Natalie Stanley

According to our database, Natalie Stanley authored at least 20 papers between 2015 and 2024.

Collaborative distances:

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

2024

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., December, 2024

Conditional Similarity Triplets Enable Covariate-Informed Representations of Single-Cell Data.

Chi-Jane Chen, Haidong Yi, Natalie Stanley

CoRR, 2024

2023

Large-scale correlation network construction for unraveling the coordination of complex biological systems.

Martin Becker, 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, Qun Liu, Yeasul Kim, Ivana Maric, Samson Mataraso, Seyedeh Neelufar Payrovnaziri, Thanaphong Phongpreecha, Neal G. Ravindra, Natalie Stanley, Sayane Shome, Yuqi Tan, Melan Thuraiappah, Maria Xenochristou, Lei Xue, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Nat. Comput. Sci., 2023

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, Ramin Fallahzadeh, Huda Nassar, Martin Becker, Maria Xenochristou, Camilo Espinosa, Davide De Francesco, Mohammad S. Ghaemi, Elizabeth K. Costello, Anthony Culos, Xuefeng Bruce Ling, Karl G. Sylvester, Gary L. Darmstadt, Virginia D. Winn, Gary M. Shaw, David A. Relman, Stephen R. Quake, Martin S. Angst, Michael P. Snyder, David K. Stevenson, Brice Gaudilliere, Nima Aghaeepour

Patterns, 2022

Interpretable Single-Cell Set Classification with Kernel Mean Embeddings.

Siyuan Shan, Vishal Baskaran, Haidong Yi, Jolene Ranek, Natalie Stanley, Junier Oliva

CoRR, 2022

CytoEMD: detecting and visualizing between-sample variation in relation to phenotype with earth mover's distance.

Haidong Yi, Natalie Stanley

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

Transparent single-cell set classification with kernel mean embeddings.

Siyuan Shan, Vishal Athreya Baskaran, Haidong Yi, Jolene Ranek, Natalie Stanley, Junier B. Oliva

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

Distribution-based sketching of single-cell samples.

Vishal Athreya Baskaran, Jolene Ranek, Siyuan Shan, Natalie Stanley, Junier B. Oliva

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

2021

CytoSet: predicting clinical outcomes via set-modeling of cytometry data.

Haidong Yi, Natalie Stanley

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2020

Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions.

Anthony Culos, Amy Tsai, Natalie Stanley, Martin Becker, Mohammad Sajjad Ghaemi, David Mcilwain, Ramin Fallahzadeh, Athena Tanada, Huda Nassar, Camilo Espinosa, Maria Xenochristou, Edward Ganio, Laura Peterson, Xiaoyuan Han, Ina A. Stelzer, Kazuo Ando, Dyani Gaudilliere, Thanaphong Phongpreecha, Ivana Maric, Alan L. Chang, Gary M. Shaw, David K. Stevenson, Sean Bendall, Kara L. Davis, Wendy J. Fantl, Garry P. Nolan, Trevor Hastie, Robert Tibshirani, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Nat. Mach. Intell., 2020

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, Anthony Culos, Natalie Stanley, Athena Tanada, Amy Tsai, Dyani Gaudilliere, Edward Ganio, Xiaoyuan Han, Kazuo Ando, Leslie McNeil, Martha Tingle, Paul H. Wise, Ivana Maric, Marina Sirota, Tony Wyss-Coray, Virginia D. Winn, Maurice L. Druzin, Ronald Gibbs, Gary L. Darmstadt, David B. Lewis, Vahid Partovi Nia, Bruno Agard, Robert Tibshirani, Garry P. Nolan, Michael P. Snyder, David A. Relman, Stephen R. Quake, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour

Bioinform., 2019

Stochastic block models with multiple continuous attributes.

Natalie Stanley, Thomas Bonacci, Roland Kwitt, Marc Niethammer, Peter J. Mucha

Appl. Netw. Sci., 2019

2018

Adapting Community Detection Approaches to Large, Multilayer, and Attributed Networks.

Natalie Stanley

PhD thesis, 2018

Testing Alignment of Node Attributes with Network Structure Through Label Propagation.

Natalie Stanley, Marc Niethammer, Peter J. Mucha

CoRR, 2018

Multi-layer Large-Scale Functional Connectome Reveals Infant Brain Developmental Patterns.

Han Zhang, Natalie Stanley, Peter J. Mucha, Weiyan Yin, Weili Lin, Dinggang Shen

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, 2018

2017

Compressing networks with super nodes.

Natalie Stanley, Roland Kwitt, Marc Niethammer, Peter J. Mucha

CoRR, 2017

Case studies in network community detection.

Saray Shai, Natalie Stanley, Clara Granell, Dane Taylor, Peter J. Mucha

CoRR, 2017

Identifying Security Critical Properties for the Dynamic Verification of a Processor.

Rui Zhang, Natalie Stanley, Christopher Griggs, Andrew Chi, Cynthia Sturton

Proceedings of the Twenty-Second International Conference on Architectural Support for Programming Languages and Operating Systems, 2017

2016

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

2015

Enhanced detectability of community structure in multilayer networks through layer aggregation.

Dane Taylor, Saray Shai, Natalie Stanley, Peter J. Mucha

CoRR, 2015