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Yoav Gilad

TitleProfessor
InstitutionUniversity of Chicago
DepartmentMedicine
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    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.

    Collapse Biography 
    Collapse education and training
    Weizmann Institute of Science, Rehovot, IsraelPh.D.08/2003Molecular Genetics
    Weizamnn Institute of Science, Rehovot, IsraelM.Sc. 09/2000Molecular Genetics
    Ben Gurion University, Beer-Sheva, IsraelB.Sc.08/1998Molecular Genetics and Biochemistry

    Collapse Research 
    Collapse research activities and funding
    R01HG010772     (GILAD, YOAV)Sep 1, 2019 - Jun 30, 2023
    NIH
    Development of iPSCs for comparative genomics in primates
    Role: Principal Investigator

    R35GM131726     (GILAD, YOAV)Jun 1, 2019 - May 31, 2024
    NIH
    Characterizing and Understanding Variation in Gene Regulatory Mechanisms Within and Between Species'
    Role: Principal Investigator

    R01HL139447     (GILAD, YOAV)Jan 1, 2018 - Apr 30, 2018
    NIH
    Characterizing and mapping gene regulatory robustness in cardiomyoctes
    Role: Principal Investigator

    R01GM122930     (GILAD, YOAV)Jul 1, 2017 - Mar 31, 2021
    NIH
    Using single cell RNA-seq to study regulatory noise and robustness
    Role: Principal Investigator

    U01TR001810     (KOTTON, DARRELL N.)Sep 15, 2016 - Jun 30, 2021
    NIH
    A National iPS Cell Network with Deep Phenotyping for Translational Research
    Role: Co-Principal Investigator

    R01ES023195     (FUREY, TERRENCE S.)Aug 26, 2013 - May 31, 2018
    NIH
    Genes, genomes, and genotoxicity: in vivo epigenetic toxicology of 1,3-butadiene
    Role: Co-Principal Investigator

    R01HG006123     (GILAD, YOAV)Apr 14, 2011 - Feb 28, 2015
    NIH
    Mapping QTLs Associated with Variation in RNA Decay Rates
    Role: Principal Investigator

    R01AI087658     (GILAD, YOAV)Jan 1, 2011 - Dec 31, 2015
    NIH
    Mapping eQTLs that affect susceptibility to Tuberculosis
    Role: Principal Investigator

    R01GM084996     (GILAD, YOAV)Mar 1, 2010 - Feb 28, 2014
    NIH
    The evolution of human specific regulatory pathways
    Role: Principal Investigator

    R01MH084703     (GILAD, YOAV)Sep 25, 2008 - Aug 31, 2016
    NIH
    Analysis and interpretation of noncoding regulatory variation
    Role: Principal Investigator

    R01HL092206     (GILAD, YOAV)Apr 1, 2008 - Apr 30, 2022
    NIH
    eQTL mapping in iPSC-derived differentiated cardiomyocytes
    Role: Principal Investigator

