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Stephanie C. Hicks

johns hopkins university

44H-index
306Paper Count
1.1WCitation Count
Published Papers 55
Publication Date
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Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
errGENOME RESEARCH
IF5.5
err2025-12-01
err1
PREAI
errWang, An; Hicks, Stephanie; Geman, Donald; Younes, Laurent
errShare
errSave
Spherical PCA: a transparent and scalable approach to quantifying the Waddington Landscape in single-cell RNA-seq data
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errYuan, Long; Li, Xuyang; Hicks, Stephanie C.; Taube, Janis M.; Szalay, Alexander S.
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errSave
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
errScience Advances
IF12.5
err2025-09-17
err0
errOAAI
errMichael S. Totty; Rita Cervera Juanes; Svitlana V. Bach; Lamya Ben Ameur; Madeline R. Valentine; Evan Simons; McKenna D. Romac; Hoa Trinh; Krystal Henderson; Ishbel Del Rosario; Madhavi Tippani; Ryan A. Miller; Joel E. Kleinman; Stephanie Cerceo Page; Arpiar Saunders; Thomas M. Hyde; Keri Martinowich; Stephanie C. Hicks; Vincent D. Costa
errShare
errSave
Spatial mutual nearest neighbors for spatial transcriptomics data
errBIOINFORMATICS
IF5.4
err2025-08-01
err1
errOAAI
errZhou, Haowen; Panwar, Pratibha; Guo, Boyi; Hallinan, Caleb; Ghazanfar, Shila; Hicks, Stephanie C.
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errSave
An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus
errNature Neuroscience
IF20
err2025-07-30
err0
errOAAI
errJacqueline R. Thompson; 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; Christine Hou; Joel E. Kleinman; Leonardo Collado-Torres; Shizhong Han; Kristen R. Maynard; Thomas M. Hyde; Keri Martinowich; Stephanie C. Page; Stephanie C. Hicks
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errSave
Transcriptional Dynamics of Sleep Deprivation and Subsequent Recovery Sleep in the Male Mouse Cortex
errSLEEP
IF4.9
err2025-05-19
err0
PREAI
errOttaway, Caitlin; Popescu, Alexander; Ford, Kaitlyn; Patterson, Taylor; Ingiosi, Ashley; Medina, Elizabeth; Hicks, Stephanie; Singletary, Kristan; Peixoto, Lucia
errShare
errSave
lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression
errBMC GENOMICS
IF3.7
err2025-05-01
err0
errOAAI
errMaden, Sean K.; Huuki-Myers, Louise A.; Kwon, Sang Ho; Collado-Torres, Leonardo; Maynard, Kristen R.; Hicks, Stephanie C.
errShare
errSave
Missing cell types in single-cell references impact deconvolution of bulk data but are detectable
errGENOME BIOLOGY
IF9.4
err2025-04-07
err0
errOAAI
errIvich, Adriana; Davidson, Natalie R.; Grieshober, Laurie; Li, Weishan; Hicks, Stephanie C.; Doherty, Jennifer A.; Greene, Casey S.
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errSave
Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex
errGENOME BIOLOGY
IF9.4
err2025-04-07
err3
errOAAI
errHuuki-Myers, Louise A.; Montgomery, Kelsey D.; Kwon, Sang Ho; Cinquemani, Sophia; Eagles, Nicholas J.; Gonzalez-Padilla, Daianna; Maden, Sean K.; Kleinman, Joel E.; Hyde, Thomas M.; Hicks, Stephanie C.; Maynard, Kristen R.; Collado-Torres, Leonardo
errShare
errSave
Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
errCELL REPORTS
IF6.9
err2025-02-01
err0
errOAAI
errRamnauth, Anthony D.; Tippani, Madhavi; Divecha, Heena R.; Papariello, Alexis R.; Miller, Ryan A.; Nelson, Erik D.; Thompson, Jacqueline R.; Pattie, Elizabeth A.; Kleinman, Joel E.; Maynard, Kristen R.; Collado-Torres, Leonardo; Hyde, Thomas M.; Martinowich, Keri; Hicks, Stephanie C.; Page, Stephanie C.
errShare
errSave
Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species
errISCIENCE
IF4.1
err2025-02-01
err1
errOAAI
errPhillips III, Robert A.; Oh, Seyun; Bach, Svitlana V.; Du, Yufeng; Miller, Ryan A.; Kleinman, Joel E.; Hyde, Thomas M.; Hicks, Stephanie C.; Page, Stephanie C.
