Stephanie C Hicks (Stephanie Hicks)

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 79

Top Venues

bioRxiv : the preprint server for biology

Biological imaging

Nature methods

Bioinformatics advances

Johns Hopkins Bloomberg School of Public Health

Rice University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Johns Hopkins Bloomberg School of Public Health Feb 01 2018

United States

Assistant Professor :: Biostatistics

Dana-Farber Cancer Institute - Jan 31 2018

United States

Postdoctoral Research Fellow :: Biostatistics and Computational Biology

Education History

Rice University

United States

PHD :: Statistics

Louisiana State University

United States

BSC :: Mathematics

Publications

Lukas M Weber, Heena R Divecha, Matthew N Tran, Sang Ho Kwon, Abby Spangler, Kelsey D Montgomery, Madhavi Tippani, Rahul Bharadwaj, Joel E Kleinman, Stephanie Cerceo Page, Thomas M Hyde, Leonardo Collado-Torres, Kristen R Maynard, Keri Martinowich, Stephanie C Hicks
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 12 (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede C A da Conceição, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: enhancing omic data analyses. Nature methods 21 (7) (2024)
Bo-Yi Guo, Wodan Ling, Sang Ho Kwon, Pratibha Panwar, Shila Ghazanfar, Keri Martinowich, Stephanie C Hicks
Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities. ArXiv (2024)
Sean K Maden, Louise A Huuki-Myers, Sang Ho Kwon, Leonardo Collado-Torres, Kristen R Maynard, Stephanie C Hicks
lute : estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew N Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard, null null
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science (New York, N.Y.) 384 (6698) (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J Eagles, Daianna Gonzalez-Padilla, Sean K Maden, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Sean K Maden, Nicholas J Eagles, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Sean K Maden, Louise A Huuki-Myers, Sang Ho Kwon, Leonardo Collado-Torres, Kristen R Maynard, Stephanie C Hicks
lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv : the preprint server for biology (2024)
Lukas M Weber, Heena R Divecha, Matthew N Tran, Sang Ho Kwon, Abby Spangler, Kelsey D Montgomery, Madhavi Tippani, Rahul Bharadwaj, Joel E Kleinman, Stephanie Cerceo Page, Thomas M Hyde, Leonardo Collado-Torres, Kristen R Maynard, Keri Martinowich, Stephanie C Hicks
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 12 (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede C A da Conceição, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: enhancing omic data analyses. Nature methods (2024)
Michael S Totty, Stephanie C Hicks, Bo-Yi Guo
SpotSweeper: spatially-aware quality control for spatial transcriptomics. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
Lukas M Weber, Heena R Divecha, Matthew N Tran, Sang Ho Kwon, Abby Spangler, Kelsey D Montgomery, Madhavi Tippani, Rahul Bharadwaj, Joel E Kleinman, Stephanie Cerceo Page, Thomas M Hyde, Leonardo Collado-Torres, Kristen R Maynard, Keri Martinowich, Stephanie C Hicks
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 12 (2024)
Robert A Phillips, Seyun Oh, Svitlana V Bach, Yufeng Du, Ryan A Miller, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Stephanie Cerceo Page, Keri Martinowich
Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species. bioRxiv : the preprint server for biology (2024)
Lukas M Weber, Heena R Divecha, Matthew N Tran, Sang Ho Kwon, Abby Spangler, Kelsey D Montgomery, Madhavi Tippani, Rahul Bharadwaj, Joel E Kleinman, Stephanie Cerceo Page, Thomas M Hyde, Leonardo Collado-Torres, Kristen R Maynard, Keri Martinowich, Stephanie C Hicks
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 12 (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J Eagles, Daianna Gonzalez-Padilla, Sean K Maden, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Sean K Maden, Louise A Huuki-Myers, Sang Ho Kwon, Leonardo Collado-Torres, Kristen R Maynard, Stephanie C Hicks
lute : estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv : the preprint server for biology (2024)
Jianing Yao, Jinglun Yu, Brian S Caffo, Stephanie Cerceo Page, Keri Martinowich, Stephanie C Hicks
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies. bioRxiv : the preprint server for biology (2024)
