Irene Kaplow

Irene Kaplow
Carnegie Mellon University | CMU · Computational Biology Department

Doctor of Philosophy

About

27
Publications
1,994
Reads
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276
Citations
Citations since 2016
20 Research Items
215 Citations
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20162017201820192020202120220204060
Introduction
I am a Lane Postdoctoral Fellow in the Pfenning Lab in the Computational Biology Department, Carnegie Mellon University. My motivation is to develop a deeper understanding of the mechanisms involved in transcriptional regulation, the process that is partially responsible for defining the differences between tissues and cell types within an organism. Specifically, I am interested in deciphering transcriptional regulatory mechanisms underlying phenotypic differences between mammals.
Education
September 2010 - January 2014
Stanford University
Field of study
  • Computer Science
September 2010 - September 2017
Stanford University
Field of study
  • Computer Science
September 2006 - June 2010
Massachusetts Institute of Technology
Field of study
  • Mathematics

Publications

Publications (27)
Article
Full-text available
DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover less than 2% of the genome and cannot account for allele-specific m...
Article
Summary: Diverse traits have evolved through cis-regulatory changes in genome sequence that influence the magnitude, timing, and cell type-specificity of gene expression. Advances in high-throughput sequencing and regulatory genomics have led to the identification of regulatory elements in individual species, but these genomic regions remain diffic...
Article
How to optimize deep-brain stimulation Deep-brain stimulation as presently used in clinical settings, for example, to treat Parkinson’s disease, does not differentiate between different neural circuitries. Considerable improvements could thus be achieved with selective stimulation that targets particular neuronal populations. Spix et al . used opto...
Article
Full-text available
Background Evolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleot...
Article
Full-text available
Background Many transcription factors (TFs), such as multi zinc-finger (ZF) TFs, have multiple DNA binding domains (DBDs), and deciphering the DNA binding motifs of individual DBDs is a major challenge. One example of such a TF is CCCTC-binding factor (CTCF), a TF with eleven ZFs that plays a variety of roles in transcriptional regulation, most not...
Preprint
Full-text available
Alzheimer's disease (AD) involves aggregation of amyloid β and tau, neuron loss, cognitive decline, and neuroinflammatory responses. Both resident microglia and peripheral immune cells have been associated with the immune component of AD. However, the relative contribution of resident and peripheral immune cell types to AD predisposition has not be...
Preprint
Full-text available
Genetic studies are rapidly identifying non-protein-coding human disease-associated loci. Understanding the regulatory mechanisms underlying these loci remains a challenge because the causal variants and the tissues in which they act are often unclear. Massively parallel reporter assays (MPRAs) have the potential to link differences in genome seque...
Preprint
Full-text available
Protein-coding differences between mammals often fail to explain phenotypic diversity, suggesting involvement of enhancers, often rapidly evolving regions that regulate gene expression. Identifying associations between enhancers and phenotypes is challenging because enhancer activity is context-dependent and may be conserved without much sequence c...
Article
Full-text available
Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations within heterogeneous tissue. Available approaches for engineering-targeted technologies for new neuron subtypes are low yield, involving intensive transgenic strain or virus screening. Here, we present Specific...
Preprint
Full-text available
Background Many transcription factors (TFs), such as multi zinc-finger (ZF) TFs, have multiple DNA binding domains (DBDs) with multiple components, and deciphering the DNA binding motifs of individual components is a major challenge. One example of such a TF is CCCTC-binding factor (CTCF), a TF with eleven ZFs that plays a variety of roles in trans...
Article
Full-text available
Recent large genome-wide association studies have identified multiple confident risk loci linked to addiction-associated behavioral traits. Most genetic variants linked to addiction-associated traits lie in noncoding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific and may con...
Preprint
Full-text available
Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations, enabling characterization of their roles in behavior and in disease states. Available approaches for engineering targeted technologies for new neuron subtypes are low-yield, involving intensive transgenic stra...
Preprint
Full-text available
Background Evolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleot...
Preprint
Full-text available
In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofaci...
Preprint
Full-text available
Recent large genome-wide association studies (GWAS) have identified multiple confident risk loci linked to addiction-associated behavioral traits. Genetic variants linked to addiction-associated traits lie largely in non-coding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific...
Article
Full-text available
Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a off-target activity in screens for essential regulatory elements. The sgRNAs with the large...
Preprint
Full-text available
Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted a genome-scale screen for essential CTCF loop anchors in the K562 leukemia cell line. Surprisingly,...
Article
Full-text available
Genome-wide association studies (GWAS) are a powerful approach for connecting genotype to phenotype. Most GWAS hits are located in cis-regulatory regions, but the underlying causal variants and their molecular mechanisms remain unknown. To better understand human cis-regulatory variation, we mapped quantitative trait loci for chromatin accessibilit...
Article
Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted a genome-scale screen for essential CTCF loop anchors in the K562 leukemia cell line. Surprisingly,...
Preprint
Full-text available
Genome-wide association studies (GWAS) are a powerful approach for connecting genotype to phenotype. Most GWAS hits are located in cis -regulatory regions, but the underlying causal variants and their molecular mechanisms remain unknown. To better understand human cis -regulatory variation, we mapped quantitative trait loci for chromatin accessibil...
Preprint
Full-text available
DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover less than 2% of the genome and cannot account for allele-specific m...
Article
Full-text available
Individual cells from a genetically identical population exhibit substantial variation in gene expression. A significant part of this variation is due to noise in the process of transcription that is intrinsic to each gene and is determined by factors such as the rate with which the promoter transitions between transcriptionally active and inactive...
Article
Full-text available
Motivation: Genome-wide association studies are commonly used to identify possible associations between genetic variations and diseases. These studies mainly focus on identifying individual single nucleotide polymorphisms (SNPs) potentially linked with one disease of interest. In this work, we introduce a novel methodology that identifies similarit...
Article
Full-text available
Biochemical reaction databases capture the sum of human knowledge of biochemical reactions and chemical com-pounds. As the amount of data available on metabolic reactions and chemical substrates increases, the necessity of central repositories increases as well. Unfortunately, there is no established algorithm for being able to calculate the degree...

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