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  4. Yoav Gilad

Yoav Gilad

Professor
ygilad@bsd.uchicago.edu
Research Summary
The Gilad lab focuses on studying genetic and regulatory differences between humans and our close evolutionary relatives. Our long term goal is to identify the genetic basis of human-specific traits, including genetic variation that underlies higher susceptibility to certain diseases and disorders in humans than in other primates.
Education
  • Weizmann Institute of Science, Rehovot, Israel, Ph.D. Molecular Genetics 08/2003
  • Weizamnn Institute of Science, Rehovot, Israel, M.Sc. Molecular Genetics 09/2000
  • Ben Gurion University, Beer-Sheva, Israel, B.Sc. Molecular Genetics and Biochemistry 08/1998
Biosciences Graduate Program Association
Publications

  1. Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. PLoS Genet. 2022 03; 18(3):e1010073. View in: PubMed

  2. Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types. Elife. 2022 02 10; 11. View in: PubMed

  3. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet. 2022 01; 18(1):e1009666. View in: PubMed

  4. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021 10 14; 22(1):291. View in: PubMed

  5. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. Elife. 2021 05 14; 10. View in: PubMed

  6. Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. Elife. 2021 02 17; 10. View in: PubMed

  7. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. Elife. 2021 02 08; 10. View in: PubMed

  8. A TAD Skeptic: Is 3D Genome Topology Conserved? Trends Genet. 2021 03; 37(3):216-223. View in: PubMed

  9. Gene expression variability in human and chimpanzee populations share common determinants. Elife. 2020 10 21; 9. View in: PubMed

  10. Where Are the Disease-Associated eQTLs? Trends Genet. 2021 02; 37(2):109-124. View in: PubMed

  11. Alternative polyadenylation mediates genetic regulation of gene expression. Elife. 2020 06 25; 9. View in: PubMed

  12. Prime time for primate functional genomics. Curr Opin Genet Dev. 2020 06; 62:1-7. View in: PubMed

  13. Effective study design for comparative functional genomics. Nat Rev Genet. 2020 07; 21(7):385-386. View in: PubMed

  14. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 2020 04; 30(4):611-621. View in: PubMed

  15. Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation. Sci Rep. 2020 01 30; 10(1):1535. View in: PubMed

  16. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res. 2020 02; 30(2):250-262. View in: PubMed

  17. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. PLoS Genet. 2019 07; 15(7):e1008278. View in: PubMed

  18. Dynamic genetic regulation of gene expression during cellular differentiation. Science. 2019 06 28; 364(6447):1287-1290. View in: PubMed

  19. Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045. View in: PubMed

  20. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. Elife. 2019 04 08; 8. View in: PubMed

  21. A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. Sci Rep. 2018 10 17; 8(1):15312. View in: PubMed

  22. A comparative study of endoderm differentiation in humans and chimpanzees. Genome Biol. 2018 10 15; 19(1):162. View in: PubMed

  23. A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. Sci Rep. 2018 08 14; 8(1):12106. View in: PubMed

  24. Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. Elife. 2018 05 08; 7. View in: PubMed

  25. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. Elife. 2018 04 12; 7. View in: PubMed

  26. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131. View in: PubMed

  27. Human genomics: Cracking the regulatory code. Nature. 2017 10 11; 550(7675):190-191. View in: PubMed

  28. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep. 2017 07 18; 7(1):5702. View in: PubMed

  29. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Sci Rep. 2017 05 26; 7(1):2451. View in: PubMed

  30. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome. 2017 02 01; 5(1):16. View in: PubMed

  31. Batch effects and the effective design of single-cell gene expression studies. Sci Rep. 2017 01 03; 7:39921. View in: PubMed

  32. Gene expression in local stroma reflects breast tumor states and predicts patient outcome. Sci Rep. 2016 12 16; 6:39240. View in: PubMed

  33. DNA methylation in lung cells is associated with asthma endotypes and genetic risk. JCI Insight. 2016 12 08; 1(20):e90151. View in: PubMed

  34. The human olfactory transcriptome. BMC Genomics. 2016 08 11; 17(1):619. View in: PubMed

  35. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5. View in: PubMed

  36. RNA splicing is a primary link between genetic variation and disease. Science. 2016 Apr 29; 352(6285):600-4. View in: PubMed

  37. Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S100-1. View in: PubMed

  38. Integrated analyses of gene expression and genetic association studies in a founder population. Hum Mol Genet. 2016 05 15; 25(10):2104-2112. View in: PubMed

  39. Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLoS Genet. 2016 Jan; 12(1):e1005793. View in: PubMed

  40. Synthesis, biological studies and molecular dynamics of new anticancer RGD-based peptide conjugates for targeted drug delivery. Bioorg Med Chem. 2016 Jan 15; 24(2):294-303. View in: PubMed

  41. Dual-drug RGD conjugates provide enhanced cytotoxicity to melanoma and non-small lung cancer cells. Biopolymers. 2016 Mar; 106(2):160-171. View in: PubMed

  42. Mycobacterial infection induces a specific human innate immune response. Sci Rep. 2015 Nov 20; 5:16882. View in: PubMed

  43. Genome-Wide Association Studies of the Human Gut Microbiota. PLoS One. 2015; 10(11):e0140301. View in: PubMed

  44. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015; 10(9):e0138030. View in: PubMed

