Research Topics
Species | Yoav GiladSummaryAffiliation: University of Chicago Country: USA Publications
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Publications
Using genomic tools to study regulatory evolutionYoav Gilad
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
Methods Mol Biol 856:335-61. 2012....- Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarrayXiaohong Zhang
Department of Biological Sciences, Columbia University, New York, NY 10027, USA
Genome Biol 8:R86. 2007..To rectify this, we have developed a DNA microarray that contains probes for most predicted human OR loci and used that array to examine OR gene expression profiles in olfactory epithelium tissues from three individuals... - Characterizing natural variation using next-generation sequencing technologiesYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 25:463-71. 2009..A better understanding of the sources of error and bias in sequencing data is essential, especially in the context of studies of variation at dynamic quantitative traits... - Revealing the architecture of gene regulation: the promise of eQTL studiesYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 24:408-15. 2008.... - Using DNA microarrays to study natural variationYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Curr Opin Genet Dev 16:553-8. 2006..In studies of natural variation, this assumption does not always hold, raising a number of new challenges... - Natural selection on gene expressionYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 22:456-61. 2006..An important implication is that mutations affecting gene expression will often be deleterious and might underlie many human diseases... - Expression profiling in primates reveals a rapid evolution of human transcription factorsYoav Gilad
Department of Genetics, Yale University, New Haven, Connecticut 06510, USA
Nature 440:242-5. 2006..Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee... - Understanding mechanisms underlying human gene expression variation with RNA sequencingJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago 60637, USA
Nature 464:768-72. 2010..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals... - DNase?I sensitivity QTLs are a major determinant of human expression variationJacob F Degner
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Nature 482:390-4. 2012..Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation... - DNA methylation patterns associate with genetic and gene expression variation in HapMap cell linesJordana T Bell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Biol 12:R10. 2011..Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available... - Gene regulation in primates evolves under tissue-specific selection pressuresRan Blekhman
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 4:e1000271. 2008..These observations are consistent with the notion that adaptive circumscribed changes in gene regulation have fewer deleterious pleiotropic effects compared with changes at the protein sequence level... - Gene expression differences among primates are associated with changes in a histone epigenetic modificationCarolyn E Cain
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genetics 187:1225-34. 2011..Our results suggest a modest, yet important role for epigenetic changes in gene expression differences between primates... - Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infectionLuis B Barreiro
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 109:1204-9. 2012..We thus identified a number of candidate loci, including the MAPK phosphatase DUSP14 in particular, that are promising susceptibility genes to pulmonary TB... - Sex-specific and lineage-specific alternative splicing in primatesRan Blekhman
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 20:180-9. 2010.... - High-resolution mapping of expression-QTLs yields insight into human gene regulationJean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
PLoS Genet 4:e1000214. 2008..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation... - Noisy splicing drives mRNA isoform diversity in human cellsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 6:e1001236. 2010..7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution... - Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility dataRoger Pique-Regi
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 21:447-55. 2011..We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions... - Multi-species microarrays reveal the effect of sequence divergence on gene expression profilesYoav Gilad
Yale University School of Medicine, Department of Genetics, Yale University, New Haven, CT 06520, USA
Genome Res 15:674-80. 2005..Our results indicate that naive use of single-species arrays in direct interspecies comparisons can yield spurious results... - Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing dataJacob F Degner
Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 507, Chicago, IL 60637, USA
Bioinformatics 25:3207-12. 2009..Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE)... - Comparative RNA sequencing reveals substantial genetic variation in endangered primatesGeorge H Perry
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 22:602-10. 2012..Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success... - Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array DataJean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
PLoS ONE 7:e30629. 2012..Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation... - False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regionsJoseph K Pickrell
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Bioinformatics 27:2144-6. 2011..Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy... - A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathwayPaola de Candia
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
PLoS ONE 3:e1670. 2008..We concentrated on this gene because of its known role in the regulation of metabolism and in longevity... - A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissuesAthma A Pai
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 7:e1001316. 2011..In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees... - A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from MadagascarGeorge H Perry
Department of Human Genetics, University of Chicago
Genome Biol Evol 4:126-35. 2012..Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests... - Functional comparison of innate immune signaling pathways in primatesLuis B Barreiro
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 6:e1001249. 2010..Put together, our observations lend strong support to the notion that lineage-specific immune responses may help explain known inter-species differences in susceptibility to infectious diseases... - Expression quantitative trait loci detected in cell lines are often present in primary tissuesKevin Bullaughey
