| Year |
Citation |
Score |
| 2023 |
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 Biology. 24: 207. PMID 37697401 DOI: 10.1186/s13059-023-03019-3 |
0.381 |
|
| 2023 |
Lin W, Wall JD, Li G, Newman D, VandeBerg JL, Yang Y, Abney M, Olivier M, Gilad Y, Cox LA. GEGenetic regulatory effects in response to a high cholesterol, high fat diet in baboons. Biorxiv : the Preprint Server For Biology. PMID 37577666 DOI: 10.1101/2023.08.01.551489 |
0.339 |
|
| 2022 |
Housman G, Briscoe E, Gilad Y. Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. Plos Genetics. 18: e1010073. PMID 35263340 DOI: 10.1371/journal.pgen.1010073 |
0.4 |
|
| 2022 |
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. 11. PMID 35142607 DOI: 10.7554/eLife.71361 |
0.402 |
|
| 2022 |
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 Genetics. 18: e1009666. PMID 35061661 DOI: 10.1371/journal.pgen.1009666 |
0.308 |
|
| 2021 |
Shah A, Mittleman BE, Gilad Y, Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biology. 22: 291. PMID 34649612 DOI: 10.1186/s13059-021-02502-z |
0.688 |
|
| 2021 |
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. 10. PMID 33988505 DOI: 10.7554/eLife.67077 |
0.4 |
|
| 2021 |
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. 10. PMID 33595436 DOI: 10.7554/eLife.62548 |
0.771 |
|
| 2021 |
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. 10. PMID 33554857 DOI: 10.7554/eLife.57345 |
0.343 |
|
| 2020 |
Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. Elife. 9. PMID 33084571 DOI: 10.7554/eLife.59929 |
0.812 |
|
| 2020 |
Umans BD, Battle A, Gilad Y. Where Are the Disease-Associated eQTLs? Trends in Genetics : Tig. PMID 32912663 DOI: 10.1016/j.tig.2020.08.009 |
0.818 |
|
| 2020 |
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. 9. PMID 32584258 DOI: 10.7554/eLife.57492 |
0.754 |
|
| 2020 |
Housman G, Gilad Y. Prime time for primate functional genomics. Current Opinion in Genetics & Development. 62: 1-7. PMID 32544775 DOI: 10.1016/j.gde.2020.04.007 |
0.366 |
|
| 2020 |
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 Research. PMID 32312741 DOI: 10.1101/Gr.247759.118 |
0.387 |
|
| 2020 |
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. Scientific Reports. 10: 1535. PMID 32001747 DOI: 10.1038/S41598-020-58327-6 |
0.354 |
|
| 2020 |
Blake LE, Roux J, Hernando-Herraez I, Banovich N, Garcia Perez R, 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 Research. PMID 31953346 DOI: 10.1101/Gr.254904.119 |
0.445 |
|
| 2020 |
Mittleman BE, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, Li Y. Author response: Alternative polyadenylation mediates genetic regulation of gene expression Elife. DOI: 10.7554/Elife.57492.Sa2 |
0.447 |
|
| 2019 |
Eres IE, Luo K, Hsiao CJ, Blake LE, Gilad Y. Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. Plos Genetics. 15: e1008278. PMID 31323043 DOI: 10.1371/journal.pgen.1008278 |
0.466 |
|
| 2019 |
Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y. Dynamic genetic regulation of gene expression during cellular differentiation. Science (New York, N.Y.). 364: 1287-1290. PMID 31249060 DOI: 10.1126/science.aaw0040 |
0.463 |
|
| 2019 |
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 Genetics. 15: e1008045. PMID 31002671 DOI: 10.1371/Journal.Pgen.1008045 |
0.508 |
|
| 2019 |
Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. Elife. 8. PMID 30958265 DOI: 10.7554/eLife.42374 |
0.463 |
|
| 2018 |
Pavlovic BJ, Blake LE, Roux J, Chavarria C, Gilad Y. A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. Scientific Reports. 8: 15312. PMID 30333510 DOI: 10.1038/s41598-018-33478-9 |
0.788 |
|
| 2018 |
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 Biology. 19: 162. PMID 30322406 DOI: 10.1186/s13059-018-1490-5 |
0.753 |
|
| 2018 |
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. Scientific Reports. 8: 12106. PMID 30108239 DOI: 10.1038/S41598-018-30587-3 |
0.356 |
|
| 2018 |
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 response QTL mapping in induced cardiomyocytes. Elife. 7. PMID 29737278 DOI: 10.7554/Elife.33480 |
0.409 |
|
| 2018 |
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. 7. PMID 29648536 DOI: 10.7554/Elife.33084 |
0.799 |
|
| 2018 |
Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Author response: Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs Elife. DOI: 10.7554/Elife.33084.053 |
0.742 |
|
| 2017 |
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, et al. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Research. PMID 29208628 DOI: 10.1101/Gr.224436.117 |
0.783 |
|
| 2017 |
Ward MC, Gilad Y. Human genomics: Cracking the regulatory code. Nature. 550: 190-191. PMID 29022577 DOI: 10.1038/550190a |
0.48 |
|
| 2017 |
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. Scientific Reports. 7: 5702. PMID 28720766 DOI: 10.1038/s41598-017-05878-w |
0.342 |
|
| 2017 |
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. Scientific Reports. 7: 2451. PMID 28550296 DOI: 10.1038/S41598-017-02547-W |
0.302 |
|
| 2017 |
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. 5: 16. PMID 28143570 DOI: 10.1186/s40168-016-0227-5 |
0.308 |
|
| 2017 |
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. Scientific Reports. 7: 39921. PMID 28045081 DOI: 10.1038/Srep39921 |
0.482 |
|
| 2016 |
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. Scientific Reports. 6: 39240. PMID 27982086 DOI: 10.1038/Srep39240 |
0.735 |
|
| 2016 |
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. 1: e90151. PMID 27942592 DOI: 10.1172/Jci.Insight.90151 |
0.341 |
|
| 2016 |
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. 17: 619. PMID 27515280 DOI: 10.1186/S12864-016-2960-3 |
0.529 |
|
| 2016 |
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. 5. PMID 27232982 DOI: 10.7554/Elife.13328 |
0.352 |
|
| 2016 |
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 (New York, N.Y.). 352: 600-4. PMID 27126046 DOI: 10.1126/Science.Aad9417 |
0.482 |
|
| 2016 |
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. Human Molecular Genetics. PMID 26931462 DOI: 10.1093/Hmg/Ddw061 |
0.745 |
|
| 2016 |
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 Genetics. 12: e1005793. PMID 26812582 DOI: 10.1371/journal.pgen.1005793 |
0.806 |
|
| 2016 |
Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Author response: Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling Elife. DOI: 10.7554/Elife.13328.037 |
0.312 |
|
| 2016 |
Gilad Y. Regulatory QTLs, batch effects, human-mouse differences, what happens after we die, single cell genomics, and Twitter F1000research. 5. DOI: 10.7490/F1000Research.1112708.1 |
0.396 |
|
| 2016 |
Lee J, Bainer R, Frankenberger C, Rabe D, Saleh s, Park M, An G, Gilad Y, Rosner MR. Abstract B15: Metastatic breast tumors regulate gene expression at distal mammary sites that predicts patient outcome Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Metca15-B15 |
0.723 |
|
| 2015 |
Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y. Mycobacterial infection induces a specific human innate immune response. Scientific Reports. 5: 16882. PMID 26586179 DOI: 10.1038/srep16882 |
0.319 |
|
| 2015 |
Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, Gilad Y. Genome-Wide Association Studies of the Human Gut Microbiota. Plos One. 10: e0140301. PMID 26528553 DOI: 10.1371/Journal.Pone.0140301 |
0.739 |
|
| 2015 |
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. 10: e0138030. PMID 26406244 DOI: 10.1371/Journal.Pone.0138030 |
0.344 |
|
| 2015 |
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, ... ... Gilad Y, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research. PMID 26392366 DOI: 10.1101/Gr.192005.115 |
0.715 |
|
| 2015 |
van de Geijn B, McVicker G, Gilad Y, Pritchard JK. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nature Methods. 12: 1061-3. PMID 26366987 DOI: 10.1038/Nmeth.3582 |
0.315 |
|
| 2015 |
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 pro-metastatic tumor-associated macrophages. Cancer Research. PMID 26238785 DOI: 10.1158/0008-5472.Can-14-3394 |
0.697 |
|
| 2015 |
Gilad Y, Mizrahi-Man O. A reanalysis of mouse ENCODE comparative gene expression data. F1000research. 4: 121. PMID 26236466 DOI: 10.12688/f1000research.6536.1 |
0.468 |
|
| 2015 |
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, ... ... Gilad Y, et al. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 4. PMID 26102527 DOI: 10.7554/Elife.07103 |
0.752 |
|
| 2015 |
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 Genetics. 11: e1005216. PMID 25950834 DOI: 10.1371/journal.pgen.1005216 |
0.81 |
|
| 2015 |
Çal??kan M, Baker SW, Gilad Y, Ober C. Host genetic variation influences gene expression response to rhinovirus infection. Plos Genetics. 11: e1005111. PMID 25874939 DOI: 10.1371/Journal.Pgen.1005111 |
0.428 |
|
| 2015 |
Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. The genetic architecture of gene expression levels in wild baboons. Elife. 4. PMID 25714927 DOI: 10.7554/Elife.04729 |
0.512 |
|
| 2015 |
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 (New York, N.Y.). 347: 664-7. PMID 25657249 DOI: 10.1126/Science.1260793 |
0.376 |
|
| 2015 |
Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. Plos Genetics. 11: e1004857. PMID 25569255 DOI: 10.1371/Journal.Pgen.1004857 |
0.753 |
|
| 2015 |
Romero IG, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Ben-Nun IF, Li Y, Sabatini K, Leonardo TR, ... ... Gilad Y, et al. Author response: A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics Elife. DOI: 10.7554/Elife.07103.051 |
0.753 |
|
| 2015 |
Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. Author response: The genetic architecture of gene expression levels in wild baboons Elife. DOI: 10.7554/Elife.04729.028 |
0.423 |
|
| 2015 |
Mizrahi-Man O, Gilad Y. Data files and codes used in the reanalysis of the mouse encode comparative gene expression data F1000research. 4. DOI: 10.5281/Zenodo.17606 |
0.377 |
|
| 2015 |
Rabe DC, Frankenberger CA, Bainer R, Sankarasharma D, Chada K, Krausz T, Gilad Y, Rosner MR. Abstract B35: The role of tumor associated macrophages (TAMs) in triple-negative breast cancer (TNBC) invasion revealed by species-specific RNA sequencing Cancer Research. 75. DOI: 10.1158/1538-7445.Chtme14-B35 |
0.7 |
|
| 2015 |
Frankenberger CA, Bainer RO, Rabe DC, Saleh S, Park M, Gilad Y, Rosner MR. Abstract A43: Systemic tumor-stroma interactions are prognostic indicators of breast tumor invasiveness Cancer Research. 75. DOI: 10.1158/1538-7445.Chtme14-A43 |
0.715 |
|
| 2015 |
Rabe DC, Frankenberger C, Bainer R, Sankarasharma D, Chada K, Krausz T, Gilad Y, Becker L, Rosner MR. Abstract 1557: Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of prometastatic TAMs Cancer Research. 76: 1557-1557. DOI: 10.1158/1538-7445.Am2016-1557 |
0.699 |
|
| 2014 |
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 Biology. 15: 547. PMID 25468404 DOI: 10.1186/S13059-014-0547-3 |
0.68 |
|
| 2014 |
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 Genetics. 10: e1004663. PMID 25233095 DOI: 10.1371/Journal.Pgen.1004663 |
0.429 |
|
| 2014 |
Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Current Opinion in Genetics & Development. 29: 68-74. PMID 25215415 DOI: 10.1016/J.Gde.2014.08.010 |
0.75 |
|
| 2014 |
Çal??kan M, Pritchard JK, Ober C, Gilad Y. The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. Plos One. 9: e107166. PMID 25192014 DOI: 10.1371/Journal.Pone.0107166 |
0.521 |
|
| 2014 |
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. Scientific Reports. 4: 5809. PMID 25069065 DOI: 10.1038/Srep05809 |
0.666 |
|
| 2014 |
Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. Bmc Biology. 12: 42. PMID 24885439 DOI: 10.1186/1741-7007-12-42 |
0.7 |
|
| 2014 |
Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, Gilad Y. Seasonal variation in human gut microbiome composition. Plos One. 9: e90731. PMID 24618913 DOI: 10.1371/journal.pone.0090731 |
0.301 |
|
| 2014 |
Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. Plos Genetics. 10: e1004226. PMID 24603674 DOI: 10.1371/Journal.Pgen.1004226 |
0.813 |
|
| 2014 |
Frumin I, Sobel N, Gilad Y. Does a unique olfactory genome imply a unique olfactory world? Nature Neuroscience. 17: 6-8. PMID 24369370 DOI: 10.1038/Nn.3608 |
0.301 |
|
| 2014 |
Roux J, Hernando-Herraez I, Banovich N, Perez RG, Chavarria C, Mitrano A, Pritchard J, Marques-Bonet T, Gilad Y. A genomic study of the contribution of DNA methylation to regulatory evolution in primates F1000research. 5. DOI: 10.7490/F1000Research.1096813.1 |
0.312 |
|
| 2014 |
Bainer R, Frankenberger C, Rabe D, Saleh S, Park M, Chada K, Gilad Y, Rosner M. Abstract LB-320: Systemic tumor-stroma interactions are prognostic indicators of breast tumor invasiveness Molecular and Cellular Biology. DOI: 10.1158/1538-7445.Am2014-Lb-320 |
0.663 |
|
| 2014 |
Rabe DC, Frankenberger C, Bainer R, Gilad Y, Rosner MR. Abstract 1084: Triple-negative breast cancer displays a unique subset of macrophages dependent on CCL5 signaling Cancer Research. 74: 1084-1084. DOI: 10.1158/1538-7445.Am2014-1084 |
0.695 |
|
| 2013 |
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 Biology. 14: R148. PMID 24380390 DOI: 10.1186/Gb-2013-14-12-R148 |
0.582 |
|
| 2013 |
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 (New York, N.Y.). 342: 747-9. PMID 24136359 DOI: 10.1126/Science.1242429 |
0.616 |
|
| 2013 |
Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science (New York, N.Y.). 342: 1100-4. PMID 24136357 DOI: 10.1126/Science.1242379 |
0.755 |
|
| 2013 |
Tung J, Gilad Y. Social environmental effects on gene regulation. Cellular and Molecular Life Sciences : Cmls. 70: 4323-39. PMID 23685902 DOI: 10.1007/S00018-013-1357-6 |
0.35 |
|
| 2013 |
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. 8: e53608. PMID 23308262 DOI: 10.1371/journal.pone.0053608 |
0.333 |
|
| 2013 |
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. Human Mutation. 34: 32-41. PMID 22936402 DOI: 10.1002/Humu.22212 |
0.764 |
|
| 2013 |
Frankenberger CA, Bainer RO, Menon J, Chavarria C, Michelini K, Melsted P, Gilad Y, Rosner MR. Abstract B25: Using species-specific RNAseq reveals stromal reprogramming in triple-negative breast cancer xenografts Cancer Research. 73. DOI: 10.1158/1538-7445.Tim2013-B25 |
0.734 |
|
| 2012 |
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 Genetics. 8: e1003036. PMID 23166509 DOI: 10.1371/Journal.Pgen.1003036 |
0.712 |
|
| 2012 |
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 Genetics. 8: e1003000. PMID 23071454 DOI: 10.1371/Journal.Pgen.1003000 |
0.793 |
|
| 2012 |
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, et al. Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 109: 12656-61. PMID 22797897 DOI: 10.1073/Pnas.1205199109 |
0.823 |
|
| 2012 |
Romero IG, Ruvinsky I, Gilad Y. Comparative studies of gene expression and the evolution of gene regulation. Nature Reviews. Genetics. 13: 505-16. PMID 22705669 DOI: 10.1038/Nrg3229 |
0.503 |
|
| 2012 |
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. Proceedings of the National Academy of Sciences of the United States of America. 109: 6490-5. PMID 22493251 DOI: 10.1073/Pnas.1202734109 |
0.395 |
|
| 2012 |
Pickrell JK, Gilad Y, Pritchard JK. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science (New York, N.Y.). 335: 1302; author reply 1. PMID 22422963 DOI: 10.1126/science.1210484 |
