Enhanced detectability of community structure in multilayer networks through layer aggregation. - Dane Taylor; Saray Shai; Natalie Stanley; Peter J. Mucha (CoRR, 2015)

Clustering Network Layers with the Strata Multilayer Stochastic Block Model. - Natalie Stanley; Saray Shai; Dane Taylor; Peter J. Mucha (IEEE Trans. Netw. Sci. Eng., 2016)

Identifying Security Critical Properties for the Dynamic Verification of a Processor. - Rui Zhang 068; Natalie Stanley; Christopher Griggs; Andrew Chi; Cynthia Sturton (ASPLOS, 2017)

Case studies in network community detection. - Saray Shai; Natalie Stanley; Clara Granell; Dane Taylor; Peter J. Mucha (CoRR, 2017)

Compressing networks with super nodes. - Natalie Stanley; Roland Kwitt; Marc Niethammer; Peter J. Mucha (CoRR, 2017)

Multi-layer Large-Scale Functional Connectome Reveals Infant Brain Developmental Patterns. - Han Zhang 002; Natalie Stanley; Peter J. Mucha; Weiyan Yin; Weili Lin; Dinggang Shen (MICCAI (3), 2018)

Testing Alignment of Node Attributes with Network Structure Through Label Propagation. - Natalie Stanley; Marc Niethammer; Peter J. Mucha (CoRR, 2018)

Adapting Community Detection Approaches to Large, Multilayer, and Attributed Networks. - Natalie Stanley (2018)

Stochastic block models with multiple continuous attributes. - Natalie Stanley; Thomas Bonacci; Roland Kwitt; Marc Niethammer; Peter J. Mucha (Appl. Netw. Sci., 2019)

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. - Mohammad Sajjad Ghaemi; Daniel B. DiGiulio; Kévin Contrepois; Benjamin J. Callahan; Thuy T. M. Ngo; Brittany Lee-McMullen; Benoit Lehallier; Anna Robaczewska; David Mcilwain; Yael Rosenberg-Hasson; Ronald J. Wong; Cecele Quaintance; et al. (Bioinform., 2019)

Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions. - Anthony Culos; Amy Tsai; Natalie Stanley; Martin Becker 003; Mohammad Sajjad Ghaemi; David Mcilwain; Ramin Fallahzadeh; Athena Tanada; Huda Nassar; Camilo Espinosa; Maria Xenochristou; Edward Ganio; et al. (Nat. Mach. Intell., 2020)

CytoSet: predicting clinical outcomes via set-modeling of cytometry data. - Haidong Yi; Natalie Stanley (BCB, 2021)

Distribution-based sketching of single-cell samples. - Vishal Athreya Baskaran; Jolene Ranek; Siyuan Shan; Natalie Stanley; Junier B. Oliva (BCB, 2022)

Transparent single-cell set classification with kernel mean embeddings. - Siyuan Shan; Vishal Athreya Baskaran; Haidong Yi; Jolene Ranek; Natalie Stanley; Junier B. Oliva (BCB, 2022)

CytoEMD: detecting and visualizing between-sample variation in relation to phenotype with earth mover's distance. - Haidong Yi; Natalie Stanley (BCB, 2022)

Interpretable Single-Cell Set Classification with Kernel Mean Embeddings. - Siyuan Shan; Vishal Baskaran; Haidong Yi; Jolene Ranek; Natalie Stanley; Junier Oliva (CoRR, 2022)

Early prediction and longitudinal modeling of preeclampsia from multiomics. - Ivana Maric; Kévin Contrepois; Mira N. Moufarrej; Ina A. Stelzer; Dorien Feyaerts; Xiaoyuan Han; Andy Tang; Natalie Stanley; Ronald J. Wong; Gavin M. Traber; Mathew Ellenberger; Alan L. Chang; et al. (Patterns, 2022)

Large-scale correlation network construction for unraveling the coordination of complex biological systems. - Martin Becker 003; Huda Nassar; Camilo Espinosa; Ina A. Stelzer; Dorien Feyaerts; Eloïse Berson; Neda Hajiakhoond Bidoki; Alan L. Chang; Geetha Saarunya; Anthony Culos; Davide De Francesco; Ramin Fallahzadeh; et al. (Nat. Comput. Sci., 2023)

Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. - Jamshaid A. Shahir; Natalie Stanley; Jeremy E. Purvis (BMC Bioinform., 2024)

Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis. - Chi-Jane Chen; Yuhang Chen; Sukwon Yun; Natalie Stanley; Tianlong Chen 001 (ACL (Findings), 2025)

Conditional similarity triplets enable covariate-informed representations of single-cell data. - Chi-Jane Chen; Haidong Yi; Natalie Stanley (BMC Bioinform., 2025)