    R01GM077959     (GILAD, YOAV)Apr 1, 2006 - Mar 31, 2015
    NIH
    Natural Selection on Gene Regulation in Humans
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. McIntire E, Barr KA, Gilad Y, Gonzales NM, McIntire E, Barr KA, Gonzales NM, Gilad Y. Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity. bioRxiv. 2024 Feb 12. PMID: 37502898; PMCID: PMC10370173.
      Citations:    
    2. Lin W, Wall JD, Li G, Newman D, VandeBerg JL, Yang Y, Abney M, Olivier M, Gilad Y, Cox LA, Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA, Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons. bioRxiv. 2023 Nov 20. PMID: 37577666; PMCID: PMC10418186.
      Citations:    
    3. Adegunsoye A, Gonzales NM, Gilad Y. Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility. Annu Rev Genet. 2023 11 27; 57:341-360. PMID: 37708421.
      Citations: 1     Fields:    Translation:HumansCells
    4. Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol. 2023 09 11; 24(1):207. PMID: 37697401; PMCID: PMC10496171.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    5. Housman G, Briscoe E, Gilad Y. Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. PLoS Genet. 2022 03; 18(3):e1010073. PMID: 35263340; PMCID: PMC8936463.
      Citations: 4     Fields:    Translation:AnimalsCells
    6. Rhodes K, Barr KA, Popp JM, Strober BJ, Battle A, Gilad Y. Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types. Elife. 2022 02 10; 11. PMID: 35142607; PMCID: PMC8830892.
      Citations: 5     Fields:    Translation:HumansCells
    7. Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr K, Qi G, Gilad Y, Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet. 2022 01; 18(1):e1009666. PMID: 35061661; PMCID: PMC8809621.
      Citations: 14     Fields:    Translation:HumansCells
    8. Shah A, Mittleman BE, Gilad Y, Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021 10 14; 22(1):291. PMID: 34649612; PMCID: PMC8518154.
      Citations: 12     Fields:    Translation:HumansCells
    9. Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S, Wen X, Lanfear DE, Pique-Regi R, Gilad Y, Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. Elife. 2021 05 14; 10. PMID: 33988505; PMCID: PMC8248987.
      Citations: 19     Fields:    Translation:HumansCells
    10. Mittleman BE, Pott S, Warland S, Barr K, Cuevas C, Gilad Y. Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. Elife. 2021 02 17; 10. PMID: 33595436; PMCID: PMC7954529.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    11. Ward MC, Banovich NE, Sarkar A, Stephens M, Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. Elife. 2021 02 08; 10. PMID: 33554857; PMCID: PMC7906610.
      Citations: 20     Fields:    Translation:HumansCells
    12. Eres IE, Gilad Y. A TAD Skeptic: Is 3D Genome Topology Conserved? Trends Genet. 2021 03; 37(3):216-223. PMID: 33203573; PMCID: PMC8120795.
      Citations: 23     Fields:    Translation:HumansCells
    13. Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. Elife. 2020 10 21; 9. PMID: 33084571; PMCID: PMC7644215.
      Citations: 18     Fields:    Translation:HumansAnimals
    14. Umans BD, Battle A, Gilad Y. Where Are the Disease-Associated eQTLs? Trends Genet. 2021 02; 37(2):109-124. PMID: 32912663; PMCID: PMC8162831.
      Citations: 80     Fields:    Translation:HumansAnimalsCells
    15. Kelley JL, Gilad Y. Effective study design for comparative functional genomics. Nat Rev Genet. 2020 07; 21(7):385-386. PMID: 32332928.
      Citations: 2     Fields:    Translation:HumansAnimals
    16. Mittleman BE, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, Li Y. Alternative polyadenylation mediates genetic regulation of gene expression. Elife. 2020 06 25; 9. PMID: 32584258; PMCID: PMC7338057.
      Citations: 27     Fields:    Translation:HumansCells
    17. Housman G, Gilad Y. Prime time for primate functional genomics. Curr Opin Genet Dev. 2020 06; 62:1-7. PMID: 32544775; PMCID: PMC8170550.
      Citations: 9     Fields:    Translation:HumansAnimals
    18. Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 2020 04; 30(4):611-621. PMID: 32312741; PMCID: PMC7197478.
      Citations: 34     Fields:    Translation:HumansCells
    19. Selewa A, Dohn R, Eckart H, Lozano S, Xie B, Gauchat E, Elorbany R, Rhodes K, Burnett J, Gilad Y, Pott S, Basu A. Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation. Sci Rep. 2020 01 30; 10(1):1535. PMID: 32001747; PMCID: PMC6992778.
      Citations: 41     Fields:    Translation:HumansCells
    20. Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Res. 2020 02; 30(2):250-262. PMID: 31953346; PMCID: PMC7050529.
      Citations: 49     Fields:    Translation:HumansAnimalsCells
    21. 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 07; 15(7):e1008278. PMID: 31323043; PMCID: PMC6668850.
      Citations: 34     Fields:    Translation:HumansAnimals
    22. 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. PMID: 31249060; PMCID: PMC6623972.
      Citations: 67     Fields:    Translation:HumansCells
    23. 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. PMID: 31002671; PMCID: PMC6474585.
      Citations: 32     Fields:    Translation:HumansCells
    24. Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. Elife. 2019 04 08; 8. PMID: 30958265; PMCID: PMC6538380.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    25. 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. PMID: 30333510; PMCID: PMC6193013.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    26. 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. PMID: 30322406; PMCID: PMC6191992.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    27. 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. PMID: 30108239; PMCID: PMC6092387.
      Citations:    Fields:    Translation:HumansCells
    28. 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. PMID: 29737278; PMCID: PMC6010343.
      Citations: 48     Fields:    Translation:HumansCells
    29. 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. PMID: 29648536; PMCID: PMC5943035.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    30. 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. PMID: 29208628; PMCID: PMC5749177.
      Citations: 62     Fields:    Translation:HumansCells
    31. Ward MC, Gilad Y. Human genomics: Cracking the regulatory code. Nature. 2017 10 11; 550(7675):190-191. PMID: 29022577.
      Citations: 11     Fields:    Translation:Humans
    32. Blischak JD, Tailleux L, Myrthil M, Morizot G, Platen CV, Brosch R, Gilad Y, Charlois C, Bergot E, Dinh A, Chény O, Herrmann JL, Barreiro LB. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep. 2017 07 18; 7(1):5702. PMID: 28720766; PMCID: PMC5516010.
      Citations: 4     Fields:    Translation:HumansCells
    33. 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. PMID: 28550296; PMCID: PMC5446398.
      Citations: 28     Fields:    Translation:HumansCells
    34. 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. PMID: 28143570; PMCID: PMC5286564.
      Citations: 35     Fields:    Translation:HumansCells
    35. 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. PMID: 28045081; PMCID: PMC5206706.
      Citations: 139     Fields:    Translation:HumansCells
    36. 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. PMID: 27982086; PMCID: PMC5159815.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    37. 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. PMID: 27942592; PMCID: PMC5139904.
      Citations: 72     Fields:    Translation:HumansCells
    38. 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. PMID: 27515280; PMCID: PMC4982115.
      Citations: 47     Fields:    Translation:HumansAnimalsCells
    39. 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. PMID: 27232982; PMCID: PMC4940163.
      Citations: 68     Fields:    Translation:HumansCells
    40. 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. PMID: 27126046; PMCID: PMC5182069.
      Citations: 291     Fields:    Translation:HumansCells
    41. 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. PMID: 27027937; PMCID: PMC5015738.
      Citations: 1     Fields:    
    42. 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. PMID: 26715008.
      Citations: 15     Fields:    
    43. Elias JA, Chupp GL, Lang RM, Shah SJ, Decara JM, Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, 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. PMID: 26931462; PMCID: PMC5062579.
      Citations: 11     Fields:    Translation:Humans
    44. 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. PMID: 26812582; PMCID: PMC4727884.
      Citations: 74     Fields:    Translation:HumansCells
    45. 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. PMID: 26719208.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    46. Blischak JD, Tailleux L, Mitrano A, Gilad Y, Barreiro LB. Mycobacterial infection induces a specific human innate immune response. Sci Rep. 2015 Nov 20; 5:16882. PMID: 26586179; PMCID: PMC4653619.
      Citations: 34     Fields:    Translation:HumansCells
    47. 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. PMID: 26528553; PMCID: PMC4631601.
      Citations: 124     Fields:    Translation:HumansAnimalsCells
    48. 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. PMID: 26406244; PMCID: PMC4583425.
      Citations: 19     Fields:    Translation:HumansCells
    49. Pacis A, Tailleux L, Morin AM, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB, Lambourne J, Pastinen T. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec; 25(12):1801-11. PMID: 26392366; PMCID: PMC4665002.
      Citations: 105     Fields:    Translation:HumansCells
    50. 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. PMID: 26366987; PMCID: PMC4626402.
      Citations: 255     Fields:    Translation:Humans
    51. 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. PMID: 26238785; PMCID: PMC4592465.
