Publications

Scientific Reports. 2017. Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin.

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


Aging epigenetics: changes and challenges, 2017 Book chapter in Epigenetics of Aging and Longevity, Elsevier press.  

Authors: Duygu Ucar* , Bérénice A. Benayoun*. 

JEM. 2017. The chromatin accessibility signature of human immune aging stems from CD8+ T cells

Authors: 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*.


 Trends in Genetics. 2017. Genomics of Islet (Dys)function and Type 2 Diabetes 

 Authors: Nathan LawlorShubham Khetan Duygu UcarMichael L. Stitzel.


 Biology Direct, 2016. Computational inference of a genomic pluripotency signature in human and mouse stem cells.

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


Nature Communications. 2016. Leukemia cell of origin identified by chromatin landscape of bulk tumour cells. 2016.

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


PLOS Computational Biology. 2016. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. 

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


PNAS. 2016. The tandem duplicator phenotype as a distinct genomic configuration in cancer. 

Authors : 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.


 PeerJ. 2016. Computational inference of H3K4me3 and H3K27ac domain length.

Authors : Julian ZubekMichael L. Stitzel Duygu Ucar​*Dariusz M. Plewczynski*.


 Molecular and Clinical Ontology. 2015. Amplification of the bromodomain-containing protein 4 gene in ovarian high‑grade serous carcinoma is associated with worse prognosis and survival. 

​Authors : Duygu Ucar , Douglas I. Lin.


 Current Diabetes Report. 2015. Transcriptional Regulation of the Pancreatic Islet: Implications for Islet Function.

​Authors : Michael L. Stitzel , Ina KyciaRomy Kursawe , Duygu Ucar.


 Epigenomics. 2015. Cell-specific gene promoters are marked by broader spans of H3K4me3 and are associated with robust gene expression patterns.

Authors : Duygu Ucar , Dashzeveg Bayarsaihan.


Cell. 2014. Broad H3K4me3 domains promote transcriptional stability at key cell identity and function genes.

Authors :  Bérénice A.Benayoun’ Elizabeth A.Pollina’ Duygu Ucar’ Salah Mahmoudi .

 KalpanaKarra Edith D.Wong KeerthanaDevarajan Aaron C.Daugherty Anshul B.Kundaje 

ElenaMancini Benjamin C.Hitz RakhiGupta ,Thomas A.Rando Julie C.Baker Michael P.Snyder , J. MichaelCherry AnneBrunet.


 Cell Reports. 2013. FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis.

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

 


Nature Cell Biology. 2013. Expansion of oligodendrocyte progenitor cells following SIRT1 inactivation in the adult brain.

Authors : 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.


 Bioinformatics. 2010. Discovering Regulatory DNA Elements Using Chromatin Signatures and Artificial Neural Network.

Authors : Hiram A. Firpi , Duygu Ucar ​, Kai Tan.


Nucleic Acids Research. 2011. Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.

Authors : Duygu Ucar ​, Qingyang Hu , Kai Tan.


 Bioinformatics. 2009. Predicting functionality of protein-DNA interactions by integrating diverse evidence.

Authors : Duygu Ucar​ , Andreas Beyer , Srinivasan Parthasarathy , Christopher T. Workman.


Bioinformatics. 2009. Construction of a Reference Gene Association Network from Multiple Profiling Data: Application to HIV Data Analysis. 

Authors : Duygu Ucar Isaac Neuhaus , Petra Ross-MacDonald , Charles Tilford , Srinivasan Parthasarathy , Nathan Siemers , Rui-Ru Ji.

 

 

 Full list can be found at Google Scholar.