Publications

1. Eishani Kumar Sokolowski, Romy Kursawe, Vijay Selvam, Redwan Bhuiyan, Asa Thibodeau, Chi Zhao, Cassandra Spracklen, Duygu Ucar*, Michael L. Stitzel*. Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics. Cell Metabolism. In press. (Article, Co-senior). Read the article

2. Sathyabaarathi Ravichandran⁺, Fernando Erra-Diaz⁺, Emin Onur Karakaslar⁺, Radu Marches, Lisa Kenyon-Pesce, Robert Rossi, Damien Chaussabel, Djamel Nehar-Belaid, David C. LaFon, Virginia Pascual, Karolina Palucka, Silke Paust, Moon H Nahm, George A Kuchel, Jacques Banchereau, Duygu Ucar. Distinct baseline immune characteristics associated with responses to conjugated and unconjugated pneumococcal polysaccharide vaccines in older adults. Nature Immunology. 2024;25(2):316-29. PMID: 38182669 (Article) (Senior) Read the article

3. Jin-Gyu Cheong, Arjun Ravishankar, Siddhartha Sharma, Christopher N Parkhurst, Simon A Grassmann, Claire K Wingert, Paoline Laurent, Sai Ma, Lucinda Paddock, Isabella C Miranda, Emin Onur Karakaslar, Djamel Nehar-Belaid, Asa Thibodeau, Michael J Bale, Vinay K Kartha, Jim K Yee, Minh Y Mays, Chenyang Jiang, Andrew W Daman, Alexia Martinez de Paz, Dughan Ahimovic, Victor Ramos, Alexander Lercher, Erik Nielsen, Sergio Alvarez-Mulett, Ling Zheng, Andrew Earl, Alisha Yallowitz, Lexi Robbins, Elyse LaFond, Karissa L Weidman, Sabrina Racine-Brzostek, He S Yang, David R Price, Louise Leyre, André F Rendeiro, Hiranmayi Ravichandran, Junbum Kim, Alain C Borczuk, Charles M Rice, R Brad Jones, Edward J Schenck, Robert J Kaner, Amy Chadburn, Zhen Zhao, Virginia Pascual, Olivier Elemento, Robert E Schwartz, Jason D Buenrostro, Rachel E Niec, Franck J Barrat, Lindsay Lief, Joseph C Sun, Duygu Ucar*, Steven Z Josefowicz*. Epigenetic memory of COVID-19 in innate immune cells and their progenitors. Cell. 2023 186(18). 3882-3902. PMID: 37597510 (Article) (Co-Senior). Read the article
4. Emin Onur Karakaslar⁺, Neerja Katiyar⁺, Muneer Hasham, Ahrim Youn, Siddhartha Sharma, Cheng-han Chung, Radu Marches, Ron Korstanje, Jacques Banchereau, Duygu Ucar. 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. February 2023. (Article) (Senior). Read the article

5. Fernando Erra Diaz, Ignacio Mazzitelli, Lucía Bleichmar, Claudia Melucci, Asa Thibodeau, Tomás Dalotto Moreno, Radu Marches, Gabriel A. Rabinovich, Duygu Ucar*, Jorge Geffner*. Concomitant inhibition of PPARγ and mTORC1 induce the differentiation of human monocytes into highly immunogenic dendritic cells. Cell Reports. 42(3). February 2023. (Article) (Co-Senior). Read the article

6. Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L Stitzel, Duygu Ucar. CoRE-ATAC: A Deep Learning model for the functional Classification of Regulatory Elements from single cell and bulk ATAC-seq data. PLOS Computational Biology. December 2021. 17 (12). e1009670. (Article) (Senior)
7. Asa Thibodeau⁺, Alper Eroglu⁺, Christopher S McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N Conrad, George A Kuchel, Zev J Gartner, Jacques Banchereau, Michael L Stitzel, A Ercument Cicek, Duygu Ucar. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biology. December 2021. 1. 1-19. (Article) (Senior)

8. Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C Ulirsch, Steven K Reilly, Duygu Ucar, Ryan Tewhey, Michael L Stitzel. Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation. September 2021. Nature Communications. 12(1). 5242. (Article). Read the article

9. Nathan T Lawlor, Djamel Nehar-Belaid, Jessica Grassmann, Marlon Stoeckius, Peter Smibert, Michael L Stitzel, Virginia Pascual, Jacques Banchereau^*, Adam Williams^*, Duygu Ucar^*. Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes. Frontiers in Immunology, March 2021. 12, 636720. (Article) (Co-Senior). Read the article

10. D Gilroy, B Pereira, R De Maeyer, D Nehar-Belaid, A Lanna, S Ward, R Marches, E CHAMBERS, D Gomes, N Riddell, M Maini, V Teixeira, S Janes, A Larbi, N Mabbott, Duygu Ucar, G Kuchel, S Henson, J Strid, J Lee, J Banchereau, A Akbar. Sestrins Induce Natural Killer Function In Senescent-like CD8+ T Cells. Nature Immunology. March 2020. 21 (6), 684-694. (Article). Read the article
11. Nathan Lawlor, Eladio J. Marquez, Donghyung Lee, and Duygu Ucar. V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data. Bioinformatics. March 2020, 10.1093/bioinformatics/btaa128. (Article) (Senior). Read the article

12. Eladio J. Marquez, Djamel Nehar-belaid, Cheng-han Chung, Radu Marches, Robert Rossi, Karolina Palucka, Virginia Pascual,  George  A  Kuchel^*,  Jacques  Banchereau^*,  Duygu  Ucar^*.  Sexual dimorphism in human immune system aging. Nature Communications. February 2020. 11 (1), 1-17. (Article) (Co-Senior). Read the article

13. Arushi Varshney, Hadley VanRenterghem, Peter Orchard, Alan P. Boyle, Michael S. Stitzel, Duygu Ucar, Stephen C. J. Parker. (2019) Cell specificity of human regulatory annotations and their genetic effects on gene expression. Genetics. February 1, 2019 vol. 211 no. 2 549-562. (Article). Read the article

14. Nathan Lawlor, Eladio J. M´arquez, Peter Orchard, Narisu Narisu, Muhammad Saad Shamim, Asa Thibodeau, Arushi Varshney, Romy Kursawe, Michael R. Erdos, Matt Kanke, Huiya Gu, Evgenia Pak, Amalia Dutra, Sheikh Russel, Xingwang Li, Emaly Piecuch, Oscar Luo, Peter S. Chines, Christian Fuchbserger, Praveen Sethupathy, Aviva Presser Aiden, Yijun Ruan, Erez Lieberman Aiden, Francis S. Collins, Duygu Ucar, Stephen C.J. Parker, and Michael L. Stitzel. (2019). Multiomic profiling identifies cis-regulatory networks underlying human pancreatic cell identity and function.  Cell Reports.  26, 788–801. (Article). Read the article
15. Simone Caielli, Diogo Troggian Veiga, Preetha Balasubramanian, Shruti Athale, Bojana Domic, Elise Murat, Romain Banchereau, Zhaohui Xu, Manjari Chandra, Cheng-Han Chung, Lynnette Walters, Jeanine Baisch, Tracey Wright, Marilynn Punaro, Lorien Nassi, Katie Stewart, Julie Fuller, Duygu Ucar, Hideki Ueno, Joseph Zhou, Jacques Banchereau*, Virginia Pascual* (2019). A CD4+ T cell population expanded in SLE blood provides B cell help through IL10 and succinate. Nature Medicine 25 (1), 75. (Article). Read the article

16. Ahrim Youn, Eladio J. Marquez, Nathan Lawlor, Michael L. Stitzel, Duygu Ucar. (2019) BiFET: A Bias-free Transcription Factor Footprint Enrichment Test. Nucleic Acids Research. January 2019, Vol. 47, No. 2 e11. (Article) (Senior). Read the article

17. Donghyung Lee*, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar*. (2018) A statistical framework for the robust detection of hidden variation in single cell transcriptomes. Scientific Reports, 8 (1), 17040. (Article) (Senior).

18. Asa Thibodeau+, Asli Uyar+, Shubham Khetan, Michael Stitzel, Duygu Ucar. (2018) A neural network based model effectively predicts enhancers from clinical ATAC-seq samples. Scientific Reports, 8: 16048. (Article) (Senior). Read the article

19. Shubham Khetan, Romy Kursawe, Ahrim Youn, Nathan Lawlor, Eladio J Marquez, Duygu Ucar*, and Michael L. Stitzel*. (2018) Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis-regulatory element use in human islets. Diabetes, db180393. (Article) (Co-Senior). Read the article

20. Ina Kycia, Brooke N. Wolford, Jeroen Huyghe, Christian Fuchsberger, Swarooparani Vadlamudi, Romy Kursawe, Asli Uyar, Shubham Khetan, Mohan Bolisetty, Anubhuti Mathur, Johanna Kuu- sisto, Markku Laakso, Duygu Ucar, Karen L. Mohlke, Michael Boehnke, Francis S. Collins, Stephen Parker, and Michael L. Stitzel. (2018) A common functional variant in a type 2 diabetes locus potentiates activity of an evolutionarily conserved islet stretch enhancer and C2CD4A/B expression. The American Journal of Human Genetics (AJHG), 102 (4), 620-635. (Article). Read the article

21. Zeeshan Ahmed*, Duygu Ucar* (2017) I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples PeerJ, 5, e4040. (Article) (Co-Senior). Read the article

22. Asa Thibodeau, Eladio J. Marquez, Dong-Guk Shin, Paola Vera-Licona*, Duygu Ucar*. (2017) Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin Scientific Reports, 7 (1), 14466. (Article) (Co-Senior). Read the article

23. Duygu Ucar*+, Eladio J. Marquez+, Cheng-han Chung+, Radu Marches, Robert Rossi, Asli Uyar, Te-Chia Wu, Joshy George, Michael Stitzel, Karolina Palucka, George A Kuchel*, and Jacques Banchereau*. (2017) The chromatin accessibility signature of aging in human blood leukocytes stems from CD8+ T cells. The Journal of Experimental Medicine (JEM), 214 (10), 3123-3144. (Article) (Co-Senior). Read the article

24. Nathan Lawlor+, Ahrim Youn+, Kursawe Romy, Duygu Ucar*, Michael L. Stitzel*. (2017) Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts Scientific Reports, 7 (1), 11959. (Article) (Co-Senior). Read the article

25. Esra Kurum, Berenice A. Benayoun, Ankit Malhotra, Joshy George, and Duygu Ucar. (2016) Computational inference of a genomic pluripotency signature in human and mouse stem cells Biology Direct, 11(1) 47. (Article) (Senior). Read the article

26. Asa Thibodeau, Eladio Marquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar. (2016) QuIN: A web server for Querying and visualizing Chromatin Interaction Networks. PLOS Computational Biology, 12(6): p. e1004809.PMCID:  4919057. (Article) (Senior). Read the article

27. Joshy George, Asli Uyar, Kira Young, Lauren Kuffler, Kaiden Waldron-Francis, Eladio Marquez, Duygu Ucar, Jennifer Trowbridge. (2016) Leukaemia cell of origin identified by chromatin land- scape of bulk tumour cells. Nature Communications, 7(Article number: 12166). (Article). Read the article

28. Francesca Menghi, Koichiro Inaki, Xing Yi Woob, Pooja Kumara, Krzysztof Grzedaa, Ankit Malhotra, Hyunsoo Kima, Duygu Ucar, Phung Trang Shreckengast , Joel P. Wagner, Jeff Chuang, and Edison T. Liu. (2016) The tandem duplicator phenotype in cancer genomes. PNAS, 26;113(17):E2373- 82. (Article). Read the article

29. Julian Zubek, Michael Stitzel, Duygu Ucar*, and Dariusz Plewczynski*. (2016) Computational inference of H3K4me3 and H3K27ac domain length. PeerJ, 2016 Mar 14;4:e1750. doi: 10.7717/peerj.1750. (Article) (Co-Senior). Read the article

30. Duygu Ucar and Douglas Lin (2015). Amplificaiton of the bromodomain-containing protein 4 gene in ovarian high-grade serous carcinoma is associated with worse prognosis and survival. Molecular and Clinical Oncology, 2015 Nov;3(6):1291-1294. (Article). Read the article