      Citations: 66     Fields:    Translation:HumansAnimalsCells
    52. Gallego Romero I, Pavlovic BJ, 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, Laurent LC, Loring JF, Gilad Y, Hernando-Herraez I, Marques-Bonet T. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015 Jun 23; 4:e07103. PMID: 26102527; PMCID: PMC4502404.
      Citations: 61     Fields:    Translation:HumansAnimalsCells
    53. Gilad Y, Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000Res. 2015; 4:121. PMID: 26236466; PMCID: PMC4516019.
      Citations: 55     Fields:    
    54. 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. PMID: 25950834; PMCID: PMC4423863.
      Citations: 19     Fields:    Translation:HumansCells
    55. Baker SW, Gilad Y, Ober C, Çaliskan M. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 2015 Apr; 11(4):e1005111. PMID: 25874939; PMCID: PMC4395341.
      Citations: 35     Fields:    Translation:HumansCells
    56. 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. PMID: 25714927; PMCID: PMC4383332.
      Citations: 52     Fields:    Translation:Animals
    57. Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan; 11(1):e1004857. PMID: 25569255; PMCID: PMC4287341.
      Citations: 81     Fields:    Translation:HumansCells
    58. 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. PMID: 25657249; PMCID: PMC4507520.
      Citations: 223     Fields:    Translation:HumansCells
    59. 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. PMID: 25233095; PMCID: PMC4169251.
      Citations: 154     Fields:    Translation:HumansCells
    60. Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Dec; 29:68-74. PMID: 25215415; PMCID: PMC4258459.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    61. Pritchard JK, Ober C, Gilad Y, Çaliskan M. The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. PLoS One. 2014; 9(9):e107166. PMID: 25192014; PMCID: PMC4156430.
      Citations: 14     Fields:    Translation:HumansCells
    62. 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. PMID: 25069065; PMCID: PMC4894427.
      Citations: 13     Fields:    Translation:HumansAnimals
    63. 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. PMID: 24885439; PMCID: PMC4071332.
      Citations: 191     Fields:    Translation:HumansCells
    64. 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. PMID: 24618913; PMCID: PMC3949691.
      Citations: 128     Fields:    Translation:Humans
    65. Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 2014 Mar; 10(3):e1004226. PMID: 24603674; PMCID: PMC3945204.
      Citations: 115     Fields:    Translation:HumansCells
    66. Frumin I, Sobel N, Gilad Y. Does a unique olfactory genome imply a unique olfactory world? Nat Neurosci. 2014 Jan; 17(1):6-8. PMID: 24369370.
      Citations: 2     Fields:    Translation:Humans
    67. 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. PMID: 25468404; PMCID: PMC4290387.
      Citations: 38     Fields:    Translation:HumansAnimalsCells
    68. 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. PMID: 24380390; PMCID: PMC4056453.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    69. 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. PMID: 24136359; PMCID: PMC3947669.
      Citations: 247     Fields:    Translation:HumansCells
    70. 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. PMID: 24136357; PMCID: PMC3994702.
      Citations: 125     Fields:    Translation:HumansAnimalsCells
    71. Tung J, Gilad Y. Social environmental effects on gene regulation. Cell Mol Life Sci. 2013 Nov; 70(22):4323-39. PMID: 23685902; PMCID: PMC3809334.
      Citations: 23     Fields:    Translation:HumansAnimals
    72. 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. PMID: 23308262; PMCID: PMC3538547.
      Citations: 121     Fields:    
    73. 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. PMID: 23166509; PMCID: PMC3499251.
      Citations: 158     Fields:    Translation:HumansCells
    74. 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. PMID: 23071454; PMCID: PMC3469421.
      Citations: 63     Fields:    Translation:HumansCells
    75. 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. PMID: 22936402; PMCID: PMC3627721.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    76. Ecker JR, Bickmore WA, Pritchard JK, Gilad Y, Segal E, Barroso I. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. PMID: 22955614.
      Citations: 102     Fields:    Translation:HumansCells
    77. 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. PMID: 22797897; PMCID: PMC3411951.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    78. 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. PMID: 22705669; PMCID: PMC4034676.
      Citations: 207     Fields:    Translation:Animals
    79. 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. PMID: 22493251; PMCID: PMC3340061.
