Gilad Lab

Publications

Preprints

Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons

Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA

bioRxiv; 2023

Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity

McIntire E, Barr KA, Gonzales NM, Gilad Y

bioRxiv; 2023

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

Gallego Romero I, Gopalakrishnan, S and Gilad Y

bioRxiv; 2018

2023

Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility

Adegunsoye, A, Gonzales, NM and Gilad Y

Annu Rev Genet; 2023

The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees

Barr KA, Rhodes KL, and Gilad Y

Genome Biology; 2023

2022

Characterizing gene expression in an in vitro biomechanical strain model of joint health [version 2; peer review: 1 approved, 1 not approved]

Hung A, Housman G, Briscoe EA, Cuevas C and Gilad Y

F1000 Research; 2022

 

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

Housman G, Briscoe E, and Gilad Y

PLoS Genetics; 2022

Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

Rhodes K, Barr KA, Popp JM, Strober BJ, Battle A, and Gilad Y

eLife; 2022

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

Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr KA, Qi G, Gilad Y, and Battle A

PLoS Genetics; 2022

Supplementary data: upload pending

2021

Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation

Shah A, Mittleman BE, Gilad Y, and Li YI

Genome Biology; 2021

eLife; 2021

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

Mittleman BE, Pott S, Warland S, Barr K, Cuevas C, and Gilad Y

eLife; 2021

Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

Ward MC, Banovich NE, Sarkar A, Stephens M, and Gilad Y

eLife; 2021

A TAD Skeptic: Is 3D Genome Topology Conserved?

Eres IE & Gilad Y

Trends in Genetics; 2022.

2020

Gene expression variability in human and chimpanzee populations share common determinants

Fair B, Blake LE, Sarkar A, Pavlovic B.J. Cuevas C, and Gilad Y.

eLife; 2020

Where Are the Disease-Associated eQTLs?

Umans BD, Battle A, and Gilad Y.

Trends in Genetics; 2020

Alternative polyadenylation mediates genetic regulation of gene expression

Mittleman BE, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, and Li YI

eLife; 2020

Prime time primate functional genomics

Housman G. and Gilad Y

Current Opinion in Genetics and Development; 2020

Effective study design for comparative functional genomics

Kelley JL and Gilad Y

Nature Reviews Genetics; 2020

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

Hsiao CJ, Tung P, Blischak JD, Burnett J, Barr K, Dey KK, Stephens M, and Gilad Y

Genome Research; 2020

Supplementary data: TAR.GZ file

Systematic comparison of high-throughput single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation

Selewa A, Dohn R, Eckart H, Lozano S, Xie B, Gauchat E, Elorbany R, Rhodes K, Burnett J, Gilad Y, Pott S, and Basu A

Scientific Reports; 2020

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

Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Garcia Perez R, Hsiao CJ, Eres I, Chavarria C, Marquez-Bonet T and Gilad YA

Genome Research; 2020

2019

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

Eres IE, Luo K, Hsiao CJ, Blake LE and Gilad Y

PLOS Genetics; 2019

Dynamic genetic regulation of gene expression during cellular differentiation

Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, and Gilad Y

Science; 2019

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

Sarkar AK, Tung P, Blischak JD, Burnett JE, Li Yi, Stephens M, and Gilad Y

PLOS Genetics; 2019

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

Ward MC, and Gilad Y

eLife; 2019

2018

A comparative study of endoderm differentiation in humans and chimpanzees

Blake LE, Thomas SJ, Blischak JD, Hsiao C, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ

Genome Biology; 2018

Supplementary data: XLS file

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

Pavlovic BJ, Blake LE, Roux J, Chavarria C, and Gilad Y

Scientific Reports; 2018

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes

Engelmann BW, Hsiao CJ, Blischak JD, Fourne Y, Ford M, and Gilad Y

Scientific Reports; 2018

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Ober C, Pritchard JK, and Gilad Y

eLife; 2018.

Silencing of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution in Primate iPSCs

Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, and Gilad Y

eLife; 2018

2017

Impact of regulatory variation across human iPSCs and differentiated cells

Banovich N, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung P, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Gallego Romero I, Pavlovic BJ, Kundaje A, Pritchard JK, and Gilad Y

Genome Research; 2017

Human genomics: Cracking the regulatory code

Ward MC and Gilad Y

Nature; 2017

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

Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann J, Brosch R, Barreiro LB, and Gilad Y

Scientific Reports; 2017

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

Montefiori L, Hernandez L, Zhang Z, Gilad Y, Ober C, Crawford G, Nobrega M, and Jo Sakabe N

