design of synthetic microbial communities
Microbial communities permeate the world around us, inhabiting a range of environments where they play crucial roles in environmental resources cycles, agriculture, and human health, highlighted by recent interest in the ... -
Modeling the effects of site-specific amino-acid preferences on protein evolution.
An important goal in the study of protein evolution is understanding which genetic changes that fixed in nature were selected for and why. However, understanding the functional consequence of any given mutation is a challenge ... -
Molecular Diversification and Species-Specific Interactions of Gamete Recognition Proteins
Reproductive proteins mediating fertilization commonly exhibit rapid sequence diversification driven by positive selection. This pattern has been observed among nearly all taxonomic groups, including mammals, invertebrates, ... -
Molecular tagging to overcome limitations of massively parallel sequencing
(2013-04-17)Massively parallel technologies have dramatically reduced the cost and increased the throughput of DNA sequencing, transforming the study of patterns of genetic variation in human and model organisms, the genetic basis of ... -
MSY4, a sequence-specific RNA binding protein expressed during mouse spermatogenesis
(2000)Translational control is an important mechanism of gene regulation, especially in gametogenesis and early embryogenesis, where there are periods of time in which there is no transcription. Previously transcribed mRNAs must ... -
Multiplex single-cell RNA sequencing for chemical genomics and spatial transcriptomics
Each of us begins life as a single fertilized cell. Following a seemingly predetermined set of cell divisions, the single cell morphs into a rough mass, then a hollowed tube, and finally becomes a recognizable neonatal ...