Marc S. Halfon
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View article: EnhancerMatcher: comparing cell-type-specific enhancer activity of DNA sequences using deep convolutional neural networks and explainable AI
EnhancerMatcher: comparing cell-type-specific enhancer activity of DNA sequences using deep convolutional neural networks and explainable AI Open
Transcriptional enhancers—unlike promoters—are challenging to identify computationally due to their variable distance and orientation relative to target genes. The scarcity of experimentally confirmed enhancers often limits the training of…
View article: Redundant and Singular Regulatory Elements Underlie the Rapidly Evolving Pigmentation of <i>Drosophila</i>
Redundant and Singular Regulatory Elements Underlie the Rapidly Evolving Pigmentation of <i>Drosophila</i> Open
A major hurdle in understanding the molecular changes responsible for metazoan diversity is the characterization of cis-regulatory elements (CREs) for gene regulatory networks (GRNs). CRE changes are suspected to be commonplace in trait ev…
View article: <i>EnhancerDetector</i> : Enhancer Discovery from Human to Fly via Interpretable Deep Learning
<i>EnhancerDetector</i> : Enhancer Discovery from Human to Fly via Interpretable Deep Learning Open
Enhancers are essential non-coding DNA elements that regulate gene expression, yet their accurate identification remains a major challenge. We introduce EnhancerDetector , a convolutional neural network-based framework for cross-species en…
View article: SCRMshaw: Supervised cis-regulatory module prediction for insect genomes
SCRMshaw: Supervised cis-regulatory module prediction for insect genomes Open
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation of their regulatory component. SCRMshaw is a computational tool designed to predict cis -regulatory modules (“enhancers…
View article: Regulatory genome annotation of 33 insect species
Regulatory genome annotation of 33 insect species Open
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 rem…
View article: Regulatory genome annotation of 33 insect species
Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Mechanisms of transcriptional regulation in <i>Anopheles gambiae</i> revealed by allele-specific expression
Mechanisms of transcriptional regulation in <i>Anopheles gambiae</i> revealed by allele-specific expression Open
Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In d…
View article: Identification of a novel downstream single-minded midline regulatory element in Drosophila melanogaster
Identification of a novel downstream single-minded midline regulatory element in Drosophila melanogaster Open
Development of the Drosophila melanogaster central nervous system midline depends on the gene single-minded (sim). Although sim regulation has been studied extensively, the fact that an enhancer mediating late embryonic sim transcription h…
View article: Regulatory genome annotation of 33 insect species
Regulatory genome annotation of 33 insect species Open
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 rem…
View article: Author response: Regulatory genome annotation of 33 insect species
Author response: Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Regulatory genome annotation of 33 insect species
Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Reviewer #2 (Public Review): Regulatory genome annotation of 33 insect species
Reviewer #2 (Public Review): Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Reviewer #3 (Public Review): Regulatory genome annotation of 33 insect species
Reviewer #3 (Public Review): Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Reviewer #1 (Public Review): Regulatory genome annotation of 33 insect species
Reviewer #1 (Public Review): Regulatory genome annotation of 33 insect species Open
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 reme…
View article: Improved methodology for fixation and preparation of Aedes aegypti embryos
Improved methodology for fixation and preparation of Aedes aegypti embryos Open
The yellow fever mosquito Aedes aegypti is a major disease vector and an increasingly popular emerging model research organism. We present here an improved protocol for the collection, fixation, and preparation of A. aegypti embryos for im…
View article: Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression
Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression Open
Transcriptional cis -regulatory modules, e.g., enhancers, control the time and location of metazoan gene expression. While changes in enhancers can provide a powerful force for evolution, there is also significant deep conservation of enha…
View article: Regulatory genome annotation of 33 insect species
Regulatory genome annotation of 33 insect species Open
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 rem…
View article: EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networks
EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networks Open
Motivation Transcriptional enhancers — unlike promoters — are unrestrained by distance or strand orientation with respect to their target genes, making their computational identification a challenge. Further, there are insufficient numbers…
View article: Mechanisms of transcriptional regulation in<i>Anopheles gambiae</i>revealed by allele specific expression
Mechanisms of transcriptional regulation in<i>Anopheles gambiae</i>revealed by allele specific expression Open
Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In d…
View article: Conserved and novel enhancers in the<i>Aedes aegypti single-minded</i>locus recapitulate embryonic ventral midline gene expression
Conserved and novel enhancers in the<i>Aedes aegypti single-minded</i>locus recapitulate embryonic ventral midline gene expression Open
Transcriptional cis -regulatory modules, e.g., enhancers, control the time and location of metazoan gene expression. While changes in enhancers can provide a powerful force for evolution, there is also significant deep conservation of enha…
View article: Evaluation of metric and representation learning approaches: Effects of representations driven by relative distance on the performance
Evaluation of metric and representation learning approaches: Effects of representations driven by relative distance on the performance Open
Several deep neural network architectures have emerged recently for metric learning. We asked which architecture is the most effective in measuring the similarity or dissimilarity among images. To this end, we evaluated six networks on a s…
View article: A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait
A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait Open
Animal traits develop through the expression and action of numerous regulatory and realizator genes that comprise a gene regulatory network (GRN). For each GRN, its underlying patterns of gene expression are controlled by cis -regulatory e…
View article: Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences
Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences Open
Background Transcriptional enhancers are essential for gene regulation, but how these regulatory elements are best defined remains a significant unresolved question. Traditional definitions rely on activity-based criteria such as reporter …
View article: Additional file 1 of Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences
Additional file 1 of Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences Open
Additional file 1.
View article: Additional file 2 of Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences
Additional file 2 of Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences Open
Additional file 2.
View article: Challenges in Improving Genomic Literacy: Results from National and Regional Surveys of Genomic Knowledge, Attitudes, Concerns, and Behaviors
Challenges in Improving Genomic Literacy: Results from National and Regional Surveys of Genomic Knowledge, Attitudes, Concerns, and Behaviors Open
Purpose Information about genomics is increasingly available to mainstream society, with more and more emphasis on using genomic information to make health care decisions. To determine how prepared people are to use this knowledge to make …
View article: REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics Open
We provide here an updated description of the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, a unique resource that provides regulatory annotation for the genome of Drosophila and other insect…