Publications

You are here: / Publications

A neural network based model effectively predicts enhancers from clinical copie
——————————————-

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
Scientific Reports · 20 Sep 2017

A common type 2 diabetes risk variant potentiates activity of an evolutionary conserved copieAlpha tC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional copie
The American Journal of Human Genetics 102, 620–635, April 5, 2018

A CD4+ T cell population expanded in lupus blood orovides B cell help through copieA common type 2 diabetes risk variant potentiates activity of an evolutionary conserved copieAlpha tC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional copie
NATURE MEDiCiNE | VOL 25 | JANUARY 2019 | 75–81

A standalone software platform for the interactive management and pre processing of ATAX seq samples copie

Amplification of the bromodomain-containing protein 4 gene in ovarian high-grade serious carcinoma copie
——————————————-

baseline immune characteristics linked to pneumoccal vaccine responsiveness in older adults copie

Baseline-immune-states-bis-associated-with-vaccine-responsiveness-and-factors-that-shape-the-BIS

biFET-sequencing-Bias-free-transcription-factor-footprint-enrichment-test

cell-specific-gene-promoters-are-marked-mby-broader-spans-of-H3K4me3-and-are-associated-with-robust-gene-expression-patterns

Cell-specificity-of-human-regulatory-annoatations-and-their-genetic-effects-on-gene-expression

Challenges-and-opportunities-for-modeling-aging-and-cancer

Chromatin-interaction-networks-revealed-unique-connectivity-patterns

cinaR-a-comprehensive-R-package-for-the-differential-analyses-and-functional-interpretation-of-ATAC-seq-data

comparative-multi-omic-mapping-of-human-panreactic-islet-endoplasmic-reticulum-and-cytokine-stress-responses-provides-nsights-into-type-2-diabetes-genetics

Computational-inference-of-a-genomic-pluripotency-signature-in-human-and-mouse-stem-cells

Computational-inference-of-H3K4me3-and-H3K27az-domain-length

Concomitant-inference-of-a-genomic-pluripotency-signature-in-human-and-mouse-stem-cells

Distinct-baseline-immune-characteristics-associated-with-reponses-to-conjugated-and-uncojugated-pneumococcal-polysaccharide-vaccines-in-older-adults

epigenetic-memory-of-coronavirus-infection-in-innate-immune-cells

Functional-characterization-of-T2D-associated-SNP-effects-on-baseline-and-ER-stress-responsive-B-CELL

Genomics-of-Islet-Dysfunction-and-Type-2-diabetes

IMMUNOGENOMIC-RESPONSES-TO-VACCINATION-IN-AGING-INSIGHTS-INTO-IMMUNE-RESILIENCE

Leukaemia-cell-of-origin-identified-by-chromatin

Leukemia-cell-of-orgin-identified-by-chromatin-landscape-of-bulk-tumor-cells

Multiomic-profiling-identifies-cis-regulatory-networks-underlying-human-pancreatic

Network-topology-of-biological-aging-and-geroscience-guided-approaches-to-COVID-19

QuIN-A-Web-server-for-querying-and-visualizing-chromatin-interaction-networks

Sestrins-induce-natural-killer-function-in-senescent-like-CD8

Sexual-dimorphism-in-human-immune-system

single-cell-analysis-of-blood-mononuclear-cells-stimulated-through-either-LPS-or-anti-CD3

The-Chromatin-accessibility-signature-of-human-immune-aging-stems

The-tandem-duplicator-phenotype-as-a-distinct

Transcriptional-activation-of-Jun-and-Fos-members-of-the-AP‐1-complex-is-a-conserved-1

Type-2-diabetes-associated-genetic-variants-regulate-chromatin-accessibility-in-human-islets

V-SVA-an-R-Shiny-application-for-detecting-and-annotating-hidden-sources-of-varaition-in-single-cell-RNA

  1. 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. In press. (Article) (Senior) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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. March 2020, 10.1093/bioinformatics/btaa128. (Article) (Senior) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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: (Article) (Senior) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. 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) Roles:
  1. Rakhi Gupta, Andrea Wills, Duygu Ucar, Julie Baker. (2014)  Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus Developmental Biology, 395(1):38-49. (Article) Roles:
  1. Berenice A. Benayoun+, Elizabeth A. Pollina+, Duygu Ucar+, Edith D. Wong, Elena Mancini, Salah Mahmoudi, Benjamin C. Hitz, Keerthana Devarajan, Rakhi Gupta, Thomas A. Rando, Julie C. Baker, Michael P. Snyder, J. Michael Cherry, and Anne Brunet (2014) H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell, 158(3):673-688. (Article) Roles:
  1. Ashley E. Webb, Elizabeth A. Pollina, Thomas Vierbuchen, Noelia Urban, Duygu Ucar, Dena S. Leeman, Ben Martynoga, Madhavi Sewak, Thomas A. Rando, Francois Guillemot, Marius Wernig and Anne Brunet (2013) FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis (2013). Cell Reports, 4(3):477-491. (Article) Roles:
  1. Victoria A Rafalski, PP Ho, Jamie  O  Brett,  Duygu  Ucar,  JC  Dugas,  Elizabeth    Pollina, LM Chow, A Ibrahim, SJ Baker , BA Barres , L Steinman , and Anne Brunet (2013) Expansion of oligodendrocyte progenitor cells following SIRT1 inactivation in the adult brain. Nature Cell Biology, 15(6):614-24. (Article) Roles:
  1. Dervis A.M. Salih, Asim J. Rashid, Damien Colas, Luis de la Torre-Ubieta, Ruo P. Zhu, Alexander A. Morgan, Evan E. Santo, Duygu Ucar, Keerthana Devarajan, Christina J. Cole, Daniel V. Madison, Mehrdad Shamloo, Atul J. Butte, Azad Bonni, Sheena A. Josselyn, Anne Brunet (2012) FoxO6 regulates memory consolidation and synaptic function Genes Development, 26(24): 2780-2801. (Article) Roles:
  1. Eric L. Greer, Travis J. Maures, Duygu Ucar, Anna G. Hauswirth, Elena Mancini, Jana P. Lim, Berenice Benayoun, Yang Shi, and Anne Brunet (2011) Transgenerational Epigenetic Inheritance of Longevity in C. elegans. Nature, 479(7373): 365-371. (Article) Roles:
  1. Duygu Ucar, Qingyang Hu, and Kai Tan (2011) Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Research, 39(10):4063-4075. (Article) Roles:
  1. Hiram Firpi, Duygu Ucar, and Kai Tan (2010) Discovering Regulatory DNA Elements Using Chromatin Signatures and Artificial Neural Network Bioinformatics, 26(13):1579-1586. (Article) Roles:
  1. Sitaram Asur, Srinivasan Parthasarathy, and Duygu Ucar (2009) An Event-based Framework for Characterizing the Evolutionary Behavior of Interaction Graphs. ACM Transactions on Knowledge Discovery from  Data  (TKDD), 3(4). (Article) Roles:
  1. Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, and Christopher T. Workman (2009) Pre- dicting functionality of protein-DNA interactions by integrating diverse evidence. Bioinformatics (ISMB’09 Proceedings), 25(12): 137-144. (Article) Roles:
  1. Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan Parthasarathy, Nathan Siemers, and Rui-Ru Ji (2007) Construction of a Reference Gene Association Network from Multiple Profiling Data: Application to HIV Data Analysis.  Bioinformatics, 23(20):  2716-2724. (Article) Roles:
  1. Sitaram Asur, Duygu Ucar, and Srinivasan Parthasarathy (2007) An Ensemble Framework for Clustering Protein-Protein Interaction Networks. Bioainformatics (ISMB’07 Proceedings), 23(13): 29-40. (Article) Roles:
  1. Hui Yang, Srinivasan Parthasarathy, and Duygu Ucar (2007) A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories. Algorithms for Molecular Biology, 2:3. (Article) Roles: