A5086649415- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Speech Recognition and Synthesis
- Insect symbiosis and bacterial influences
- Speech and Audio Processing
- Insect Resistance and Genetics
- Insect behavior and control techniques
- Invertebrate Immune Response Mechanisms
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Music and Audio Processing
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
University at Buffalo, State University of New York
2019-2024
Miami University
2024
Jacobs (United States)
2023
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation their regulatory component. SCRMshaw computational tool designed predict cis-regulatory modules (CRMs) in various species (Kantorovitz 2009; Kazemian 2011; Asma Halfon 2019; 2024). One key advantages its accessibility. It requires minimal resources—just genome sequence training data from known Drosophila CRMs, which are readily available download. Even users with modest...
Animal traits develop through the expression and action of numerous regulatory realizator genes that comprise a gene network (GRN). For each GRN, its underlying patterns are controlled by cis -regulatory elements (CREs) bind activating repressing transcription factors. These interactions drive cell-type developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, major barrier to this daunting task is CRE identification. Here, we used an in...
Annotation of newly sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation insect regulatory sequences, provide searchable database resource with enhancer predictions 33 genomes. Using our previously developed SCRMshaw computational prediction method, predict...
ABSTRACT Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation insect regulatory sequences, provide searchable database resource with enhancer predictions 33 genomes. Using our previously-developed SCRMshaw computational prediction...
Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved elevated expression of detoxifying enzymes that metabolize insecticide. In diploid organisms, gene regulated both in cis , regulatory sequences same chromosome, and trans acting factors, affecting alleles equally. Differing levels transcription caused mutations -regulatory modules (CRM), few these have been identified mosquitoes. We...
Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods for CRM discovery, but it critical that we develop effective means evaluate their performance in terms estimating sensitivity specificity. We introduce here pCRMeval, pipeline silico evaluation any enhancer prediction tools are flexible enough be applied the Drosophila melanogaster...
Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation insect regulatory sequences, provide searchable database resource with enhancer predictions 33 genomes. Using our previously-developed SCRMshaw computational prediction method, predict...
Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation insect regulatory sequences, provide searchable database resource with enhancer predictions 33 genomes. Using our previously-developed SCRMshaw computational prediction method, predict...
Abstract Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved elevated expression of detoxifying enzymes that metabolize insecticide. In diploid organisms, gene regulated both in cis , regulatory sequences same chromosome, and trans acting factors, affecting alleles equally. Differing levels transcription caused mutations -regulatory modules (CRM), few these have been identified mosquitoes....
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation their regulatory component. SCRMshaw computational tool designed predict cis-regulatory modules (CRMs) in various species (Kantorovitz 2009; Kazemian 2011; Asma Halfon 2019; 2024). One key advantages its accessibility. It requires minimal resources—just genome sequence training data from known Drosophila CRMs, which are readily available download. Even users with modest...
Annotation of newly sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis -regulatory modules—e.g., enhancers and silencers—that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation insect regulatory sequences, provide searchable database resource with enhancer predictions 33 genomes. Using our previously developed SCRMshaw computational prediction method, predict...
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation their regulatory component. SCRMshaw computational tool designed predict cis -regulatory modules (“enhancers”) in various species. A key advantage its accessibility. It requires minimal resources—just genome sequence training data from known Drosophila sequences, which are readily available download. Even users with modest skills can run on desktop computer basic...