Publications | Ucar Lab

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar

PLOS Computational Biology · 13 Dec 2021

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

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

Genome Biology · 01 Sep 2021

Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28

Nathan Lawlor, Djamel Nehar-Belaid, Jessica D.S. Grassmann, Marlon Stoeckius, Peter Smibert, Michael L. Stitzel, Virginia Pascual, Jacques Banchereau, Adam Williams, Duygu Ucar

Frontiers in Immunology · 17 Mar 2021

The lethal sex gap: COVID-19

Eladio J. Márquez, Jennifer Trowbridge, George A. Kuchel, Jacques Banchereau, Duygu Ucar

Immunity & Ageing · 21 May 2020

Sestrins induce natural killer function in senescent-like CD8+ T cells

Branca I. Pereira, Roel P. H. De Maeyer, Luciana P. Covre, Djamel Nehar-Belaid, Alessio Lanna, Sophie Ward, Radu Marches, Emma S. Chambers, Daniel C. O. Gomes, Natalie E. Riddell, Mala K. Maini, Vitor H. Teixeira, Samuel M. Janes, Derek W. Gilroy, Anis Larbi, Neil A. Mabbott, Duygu Ucar, George A. Kuchel, Sian M. Henson, Jessica Strid, Jun H. Lee, Jacques Banchereau, Arne N. Akbar

Nature Immunology · 30 Mar 2020

V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data

Nathan Lawlor, Eladio J Marquez, Donghyung Lee, Duygu Ucar

Bioinformatics · 02 Mar 2020

Sexual-dimorphism in human immune system aging

Eladio J. Márquez, Cheng-han Chung, Radu Marches, Robert J. Rossi, Djamel Nehar-Belaid, Alper Eroglu, David J. Mellert, George A. Kuchel, Jacques Banchereau, Duygu Ucar

Nature Communications · 06 Feb 2020

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function

Nathan Lawlor, Eladio J. Márquez, 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 Russell, 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, Michael L. Stitzel

Cell Reports · 01 Jan 2019

Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA)

Donghyung Lee, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar

Scientific Reports · 19 Nov 2018

BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test

Ahrim Youn, Eladio J Marquez, Nathan Lawlor, Michael L Stitzel, Duygu Ucar

Nucleic Acids Research · 14 Nov 2018

A neural network based model effectively predicts enhancers from clinical ATAC-seq samples

Asa Thibodeau, Asli Uyar, Shubham Khetan, Michael L. Stitzel, Duygu Ucar

Scientific Reports · 30 Oct 2018

Type 2 Diabetes–Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets

Shubham Khetan, Romy Kursawe, Ahrim Youn, Nathan Lawlor, Alexandria Jillette, Eladio J. Marquez, Duygu Ucar, Michael L. Stitzel

Diabetes · 04 Sep 2018

A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression

Ina Kycia, Brooke N. Wolford, Jeroen R. Huyghe, Christian Fuchsberger, Swarooparani Vadlamudi, Romy Kursawe, Ryan P. Welch, Ricardo d’Oliveira Albanus, Asli Uyar, Shubham Khetan, Nathan Lawlor, Mohan Bolisetty, Anubhuti Mathur, Johanna Kuusisto, Markku Laakso, Duygu Ucar, Karen L. Mohlke, Michael Boehnke, Francis S. Collins, Stephen C.J. Parker, Michael L. Stitzel

The American Journal of Human Genetics · 01 Apr 2018

Aging Epigenetics

Duygu Ucar, Bérénice A. Benayoun

Epigenetics of Aging and Longevity · 01 Jan 2018

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

Zeeshan Ahmed, Duygu Ucar

PeerJ · 22 Nov 2017

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin

Asa Thibodeau, Eladio J. Márquez, Dong-Guk Shin, Paola Vera-Licona, Duygu Ucar

Scientific Reports · 31 Oct 2017

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

The chromatin accessibility signature of human immune aging stems from CD8+ T cells

Duygu Ucar, Eladio J. Márquez, Cheng-Han Chung, Radu Marches, Robert J. Rossi, Asli Uyar, Te-Chia Wu, Joshy George, Michael L. Stitzel, A. Karolina Palucka, George A. Kuchel, Jacques Banchereau

Journal of Experimental Medicine · 13 Sep 2017

Genomics of Islet (Dys)function and Type 2 Diabetes

Nathan Lawlor, Shubham Khetan, Duygu Ucar, Michael L. Stitzel

Trends in Genetics · 01 Apr 2017

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

Esra Kurum, Bérénice A. Benayoun, Ankit Malhotra, Joshy George, Duygu Ucar

Biology Direct · 17 Sep 2016

Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells

Joshy George, Asli Uyar, Kira Young, Lauren Kuffler, Kaiden Waldron-Francis, Eladio Marquez, Duygu Ucar, Jennifer J. Trowbridge

Nature Communications · 11 Jul 2016

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

Asa Thibodeau, Eladio J. Márquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar

PLOS Computational Biology · 23 Jun 2016

The tandem duplicator phenotype as a distinct genomic configuration in cancer

Francesca Menghi, Koichiro Inaki, XingYi Woo, Pooja A. Kumar, Krzysztof R. Grzeda, Ankit Malhotra, Vinod Yadav, Hyunsoo Kim, Eladio J. Marquez, Duygu Ucar, Phung T. Shreckengast, Joel P. Wagner, George MacIntyre, Krishna R. Murthy Karuturi, Ralph Scully, James Keck, Jeffrey H. Chuang, Edison T. Liu

Proceedings of the National Academy of Sciences · 07 Apr 2016

Computational inference of H3K4me3 and H3K27ac domain length

Julian Zubek, Michael L. Stitzel, Duygu Ucar, Dariusz M. Plewczynski

PeerJ · 14 Mar 2016

Transcriptional Regulation of the Pancreatic Islet: Implications for Islet Function

Michael L. Stitzel, Ina Kycia, Romy Kursawe, Duygu Ucar

Current Diabetes Reports · 14 Aug 2015

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

Duygu Ucar, Dashzeveg Bayarsaihan

Epigenomics · 01 Apr 2015

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

Bérénice A. Benayoun, Elizabeth A. Pollina, Duygu Ucar, Salah Mahmoudi, Kalpana Karra, Edith D. Wong, Keerthana Devarajan, Aaron C. Daugherty, Anshul B. Kundaje, Elena Mancini, Benjamin C. Hitz, Rakhi Gupta, Thomas A. Rando, Julie C. Baker, Michael P. Snyder, J. Michael Cherry, Anne Brunet

Cell · 01 Jul 2014

FOXO3 Shares Common Targets with ASCL1 Genome-wide and Inhibits ASCL1-Dependent Neurogenesis

Ashley E. Webb, Elizabeth A. Pollina, Thomas Vierbuchen, Noelia Urbán, Duygu Ucar, Dena S. Leeman, Ben Martynoga, Madhavi Sewak, Thomas A. Rando, François Guillemot, Marius Wernig, Anne Brunet

Cell Reports · 01 Aug 2013

Expansion of oligodendrocyte progenitor cells following SIRT1 inactivation in the adult brain

Victoria A. Rafalski, Peggy P. Ho, Jamie O. Brett, Duygu Ucar, Jason C. Dugas, Elizabeth A. Pollina, Lionel M. L. Chow, Adiljan Ibrahim, Suzanne J. Baker, Ben A. Barres, Lawrence Steinman, Anne Brunet

Nature Cell Biology · 05 May 2013