List of works - Yoav Gilad

A TAD Skeptic: Is 3D Genome Topology Conserved?

scientific article published on 14 November 2020

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway

scientific article

A comparison of gene expression and DNA methylation patterns across tissues and species

scientific article published on 17 January 2020

A framework for exploring functional variability in olfactory receptor genes

scientific article

A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees

scientific article published on 08 April 2019

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

scientific article (publication date: 2012)

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

scientific article

A reanalysis of mouse ENCODE comparative gene expression data

scientific article

Absence of the TAP2 human recombination hotspot in chimpanzees

scientific article

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

scientific article

Alternative polyadenylation mediates genetic regulation of gene expression

scientific article published on 25 June 2020

An evolutionarily conserved sexual signature in the primate brain

scientific article

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

scientific article published on 20 April 2020

Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray

scientific article

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

scientific article

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

scientific article (publication date: April 2012)

Comparative studies of gene expression and the evolution of gene regulation

scientific article

Controls of nucleosome positioning in the human genome.

scientific article

Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta)

scientific article (publication date: 2009)

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

scientific article

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

scientific article published on 10 January 2012

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

scientific article published on 19 April 2019

Does a unique olfactory genome imply a unique olfactory world?

scientific article published on 01 January 2014

Dynamic genetic regulation of gene expression during cellular differentiation

scientific article published on 01 June 2019

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

scientific article

Effective study design for comparative functional genomics

scientific article published on 24 April 2020

Epigenetic modifications are associated with inter-species gene expression variation in primates

scientific article

Evidence for positive selection and population structure at the human MAO-A gene

scientific article

Evolution of bitter taste receptors in humans and apes

scientific article

Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

scientific article published on 09 March 2022

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data ⬇️

scientific article (publication date: 2012)

Expression profiling in primates reveals a rapid evolution of human transcription factors

scientific article

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

scientific article

Functional comparison of innate immune signaling pathways in primates

scientific article

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

scientific article published on 14 May 2021

Gene expression differences among primates are associated with changes in a histone epigenetic modification

scientific article

Gene expression variability in human and chimpanzee populations share common determinants

scientific article published on 21 October 2020

Gene regulation in primates evolves under tissue-specific selection pressures

scientific article

Genome-Wide Association Studies of the Human Gut Microbiota

scientific article published on 3 November 2015

Genomic-scale capture and sequencing of endogenous DNA from feces

scientific article

Genomics: ENCODE explained

scientific article

High-resolution mapping of expression-QTLs yields insight into human gene regulation

scientific article

Host genetic variation influences gene expression response to rhinovirus infection

scientific article

Human specific loss of olfactory receptor genes

scientific article

Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates

scientific article published in January 2004

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels

scientific article

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

scientific article

Natural selection on the olfactory receptor gene family in humans and chimpanzees

scientific article

Noisy splicing drives mRNA isoform diversity in human cells.

scientific article

Population differences in the human functional olfactory repertoire

scientific article

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

scientific article

Prime time for primate functional genomics

scientific article published on 13 June 2020

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

scientific article

RNA-seq: impact of RNA degradation on transcript quantification

scientific article

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9.

scientific article

Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates

scientific article published on 19 July 2019

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

scientific article published on 7 May 2015

Revealing the architecture of gene regulation: the promise of eQTL studies

scientific article

Seasonal variation in human gut microbiome composition

scientific article

Sex-specific and lineage-specific alternative splicing in primates

scientific article

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.

scientific article published on 12 April 2018

Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation

scientific article published on 21 January 2022

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

scientific article published on 30 January 2020

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs

scientific article

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

scientific article

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

scientific article

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines

scientific article

The functional consequences of variation in transcription factor binding.

scientific article

The genetic and mechanistic basis for variation in gene regulation

scientific article

The genetic architecture of gene expression levels in wild baboons

scientific article

Time-dependent transcriptional profiling links gene expression to mitogen-activated protein kinase kinase 4 (MKK4)-mediated suppression of omental metastatic colonization ⬇️

scientific article published on February 21, 2012

Using genomic tools to study regulatory evolution

scientific article

Where Are the Disease-Associated eQTLs?

scientific article published on 07 September 2020

List of works by Yoav Gilad

A TAD Skeptic: Is 3D Genome Topology Conserved?

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway

A comparison of gene expression and DNA methylation patterns across tissues and species

A framework for exploring functional variability in olfactory receptor genes

A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

A reanalysis of mouse ENCODE comparative gene expression data

Absence of the TAP2 human recombination hotspot in chimpanzees

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Alternative polyadenylation mediates genetic regulation of gene expression

An evolutionarily conserved sexual signature in the primate brain

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Comparative studies of gene expression and the evolution of gene regulation

Controls of nucleosome positioning in the human genome.

Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta)

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

Does a unique olfactory genome imply a unique olfactory world?

Dynamic genetic regulation of gene expression during cellular differentiation

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Effective study design for comparative functional genomics

Epigenetic modifications are associated with inter-species gene expression variation in primates

Evidence for positive selection and population structure at the human MAO-A gene

Evolution of bitter taste receptors in humans and apes

Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data ⬇️

Expression profiling in primates reveals a rapid evolution of human transcription factors

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

Functional comparison of innate immune signaling pathways in primates

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

Gene expression differences among primates are associated with changes in a histone epigenetic modification

Gene expression variability in human and chimpanzee populations share common determinants

Gene regulation in primates evolves under tissue-specific selection pressures

Genome-Wide Association Studies of the Human Gut Microbiota

Genomic-scale capture and sequencing of endogenous DNA from feces

Genomics: ENCODE explained

High-resolution mapping of expression-QTLs yields insight into human gene regulation

Host genetic variation influences gene expression response to rhinovirus infection

Human specific loss of olfactory receptor genes

Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Natural selection on the olfactory receptor gene family in humans and chimpanzees

Noisy splicing drives mRNA isoform diversity in human cells.

Population differences in the human functional olfactory repertoire

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

Prime time for primate functional genomics

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

RNA-seq: impact of RNA degradation on transcript quantification

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9.

Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

Revealing the architecture of gene regulation: the promise of eQTL studies

Seasonal variation in human gut microbiome composition

Sex-specific and lineage-specific alternative splicing in primates

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.

Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation

Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines

The functional consequences of variation in transcription factor binding.

The genetic and mechanistic basis for variation in gene regulation

The genetic architecture of gene expression levels in wild baboons

Time-dependent transcriptional profiling links gene expression to mitogen-activated protein kinase kinase 4 (MKK4)-mediated suppression of omental metastatic colonization ⬇️

Using genomic tools to study regulatory evolution

Where Are the Disease-Associated eQTLs?

Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells