Understanding the 3D structure of the human genome
Natalie Sauerwald, Carl Kingsford (2021). Capturing the complexity of topologically associating domains through multi-feature optimization. bioRxiv.
Yihang Shen, Carl Kingsford (2020). Probabilistic method corrects previously uncharacterized Hi-C artifact. bioRxiv.
Natalie Sauerwald (2020). Algorithms for the study of chromosomal structure variability. Ph.D. Dissertation.
Natalie Sauerwald, Akshat Singhal, Carl Kingsford (2019). Analysis of the structural variability of topologically associated domains as revealed by Hi-C. Nuc. Acids Res. Genomics and Bioinformatics 2(1):lqz008 (2020).
Natalie Sauerwald, Yihang Shen, Carl Kingsford (2019). Topological data analysis reveals principles of chromosome structure throughout cellular differentiation. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 23:1–23:16 (2019).
Natalie Sauerwald, Carl Kingsford (2018). Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics (ISMB) 34(13):i475-i483.
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar (2017). Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Research 45(7):3663-3673.
Hiren Karathia, Carl Kingsford, Michelle Girvan, Sridhar Hannenhalli (2016). A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports 6:39279.
Emre Sefer, Geet Duggal, Carl Kingsford (2016). Deconvolution of ensemble chromatin interaction data reveals the latent mixing structures in cell subpopulations. Journal of Computational Biology 23(6):425-438.
Emre Sefer, Carl Kingsford (2015). Semi-nonparametric modeling of topological domain formation from epigenetic data. International Workshop on Algorithms in Bioinformatics, pages 148-161.
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford (2014). Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology, 914.
Geet Duggal, Hao Wang, Carl Kingsford (2013). Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Research 42(1):87-96.
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford (2013). Multiscale identification of topological domains in chromatin. International Workshop on Algorithms in Bioinformatics, pages 300-312.
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford (2013). Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms for Molecular Biology 8:8.
Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford (2013). Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, pages 306-315.
Geet Duggal, Carl Kingsford (2012). Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. BMC Bioinformatics 13:241.