Research Description

One of the main challenges for geneticists in the 'post-genome' era is to understand the genetic architecture of gene regulation and how differences in gene regulation affect complex phenotypes, including human diseases. While many groups are studying gene regulatory mechanisms in model organisms, we reasoned that, although more challenging, the study of gene regulation in primates may carry rewards that are immediately applicable to humans. By collecting valuable samples, developing and adapting new technologies, and combining expertise in evolutionary biology, comparative genetics, and genomics, our lab has made key contributions to the study of gene regulation in humans.

Selected Publications

Comparative studies of gene expression and the evolution of gene regulation.

Romero IG, Ruvinsky I, Gilad Y

(Jul 2012) Nature reviews. Genetics 13(7):505-16 PMID:22705669

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, Gilad Y

(May 2012) Human molecular genetics 21(9):2111-23 PMID:22286170 (Full Text)

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, Gilad Y

(Apr 2012) Proceedings of the National Academy of Sciences of the United States of America 109(17):6490-5 PMID:22493251 (Full Text)

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, Pritchard JK

(Feb 2012) Nature 482(7385):390-4 PMID:22307276

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, Pritchard JK

(2012) Genome biology 13(1):R7 PMID:22293038 (Full Text)

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

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

(Jan 2012) Proceedings of the National Academy of Sciences of the United States of America 109(4):1204-9 PMID:22233810 (Full Text)

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

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

(Mar 2011) Genome research 21(3):447-55 PMID:21106904 (Full Text)

Genomic-scale capture and sequencing of endogenous DNA from feces.

Perry GH, Marioni JC, Melsted P, Gilad Y

(Dec 2010) Molecular ecology 19(24):5332-44 PMID:21054605 (Full Text)

Functional comparison of innate immune signaling pathways in primates.

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

(Dec 2010) PLoS genetics 6(12):e1001249 PMID:21187902 (Full Text)

Noisy splicing drives mRNA isoform diversity in human cells.

Pickrell JK, Pai AA, Gilad Y, Pritchard JK

(2010) PLoS genetics 6(12):e1001236 PMID:21151575 (Full Text)

Natural selection on gene expression

Gilad, Y., Oshlack, A. and Rifkin, S.

(2006)Trends in Genetics. 8: 456-461

The evolution of the human olfactory receptor gene repertoire

Gilad, Y.

(2006)New Encyclopedia of Neuroscience

Using DNA microarrays to study natural variation.

Gilad Y, Borevitz J

(Dec 2006) Current opinion in genetics & development 16(6):553-8 PMID:17008090

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

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

(Mar 2006) Nature 440(7081):242-5 PMID:16525476

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

(Sep 2005) Nature 437(7055):69-87 PMID:16136131

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

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

(May 2005) Genome research 15(5):674-80 PMID:15867429 (Full Text)

A comparison of the human and chimpanzee olfactory receptor gene repertoires.

Gilad Y, Man O, Glusman G

(Feb 2005) Genome research 15(2):224-30 PMID:15687286 (Full Text)

Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons.

Man O, Gilad Y, Lancet D

(Jan 2004) Protein science : a publication of the Protein Society 13(1):240-54 PMID:14691239 (Full Text)

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

Gilad Y, Wiebe V, Przeworski M, Lancet D, Pääbo S

(Jan 2004) PLoS biology 2(1):E5 PMID:14737185 (Full Text)

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

Gilad Y, Bustamante CD, Lancet D, Pääbo S

(Sep 2003) American journal of human genetics 73(3):489-501 PMID:12908129 (Full Text)

Different noses for different people.

Menashe I, Man O, Lancet D, Gilad Y

(Jun 2003) Nature genetics 34(2):143-4 PMID:12730696

Human specific loss of olfactory receptor genes.

Gilad Y, Man O, Pääbo S, Lancet D

(Mar 2003) Proceedings of the National Academy of Sciences of the United States of America 100(6):3324-7 PMID:12612342 (Full Text)