Scientific Reports; 2017

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, and Ober C

Microbiome; 2017

Batch effects and the effective design of single-cell gene expression studies

Tung P, Blischak JD, Hsiao C, Knowles DA, Burnett JE, Pritchard JK, and Gilad Y

Scientific Reports; 2017

2016

Gene expression in local stroma reflects breast tumor states and predicts patient outcome

Bainer R, Frankenberger C, Rabe D, An G, Gilad Y, and Rosner MR

Scientific Reports; 2016

DNA methylation in lung cells is associated with asthma endotypes and genetic risk

Nicodemus-Johnson J, Myers RA, Sakabe NJ, Sobreira DR, Hogarth DK, Naureckas ET, Sperling AI, Solway J, White SR, Nobrega MA, Nicolae DL, Gilad Y, and Ober C

JCI Insight; 2016

The human olfactory transcriptome

Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, and Lancet D

BMC Genomics; 2016

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, and Pritchard JK

eLife; 2016

RNA splicing is a primary link between genetic variation and diseases

Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, and Pritchard JK

Science; 2016

Integrated Analyses of Gene Expression and Genetic Association Studies in a Founder Population

Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, DeCara JM, Gilad Y, and Ober C

Human Molecular Genetics; 2016

Supplementary data: ZIP file

 

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs

Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, and Gilad Y

PLoS Genetics; 2016

Supplementary data: ZIP file

2015

Mycobacterial infection induces a specific human innate immune response

Blischak JD, Tailleux L, Mitrano A, Barreiro L, and Gilad Y

Scientific Reports; 2015

Supplementary data: ZIP file

Genome-Wide Association Studies of the Human Gut Microbiota

Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, and Gilad Y

PLoS One; 2015

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding

Raj A, Shim H, Gilad Y, Pritchard JK, and Stephens M

PLoS One; 2015

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

Pacis A, Tailleux L, Morin AM, Lambourne J, Maclsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, and Barreiro LB

Genome Research; 2015

WASP: allele-specific software for robust molecular quantitative trait locus discovery

van de Geijn B, McVicker G, Gilad Y, Pritchard JK

Nature Methods; 2015

Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of pro-metastatic tumor-associated macrophages

Frankenberger C, Rabe D, Bainer R, Sankarasharma D, Chada K, Krausz T, Gilad Y, Becker L, and Rosner MR

Cancer Research; 2015

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y

eLife; 2015

Supplementary data: TXT file

A reanalysis of mouse ENCODE comparative gene expression data

Mizrahi-Man O and Gilad Y

F1000 Research; 2015

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

Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, and Gilad Y

PLoS Genetics; 2015

Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection

Çalışkan M, Baker SW, Gilad Y, and Ober C.

PLoS Genetics; 2015

The genetic architecture of gene expression levels in wild baboons

Tung J, Zhou X, Alberts SC, Stephens M, and Gilad Y

eLife; 2015

The Genetic and Mechanistic Basis for Variation in Gene Regulation

Pai AA, Pritchard JK, and Gilad Y

PLoS Genetics; 2015

Impact of regulatory variation from RNA to protein

Battle A, Kahn Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, and Gilad Y

Science; 2015

Supplementary data: ZIP file

Genotype data and RNA sequencing data from the 72 YRI LCL lines used in this study are available on GEO (GSE19480 ) and GEUVADIS (E-GEUV-3; ArrayExpress), as is the ribosome profiling data generated in this study (GSE61742). The YRI LCLs have also been used to measure a variety of genomic phenotypes, including H3K27ac (GSE58852), DNA methylation (GSE57483), chromatin accessibility (DNAse-seq; GSE31388), transcriptional elongation rates and initiation frequencies (4sU-seq; GSE75220), RNA decay (GSE37451), and protein levels (PXD001406).

2014

Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates

Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, and Gilad Y

Genome Biology; 2014

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, and Gilad Y

PLoS Genetics; 2014

Supplementary data: TXT file

Comparative studies of gene regulatory mechanisms

Pai AA and Gilad Y

Current Opinion in Genetics and  Development; 2014

The Effect of Freeze-Thaw Cycles on Gene Expression Levels in Lymphoblastoid Cell Lines

Calışkan M, Pritchard JK, Ober C, and Gilad Y

PLoS One; 2014

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence

Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AC, and Gilad Y

Scientific Reports; 2014

RNA-seq: Impact of RNA degradation on transcript quantification

Gallego Romero I, Pai AA, Tung J, and Gilad Y

BMC Biology; 2014

Seasonal variation in human gut microbiome composition

Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, and Gilad Y

PLoS One; 2014

The functional consequences of variation in transcription factor binding

Cusanovich DA, Pavlovic B, Pritchard JK, and Gilad Y

PLoS Genetics; 2014

Does a unique olfactory genome imply a unique olfactory world?

