Publications
2009
Degner, J.F., Marioni, J.C., Pai, A.A., Pickrell, J.K., Nkadori, E., Gilad, Y., Pritchard, J.K. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009 Oct 6 (Epub ahead of print).
Gilad, Y., Pritchard, J.K., Thornton, K. Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics. 2009 Oct 2 (Epub ahead of print).
Bullaughey, K., Chavarria, C.I., Coop, G., Gilad, Y. Expression quantitative trait loci detected in cell-lines are often present in primary tissues. Hum Mol Genet. 2009 Aug 11 (Epub ahead of print).
Blekhman, R., Oshlack, A., and Gilad, Y. Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics 2009 182(2):627-30.
Degenhardt, J.D., de Candia, P., Chabot, A., Schwartz, S., Henderson, L., Ling, B., Hunter, M., Jiang, Z., Palermo, R.E., Katze, M., Eichler, E.E., Ventura, M., Rogers, J., Marx, P., *Gilad, Y., and *Bustamante, C.D. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in rhesus macaques (Macaca mulatta). PLoS Genetics 2009 Jan 23, 5(1):e1000346.
Gilad, Y. Olfactory receptor genes: Human loss during evolution. Squire LR (ed.) Encyclopedia of Neuroscience, Oxford: Academic Press 2009, volume 7: 157-161.
2008
De la Cruz, O., Blekhman, R., Zhang, X., Nicolae, D., Firestein, S., and Gilad, Y. A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes. Mol. Biol. and Evol. 2008 Dec 22; [Epub ahead of print].
Ober, C., Loisel, D.A., and Gilad, Y. Sex-specific genetic architecture of human disease. Nature Reviews Genetics 2008 Dec; 9: 911-22.
Blekhman, R., Oshlack, A., Chabot, A.E., Smyth, G.K., and Gilad, Y. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genetics 2008 Nov 21; 4(11): e1000271.
Veyrieras, J.B., Kudaravalli, S., Kim, S.Y., Dermitzakis, E.T., Gilad, Y., Stephens, M., and Pritchard, J.K. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genetics 2008 Oct 10; 4(10): e1000214.
Marioni, J.C., Mason, C.E., Shrikant, M.M., Stephens, M., and Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 2008 Sep;18(9):1509-17.
Gilad, Y., Rifkin, S.A., and Pritchard, J.K. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends in Genetics, 2008 Aug;24(8):408-415.
Reinius, B., Saetre, P., Leonard, J.A., Blekhman, R., Martinez, R., Gilad, Y., and Jazin, H. An evolutionarily conserved sexual signature in the primate brain. PLoS Genetics, 2008 Jun 20;4(6):e1000100.
de Candia, P., Blekhman, R., Chabot, A.E., Oshlack, A. and Gilad, Y. A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway. PLoS One 2008, Feb 27;3(2):e1670.
2007
Man, O., Willhite, D.C., Crasto, C.J., Shepherd, G.M. and Gilad, Y. A framework for exploring functional variability in olfactory receptor genes. PLoS One 2007, Aug 1;2:e682.
Chabot, A.E., Shrit, R.A., Blekhman, R. and Gilad Y. Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics 2007 176(4):2069-76
Zhang, X., De la Cruz, O., Pinto, J.M., Nicolae, D., Firestein, S. and Gilad, Y. Characterizing the expression of human olfactory receptor genes. Genome Biology 2007 May 17;8(5):R86
Oshlack, A., Chabot, A.E., Smyth, G.K. and Gilad, Y. Using DNA microarrays to study gene expression in closely related species. Bioinformatics 2007, 23(10):1235-42
2006
Gilad, Y. and Borevitz, J. Using microarrays to study natural variation. Current Opinion in Genetics and Development 2006, 16: 553-558.
Gilad, Y., Oshlack, A. and Rifkin, S. Natural selection on gene expression. Trends in Genetics 2006, 8: 456-461.
Gilad, Y., Oshlack, A., Smyth, G.K., Speed, T.P. and White, K.P. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 2006, 440: 242-245.
2000-2005
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome Nature 2005, 437: 69-87.
Gilad, Y., Rifkin, S.A., Bertone, P., Gerstein, M. and White, K.P. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research. 2005, 15(5):674-680.
Gilad, Y., Man, O. and Glusman. G. A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Research. 2005, 15: 224-230.
Fischer, A., Gilad, Y., Man, O. and Pääbo, S. Evolution of bitter taste receptors in primates. Mol. Biol. and Evol. 2005, 22(3):432-436.
Ptak, S.E., Roeder, A.D., Stephens, M., Gilad, Y., Pääbo, S. and Przeworski, M. Absence of the TAP2 human recombination hotspot in chimpanzee. PLoS Biology. 2004, 2(6): 849-855.
Gilad, Y., Wiebe, V., Przeworski, M., Lancet, D. and Pääbo, S. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biology. 2004, 2(1): 120-125.
Man, O., Gilad, Y. and Lancet, D. Predicting the binding site of olfactory receptors by human-mouse comparisons. Protein Science. 2004, 13(1): 240-254.
Gilad, Y., Bustamante, C.D., Lancet, D. and Pääbo, S. Natural selection on the olfactory receptor gene family in humans and chimpanzees. Am. J. Hum. Gen. 2003, 73(3):489-501.
Menashe, I. , Man, O., Lancet, D. and Gilad, Y. Different noses to different people. Nature Genetics. 2003, 34(2):143-144.
Gilad, Y., Man O., Pääbo, S, and Lancet D. Human specific loss of olfactory receptor genes. Proc. Natl. Acad. Sci. 2003, 100(6): 3324-3327.
Gilad, Y. and Lancet D. Population differences in the human functional olfactory repertoire. Mol. Biol. and Evol. 2003, 20(3): 307-314.
Menashe, I. , Man, O., Lancet, D. and Gilad, Y. Population differences in haplotype structure within a human olfactory receptor gene cluster. Hum. Mol. Genet. 2002, 11(12): 1381-1390.
Gilad, Y., Rozenberg, S., Przeworski, M., Lancet, D. and Skorecki, K. Evidence for positive selection and population structure at the human MAO-A gene. Proc. Natl. Acad. Sci. 2002, 99(2): 862-867.
Conticello, G. S., Gilad, Y., Avidan, N., Ben-Asher, E., Levy, Z. and Fainzilber, M. Mechanisms for evolving hypervariability: the case of conopeptides. Mol. Biol. and Evol. 2001, 18(2):120-131.
Lapidot, M., Pilpel, T., Gilad, Y., Falcovits, A., Haaf T. and Lancet, D. Mouse- Human Orthology relationships in an Olfactory Receptor Gene Cluster. Genomics. 2001, 71(3): 296-306.
Gilad, Y., Segré, D., Skorecki, K., Nachman, W.M., Lancet, D. and Sharon , D. Dichotomy of single- nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nature Genetics. 2000, 26(2): 221-224.
Sharon , D., Gilad, Y., Glusman, G., Khen, M., Lancet, D. and Kalush, F. Identification and characterization of coding single- nucleotide polymorphisms within a human olfactory receptor gene cluster. Genes. 2000, 260(1-2): 87-94.