errShare
errSave
SPATIAL-MOLECULAR SEX DIFFERENCES IN THE HUMAN VENTROMEDIAL AND ARCUATE HYPOTHALAMUS
errEUROPEAN NEUROPSYCHOPHARMACOLOGY
IF6.7
err2024-10-01
err0
PREAI
errMulvey, Bernard; Wang, Yi; Divecha, Heena R.; Bach, Svitlana; Montgomery, Kelsey D.; Cinquemani, Sophia; Du, Yufeng; Miller, Ryan; Kleinman, Joel E.; Page, Stephanie Cerceo; Hyde, Thomas M.; Hicks, Stephanie C.; Hansen, Kasper D.; Martinowich, Keri; Maynard, Kristen R.
errShare
errSave
The tidyomics ecosystem: enhancing omic data analyses
errNATURE METHODS
IF32.1
err2024-06-14
err2
PREAI
errHutchison, William J.; Keyes, Timothy J.; Crowell, Helena L.; Serizay, Jacques; Soneson, Charlotte; Davis, Eric S.; Sato, Noriaki; Moses, Lambda; Tarlinton, Boyd; Nahid, Abdullah A.; Kosmac, Miha; Clayssen, Quentin; Yuan, Victor; Mu, Wancen; Park, Ji-Eun; Mamede, Izabela; Ryu, Min Hyung; Axisa, Pierre-Paul; Paiz, Paulina; Poon, Chi-Lam; Tang, Ming; Gottardo, Raphael; Morgan, Martin; Lee, Stuart; Lawrence, Michael; Hicks, Stephanie C.; Nolan, Garry P.; Davis, Kara L.; Papenfuss, Anthony T.; Love, Michael I.; Mangiola, Stefano
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errSave
Partnering With Authors to Enhance Reproducibility at JASA
errJOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
IF3
err2024-04-25
err1
PREAI
errWrobel, Julia; Hector, Emily C.; Crawford, Lorin; Mcgowan, Lucy D'Agostino; da Silva, Natalia; Goldsmith, Jeff; Hicks, Stephanie; Kane, Michael; Lee, Youjin; Mayrink, Vinicius; Paciorek, Christopher J.; Usher, Therri; Wolfson, Julian
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errSave
Detecting differential transcript usage in complex diseases with SPIT
errCELL REPORTS METHODS
IF4.5
err2024-03-01
err0
errOAAI
errErdogdu, Beril; Varabyou, Ales; Hicks, Stephanie C.; Salzberg, Steven L.; Pertea, Mihaela
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errSave
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
errELIFE
IF0
err2024-01-24
err7
errOAAI
errWeber, Lukas M.; Divecha, Heena R.; Tran, Matthew N.; Kwon, Sang Ho; Spangler, Abby; Montgomery, Kelsey D.; Tippani, Madhavi; Bharadwaj, Rahul; Kleinman, Joel E.; Page, Stephanie C.; Hyde, Thomas M.; Collado-Torres, Leonardo; Maynard, Kristen R.; Martinowich, Keri; Hicks, Stephanie C.
errShare
errSave
Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
errGENOME BIOLOGY
IF9.4
err2023-12-14
err13
errOAAI
errMaden, Sean K.; Kwon, Sang Ho; Huuki-Myers, Louise A.; Collado-Torres, Leonardo; Hicks, Stephanie C.; Maynard, Kristen R.
errShare
errSave
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples
errNATURE COMMUNICATIONS
IF15.7
err2023-11-10
err13
errOAAI
errHou, Wenpin; Ji, Zhicheng; Chen, Zeyu; Wherry, E. John; Hicks, Stephanie C.; Ji, Hongkai
errShare
errSave
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
errGENOME BIOLOGY
IF9.4
err2023-10-20
err5
errOAAI
errHippen, Ariel A.; Omran, Dalia K.; Weber, Lukas M.; Jung, Euihye; Drapkin, Ronny; Doherty, Jennifer A.; Hicks, Stephanie C.; Greene, Casey S.
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errSave
Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
errGENOME BIOLOGY
IF9.4
err2023-10-16
err2
errOAAI
errHuuki-Myers, Louise A.; Montgomery, Kelsey D.; Kwon, Sang Ho; Page, Stephanie C.; Hicks, Stephanie C.; Maynard, Kristen R.; Collado-Torres, Leonardo
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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Richard A. Gibbs
H-index: 190 · Papers: 1.3K
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Steven L. Salzberg
H-index: 160 · Papers: 600
M
Michael Diamond
H-index: 160 · Papers: 1.5K
D
Donna M. Muzny
H-index: 156 · Papers: 693
D
David A. Wheeler
H-index: 147 · Papers: 602
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