0.351 |
|
| 2012 |
Gilad Y. Using genomic tools to study regulatory evolution. Methods in Molecular Biology (Clifton, N.J.). 856: 335-61. PMID 22399466 DOI: 10.1007/978-1-61779-585-5_14 |
0.52 |
|
| 2012 |
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. 7: e30629. PMID 22359548 DOI: 10.1371/Journal.Pone.0030629 |
0.484 |
|
| 2012 |
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. Clinical & Experimental Metastasis. 29: 397-408. PMID 22350525 DOI: 10.1007/S10585-011-9448-Y |
0.761 |
|
| 2012 |
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. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808 |
0.776 |
|
| 2012 |
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 Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7 |
0.757 |
|
| 2012 |
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. Human Molecular Genetics. 21: 2111-23. PMID 22286170 DOI: 10.1093/Hmg/Dds021 |
0.812 |
|
| 2012 |
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. Proceedings of the National Academy of Sciences of the United States of America. 109: 1204-9. PMID 22233810 DOI: 10.1073/Pnas.1115761109 |
0.713 |
|
| 2012 |
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 Research. 22: 602-10. PMID 22207615 DOI: 10.1101/Gr.130468.111 |
0.757 |
|
| 2012 |
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 Biology and Evolution. 4: 126-35. PMID 22155688 DOI: 10.1093/Gbe/Evr132 |
0.374 |
|
| 2011 |
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 (Oxford, England). 27: 2144-6. PMID 21690102 DOI: 10.1093/bioinformatics/btr354 |
0.326 |
|
| 2011 |
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 Genetics. 7: e1001316. PMID 21383968 DOI: 10.1371/Journal.Pgen.1001316 |
0.751 |
|
| 2011 |
Cain CE, Blekhman R, Marioni JC, Gilad Y. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics. 187: 1225-34. PMID 21321133 DOI: 10.1534/Genetics.110.126177 |
0.793 |
|
| 2011 |
Caliskan M, Cusanovich DA, Ober C, Gilad Y. The effects of EBV transformation on gene expression levels and methylation profiles. Human Molecular Genetics. 20: 1643-52. PMID 21289059 DOI: 10.1093/Hmg/Ddr041 |
0.781 |
|
| 2011 |
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 Biology. 12: R10. PMID 21251332 DOI: 10.1186/Gb-2011-12-1-R10 |
0.743 |
|
| 2011 |
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 Research. 21: 447-55. PMID 21106904 DOI: 10.1101/Gr.112623.110 |
0.748 |
|
| 2011 |
Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Genome Biology. 12. DOI: 10.1186/Gb-2011-12-6-405 |
0.706 |
|
| 2010 |
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. Plos Genetics. 6: e1001249. PMID 21187902 DOI: 10.1371/Journal.Pgen.1001249 |
0.65 |
|
| 2010 |
Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. Plos Genetics. 6: e1001236. PMID 21151575 DOI: 10.1371/Journal.Pgen.1001236 |
0.742 |
|
| 2010 |
Perry GH, Marioni JC, Melsted P, Gilad Y. Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology. 19: 5332-44. PMID 21054605 DOI: 10.1111/J.1365-294X.2010.04888.X |
0.337 |
|
| 2010 |
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. 464: 768-72. PMID 20220758 DOI: 10.1038/Nature08872 |
0.766 |
|
| 2010 |
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Research. 20: 180-9. PMID 20009012 DOI: 10.1101/Gr.099226.109 |
0.734 |
|
| 2010 |
Bainer R, Marioni J, Barriero L, Blekhman R, Onel K, Gilad Y. Abstract LB-332: MDM4 transcription is discordantly regulated by common variants of p53 Cancer Research. 70. DOI: 10.1158/1538-7445.Am10-Lb-332 |
0.794 |
|
| 2009 |
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 (Oxford, England). 25: 3207-12. PMID 19808877 DOI: 10.1093/Bioinformatics/Btp579 |
0.706 |
|
| 2009 |
Gilad Y, Pritchard JK, Thornton K. Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics : Tig. 25: 463-71. PMID 19801172 DOI: 10.1016/j.tig.2009.09.003 |
