Publications (old)

Current Preprints 

Barr KA, Rhodes KL, and Gilad Y. Embryoid bodies facilitate comparative analysis of gene expression in humans and chimpanzees across dozens of cell types. bioRxiv; 500831; doi: https://doi.org/10.1101/2022.07.20.500831

Gallego Romero I, Gopalakrishnan, S and Gilad Y. Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells. bioRxiv; 466631; doi: https://doi.org/10.1101/466631

Publications

2022

Hung A, Housman G, Briscoe EA, Cuevas C and Gilad Y. Characterizing gene expression in an in vitro biomechanical strain model of joint health [version 1; peer review: awaiting peer review]. F1000 Research; 2022; 11:296. doi: https://doi.org/10.12688/f1000research.109602.1

Housman G, Briscoe E, and Gilad Y. Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. PLoS Genetics; 2022; 18(3):e1010073. doi: https://doi.org.10.1371/journal.pgen.1010073

Rhodes K, Barr KA, Popp JM, Strober BJ, Battle A, and Gilad Y. Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types. eLife; 2022 Feb 10; 11:e71361. doi: https://doi.org/10.7554/eLife.71361.

Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr KA, Qi G, Gilad Y, and Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genetics; 18(1):e1009666. doi: https://doi.org/10.1371/journal.pgen.1009666

2021

Shah A, Mittleman BE, Gilad Y, and Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biology. 2021 Oct 14; 22(1):291; doi: doi.org/10.1186/s13059-021-02502-z

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, and Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. Elife. 2021 May 14;e67077. doi: doi.org/10.7554/eLife.67077

Mittleman BE, Pott S, Warland S, Barr K, Cuevas C, and Gilad Y. Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. Elife. 2021 Feb 17;10:e62548. doi: doi.org/10.7554/eLife.62548

Ward MC, Banovich NE, Sarkar A, Stephens M, and Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. Elife. 2021 Feb 8;10:e57345. doi: doi.org/10.7554/eLife.57345

Eres IE & Gilad Y. A TAD Skeptic: Is 3D Genome Topology Conserved? Trends in Genetics. 2021 Mar;37(3):216-223; doi: 10.1016/j.tig.2020.10.00

2020

Fair B, Blake LE, Sarkar A, Pavlovic B.J. Cuevas C, and Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. Elife. 2020 Oct 21; 9:e59929. doi: 10.7554/eLife.59929

Umans BD, Battle A, and Gilad Y. Where Are the Disease-Associated eQTLs? 2020 Sep 7; S0168-9525(20)30209-2; Trends in Genetics.  doi: 10.1016/j.tig.2020.08.009

Mittleman BE, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, and Li YI. Alternative polyadenylation mediates genetic regulation of gene expression. 2020 June 25; eLife 2020;9:e57492;  doi: 10.7554/eLife.57492 

Housman G and Gilad Y. Prime time primate functional genomics. Current Opinion in Genetics and Development. 2020 June 13; doi: https://doi.org/10.1016/j.gde.2020.04.007

Kelley JL and Gilad Y. Effective study design for comparative functional genomics. Nature Reviews Genetics. 2020 April 24; doi: https://doi.org/10.1038/s41576-020-0242-z

Hsiao CJ, Tung P, Blischak JD, Burnett J, Barr K, Dey KK, Stephens M, and Gilad Y. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Research. 2020, April 20; doi:10.1101/gr.247759.118 

Selewa A, Dohn R, Eckart H, Lozano S, Xie B, Gauchat E, Elorbany R, Rhodes K, Burnett J, Gilad Y, Pott S, and Basu A. Systematic comparison of high-throughput single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation. 2020 Jan 30 Scientific Reports. 10(1535); doi:  https://doi.org/10.1038/s41598-020-58327-6

Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Garcia Perez R, Hsiao CJ, Eres I, Chavarria C, Marquez-Bonet T and Gilad Y. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Research.  2020, Jan 17; doi: 10.1101/gr.254904.119

2019

Eres IE, Luo K, Hsiao CJ, Blake LE and Gilad Y. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. PLOS Genetics; 2019; doi: https://doi.org/10.1371/journal.pgen.1008278

Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, and Gilad Y. Dynamic genetic regulation of gene expression during cellular differentiation. Science. 2019; 364(6447); doi: 10.1126/science.aaw0040 https://science.sciencemag.org/content/364/6447/1287?fbclid=IwAR3fogSPVd-WofbUsz6Sz3Z0u9IEZKQkX-IjODzWWTXshWZYdg5C-Qk772E

Sarkar AK, Tung P, Blischak JD, Burnett JE, Li Yi, Stephens M, and Gilad Y. Discovery and charactirzation of variance QTLs in human induced pluripotent stem cells. PLOS Genetics 2019; 10.1371; doi: https://doi.org/10.1371/journal.pgen.1008045

Ward MC, and Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from human cimpanzees. eLife 2019; 8:e42374; doi:10.7554 https://elifesciences.org/articles/42374

2018

Blake LE, Thomas SJ, Blischak JD, Hsiao C, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ. A comparative study of endoderm differentiation in humans and chimpanzees. Genome Biology 2018; 19(162); doi:10.1186 https://doi.org/10.1186/s13059-018-1490-5

Pavlovic BJ, Blake LE, Roux J, Chavarria C, and Gilad Y. A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. Sci Rep. 2018; 8(15312); doi:10.1038/s41598-018-33478-9 https://www.nature.com/articles/s41598-018-33478-9

Engelmann BW, Hsiao CJ, Blischak JD, Fourne Y, Ford M, and Gilad Y. A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. Sci Rep. 2018; 8(1); doi:10.1038/s41598-018-30587-3 https://www.nature.com/articles/s41598-018-30587-3

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Ober C, Pritchard JK, and Gilad Y. Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. Elife. 2018 May 8 212381. doi: 10.7554/eLife.33480. [epub ahead of print]

Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, and Gilad Y. Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution in Primate iPSCs. Elife. 2018 Apr 12;7:e33084. doi: 10.7554/eLife.33084. [epub ahead of print]

2017

Banovich N, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung P, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Gallego Romero I, Pavlovic BJ, Kundaje A, Pritchard JK, and Gilad Y. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2017 Dec 5: 117. doi: 10.1101/gr.224436. [epub ahead of print]

Ward MC and Gilad Y. Human genomics: Cracking the regulatory code. Nature. 2017 Oct 11;550(7675):190-191. doi: 10.1038/550190a.

Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann J, Brosch R, Barreiro LB, and Gilad Y. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep. 2017 Jul 18;7(1):5702. doi: 10.1038/s41598-017-05878-w.

Montefiori L, Hernandez L, Zhang Z, Gilad Y, Ober C, Crawford G, Nobrega M, and Jo Sakabe N. Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9. Sci Rep. 2017 May 26;7(1):2451. doi: 10.1038/s41598-017-02547-w.

Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, and Ober C. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome. 2017 Feb 1;5:16. doi: 10.1186/s40168-016-0227-5.

Tung P, Blischak JD, Hsiao C, Knowles DA, Burnett JE, Pritchard JK, and Gilad Y. Batch effects and the effective design of single-cell gene expression studies. Sci Rep. 2017 Jan 3;7:39921. doi: 10.1038/srep39921.

2016

Bainer R, Frankenberger C, Rabe D, An G, Gilad Y, and Rosner MR. Gene expression in local stroma reflects breast tumor states and predicts patient outcome. Sci Rep. 2016 Dec 16;6:39240. doi:10.1038/srep39240.

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, and Ober C. DNA methylation in lung cells is associated with asthma endotypes and genetic risk. JCI Insight. 2016 Dec 8;1(20):e90151. doi: 10.1172/jci.insight.90151.

Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, and Lancet D. The human olfactory transcriptome. BMC Genomics. 2016 Aug 11;17(1):619. doi: 10.1186/s12864-016-2960-3.

Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, and Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 May 27;5. doi: 10.7554/eLife.13328. [epub ahead of print]

Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, and Pritchard JK. RNA splicing is a primary link between genetic variation and disease. Science. 2016 Apr 29; 352(6285): 600-604. doi: 10.1126/science.aad9417.

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, and Ober C. Integrated Analyses of Gene Expression and Genetic Association Studies in a Founder Population. Hum Mol Genet. 2016 Feb 29. doi: 10.1093/hmg/ddw061. [epub ahead of print]

Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, and Gilad Y. Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLoS Genet. 2016 Jan 26;12(1):e1005793. doi: 10.1371/journal.pgen.1005793.

2015

Blischak JD, Tailleux L, Mitrano A, Barreiro L, and Gilad Y. Mycobacterial infection induces a specific human innate immune response. Sci Rep. 2015 Nov 20;5:16882. doi: 10.1038/srep16882.

Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, and Gilad Y. Genome-Wide Association Studies of the Human Gut Microbiota. PLoS One. 2015 Nov 3;10(10):e0140301. doi: 10.1371/journal.pone.0140301.

Raj A, Shim H, Gilad Y, Pritchard JK, and Stephens M. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030.

Pacis A, Tailleux L, Morin AM, Lambourne J, Maclsaac 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, and Barreiro LB. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Sep 21. pii: gr.192005.115.

van de Geijn B, McVicker G, Gilad Y, Pritchard JK. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015 Sep 14. doi: 10.1038/nmeth.3582.

Frankenberger C, Rabe D, Bainer R, Sankarasharma D, Chada K, Krausz T, Gilad Y, Becker L, and Rosner MR. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of pro-metastatic tumor-associated macrophages. Cancer Res. 2015 Aug 3. pii: canres.3394.2014.

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. doi: 10.7554/eLife.07103.

Mizrahi-Man O and Gilad Y. A reanalysis of mouse ENCODE comparative gene expression data. F1000Research. 2015 May: http://dx.doi.org/10.12688/f1000research.6536.1

Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, and Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet. 2015 May 7;11(5):e1005216.

Çalışkan M, Baker SW, Gilad Y, and Ober C. Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection. PLoS Genetics. 2015 April 13;11(4):e1005111.

Tung J, Zhou X, Alberts SC, Stephens M, and Gilad Y. The genetic architecture of gene expression levels in wild baboons. eLife. Feb 2015;4:e04729.

Pai AA, Pritchard JK, and Gilad Y. The Genetic and Mechanistic Basis for Variation in Gene Regulation. PLoS Genet. 2015 Jan 8;11(1):e1004857.

2014

Battle A, Kahn Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, and Gilad Y. Impact of regulatory variation from RNA to protein. Science. 2014 Dec 18. [epub ahead of print]

Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, and Gilad Y. Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates. Genome Biology. 2014 Dec 3; 15:547.

Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, and Gilad Y. Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels. PLoS Genetics 2014 Sep 18;10(9):e1004663.

Pai AA and Gilad Y. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Sep 9;29C:68-74. [epub ahead of print]Calışkan M, Pritchard JK, Ober C, and Gilad Y. The Effect of Freeze-Thaw Cycles on Gene Expression Levels in Lymphoblastoid Cell Lines. PLoS One. 2014 Sep 5;9(9):e107166.

Blekhman R, Perry GH, Shahbaz S, Fiehn O, Clark AC, and Gilad Y. Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence. Scientific Reports. 2014 July 28;4:5809.

Gallego Romero I, Pai AA, Tung J, and Gilad Y. RNA-seq: Impact of RNA degradation on transcript quantification. BMC Biol. 2014 May 30; 12(1):42 (epub ahead of print)

Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, and Gilad Y. Seasonal variation in human gut microbiome composition. PLoS One. 2014;9(3):e90731 (epub 2014 Mar 11)

Cusanovich DA, Pavlovic B, Pritchard JK, and Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genetics. 2014;10(3):e1004226 (epub 2014 Mar 6)

2013

Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, and Flicek P. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biology. 2013 Dec 31;14(12):R148 [epub ahead of print]

Frumin I, Sobel N, and Gilad Y. Does a unique olfactory genome imply a unique olfactory world? Nat. Neurosci. 2014 Jan 17;17(1):6-8 (epub 2013 Dec 26)

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, and Pritchard JK. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 8;342(6159):747-9

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

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

Mizrahi-Man O, Davenport ER, and Gilad Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: Evaluation of effective study designs. PLoS One. 2013;8(1):e53608 (epub 2013 Jan 7)

2012

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, and Pritchard JK. Controls of nucleosome positioning in the human genome. PLoS Genetics. 2012;8(11):e1003036 (epub 2012 Nov 15)

Pai AA, Cain CC, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, and Gilad Y. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genetics. 2012;8(10):e1003000 (epub 2012 Oct 11)

Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, and Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 6;489(7414):52-55

Keydar I, Ben-Asher E, Feldmesser E, Nativ N, Oshimoto A, Restrepo D, Matsunami H, Chien MS, Pinto JM, Gilad Y, Olender T, and Lancet D. General olfactory sensitivity database (GOSdb): Candidate genes and their genomic variations. Human Mutation. 2013 Jan;34(1):32-41 (Epub Aug 30)

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, and Lee C. Regulatory element copy number differences shape primate expression profiles. PNAS. 2012 July 31;109(31):12656-61

Gallego Romero I, Ruvisnky I, and Gilad Y. Comparative studies of gene expression and the evolution of gene regulation. Nature Reviews Genetics. 2012 June 18;13(7):505-516

Bainer RO, Veneris JT, Yamada SD, Montag A, Lingen MW, Gilad Y, and Rinker-Schaeffer CW. Time-dependent transcriptional profiling links gene expression to mitogen-activated protein kinase kinase 4 (MKK4)-mediated suppression of omental metastatic colonization. Clinical Experimental Metastasis. 2012 Jun;29(5):397-408.

Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, and Gilad Y. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Human Molecular Genetics. 2012 May1;21(9):2111-23.

Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, and Gilad Y. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. PNAS. 2012 Apr 24;109(17):6490-5.

Pickrell JK, Gilad Y, and Pritchard JK. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”. Science. 2012 March 16;335(6074):1302; author reply 1302.

Gilad Y. Using genomic tools to study regulatory evolution. Methods in Molecular Biology. 2012;856:335-61.

Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, and Pritchard JK. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One. 2012;7(2):e30629 (epub 2012 Feb 16)

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, and Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 5;482(7385):390-4

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

Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, and Gilad Y. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. PNAS. 2012 Jan 24;109(4):1204-9

2011

Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, and Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research. 2012 Apr; 22(4):602-10. Epub 2011 Dec 29

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, and Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution. 2012 Jan;4(2):126-135. Epub 2011 Dec 7

Pickrell JK, Gaffney DJ, Gilad Y, and Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 1;27(15):2144-6.

Pai AA, Bell JT, Marioni JC, Pritchard JK, and Gilad Y. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genetics. 2011 Feb 24; 7(2): e1001316.

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

Çalışkan M, Cusanovich DA, Ober C, and Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Human Molecular Genetics. 2011 Apr; 20(8):1643-52.

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

2010

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

Pickrell JK, Pai AA, Gilad Y, and Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genetics. 2010 Dec 9; 6(12): e1001236.

*Perry GH, *Marioni JC, Melsted P, and Gilad Y. Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology. 2010 Dec; 19(24):5332-44.

*Pique-Regi R, *Degner JF, Pai AA, Gaffney DJ, Gilad Y, and Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research. 2011 Mar; 21(3):447-55. Epub 2010 Nov 24.

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, and Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 1. 464(7289):768-72.

2009

*Blekhman R, *Marioni JC, Zumbo P, Stephens M, and Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Research. 2010 20:180-189. Epub 2009 Dec 15.

Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, and Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009 25(24):3207-12.

Gilad Y, Pritchard JK, and Thornton K. Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics. 2009 25(10):463-71.

Bullaughey K, Chavarria CI, Coop G, and Gilad Y. Expression quantitative trait loci detected in cell-lines are often present in primary tissues. Hum Mol Genet. 2009 18(22):4296-303.

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 JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, *Gilad Y, and *Bustamante CD. 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. 2009 26(3):491-494. Epub 2008 Dec 22.

Ober C, Loisel DA, and Gilad Y. Sex-specific genetic architecture of human disease. Nature Reviews Genetics 2008 Dec; 9: 911-22.

Blekhman R, Oshlack A, Chabot AE, Smyth GK, 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 SY, Dermitzakis ET, Gilad Y, Stephens M, and Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genetics 2008 Oct 10; 4(10): e1000214.

Marioni JC, Mason CE, Shrikant MM, 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 SA, and Pritchard JK. 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 JA, 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 AE, 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 DC, Crasto CJ, Shepherd GM and Gilad Y. A framework for exploring functional variability in olfactory receptor genes. PLoS One 2007, Aug 1;2:e682.

Chabot AE, Shrit RA, 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 JM, Nicolae D, Firestein S and Gilad Y. Characterizing the expression of human olfactory receptor gene family using a novel DNA microarray. Genome Biology 2007 May 17;8(5):R86

Oshlack A, Chabot AE, Smyth GK 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 SA. Natural selection on gene expression. Trends in Genetics 2006, 8: 456-461.

Gilad Y, Oshlack A, Smyth GK, Speed TP and White KP. 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 SA, Bertone P, Gerstein M and White KP. 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 humans and apes. Mol. Biol. and Evol. 2005, 22(3):432-436.

Ptak SE, Roeder AD, 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, Przeworski M, and Lancet D. 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. Prediction of the odorant binding site of olfactory receptors by human-mouse comparisons. Protein Science. 2004, 13(1): 240-254.

Gilad Y, Bustamante CD, 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 for 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 GS, 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 MW, 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.