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Hum Mol Genet 18:4296-303. 2009..Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues... - The effects of EBV transformation on gene expression levels and methylation profilesMinal Caliskan
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
Hum Mol Genet 20:1643-52. 2011..In contrast, inference based on functional studies in LCLs may be more limited to the cell lines... - Using reporter gene assays to identify cis regulatory differences between humans and chimpanzeesAdrien Chabot
Department of Human Genetics, University of Chicago, 920 E 58th Street, Chicago, IL 60637, USA
Genetics 176:2069-76. 2007..High-throughput application of this approach can provide a map of regulatory element differences between humans and our close evolutionary relatives... - Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"Joseph K Pickrell
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Science 335:1302; author reply 1302. 2012..We found that at least 88% of these sequence mismatches can likely be explained by technical artifacts such as errors in mapping sequencing reads to a reference genome, sequencing errors, and genetic variation... - RNA-seq: an assessment of technical reproducibility and comparison with gene expression arraysJohn C Marioni
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 18:1509-17. 2008..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology... - A comparison of the human and chimpanzee olfactory receptor gene repertoiresYoav Gilad
Yale University School of Medicine, Department of Genetics, New Haven, Connecticut 06520, USA
Genome Res 15:224-30. 2005..Thus, although overall there is relaxed constraint on human olfaction relative to chimpanzee, species-specific sensory requirements appear to have shaped the evolution of the functional OR gene repertoires in both species... - Genomic-scale capture and sequencing of endogenous DNA from fecesGeorge H Perry
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Mol Ecol 19:5332-44. 2010..585%), western chimpanzees have a low ratio (0.42) of X chromosomal (? = 0.034%) to autosomal (chromosome 21 ? = 0.081%) sequence diversity, a pattern that may reflect an unusual demographic history of this subspecies... - Sex-specific genetic architecture of human diseaseCarole Ober
Department of Human Genetics, 920 East 58th Street, The University of Chicago, Chicago, Illinois 60637, USA
Nat Rev Genet 9:911-22. 2008..Genetic studies that ignore sex-specific effects in their design and interpretation could fail to identify a significant proportion of the genes that contribute to risk for complex diseases... - Human specific loss of olfactory receptor genesYoav Gilad
Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, Leipzig D 04103, Germany
Proc Natl Acad Sci U S A 100:3324-7. 2003..As a consequence, the fraction of OR pseudogenes in humans is almost twice as high as in the non-human primates, suggesting a human-specific process of OR gene disruption, likely due to a reduced chemosensory dependence relative to apes... - Different noses for different peopleIdan Menashe
Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel
Nat Genet 34:143-4. 2003..The results show an unprecedented prevalence of segregating pseudogenes, identifying one of the most pronounced cases of functional population diversity in the human genome... - Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primatesYoav Gilad
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
PLoS Biol 2:E5. 2004..Our findings suggest that the deterioration of the olfactory repertoire occurred concomitant with the acquisition of full trichromatic color vision in primates... - Absence of the TAP2 human recombination hotspot in chimpanzeesSusan E Ptak
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
PLoS Biol 2:e155. 2004.... - Using DNA microarrays to study gene expression in closely related speciesAlicia Oshlack
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3050, Australia
Bioinformatics 23:1235-42. 2007..Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach... - An evolutionarily conserved sexual signature in the primate brainBjörn Reinius
Department of Development and Genetics, Uppsala University, Uppsala, Sweden
PLoS Genet 4:e1000100. 2008..Genes within sexual expression profiles may underlie important functional differences between the sexes, with possible importance during primate evolution... - Evolution of bitter taste receptors in humans and apesAnne Fischer
Max Plank Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
Mol Biol Evol 22:432-6. 2005..However, in contrast to the olfactory receptor gene repertoire, where humans have a higher proportion of pseudogenes than apes, there is no evidence that the rate of loss of bitter taste receptor genes varies among humans and apes... - Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisonsOrna Man
Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel
Protein Sci 13:240-54. 2004..This conclusion is supported by the observation that all but one of the predicted binding site residues correspond to ligand-contact positions in other rhodopsin-like GPCRs... - Natural selection on the olfactory receptor gene family in humans and chimpanzeesYoav Gilad
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Am J Hum Genet 73:489-501. 2003..These observations are likely due to differences in lifestyle, between humans and great apes, that have led to distinct sensory needs... - Evidence for positive selection and population structure at the human MAO-A geneYoav Gilad
Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 99:862-7. 2002.... - Population differences in the human functional olfactory repertoireYoav Gilad
Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot, Israel
Mol Biol Evol 20:307-14. 2003..Our observations are unlikely to be accounted for by simple demographic models but may be explained by positive selection acting on OR loci in Caucasians...
Research Grants
- Integrating genomics and gene expression analyses to map CVD-associated lociYoav Gilad; Fiscal Year: 2010....
- Natural Selection on Gene Regulation in HumansYoav Gilad; Fiscal Year: 2010..abstract_text> ..
- The evolution of human specific regulatory pathwaysYoav Gilad; Fiscal Year: 2010..PUBLIC HEALTH RELEVANCE: The goal of the proposed study is to identify a first set of regulatory pathways that have been remodeled in humans, and learn about the genetic basis of gene regulatory changes in primates. ..
- Natural Selection on Gene Regulation in HumansYoav Gilad; Fiscal Year: 2007....