Duygu Ucar

According to our database, Duygu Ucar authored at least 14 papers between 2005 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

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 Comput. Biol., 2021

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. Márquez, Donghyung Lee, Duygu Ucar

Bioinform., 2020

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 Comput. Biol., 2016

2010

A Survey of Graph Mining Techniques for Biological Datasets.

Srinivasan Parthasarathy, Shirish Tatikonda, Duygu Ucar

Proceedings of the Managing and Mining Graph Data, 2010

Discover regulatory DNA elements using chromatin signatures and artificial neural network.

Hiram A. Firpi, Duygu Ucar, Kai Tan

Bioinform., 2010

Markov clustering of protein interaction networks with improved balance and scalability.

Venu Satuluri, Srinivasan Parthasarathy, Duygu Ucar

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009

An event-based framework for characterizing the evolutionary behavior of interaction graphs.

Sitaram Asur, Srinivasan Parthasarathy, Duygu Ucar

ACM Trans. Knowl. Discov. Data, 2009

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

Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, Christopher T. Workman

Bioinform., 2009

Mutual Information Based Extrinsic Similarity for Microarray Analysis.

Duygu Ucar, Fatih Altiparmak, Hakan Ferhatosmanoglu, Srinivasan Parthasarathy

Proceedings of the Bioinformatics and Computational Biology, 2009

2007

Construction of a reference gene association network from multiple profiling data: application to data analysis.

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

Bioinform., 2007

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories.

Hui Yang, Srinivasan Parthasarathy, Duygu Ucar

Algorithms Mol. Biol., 2007

An ensemble framework for clustering protein-protein interaction networks.

Sitaram Asur, Duygu Ucar, Srinivasan Parthasarathy

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-Induced Subgraphs.

Duygu Ucar, Sitaram Asur, Ümit V. Çatalyürek, Srinivasan Parthasarathy

Proceedings of the Knowledge Discovery in Databases: PKDD 2006, 2006

2005

Effective Pre-Processing Strategies for Functional Clustering of a Protein-Protein Interactions Network.

Duygu Ucar, Srinivasan Parthasarathy, Sitaram Asur, Chao Wang

Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005