Effective Pre-Processing Strategies for Functional Clustering of a Protein-Protein Interactions Network. - Duygu Ucar; Srinivasan Parthasarathy 001; Sitaram Asur; Chao Wang 050 (BIBE, 2005)

Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-Induced Subgraphs. - Duygu Ucar; Sitaram Asur; Ümit V. Çatalyürek; Srinivasan Parthasarathy 001 (PKDD, 2006)

An ensemble framework for clustering protein-protein interaction networks. - Sitaram Asur; Duygu Ucar; Srinivasan Parthasarathy 001 (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories. - Hui Yang 002; Srinivasan Parthasarathy 001; Duygu Ucar (Algorithms Mol. Biol., 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 001; Nathan O. Siemers; Rui-Ru Ji (Bioinform., 2007)

Mutual Information Based Extrinsic Similarity for Microarray Analysis. - Duygu Ucar; Fatih Altiparmak; Hakan Ferhatosmanoglu; Srinivasan Parthasarathy 001 (BICoB, 2009)

Predicting functionality of protein-DNA interactions by integrating diverse evidence. - Duygu Ucar; Andreas Beyer; Srinivasan Parthasarathy 001; Christopher T. Workman (Bioinform., 2009)

An event-based framework for characterizing the evolutionary behavior of interaction graphs. - Sitaram Asur; Srinivasan Parthasarathy 001; Duygu Ucar (ACM Trans. Knowl. Discov. Data, 2009)

Markov clustering of protein interaction networks with improved balance and scalability. - Venu Satuluri; Srinivasan Parthasarathy 001; Duygu Ucar (BCB, 2010)

Discover regulatory DNA elements using chromatin signatures and artificial neural network. - Hiram A. Firpi; Duygu Ucar; Kai Tan 001 (Bioinform., 2010)

A Survey of Graph Mining Techniques for Biological Datasets. - Srinivasan Parthasarathy 001; Shirish Tatikonda; Duygu Ucar (Managing and Mining Graph Data, 2010)

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)

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)

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)