0.356 |
|
| 2009 |
Bullaughey K, Chavarria CI, Coop G, Gilad Y. Expression quantitative trait loci detected in cell lines are often present in primary tissues. Human Molecular Genetics. 18: 4296-303. PMID 19671653 DOI: 10.1093/Hmg/Ddp382 |
0.465 |
|
| 2009 |
Blekhman R, Oshlack A, Gilad Y. Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics. 182: 627-30. PMID 19332884 DOI: 10.1534/Genetics.108.099960 |
0.725 |
|
| 2009 |
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, et al. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). Plos Genetics. 5: e1000346. PMID 19165326 DOI: 10.1371/Journal.Pgen.1000346 |
0.369 |
|
| 2009 |
De la Cruz O, Blekhman R, Zhang X, Nicolae D, Firestein S, Gilad Y. A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes. Molecular Biology and Evolution. 26: 491-4. PMID 19103638 DOI: 10.1093/Molbev/Msn294 |
0.708 |
|
| 2009 |
Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures Plos Genetics. 5. DOI: 10.1371/Annotation/06105Fdb-F0Fa-4Fe2-88D0-Db9F6036509F |
0.611 |
|
| 2008 |
Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. Gene regulation in primates evolves under tissue-specific selection pressures. Plos Genetics. 4: e1000271. PMID 19023414 DOI: 10.1371/Journal.Pgen.1000271 |
0.729 |
|
| 2008 |
Ober C, Loisel DA, Gilad Y. Sex-specific genetic architecture of human disease. Nature Reviews. Genetics. 9: 911-22. PMID 19002143 DOI: 10.1038/Nrg2415 |
0.373 |
|
| 2008 |
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 Genetics. 4: e1000214. PMID 18846210 DOI: 10.1371/Journal.Pgen.1000214 |
0.46 |
|
| 2008 |
Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends in Genetics : Tig. 24: 408-15. PMID 18597885 DOI: 10.1016/J.Tig.2008.06.001 |
0.513 |
|
| 2008 |
Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E. An evolutionarily conserved sexual signature in the primate brain. Plos Genetics. 4: e1000100. PMID 18566661 DOI: 10.1371/Journal.Pgen.1000100 |
0.684 |
|
| 2008 |
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research. 18: 1509-17. PMID 18550803 DOI: 10.1101/Gr.079558.108 |
0.454 |
|
| 2008 |
de Candia P, Blekhman R, Chabot AE, Oshlack A, Gilad Y. A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway. Plos One. 3: e1670. PMID 18301748 DOI: 10.1371/Journal.Pone.0001670 |
0.701 |
|
| 2007 |
Man O, Willhite DC, Crasto CJ, Shepherd GM, Gilad Y. A framework for exploring functional variability in olfactory receptor genes. Plos One. 2: e682. PMID 17668060 DOI: 10.1371/Journal.Pone.0000682 |
0.562 |
|
| 2007 |
Chabot A, Shrit RA, Blekhman R, Gilad Y. Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics. 176: 2069-76. PMID 17565944 DOI: 10.1534/Genetics.107.073429 |
0.731 |
|
| 2007 |
Zhang X, De la Cruz O, Pinto JM, Nicolae D, Firestein S, Gilad Y. Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray. Genome Biology. 8: R86. PMID 17509148 DOI: 10.1186/Gb-2007-8-5-R86 |
0.422 |
|
| 2007 |
Oshlack A, Chabot AE, Smyth GK, Gilad Y. Using DNA microarrays to study gene expression in closely related species. Bioinformatics (Oxford, England). 23: 1235-42. PMID 17384014 DOI: 10.1093/bioinformatics/btm111 |
0.435 |
|
| 2006 |
Gilad Y, Borevitz J. Using DNA microarrays to study natural variation. Current Opinion in Genetics & Development. 16: 553-8. PMID 17008090 DOI: 10.1016/J.Gde.2006.09.005 |
0.422 |
|
| 2006 |
Gilad Y, Oshlack A, Rifkin SA. Natural selection on gene expression. Trends in Genetics : Tig. 22: 456-61. PMID 16806568 DOI: 10.1016/J.Tig.2006.06.002 |
0.477 |
|
| 2006 |
Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature. 440: 242-5. PMID 16525476 DOI: 10.1038/nature04559 |
0.497 |
|
| 2006 |
Thompson E, Murray C, Burkart M, Nicolae D, Gilad Y, Ober C. Haplotype Structure and Natural Selection in an Olfactory Receptor (OR) Gene on Chromosome 6p Associated with Asthma Susceptibility Journal of Allergy and Clinical Immunology. 117: S149. DOI: 10.1016/J.Jaci.2005.12.595 |
