Natalie Stanley

26 papers A* 1Journal 18Unranked 6

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Conditional similarity triplets enable covariate-informed representations of single-cell data. BMC Bioinform. Chi-Jane Chen, Haidong Yi, Natalie Stanley
2025	—	`conf`	Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis. ACL (Findings) Chi-Jane Chen, Yuhang Chen, Sukwon Yun, Natalie Stanley, Tianlong Chen
2025	J	`jnl`	Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis. CoRR Chi-Jane Chen, Yuhang Chen, Sukwon Yun, Natalie Stanley, Tianlong Chen
2024	J	`jnl`	Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks. BMC Bioinform. Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis
2024	J	`jnl`	Conditional Similarity Triplets Enable Covariate-Informed Representations of Single-Cell Data. CoRR Chi-Jane Chen, Haidong Yi, Natalie Stanley
2023	J	`jnl`	Large-scale correlation network construction for unraveling the coordination of complex biological systems. Nat. Comput. Sci. 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
2022	—	`conf`	CytoEMD: detecting and visualizing between-sample variation in relation to phenotype with earth mover's distance. BCB Haidong Yi, Natalie Stanley
2022	J	`jnl`	Distribution-based Sketching of Single-Cell Samples. CoRR Vishal Athreya Baskaran, Jolene Ranek, Siyuan Shan, Natalie Stanley, Junier B. Oliva
2022	—	`conf`	Distribution-based sketching of single-cell samples. BCB Vishal Athreya Baskaran, Jolene Ranek, Siyuan Shan, Natalie Stanley, Junier B. Oliva
2022	J	`jnl`	Early prediction and longitudinal modeling of preeclampsia from multiomics. Patterns 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
2022	J	`jnl`	Interpretable Single-Cell Set Classification with Kernel Mean Embeddings. CoRR Siyuan Shan, Vishal Baskaran, Haidong Yi, Jolene Ranek, Natalie Stanley, Junier Oliva
2022	—	`conf`	Transparent single-cell set classification with kernel mean embeddings. BCB Siyuan Shan, Vishal Athreya Baskaran, Haidong Yi, Jolene Ranek, Natalie Stanley, Junier B. Oliva
2021	—	`conf`	CytoSet: predicting clinical outcomes via set-modeling of cytometry data. BCB Haidong Yi, Natalie Stanley
2020	J	`jnl`	Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions. Nat. Mach. Intell. 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
2019	J	`jnl`	Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinform. 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
2019	J	`jnl`	Stochastic block models with multiple continuous attributes. Appl. Netw. Sci. Natalie Stanley, Thomas Bonacci, Roland Kwitt, Marc Niethammer, Peter J. Mucha
2018	—	`—`	Adapting Community Detection Approaches to Large, Multilayer, and Attributed Networks. Natalie Stanley
2018	—	`conf`	Multi-layer Large-Scale Functional Connectome Reveals Infant Brain Developmental Patterns. MICCAI (3) Han Zhang, Natalie Stanley, Peter J. Mucha, Weiyan Yin, Weili Lin, Dinggang Shen
2018	J	`jnl`	Stochastic Block Models with Multiple Continuous Attributes. CoRR Natalie Stanley, Thomas Bonacci, Roland Kwitt, Marc Niethammer, Peter J. Mucha
2018	J	`jnl`	Testing Alignment of Node Attributes with Network Structure Through Label Propagation. CoRR Natalie Stanley, Marc Niethammer, Peter J. Mucha
2017	J	`jnl`	Case studies in network community detection. CoRR Saray Shai, Natalie Stanley, Clara Granell, Dane Taylor, Peter J. Mucha
2017	J	`jnl`	Compressing networks with super nodes. CoRR Natalie Stanley, Roland Kwitt, Marc Niethammer, Peter J. Mucha
2017	A*	`conf`	Identifying Security Critical Properties for the Dynamic Verification of a Processor. ASPLOS Rui Zhang, Natalie Stanley, Christopher Griggs, Andrew Chi, Cynthia Sturton
2016	J	`jnl`	Clustering Network Layers with the Strata Multilayer Stochastic Block Model. IEEE Trans. Netw. Sci. Eng. Natalie Stanley, Saray Shai, Dane Taylor, Peter J. Mucha
2015	J	`jnl`	Clustering Network Layers With the Strata Multilayer Stochastic Block Model. CoRR Natalie Stanley, Saray Shai, Dane Taylor, Peter J. Mucha
2015	J	`jnl`	Enhanced detectability of community structure in multilayer networks through layer aggregation. CoRR Dane Taylor, Saray Shai, Natalie Stanley, Peter J. Mucha