      Citations: 136     Fields:    Translation:AnimalsCells
    80. 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. PMID: 22422963; PMCID: PMC5207799.
      Citations: 110     Fields:    Translation:Humans
    81. 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. PMID: 22350525; PMCID: PMC4026167.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    82. 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. PMID: 22359548; PMCID: PMC3281037.
      Citations: 16     Fields:    Translation:HumansCells
    83. 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. PMID: 22307276; PMCID: PMC3501342.
      Citations: 380     Fields:    Translation:HumansCells
    84. 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. PMID: 22293038; PMCID: PMC3334587.
      Citations: 125     Fields:    Translation:HumansCells
    85. 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. PMID: 22286170; PMCID: PMC3315207.
      Citations: 34     Fields:    Translation:HumansCells
    86. 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. PMID: 22233810; PMCID: PMC3268270.
      Citations: 142     Fields:    Translation:HumansCells
    87. Gilad Y. Using genomic tools to study regulatory evolution. Methods Mol Biol. 2012; 856:335-61. PMID: 22399466; PMCID: PMC4011178.
      Citations: 3     Fields:    Translation:HumansAnimals
    88. Perry GH, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y, Melsted P. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. PMID: 22207615; PMCID: PMC3317143.
      Citations: 74     Fields:    Translation:HumansAnimalsCells
    89. Perry GH, Reeves D, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y, Melsted P. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol. 2012; 4(2):126-35. PMID: 22155688; PMCID: PMC3273163.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    90. 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. PMID: 21690102; PMCID: PMC3137225.
      Citations: 54     Fields:    Translation:HumansCells
    91. 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. PMID: 21383968; PMCID: PMC3044686.
      Citations: 108     Fields:    Translation:HumansAnimalsCells
    92. 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. PMID: 21321133; PMCID: PMC3070530.
      Citations: 53     Fields:    Translation:HumansAnimalsCells
    93. 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. PMID: 21289059; PMCID: PMC3063990.
      Citations: 81     Fields:    Translation:HumansCells
    94. 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. PMID: 21251332; PMCID: PMC3091299.
      Citations: 483     Fields:    Translation:HumansCells
    95. 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. PMID: 21187902; PMCID: PMC3002988.
      Citations: 55     Fields:    Translation:HumansAnimalsCells
    96. 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. PMID: 21151575; PMCID: PMC3000347.
      Citations: 167     Fields:    Translation:HumansCells
    97. 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. PMID: 21106904; PMCID: PMC3044858.
      Citations: 332     Fields:    Translation:HumansCells
    98. Perry GH, Marioni JC, Gilad Y, Melsted P. Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol. 2010 Dec; 19(24):5332-44. PMID: 21054605; PMCID: PMC2998560.
      Citations: 42     Fields:    Translation:Animals
    99. 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. PMID: 20220758; PMCID: PMC3089435.
      Citations: 770     Fields:    Translation:HumansCells
    100. 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. PMID: 20009012; PMCID: PMC2813474.
      Citations: 159     Fields:    Translation:HumansAnimalsCells
    101. 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. PMID: 19808877; PMCID: PMC2788925.
      Citations: 277     Fields:    Translation:HumansCells
    102. Gilad Y, Pritchard JK, Thornton K. Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 2009 Oct; 25(10):463-71. PMID: 19801172; PMCID: PMC3994700.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    103. 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. PMID: 19671653; PMCID: PMC2766291.
      Citations: 35     Fields:    Translation:HumansCells
    104. Ober C, Loisel DA, Gilad Y. Sex-specific genetic architecture of human disease. Nat Rev Genet. 2008 Dec; 9(12):911-22. PMID: 19002143; PMCID: PMC2694620.
      Citations: 345     Fields:    Translation:HumansAnimals
    105. 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. PMID: 19023414; PMCID: PMC2581600.
      Citations: 97     Fields:    Translation:HumansAnimals
    106. 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. PMID: 18846210; PMCID: PMC2556086.
      Citations: 353     Fields:    Translation:HumansCells
    107. 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. PMID: 18597885; PMCID: PMC2583071.
      Citations: 269     Fields:    Translation:HumansAnimals
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