0.311 |
|
| 2005 |
Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, ... ... Gilad Y, et al. Initial sequence of the chimpanzee genome and comparison with the human genome Nature. 437: 69-87. PMID 16136131 DOI: 10.1038/Nature04072 |
0.347 |
|
| 2005 |
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research. 15: 674-80. PMID 15867429 DOI: 10.1101/Gr.3335705 |
0.478 |
|
| 2005 |
Gilad Y, Man O, Glusman G. A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Research. 15: 224-30. PMID 15687286 DOI: 10.1101/Gr.2846405 |
0.465 |
|
| 2005 |
Fischer A, Gilad Y, Man O, Pääbo S. Evolution of bitter taste receptors in humans and apes. Molecular Biology and Evolution. 22: 432-6. PMID 15496549 DOI: 10.1093/Molbev/Msi027 |
0.396 |
|
| 2004 |
Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S, Przeworski M. Absence of the TAP2 human recombination hotspot in chimpanzees. Plos Biology. 2: e155. PMID 15208713 DOI: 10.1371/Journal.Pbio.0020155 |
0.364 |
|
| 2004 |
Gilad Y, Wiebe V, Przeworski M, Lancet D, Pääbo S. Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. Plos Biology. 2: E5. PMID 14737185 DOI: 10.1371/Journal.Pbio.0020005 |
0.578 |
|
| 2004 |
Man O, Gilad Y, Lancet D. Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Science : a Publication of the Protein Society. 13: 240-54. PMID 14691239 DOI: 10.1110/Ps.03296404 |
0.508 |
|
| 2003 |
Gilad Y, Bustamante CD, Lancet D, Pääbo S. Natural selection on the olfactory receptor gene family in humans and chimpanzees. American Journal of Human Genetics. 73: 489-501. PMID 12908129 DOI: 10.1086/378132 |
0.64 |
|
| 2003 |
Menashe I, Man O, Lancet D, Gilad Y. Different noses for different people. Nature Genetics. 34: 143-4. PMID 12730696 DOI: 10.1038/Ng1160 |
0.621 |
|
| 2003 |
Gilad Y, Lancet D. Population differences in the human functional olfactory repertoire. Molecular Biology and Evolution. 20: 307-14. PMID 12644552 DOI: 10.1093/molbev/msg013 |
0.57 |
|
| 2003 |
Gilad Y, Man O, Pääbo S, Lancet D. Human specific loss of olfactory receptor genes. Proceedings of the National Academy of Sciences of the United States of America. 100: 3324-7. PMID 12612342 DOI: 10.1073/Pnas.0535697100 |
0.619 |
|
| 2002 |
Menashe I, Man O, Lancet D, Gilad Y. Population differences in haplotype structure within a human olfactory receptor gene cluster. Human Molecular Genetics. 11: 1381-90. PMID 12023980 DOI: 10.1093/Hmg/11.12.1381 |
0.584 |
|
| 2002 |
Gilad Y, Rosenberg S, Przeworski M, Lancet D, Skorecki K. Evidence for positive selection and population structure at the human MAO-A gene. Proceedings of the National Academy of Sciences of the United States of America. 99: 862-7. PMID 11805333 DOI: 10.1073/Pnas.022614799 |
0.59 |
|
| 2001 |
Lapidot M, Pilpel Y, Gilad Y, Falcovitz A, Sharon D, Haaf T, Lancet D. Mouse-human orthology relationships in an olfactory receptor gene cluster. Genomics. 71: 296-306. PMID 11170746 DOI: 10.1006/Geno.2000.6431 |
0.589 |
|
| 2001 |
Conticello SG, Gilad Y, Avidan N, Ben-Asher E, Levy Z, Fainzilber M. Mechanisms for evolving hypervariability: the case of conopeptides. Molecular Biology and Evolution. 18: 120-31. PMID 11158371 DOI: 10.1093/Oxfordjournals.Molbev.A003786 |
0.419 |
|
| 2000 |
Sharon D, Gilad Y, Glusman G, Khen M, Lancet D, Kalush F. Identification and characterization of coding single-nucleotide polymorphisms within a human olfactory receptor gene cluster. Gene. 260: 87-94. PMID 11137294 DOI: 10.1016/S0378-1119(00)00467-4 |
0.567 |
|
| 2000 |
Gilad Y, Segré D, Skorecki K, Nachman MW, Lancet D, Sharon D. Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nature Genetics. 26: 221-4. PMID 11017082 DOI: 10.1038/79957 |
0.752 |
|
| Show low-probability matches. |