Frumin I, Sobel N, and Gilad Y

Nature Neuroscience; 2014

2013

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

Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, and Flicek P

Genome Biology; 2013

Identification of genetic variants that affect histone modifications in human cells

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, and Pritchard JK

Science; 2013

Primate transcript and protein expression levels evolve under compensatory selection pressures

Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, and Gilad Y

Science; 2013

Social environmental effects on gene regulation

Tung J and Gilad Y

Cellular and Molecular Life Science; 2013

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

Mizrahi-Man O, Davenport ER, and Gilad Y

PLoS One; 2013

General olfactory sensitivity database (GOSdb): Candidate genes and their genomic variations

Keydar I, Ben-Asher E, Feldmesser E, Nativ N, Oshimoto A, Restrepo D, Matsunami H, Chien MS, Pinto JM, Gilad Y, Olender T, and Lancet D

Human Mutation; 2013

2012

Controls of nucleosome positioning in the human genome

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, and Pritchard JK

PLoS Genetics; 2012

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

Pai AA, Cain CC, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, and Gilad Y

PLoS Genetics; 2012

Genomics: ENCODE explained

Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, and Segal E

Nature; 2012

Regulatory element copy number differences shape primate expression profiles

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, and Lee C

Proceedings of the National Academy of Sciences; 2012

Comparative studies of gene expression and the evolution of gene regulation

Gallego Romero I, Ruvisnky I, and Gilad Y

Nature Reviews Genetics; 2012

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

Bainer RO, Veneris JT, Yamada SD, Montag A, Lingen MW, Gilad Y, and Rinker-Schaeffer CW

Clinical Experimental Metastasis; 2012

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

Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, and Gilad Y

Human Molecular Genetics; 2012

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, and Gilad Y

Proceedings of the National Academy of Sciences; 2012

Supplementary data: DOC file

Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”

Pickrell JK, Gilad Y, and Pritchard JK

Science; 2012

Using genomic tools to study regulatory evolution

Gilad Y

Methods in Molecular Biology; 2012

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

Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, and Pritchard JK

PLoS One; 2012

DNase I sensitivity QTLs are a major determinant of human expression variation

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, and Pritchard JK

Nature; 2012

Dissecting the regulatory architecture of gene expression QTLs

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, and Pritchard JK

Genome Biology; 2012

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

Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, and Gilad Y

Proceedings of the National Academy of Sciences; 2012

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, and Gilad Y

Genome Research; 2012

Supplemental data: Please contact us if data on Genome Research webpage doesn’t meet your needs.

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

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, and Gilad Y

Genome Biology and Evolution; 2012

Supplemental data: ZIP file

 

2011

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

Pickrell JK, Gaffney DJ, Gilad Y, and Pritchard JK

Bioinformatics; 2011

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

Pai AA, Bell JT, Marioni JC, Pritchard JK, and Gilad Y

PLoS Genetics; 2011

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

Cain CE, Blekhman R, Marioni JC, and Gilad Y

Genetics; 2011

The effects of EBV transformation on gene expression levels and methylation profiles

Çalışkan M, Cusanovich DA, Ober C, and Gilad Y

Human Molecular Genetics; 2011

Supplemental data: ZIP file

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

Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y and Pritchard JK

Genome Biology; 2011

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

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, and Pritchard JK

Genome Research; 2011

2010

Functional comparison of innate immune signaling pathways in primates

Barreiro LB, Marioni JC, Blekhman R, Stephens M, and Gilad Y

PLoS Genetics; 2010

Noisy splicing drives mRNA isoform diversity in human cells

Pickrell JK, Pai AA, Gilad Y, and Pritchard JK

PLoS Genetics; 2010

Genomic-scale capture and sequencing of endogenous DNA from feces

Perry GH, Marioni JC, Melsted P, and Gilad Y

Molecular Ecology; 2010

Supplemental data: NIH (study number SRA012374)

Understanding mechanisms underlying human gene expression variation with RNA sequencing

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, and Pritchard JK

Nature; 2010

Sex-specific and lineage-specific alternative splicing in primates

Blekhman R, Marioni JC, Zumbo P, Stephens M, and Gilad Y

Genome Research; 2010

2009

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

Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, and Pritchard JK

Bioinformatics; 2009

Characterizing natural variation using next-generation sequencing technologies

Gilad Y, Pritchard JK, and Thornton K

Trends in Genetics; 2009

Expression quantitative trait loci detected in cell-lines are often present in primary tissues

Bullaughey K, Chavarria CI, Coop G, and Gilad Y

Human Molecular Genetics; 2009

Supplementary data: ZIP file

Segmental duplications contribute to gene expression differences between humans and chimpanzees

Blekhman R, Oshlack A, and Gilad Y

Genetics; 2009

Supplementary data: ZIP file

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

Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, and Bustamante CD

PLoS Genetics; 2009

Olfactory receptor genes: Human loss during evolution. Squire LR (ed.)