Robert A Phillips, Seyun Oh, Svitlana V Bach, Yufeng Du, Ryan A Miller, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Stephanie Cerceo Page, Keri Martinowich
Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species. bioRxiv : the preprint server for biology (2024)
Erik D Nelson, Madhavi Tippani, Anthony D Ramnauth, Heena R Divecha, Ryan A Miller, Nicholas J Eagles, Elizabeth A Pattie, Sang Ho Kwon, Svitlana V Bach, Uma M Kaipa, Jianing Yao, Joel E Kleinman, Leonardo Collado-Torres, Shizhong Han, Kristen R Maynard, Thomas M Hyde, Keri Martinowich, Stephanie Cerceo Page, Stephanie C Hicks
An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J Eagles, Daianna Gonzalez-Padilla, Sean K Maden, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew N Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard, null null
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science (New York, N.Y.) 384 (6698) (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede C A da Conceição, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: enhancing omic data analyses. Nature methods (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Sean K Maden, Nicholas J Eagles, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew N Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard, null null
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science (New York, N.Y.) 384 (6698) (2024)
Michael S Totty, Stephanie C Hicks, Bo-Yi Guo
SpotSweeper: spatially-aware quality control for spatial transcriptomics. bioRxiv : the preprint server for biology (2024)
Jianing Yao, Jinglun Yu, Brian S Caffo, Stephanie Cerceo Page, Keri Martinowich, Stephanie C Hicks
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede C A da Conceição, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: enhancing omic data analyses. Nature methods 21 (7) (2024)
Robert A Phillips, Seyun Oh, Svitlana V Bach, Yufeng Du, Ryan A Miller, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Stephanie Cerceo Page, Keri Martinowich
Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species. bioRxiv : the preprint server for biology (2024)
Erik D Nelson, Madhavi Tippani, Anthony D Ramnauth, Heena R Divecha, Ryan A Miller, Nicholas J Eagles, Elizabeth A Pattie, Sang Ho Kwon, Svitlana V Bach, Uma M Kaipa, Jianing Yao, Joel E Kleinman, Leonardo Collado-Torres, Shizhong Han, Kristen R Maynard, Thomas M Hyde, Keri Martinowich, Stephanie Cerceo Page, Stephanie C Hicks
An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew N Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard, null null
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science (New York, N.Y.) 384 (6698) (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J Eagles, Daianna Gonzalez-Padilla, Sean K Maden, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Alexander Popescu, Caitlin Ottaway, Kaitlyn Ford, Taylor Wintler Patterson, Ashley M Ingiosi, Elizabeth Medina, Stephanie C Hicks, Kristan Singletary, Lucia Peixoto
Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex. bioRxiv : the preprint server for biology (2024)
Jianing Yao, Jinglun Yu, Brian S Caffo, Stephanie Cerceo Page, Keri Martinowich, Stephanie C Hicks
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
Malte Daniel Luecken, Scott A Gigante, Daniel Burkhardt, Robrecht Cannoodt, Daniel Strobl, Nikolay Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael Vinyard, Daniel Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J Otto, Michal Klein, Olga Botvinnik, Louise Deconinck, Kai Waldrant, Bastian Rieck, Constantin Ahlmann-Eltze, Eduardo da Veiga Beltrame, Andrew Benz, Carmen Bravo González-Blas, Ann Chen, Benjamin DeMeo, Can Ergen, Swann Floc'hlay, Adam Gayoso, Stephanie C Hicks, Yuge Ji, Vitalii Kleshchevnikov, Gioele La Manno, Maximilian Lombardo, Romain Lopez, Dario Righelli, Hirak Sarkar, Valentine Svensson, Alexander Tong, Galen Xing, Chenling Xu, Jonathan Bloom, Angela Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Joachim Theis, Smita Krishnaswamy
Defining and benchmarking open problems in single-cell analysis. Research square (2024)
Louise A Huuki-Myers, Kelsey D Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J Eagles, Daianna Gonzalez-Padilla, Sean K Maden, Joel E Kleinman, Thomas M Hyde, Stephanie C Hicks, Kristen R Maynard, Leonardo Collado-Torres
Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv : the preprint server for biology (2024)
Kaitlyn Ford, Elena Zuin, Dario Righelli, Elizabeth Medina, Hannah Schoch, Kristan Singletary, Christine M Muheim, Marcos G Frank, Stephanie C Hicks, Davide Risso, Lucia Peixoto
A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex. bioRxiv : the preprint server for biology (2023)
Lukas M Weber, Arkajyoti Saha, Abhirup Datta, Kaspar D Hansen, Stephanie C Hicks
nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes. Nature communications 14 (1) (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. Biological imaging 3 (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. Biological imaging 3 (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. Biological imaging 3 (2023)
Wenpin Hou, Zhicheng Ji, Zeyu Chen, E John Wherry, Stephanie C Hicks, Hongkai Ji
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nature communications 14 (1) (2023)
Albert Kuo, Kaspar D Hansen, Stephanie C Hicks
Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data. Biostatistics (Oxford, England) (2023)
Madhavi Tippani, Heena R Divecha, Joseph L Catallini, Sang H Kwon, Lukas M Weber, Abby Spangler, Andrew E Jaffe, Thomas M Hyde, Joel E Kleinman, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Stephanie C Page, Kristen R Maynard
VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological imaging 3 (2023)
Beril Erdogdu, Ales Varabyou, Stephanie C Hicks, Steven L Salzberg, Mihaela Pertea
Detecting differential transcript usage in complex diseases with SPIT. bioRxiv : the preprint server for biology (2023)
Madhavi Tippani, Heena R Divecha, Joseph L Catallini, Sang H Kwon, Lukas M Weber, Abby Spangler, Andrew E Jaffe, Thomas M Hyde, Joel E Kleinman, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Stephanie C Page, Kristen R Maynard
VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological imaging 3 (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. bioRxiv : the preprint server for biology (2023)
Madhavi Tippani, Heena R Divecha, Joseph L Catallini, Sang H Kwon, Lukas M Weber, Abby Spangler, Andrew E Jaffe, Thomas M Hyde, Joel E Kleinman, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Stephanie C Page, Kristen R Maynard
VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological imaging 3 (2023)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew Nguyen Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard
Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex. bioRxiv : the preprint server for biology (2023)
Anthony D Ramnauth, Madhavi Tippani, Heena R Divecha, Alexis R Papariello, Ryan A Miller, Elizabeth A Pattie, Joel E Kleinman, Kristen R Maynard, Leonardo Collado-Torres, Thomas M Hyde, Keri Martinowich, Stephanie C Hicks, Stephanie Cerceo Page
Spatially-resolved transcriptomics of human dentate gyrus across postnatal lifespan reveals heterogeneity in markers for proliferation, extracellular matrix, and neuroinflammation. bioRxiv : the preprint server for biology (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. bioRxiv : the preprint server for biology (2023)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew Nguyen Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard
Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex. bioRxiv : the preprint server for biology (2023)
Bo-Yi Guo, Louise A Huuki-Myers, Melissa Grant-Peters, Leonardo Collado-Torres, Stephanie C Hicks
escheR: unified multi-dimensional visualizations with Gestalt principles. Bioinformatics advances 3 (1) (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. bioRxiv : the preprint server for biology (2023)
Bo-Yi Guo, Louise A Huuki-Myers, Melissa Grant-Peters, Leonardo Collado-Torres, Stephanie C Hicks
escheR: unified multi-dimensional visualizations with Gestalt principles. Bioinformatics advances 3 (1) (2023)
Bo-Yi Guo, Louise A Huuki-Myers, Melissa Grant-Peters, Leonardo Collado-Torres, Stephanie C Hicks
escheR: unified multi-dimensional visualizations with Gestalt principles. Bioinformatics advances 3 (1) (2023)
Madhavi Tippani, Heena R Divecha, Joseph L Catallini, Sang H Kwon, Lukas M Weber, Abby Spangler, Andrew E Jaffe, Thomas M Hyde, Joel E Kleinman, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Stephanie C Page, Kristen R Maynard
VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological imaging 3 (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. Biological imaging 3 (2023)
Erik D Nelson, Kristen R Maynard, Kyndall R Nicholas, Matthew Nguyen Tran, Heena R Divecha, Leonardo Collado-Torres, Stephanie C Hicks, Keri Martinowich
Activity-regulated gene expression across cell types of the mouse hippocampus. Hippocampus (2023)
Bo-Yi Guo, Louise A Huuki-Myers, Melissa Grant-Peters, Leonardo Collado-Torres, Stephanie C Hicks
escheR: unified multi-dimensional visualizations with Gestalt principles. Bioinformatics advances 3 (1) (2023)
Louise A Huuki-Myers, Abby Spangler, Nicholas J Eagles, Kelsey D Montgomery, Sang Ho Kwon, Bo-Yi Guo, Melissa Grant-Peters, Heena R Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B Nguyen, Prashanthi Ravichandran, Matthew Nguyen Tran, Arta Seyedian, null null, Thomas M Hyde, Joel E Kleinman, Alexis J Battle, Stephanie Cerceo Page, Mina Ryten, Stephanie C Hicks, Keri Martinowich, Leonardo Collado-Torres, Kristen R Maynard
Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex. bioRxiv : the preprint server for biology (2023)
Bo-Yi Guo, Stephanie C Hicks
escheR: Unified multi-dimensional visualizations with Gestalt principles. bioRxiv : the preprint server for biology (2023)
Bo-Yi Guo, Louise A Huuki-Myers, Melissa Grant-Peters, Leonardo Collado-Torres, Stephanie C Hicks
escheR: unified multi-dimensional visualizations with Gestalt principles. Bioinformatics advances 3 (1) (2023)
Chaichontat Sriworarat, Annie B Nguyen, Nicholas J Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R Maynard, Stephanie C Hicks
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments. bioRxiv : the preprint server for biology (2023)
Dario Righelli, Lukas M Weber, Helena Lucia Crowell, Brenda Pardo, Leonardo Collado-Torres, Shila Ghazanfar, Aaron T L Lun, Stephanie C Hicks, Davide Risso
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics (Oxford, England) 38 (11) (2022)
Lukas M Weber, Ariel A Hippen, Peter F Hickey, Kristofer C Berrett, Jason Gertz, Jennifer Anne Doherty, Casey S Greene, Stephanie C Hicks
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. GigaScience 10 (9) (2022)
Yi Wang, Stephanie C Hicks, Kaspar D Hansen
Addressing the mean-correlation relationship in co-expression analysis. PLoS computational biology 18 (3) (2022)
Benjamin J Heil, Michael M Hoffman, Florian Markowetz, Su-In Lee, Casey S Greene, Stephanie C Hicks
Reproducibility standards for machine learning in the life sciences. Nature methods 18 (10) (2021)
Wenpin Hou, Zhicheng Ji, Zeyu Chen, E John Wherry, Stephanie C Hicks, Hongkai Ji
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. bioRxiv : the preprint server for biology (2021)
Ariel A Hippen, Matias M Falco, Lukas M Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vaharautio, Casey S Greene, Stephanie C Hicks
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS computational biology 17 (8) (2021)
Kristen R Maynard, Leonardo Collado-Torres, Lukas M Weber, Cedric Uytingco, Brianna K Barry, Stephen R Williams, Joseph L Catallini, Matthew Nguyen Tran, Zachary Besich, Madhavi Tippani, Jennifer Chew, Yifeng Yin, Joel E Kleinman, Thomas M Hyde, Nikhil Rao, Stephanie C Hicks, Keri Martinowich, Andrew E Jaffe
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature neuroscience 24 (3) (2021)
Stephanie C Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
mbkmeans: Fast clustering for single cell data using mini-batch k-means. PLoS computational biology 17 (1) (2021)
Ruizhu Huang, Charlotte Soneson, Felix G M Ernst, Kevin C Rue-Albrecht, Guangchuang Yu, Stephanie C Hicks, Mark D Robinson
TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research 9 (2020)
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, Kevin Christophe Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike L Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C Hicks
Orchestrating single-cell analysis with Bioconductor. Nature methods 17 (2) (2019)
Keegan Korthauer, Patrick K Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J Alm, Stephanie C Hicks
A practical guide to methods controlling false discoveries in computational biology. Genome biology 20 (1) (2019)

Stephanie C Hicks.css-eqlu8i{font-size:small;padding-left:4px;} (Stephanie Hicks)

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Stephanie C Hicks (Stephanie Hicks)