Yoav Gilad

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
Publications
  1. Eres IE, Luo K, Hsiao CJ, Blake LE, Gilad Y. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. PLoS Genet. 2019 Jul; 15(7):e1008278. View in: PubMed

  2. Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y. Dynamic genetic regulation of gene expression during cellular differentiation. Science. 2019 06 28; 364(6447):1287-1290. View in: PubMed

  3. Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y. Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045. View in: PubMed

  4. Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. Elife. 2019 04 08; 8. View in: PubMed

  5. Pavlovic BJ, Blake LE, Roux J, Chavarria C, Gilad Y. 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

  6. Blake LE, Thomas SM, Blischak JD, Hsiao CJ, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ. A comparative study of endoderm differentiation in humans and chimpanzees. Genome Biol. 2018 10 15; 19(1):162. View in: PubMed

  7. Engelmann BW, Hsiao CJ, Blischak JD, Fourne Y, Khan Z, Ford M, Gilad Y. A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. Sci Rep. 2018 08 14; 8(1):12106. View in: PubMed

  8. Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y. Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. Elife. 2018 05 08; 7. View in: PubMed

  9. Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. Elife. 2018 04 12; 7. View in: PubMed

  10. Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131. View in: PubMed

  11. Ward MC, Gilad Y. Human genomics: Cracking the regulatory code. Nature. 2017 10 11; 550(7675):190-191. View in: PubMed

  12. Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann JL, Brosch R, Barreiro LB, Gilad Y. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep. 2017 07 18; 7(1):5702. View in: PubMed

  13. Montefiori L, Hernandez L, Zhang Z, Gilad Y, Ober C, Crawford G, Nobrega M, Jo Sakabe N. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Sci Rep. 2017 05 26; 7(1):2451. View in: PubMed

  14. Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, Ober C. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome. 2017 02 01; 5(1):16. View in: PubMed

  15. Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y. Batch effects and the effective design of single-cell gene expression studies. Sci Rep. 2017 01 03; 7:39921. View in: PubMed

  16. Bainer R, Frankenberger C, Rabe D, An G, Gilad Y, Rosner MR. Gene expression in local stroma reflects breast tumor states and predicts patient outcome. Sci Rep. 2016 12 16; 6:39240. View in: PubMed

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

  18. Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, Lancet D. The human olfactory transcriptome. BMC Genomics. 2016 08 11; 17(1):619. View in: PubMed

  19. Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5. View in: PubMed

  20. Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK. RNA splicing is a primary link between genetic variation and disease. Science. 2016 Apr 29; 352(6285):600-4. View in: PubMed

  21. Igartua C, Davenport ER, Chupp GL, Elias JA, Gilad Y, Ober C, Pinto JM. 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

  22. 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, Ober C. 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

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

  24. Gilad Y, Noy E, Senderowitz H, Albeck A, Firer MA, Gellerman G. 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

  25. Gilad Y, Noy E, Senderowitz H, Albeck A, Firer MA, Gellerman G. 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

  26. Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y. Mycobacterial infection induces a specific human innate immune response. Sci Rep. 2015 Nov 20; 5:16882. View in: PubMed

  27. Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, Gilad Y. Genome-Wide Association Studies of the Human Gut Microbiota. PLoS One. 2015; 10(11):e0140301. View in: PubMed

  28. Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M. 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

  29. Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac 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, Barreiro LB. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec; 25(12):1801-11. View in: PubMed

  30. van de Geijn B, McVicker G, Gilad Y, Pritchard JK. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015 Nov; 12(11):1061-3. View in: PubMed

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

  32. Gilad Y, Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000Res. 2015; 4:121. View in: PubMed

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

  34. Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet. 2015 May; 11(5):e1005216. View in: PubMed

  35. Çaliskan M, Baker SW, Gilad Y, Ober C. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 2015 Apr; 11(4):e1005111. View in: PubMed