Gilad Y

Encyclopedia of Neuroscience, Oxford: Academic Press 2009, volume 7: 157-161.

A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes

De la Cruz O, Blekhman R, Zhang X, Nicolae D, Firestein S, and Gilad Y

Molecular Biology and Evolution; 2009

2008

Sex-specific genetic architecture of human disease

Ober C, Loisel DA, and Gilad Y

Nature Reviews Genetics; 2008

Gene regulation in primates evolves under tissue-specific selection pressures

Blekhman R, Oshlack A, Chabot AE, Smyth GK, and Gilad Y

PLoS Genetics; 2008

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

Veyrieras J-B, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, and Pritchard JK

PLoS Genetics; 2008

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

Marioni JC, Mason CE, Shrikant MM, Stephens M, and Gilad Y

Genome Research; 2008

Supplementary Data: Multiple file types

An evolutionarily conserved sexual signature in the primate brain

Reinius B, Saetre P, Leonard JA, Blekhman R, Martinez R, Gilad Y, and Jazin H

PLoS Genetics; 2008

A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway

de Candia P, Blekhman R, Chabot AE, Oshlack A and Gilad Y

PLoS One; 2008

2007

A framework for exploring functional variability in olfactory receptor genes

Man O, Willhite DC, Crasto CJ, Shepherd GM and Gilad Y

PLoS One; 2007

Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees

Chabot AE, Shrit RA, Blekhman R and Gilad Y

Genetics; 2007

Supplementary data: ZIP file

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

Zhang X, De la Cruz O, Pinto JM, Nicolae D, Firestein S and Gilad Y

Genome Biology; 2007

Using DNA microarrays to study gene expression in closely related species

Oshlack A, Chabot AE, Smyth GK and Gilad Y

Bioinformatics; 2007

Supplementary data: DOC file

2006

Using microarrays to study natural variation

Gilad Y and Borevitz J

Current Opinion in Genetics and Development; 2006

Natural selection on gene expression

Gilad Y, Oshlack A and Rifkin SA

Trends in Genetics; 2006

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

Gilad Y, Oshlack A, Smyth GK, Speed TP and White KP

Nature; 2006

2000-2005

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium

Nature; 2005

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

Gilad Y, Rifkin SA, Bertone P, Gerstein M and White KP

Genome Research; 2005

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Gilad Y, Man O and Glusman G

Genome Research; 2005

Evolution of bitter taste receptors in humans and apes

Fischer A, Gilad Y, Man O and Pääbo S

Molecular Biology  and Evolution; 2005

Absence of the TAP2 human recombination hotspot in chimpanzee

Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S and Przeworski, M

PLoS Biology; 2004

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

Gilad Y, Przeworski M, and Lancet D

PLoS Biology; 2004

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

Gilad Y, Bustamante CD, Lancet D and Pääbo S

American  Journal of  Human Genetics; 2003

Different noses for different people

Menashe I, Man O, Lancet D and Gilad Y

Nature Genetics; 2003

Population differences in the human functional olfactory repertoire

Gilad Y and Lancet D

Molecular Biology and Evolution; 2003

Population differences in haplotype structure within a human olfactory receptor gene cluster

Menashe I, Man O, Lancet D and Gilad Y

Human Molecular Genetics; 2002

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

Gilad Y, Rozenberg S, Przeworski M, Lancet D and Skorecki K

Proceedings of the National Academy of Sciences; 2002

Mechanisms for evolving hypervariability: the case of conopeptides

Conticello GS, Gilad Y, Avidan N, Ben-Asher E, Levy Z and Fainzilber M

Molecular Biology and Evolution; 2001

Mouse-Human Orthology relationships in an Olfactory Receptor Gene Cluster

Lapidot M, Pilpel T, Gilad Y, Falcovits A, Haaf T and Lancet D

Genomics; 2001

Dichotomy of single- nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes

Gilad Y, Segré D, Skorecki K, Nachman MW, Lancet D and Sharon D

Nature Genetics; 2000

Identification and characterization of coding single-nucleotide polymorphisms within a human olfactory receptor gene cluster

Sharon D, Gilad Y, Glusman G, Khen M, Lancet D and Kalush F

Genes; 2000

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