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Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.

Eres IE, Luo K, Hsiao CJ, Blake LE, Gilad Y.

PLoS Genet. 2019 Jul 19;15(7):e1008278. doi: 10.1371/journal.pgen.1008278. eCollection 2019 Jul.


Dynamic genetic regulation of gene expression during cellular differentiation.

Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y.

Science. 2019 Jun 28;364(6447):1287-1290. doi: 10.1126/science.aaw0040.


Discovery and characterization of variance QTLs in human induced pluripotent stem cells.

Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y.

PLoS Genet. 2019 Apr 19;15(4):e1008045. doi: 10.1371/journal.pgen.1008045. eCollection 2019 Apr.


A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees.

Ward MC, Gilad Y.

Elife. 2019 Apr 8;8. pii: e42374. doi: 10.7554/eLife.42374.


A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues.

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

Sci Rep. 2018 Oct 17;8(1):15312. doi: 10.1038/s41598-018-33478-9.


A comparative study of endoderm differentiation in humans and chimpanzees.

Blake LE, Thomas SM, Blischak JD, Hsiao CJ, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ.

Genome Biol. 2018 Oct 15;19(1):162. doi: 10.1186/s13059-018-1490-5.


Drug Screening Identifies Sigma-1-Receptor as a Target for the Therapy of VWM Leukodystrophy.

Atzmon A, Herrero M, Sharet-Eshed R, Gilad Y, Senderowitz H, Elroy-Stein O.

Front Mol Neurosci. 2018 Sep 18;11:336. doi: 10.3389/fnmol.2018.00336. eCollection 2018.


A cancer associated somatic mutation in LC3B attenuates its binding to E1-like ATG7 protein and subsequent lipidation.

Nuta GC, Gilad Y, Gershoni M, Sznajderman A, Schlesinger T, Bialik S, Eisenstein M, Pietrokovski S, Kimchi A.

Autophagy. 2019 Mar;15(3):438-452. doi: 10.1080/15548627.2018.1525476. Epub 2018 Oct 8.


A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes.

Engelmann BW, Hsiao CJ, Blischak JD, Fourne Y, Khan Z, Ford M, Gilad Y.

Sci Rep. 2018 Aug 14;8(1):12106. doi: 10.1038/s41598-018-30587-3.


Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes.

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y.

Elife. 2018 May 8;7. pii: e33480. doi: 10.7554/eLife.33480.


Non-canonical activation of DAPK2 by AMPK constitutes a new pathway linking metabolic stress to autophagy.

Shiloh R, Gilad Y, Ber Y, Eisenstein M, Aweida D, Bialik S, Cohen S, Kimchi A.

Nat Commun. 2018 May 1;9(1):1759. doi: 10.1038/s41467-018-03907-4.


Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.

Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y.

Elife. 2018 Apr 12;7. pii: e33084. doi: 10.7554/eLife.33084.


Impact of regulatory variation across human iPSCs and differentiated cells.

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.

Genome Res. 2018 Jan;28(1):122-131. doi: 10.1101/gr.224436.117. Epub 2017 Dec 5.


Human genomics: Cracking the regulatory code.

Ward MC, Gilad Y.

Nature. 2017 Oct 11;550(7675):190-191. doi: 10.1038/550190a. No abstract available.


Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells.

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.

Sci Rep. 2017 Jul 18;7(1):5702. doi: 10.1038/s41598-017-05878-w.


Discovery of potent molecular chimera (CM358) to treat human metastatic melanoma.

Gilad Y, Tuchinsky H, Ben-David G, Minnes R, Gancz A, Senderowitz H, Luboshits G, Firer MA, Gellerman G.

Eur J Med Chem. 2017 Sep 29;138:602-615. doi: 10.1016/j.ejmech.2017.06.066. Epub 2017 Jun 29.


Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9.

Montefiori L, Hernandez L, Zhang Z, Gilad Y, Ober C, Crawford G, Nobrega M, Jo Sakabe N.

Sci Rep. 2017 May 26;7(1):2451. doi: 10.1038/s41598-017-02547-w.


Recent Innovations in Peptide Based Targeted Drug Delivery to Cancer Cells.

Gilad Y, Firer M, Gellerman G.

Biomedicines. 2016 May 26;4(2). pii: E11. doi: 10.3390/biomedicines4020011. Review.


Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.

Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, Ober C.

Microbiome. 2017 Feb 1;5(1):16. doi: 10.1186/s40168-016-0227-5.


Batch effects and the effective design of single-cell gene expression studies.

Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y.

Sci Rep. 2017 Jan 3;7:39921. doi: 10.1038/srep39921.


Gene expression in local stroma reflects breast tumor states and predicts patient outcome.

Bainer R, Frankenberger C, Rabe D, An G, Gilad Y, Rosner MR.

Sci Rep. 2016 Dec 16;6:39240. doi: 10.1038/srep39240.


DNA methylation in lung cells is associated with asthma endotypes and genetic risk.

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.

JCI Insight. 2016 Dec 8;1(20):e90151. doi: 10.1172/jci.insight.90151.


The human olfactory transcriptome.

Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, Lancet D.

BMC Genomics. 2016 Aug 11;17(1):619. doi: 10.1186/s12864-016-2960-3.


Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK.

Elife. 2016 May 27;5. pii: e13328. doi: 10.7554/eLife.13328.


RNA splicing is a primary link between genetic variation and disease.

Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK.

Science. 2016 Apr 29;352(6285):600-4. doi: 10.1126/science.aad9417. Epub 2016 Apr 28.


Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites.

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

Ann Am Thorac Soc. 2016 Mar;13 Suppl 1:S100-1. doi: 10.1513/AnnalsATS.201508-521MG. No abstract available.


Integrated analyses of gene expression and genetic association studies in a founder population.

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.

Hum Mol Genet. 2016 May 15;25(10):2104-2112. Epub 2016 Feb 29.


Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs.

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

PLoS Genet. 2016 Jan 26;12(1):e1005793. doi: 10.1371/journal.pgen.1005793. eCollection 2016 Jan.


Synthesis, biological studies and molecular dynamics of new anticancer RGD-based peptide conjugates for targeted drug delivery.

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

Bioorg Med Chem. 2016 Jan 15;24(2):294-303. doi: 10.1016/j.bmc.2015.12.020. Epub 2015 Dec 12.


Dual-drug RGD conjugates provide enhanced cytotoxicity to melanoma and non-small lung cancer cells.

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

Biopolymers. 2016 Mar;106(2):160-171. doi: 10.1002/bip.22800.


A reliable computational workflow for the selection of optimal screening libraries.

Gilad Y, Nadassy K, Senderowitz H.

J Cheminform. 2015 Dec 11;7:61. doi: 10.1186/s13321-015-0108-0. eCollection 2015.


Mycobacterial infection induces a specific human innate immune response.

Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y.

Sci Rep. 2015 Nov 20;5:16882. doi: 10.1038/srep16882.


Genome-Wide Association Studies of the Human Gut Microbiota.

Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, Gilad Y.

PLoS One. 2015 Nov 3;10(11):e0140301. doi: 10.1371/journal.pone.0140301. eCollection 2015.


msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

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

PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030. eCollection 2015.


Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.


WASP: allele-specific software for robust molecular quantitative trait locus discovery.

van de Geijn B, McVicker G, Gilad Y, Pritchard JK.

Nat Methods. 2015 Nov;12(11):1061-3. doi: 10.1038/nmeth.3582. Epub 2015 Sep 14.


Metastasis Suppressors Regulate the Tumor Microenvironment by Blocking Recruitment of Prometastatic Tumor-Associated Macrophages.

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

Cancer Res. 2015 Oct 1;75(19):4063-73. doi: 10.1158/0008-5472.CAN-14-3394. Epub 2015 Aug 3.


A reanalysis of mouse ENCODE comparative gene expression data.

Gilad Y, Mizrahi-Man O.

F1000Res. 2015 May 19;4:121. doi: 10.12688/f1000research.6536.1. eCollection 2015.


A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.

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.

Elife. 2015 Jun 23;4:e07103. doi: 10.7554/eLife.07103.


Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature.

Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y.

PLoS Genet. 2015 May 7;11(5):e1005216. doi: 10.1371/journal.pgen.1005216. eCollection 2015 May.


Host genetic variation influences gene expression response to rhinovirus infection.

Çalışkan M, Baker SW, Gilad Y, Ober C.

PLoS Genet. 2015 Apr 13;11(4):e1005111. doi: 10.1371/journal.pgen.1005111. eCollection 2015 Apr.


The genetic architecture of gene expression levels in wild baboons.

Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y.

Elife. 2015 Feb 25;4. doi: 10.7554/eLife.04729.


Genomic variation. Impact of regulatory variation from RNA to protein.

Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y.

Science. 2015 Feb 6;347(6222):664-7. doi: 10.1126/science.1260793. Epub 2014 Dec 18.


The genetic and mechanistic basis for variation in gene regulation.

Pai AA, Pritchard JK, Gilad Y.

PLoS Genet. 2015 Jan 8;11(1):e1004857. doi: 10.1371/journal.pgen.1004857. eCollection 2015 Jan.


Epigenetic modifications are associated with inter-species gene expression variation in primates.

Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y.

Genome Biol. 2014;15(12):547.


DAPK2 is a novel regulator of mTORC1 activity and autophagy.

Ber Y, Shiloh R, Gilad Y, Degani N, Bialik S, Kimchi A.

Cell Death Differ. 2015 Mar;22(3):465-75. doi: 10.1038/cdd.2014.177. Epub 2014 Oct 31.


The programmed cell death GLuc PCA library - a powerful tool for pathway discovery and drug screening.

Gilad Y, Kimchi A.

Mol Cell Oncol. 2014 Dec 31;1(4):e969644. doi: 10.4161/23723548.2014.969644. eCollection 2014 Oct-Dec.


Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels.

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

PLoS Genet. 2014 Sep 18;10(9):e1004663. doi: 10.1371/journal.pgen.1004663. eCollection 2014 Sep.


Comparative studies of gene regulatory mechanisms.

Pai AA, Gilad Y.

Curr Opin Genet Dev. 2014 Dec;29:68-74. doi: 10.1016/j.gde.2014.08.010. Epub 2014 Sep 16. Review.


The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines.

Çalışkan M, Pritchard JK, Ober C, Gilad Y.

PLoS One. 2014 Sep 5;9(9):e107166. doi: 10.1371/journal.pone.0107166. eCollection 2014.

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