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Duygu Ucar - Publications

Affiliations: 
2011-2014 Jackson Laboratory for Genomic Medicine 
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33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Karakaslar EO, Katiyar N, Hasham M, Youn A, Sharma S, Chung CH, Marches R, Korstanje R, Banchereau J, Ucar D. Transcriptional activation of Jun and Fos members of the AP-1 complex is a conserved signature of immune aging that contributes to inflammaging. Aging Cell. e13792. PMID 36840360 DOI: 10.1111/acel.13792  0.308
2021 Thibodeau A, Khetan S, Eroglu A, Tewhey R, Stitzel ML, Ucar D. CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. Plos Computational Biology. 17: e1009670. PMID 34898596 DOI: 10.1371/journal.pcbi.1009670  0.325
2020 Pereira BI, De Maeyer RPH, Covre LP, Nehar-Belaid D, Lanna A, Ward S, Marches R, Chambers ES, Gomes DCO, Riddell NE, Maini MK, Teixeira VH, Janes SM, Gilroy DW, Larbi A, ... ... Ucar D, et al. Sestrins induce natural killer function in senescent-like CD8 T cells. Nature Immunology. PMID 32231301 DOI: 10.1038/S41590-020-0643-3  0.356
2020 Lawlor N, Marquez EJ, Lee D, Ucar D. V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data. Bioinformatics (Oxford, England). PMID 32119082 DOI: 10.1093/Bioinformatics/Btaa128  0.325
2019 Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, ... ... Ucar D, et al. Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. Cell Reports. 26: 788-801.e6. PMID 30650367 DOI: 10.1016/J.Celrep.2018.12.083  0.356
2018 Varshney A, VanRenterghem H, Orchard P, Boyle AP, Stitzel ML, Ucar D, Parker SCJ. Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics. PMID 30593493 DOI: 10.1534/Genetics.118.301525  0.512
2018 Caielli S, Veiga DT, Balasubramanian P, Athale S, Domic B, Murat E, Banchereau R, Xu Z, Chandra M, Chung CH, Walters L, Baisch J, Wright T, Punaro M, Nassi L, ... ... Ucar D, et al. A CD4 T cell population expanded in lupus blood provides B cell help through interleukin-10 and succinate. Nature Medicine. PMID 30478422 DOI: 10.1038/S41591-018-0254-9  0.344
2018 Lee D, Cheng A, Lawlor N, Bolisetty M, Ucar D. Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). Scientific Reports. 8: 17040. PMID 30451954 DOI: 10.1038/S41598-018-35365-9  0.404
2018 Youn A, Marquez EJ, Lawlor N, Stitzel ML, Ucar D. BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test. Nucleic Acids Research. PMID 30428075 DOI: 10.1093/Nar/Gky1117  0.46
2018 Thibodeau A, Uyar A, Khetan S, Stitzel ML, Ucar D. A neural network based model effectively predicts enhancers from clinical ATAC-seq samples. Scientific Reports. 8: 16048. PMID 30375457 DOI: 10.1038/S41598-018-34420-9  0.422
2018 Khetan S, Kursawe R, Youn A, Lawlor N, Jillette A, Marquez EJ, Ucar D, Stitzel ML. Type 2 Diabetes Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets. Diabetes. PMID 30181159 DOI: 10.2337/Db18-0393  0.354
2018 Kycia I, Wolford BN, Huyghe JR, Fuchsberger C, Vadlamudi S, Kursawe R, Welch RP, Albanus RD, Uyar A, Khetan S, Lawlor N, Bolisetty M, Mathur A, Kuusisto J, Laakso M, ... Ucar D, et al. A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression. American Journal of Human Genetics. 102: 620-635. PMID 29625024 DOI: 10.1016/J.Ajhg.2018.02.020  0.323
2017 Ahmed Z, Ucar D. I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples. Peerj. 5: e4040. PMID 29181276 DOI: 10.7717/Peerj.4040  0.314
2017 Thibodeau A, Márquez EJ, Shin DG, Vera-Licona P, Ucar D. Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin. Scientific Reports. 7: 14466. PMID 29089515 DOI: 10.1038/S41598-017-14389-7  0.462
2017 Lawlor N, Youn A, Kursawe R, Ucar D, Stitzel ML. Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts. Scientific Reports. 7: 11959. PMID 28931935 DOI: 10.1038/S41598-017-12335-1  0.444
2017 Ucar D, Márquez EJ, Chung CH, Marches R, Rossi RJ, Uyar A, Wu TC, George J, Stitzel ML, Palucka AK, Kuchel GA, Banchereau J. The chromatin accessibility signature of human immune aging stems from CD8(+) T cells. The Journal of Experimental Medicine. PMID 28904110 DOI: 10.1084/Jem.20170416  0.418
2016 Kurum E, Benayoun BA, Malhotra A, George J, Ucar D. Computational inference of a genomic pluripotency signature in human and mouse stem cells. Biology Direct. 11: 47. PMID 27639379 DOI: 10.1186/S13062-016-0148-Z  0.725
2016 George J, Uyar A, Young K, Kuffler L, Waldron-Francis K, Marquez E, Ucar D, Trowbridge JJ. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. Nature Communications. 7: 12166. PMID 27397025 DOI: 10.1038/Ncomms12166  0.486
2016 Thibodeau A, Márquez EJ, Luo O, Ruan Y, Menghi F, Shin DG, Stitzel ML, Vera-Licona P, Ucar D. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. Plos Computational Biology. 12: e1004809. PMID 27336171 DOI: 10.1371/Journal.Pcbi.1004809  0.344
2016 Zubek J, Stitzel ML, Ucar D, Plewczynski DM. Computational inference of H3K4me3 and H3K27ac domain length. Peerj. 4: e1750. PMID 26989607 DOI: 10.7717/Peerj.1750  0.537
2016 Trowbridge J, George J, Uyar A, Young K, Waldron-Francis K, Marquez E, Ucar D. Leukemia cell-of-origin identified by chromatin landscape of bulk tumor cells Experimental Hematology. 44. DOI: 10.1016/J.Exphem.2016.06.228  0.423
2015 Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, et al. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell. 163: 1281-1286. PMID 28930648 DOI: 10.1016/j.cell.2015.10.051  0.685
2015 Stitzel ML, Kycia I, Kursawe R, Ucar D. Transcriptional Regulation of the Pancreatic Islet: Implications for Islet Function. Current Diabetes Reports. 15: 635. PMID 26272056 DOI: 10.1007/S11892-015-0635-0  0.457
2015 Ucar D, Bayarsaihan D. Cell-specific gene promoters are marked by broader spans of H3K4me3 and are associated with robust gene expression patterns. Epigenomics. 7: 129-31. PMID 25942528 DOI: 10.2217/Epi.14.87  0.45
2014 Gupta R, Wills A, Ucar D, Baker J. Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Developmental Biology. 395: 38-49. PMID 25205067 DOI: 10.1016/J.Ydbio.2014.08.034  0.321
2014 Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 158: 673-88. PMID 25083876 DOI: 10.1016/J.Cell.2014.06.027  0.686
2013 Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A. FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis. Cell Reports. 4: 477-91. PMID 23891001 DOI: 10.1016/J.Celrep.2013.06.035  0.741
2013 Rafalski VA, Ho PP, Brett JO, Ucar D, Dugas JC, Pollina EA, Chow LM, Ibrahim A, Baker SJ, Barres BA, Steinman L, Brunet A. Expansion of oligodendrocyte progenitor cells following SIRT1 inactivation in the adult brain. Nature Cell Biology. 15: 614-24. PMID 23644469 DOI: 10.1038/Ncb2735  0.727
2012 Salih DA, Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, et al. FoxO6 regulates memory consolidation and synaptic function. Genes & Development. 26: 2780-801. PMID 23222102 DOI: 10.1101/Gad.208926.112  0.742
2011 Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature. 479: 365-71. PMID 22012258 DOI: 10.1038/Nature10572  0.706
2011 Ucar D, Hu Q, Tan K. Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Research. 39: 4063-75. PMID 21266477 DOI: 10.1093/Nar/Gkr016  0.458
2010 Firpi HA, Ucar D, Tan K. Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics (Oxford, England). 26: 1579-86. PMID 20453004 DOI: 10.1093/Bioinformatics/Btq248  0.39
2009 Ucar D, Beyer A, Parthasarathy S, Workman CT. Predicting functionality of protein-DNA interactions by integrating diverse evidence. Bioinformatics (Oxford, England). 25: i137-44. PMID 19477979 DOI: 10.1093/Bioinformatics/Btp213  0.35
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