  36. Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. The genetic architecture of gene expression levels in wild baboons. Elife. 2015 Feb 25; 4. View in: PubMed

  37. Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y. Genomic variation. Impact of regulatory variation from RNA to protein. Science. 2015 Feb 06; 347(6222):664-7. View in: PubMed

  38. Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan; 11(1):e1004857. View in: PubMed

  39. Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol. 2014; 15(12):547. View in: PubMed

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

  41. Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Dec; 29:68-74. View in: PubMed

  42. Çaliskan M, Pritchard JK, Ober C, Gilad Y. The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. PLoS One. 2014; 9(9):e107166. View in: PubMed

  43. Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AG, Gilad Y. 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

  44. Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol. 2014 May 30; 12:42. View in: PubMed

  45. Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, Gilad Y. Seasonal variation in human gut microbiome composition. PLoS One. 2014; 9(3):e90731. View in: PubMed

  46. Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 2014 Mar; 10(3):e1004226. View in: PubMed

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

  48. Frumin I, Sobel N, Gilad Y. Does a unique olfactory genome imply a unique olfactory world? Nat Neurosci. 2014 Jan; 17(1):6-8. View in: PubMed

  49. McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 08; 342(6159):747-9. View in: PubMed

  50. Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. 2013 Nov 29; 342(6162):1100-4. View in: PubMed

  51. Tung J, Gilad Y. Social environmental effects on gene regulation. Cell Mol Life Sci. 2013 Nov; 70(22):4323-39. View in: PubMed

  52. Mizrahi-Man O, Davenport ER, Gilad Y. 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

  53. Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. Controls of nucleosome positioning in the human genome. PLoS Genet. 2012; 8(11):e1003036. View in: PubMed

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

  55. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. View in: PubMed

  56. Keydar I, Ben-Asher E, Feldmesser E, Nativ N, Oshimoto A, Restrepo D, Matsunami H, Chien MS, Pinto JM, Gilad Y, Olender T, Lancet D. General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. Hum Mutat. 2013 Jan; 34(1):32-41. View in: PubMed

  57. 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, Lee C. 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

  58. Romero IG, Ruvinsky I, Gilad Y. Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet. 2012 Jun 18; 13(7):505-16. View in: PubMed

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

  60. Pickrell JK, Gilad Y, Pritchard JK. 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

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

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

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

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

  65. Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 2012 Jan 31; 13(1):R7. View in: PubMed

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

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

  68. Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. View in: PubMed

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

  70. Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK. 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

  71. Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. 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

  72. Cain CE, Blekhman R, Marioni JC, Gilad Y. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics. 2011 Apr; 187(4):1225-34. View in: PubMed

  73. Caliskan M, Cusanovich DA, Ober C, Gilad Y. 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

  74. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011; 12(1):R10. View in: PubMed

  75. Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. PLoS Genet. 2010 Dec 16; 6(12):e1001249. View in: PubMed

  76. Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 2010 Dec 09; 6(12):e1001236. View in: PubMed

  77. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar; 21(3):447-55. View in: PubMed

  78. Perry GH, Marioni JC, Melsted P, Gilad Y. Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol. 2010 Dec; 19(24):5332-44. View in: PubMed

  79. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 01; 464(7289):768-72. View in: PubMed

  80. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010 Feb; 20(2):180-9. View in: PubMed

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

  82. Gilad Y, Pritchard JK, Thornton K. Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 2009 Oct; 25(10):463-71. View in: PubMed

  83. Bullaughey K, Chavarria CI, Coop G, Gilad Y. 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

  84. Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet. 2008 Nov; 4(11):e1000271. View in: PubMed

  85. Ober C, Loisel DA, Gilad Y. Sex-specific genetic architecture of human disease. Nat Rev Genet. 2008 Dec; 9(12):911-22. View in: PubMed

  86. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 2008 Oct; 4(10):e1000214. View in: PubMed

  87. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 2008 Aug; 24(8):408-15. View in: PubMed