  45. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec; 25(12):1801-11. View in: PubMed

  46. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015 Nov; 12(11):1061-3. View in: PubMed

  47. Metastasis Suppressors Regulate the Tumor Microenvironment by Blocking Recruitment of Prometastatic Tumor-Associated Macrophages. Cancer Res. 2015 Oct 01; 75(19):4063-73. View in: PubMed

  48. A reanalysis of mouse ENCODE comparative gene expression data. F1000Res. 2015; 4:121. View in: PubMed

  49. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015 Jun 23; 4:e07103. View in: PubMed

  50. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet. 2015 May; 11(5):e1005216. View in: PubMed

  51. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 2015 Apr; 11(4):e1005111. View in: PubMed

  52. The genetic architecture of gene expression levels in wild baboons. Elife. 2015 Feb 25; 4. View in: PubMed

  53. Genomic variation. Impact of regulatory variation from RNA to protein. Science. 2015 Feb 06; 347(6222):664-7. View in: PubMed

  54. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan; 11(1):e1004857. View in: PubMed

  55. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol. 2014; 15(12):547. View in: PubMed

  56. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 2014 Sep; 10(9):e1004663. View in: PubMed

  57. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Dec; 29:68-74. View in: PubMed

  58. The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. PLoS One. 2014; 9(9):e107166. View in: PubMed

  59. Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence. Sci Rep. 2014 Jul 28; 4:5809. View in: PubMed

  60. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol. 2014 May 30; 12:42. View in: PubMed

  61. Seasonal variation in human gut microbiome composition. PLoS One. 2014; 9(3):e90731. View in: PubMed

  62. The functional consequences of variation in transcription factor binding. PLoS Genet. 2014 Mar; 10(3):e1004226. View in: PubMed

  63. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol. 2013 Dec 31; 14(12):R148. View in: PubMed

  64. Does a unique olfactory genome imply a unique olfactory world? Nat Neurosci. 2014 Jan; 17(1):6-8. View in: PubMed

  65. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 08; 342(6159):747-9. View in: PubMed

  66. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. 2013 Nov 29; 342(6162):1100-4. View in: PubMed

  67. Social environmental effects on gene regulation. Cell Mol Life Sci. 2013 Nov; 70(22):4323-39. View in: PubMed

  68. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One. 2013; 8(1):e53608. View in: PubMed

  69. Controls of nucleosome positioning in the human genome. PLoS Genet. 2012; 8(11):e1003036. View in: PubMed

  70. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 2012; 8(10):e1003000. View in: PubMed

  71. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. View in: PubMed

  72. General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. Hum Mutat. 2013 Jan; 34(1):32-41. View in: PubMed

  73. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12656-61. View in: PubMed

  74. Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet. 2012 Jun 18; 13(7):505-16. View in: PubMed

  75. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proc Natl Acad Sci U S A. 2012 Apr 24; 109(17):6490-5. View in: PubMed

  76. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science. 2012 Mar 16; 335(6074):1302; author reply 1302. View in: PubMed

  77. Using genomic tools to study regulatory evolution. Methods Mol Biol. 2012; 856:335-61. View in: PubMed

  78. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One. 2012; 7(2):e30629. View in: PubMed

  79. Time-dependent transcriptional profiling links gene expression to mitogen-activated protein kinase kinase 4 (MKK4)-mediated suppression of omental metastatic colonization. Clin Exp Metastasis. 2012 Jun; 29(5):397-408. View in: PubMed

  80. DNase?I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 05; 482(7385):390-4. View in: PubMed

  81. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 2012 Jan 31; 13(1):R7. View in: PubMed

  82. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet. 2012 May 01; 21(9):2111-23. View in: PubMed

  83. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A. 2012 Jan 24; 109(4):1204-9. View in: PubMed

  84. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. View in: PubMed

  85. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol. 2012; 4(2):126-35. View in: PubMed

  86. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 01; 27(15):2144-6. View in: PubMed

  87. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet. 2011 Feb; 7(2):e1001316. View in: PubMed

  88. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics. 2011 Apr; 187(4):1225-34. View in: PubMed

  89. The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet. 2011 Apr 15; 20(8):1643-52. View in: PubMed

  90. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011; 12(1):R10. View in: PubMed

  91. Functional comparison of innate immune signaling pathways in primates. PLoS Genet. 2010 Dec 16; 6(12):e1001249. View in: PubMed

  92. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 2010 Dec 09; 6(12):e1001236. View in: PubMed

  93. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar; 21(3):447-55. View in: PubMed

  94. Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol. 2010 Dec; 19(24):5332-44. View in: PubMed

  95. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 01; 464(7289):768-72. View in: PubMed

  96. Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010 Feb; 20(2):180-9. View in: PubMed

  97. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009 Dec 15; 25(24):3207-12. View in: PubMed

  98. Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 2009 Oct; 25(10):463-71. View in: PubMed

  99. Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet. 2009 Nov 15; 18(22):4296-303. View in: PubMed

  100. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet. 2008 Nov; 4(11):e1000271. View in: PubMed

  101. Sex-specific genetic architecture of human disease. Nat Rev Genet. 2008 Dec; 9(12):911-22. View in: PubMed

  102. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 2008 Oct; 4(10):e1000214. View in: PubMed

  103. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 2008 Aug; 24(8):408-15. View in: PubMed
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