Stephanie Hicks
@stephaniehicks.bsky.social
Associate Professor of Biostatistics and Biomedical Engineering at Johns Hopkins. stephaniehicks.com
I am very excited to share this book! It has been so much to collaborate on the project. We hope you find it useful!
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 10:11 PM
I am very excited to share this book! It has been so much to collaborate on the project. We hope you find it useful!
Today I am starting a weekly post titled "Autism: The Evidence". I hope it helps someone fight the colossal wave of misinformation that is drowning us. Part 1: I heard Autism prevalence has gone up. Is that true? If so why?
November 15, 2025 at 9:04 AM
Very excited to share that Department of Biomedical Engineering @hopkinsengineer.bsky.social is hiring for open rank tenure-track faculty in #Biomedical #DataScience!
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 6, 2025 at 6:20 AM
Very excited to share that Department of Biomedical Engineering @hopkinsengineer.bsky.social is hiring for open rank tenure-track faculty in #Biomedical #DataScience!
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
Reposted by Stephanie Hicks
Adding that you are still encouraged to apply even if you can't hit the Nov 15th date! It's just the date we plan to start reviewing, but we'll definitely continue reviewing for some time.
October 31, 2025 at 3:23 PM
Adding that you are still encouraged to apply even if you can't hit the Nov 15th date! It's just the date we plan to start reviewing, but we'll definitely continue reviewing for some time.
Come work with me! @jhubiostat.bsky.social is hiring for a tenure-track Assistant Professor position 🥳 Apps due Nov 15
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 31, 2025 at 6:58 AM
Come work with me! @jhubiostat.bsky.social is hiring for a tenure-track Assistant Professor position 🥳 Apps due Nov 15
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/176686
🧪🧬💻🧠 #StatsSky #WomenInSTEM
Looking for postdoctoral opportunities? ✅
Interested in working with me or any of the 30 other amazing @jhubiostat.bsky.social faculty? ✅
If yes, I encourage you to apply to our postdoc program in #DataScience and #AI in #Health and #Medicine!
🔗 apply.interfolio.com/174430
🧪🧬💻🧠
Interested in working with me or any of the 30 other amazing @jhubiostat.bsky.social faculty? ✅
If yes, I encourage you to apply to our postdoc program in #DataScience and #AI in #Health and #Medicine!
🔗 apply.interfolio.com/174430
🧪🧬💻🧠
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 31, 2025 at 6:40 AM
Looking for postdoctoral opportunities? ✅
Interested in working with me or any of the 30 other amazing @jhubiostat.bsky.social faculty? ✅
If yes, I encourage you to apply to our postdoc program in #DataScience and #AI in #Health and #Medicine!
🔗 apply.interfolio.com/174430
🧪🧬💻🧠
Interested in working with me or any of the 30 other amazing @jhubiostat.bsky.social faculty? ✅
If yes, I encourage you to apply to our postdoc program in #DataScience and #AI in #Health and #Medicine!
🔗 apply.interfolio.com/174430
🧪🧬💻🧠
This was a really fantastic collaboration! Congratulations @mictott.bsky.social Rita Cervera Juanes,
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
Very excited to share my second postdoc, now out in Science Advances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/13 www.science.org/doi/10.1126/...
Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates
Specialized cell types and links to psychiatric disorders are revealed by genetic mapping of primate amygdala neurons.
www.science.org
September 18, 2025 at 1:17 AM
This was a really fantastic collaboration! Congratulations @mictott.bsky.social Rita Cervera Juanes,
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
@svitlanabach.bsky.social and all co-authors! 🧪🧬💻🧠
Congratulations to @prashanthi-ravi.bsky.social @svitlana-bach.bsky.social & all co-authors! Wonderful collab btw @alexisbattle.bsky.social and @martinowk.bsky.social @kr-maynard.bsky.social spatially profiling human nucleus accumbens 🧠 #TeamScience 🧪 🧬 🖥️
Thank you #NIH #NIDA for generous funding 👏
Thank you #NIH #NIDA for generous funding 👏
(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium
September 17, 2025 at 10:56 AM
Congratulations to @prashanthi-ravi.bsky.social @svitlana-bach.bsky.social & all co-authors! Wonderful collab btw @alexisbattle.bsky.social and @martinowk.bsky.social @kr-maynard.bsky.social spatially profiling human nucleus accumbens 🧠 #TeamScience 🧪 🧬 🖥️
Thank you #NIH #NIDA for generous funding 👏
Thank you #NIH #NIDA for generous funding 👏
Thank you for the invitation @sib.swiss! I really enjoyed talking with everyone and I learned a lot over the last few days. I highly recommend this conference to anyone working in Bioinformatics. 🧬🧪💻
Our invited speakers for the parallel session on ‘Computational methods for single-cell and spatial omics’ is @stephaniehicks.bsky.social from Johns Hopkins Bloomberg School of Public Health, USA. Session is chaired by @marianna-raps.bsky.social and @julienroux.bsky.social. #bc2basel
September 10, 2025 at 7:08 PM
Thank you for the invitation @sib.swiss! I really enjoyed talking with everyone and I learned a lot over the last few days. I highly recommend this conference to anyone working in Bioinformatics. 🧬🧪💻
Congratulations @kinnaryshah.bsky.social @mictott.bsky.social @svitlanabach.bsky.social & all co-authors! Wonderful collab btw @jhubiostat.bsky.social @jhu.edu and @lieberinstitute.bsky.social spatially profiling human dACC 🧠 #TeamScience 🧪 🧬 🖥️
Thank you #NIDA #NIMH for generous funding & support 👏
Thank you #NIDA #NIMH for generous funding & support 👏
so excited to share that our preprint characterizing the dorsal anterior cingulate cortex in post-mortem human brain from @lieberinstitute.bsky.social is out! we integrated matched SRT and snRNA-seq data to investigate agranularity and von Economo neurons
July 28, 2025 at 2:29 PM
Congratulations @kinnaryshah.bsky.social @mictott.bsky.social @svitlanabach.bsky.social & all co-authors! Wonderful collab btw @jhubiostat.bsky.social @jhu.edu and @lieberinstitute.bsky.social spatially profiling human dACC 🧠 #TeamScience 🧪 🧬 🖥️
Thank you #NIDA #NIMH for generous funding & support 👏
Thank you #NIDA #NIMH for generous funding & support 👏
Excited to share a blogpost summarizing challenges, opportunities & reflections from a course @hopkinsengineer.bsky.social co-taught with @alexisbattle.bsky.social (and huge support from Seraj Grimes!) at the intersection of #deeplearning #genetics #genomics 🧪 🧬 💻
stephaniehicks.com/blog/course-...
stephaniehicks.com/blog/course-...
Translating the face-paced world of research in deep learning and genetics and genomics to the classroom – Stephanie C. Hicks, PhD
stephaniehicks.com
July 8, 2025 at 11:34 PM
Excited to share a blogpost summarizing challenges, opportunities & reflections from a course @hopkinsengineer.bsky.social co-taught with @alexisbattle.bsky.social (and huge support from Seraj Grimes!) at the intersection of #deeplearning #genetics #genomics 🧪 🧬 💻
stephaniehicks.com/blog/course-...
stephaniehicks.com/blog/course-...
Reposted by Stephanie Hicks
Benchmarking study of single-cell feature selection finds deviance to be an effective criterion: doi.org/10.1093/bib/... . Try it yourself with our ( @kstreet.bsky.social @stephaniehicks.bsky.social @davi1893.bsky.social ) scry package @bioconductor.bsky.social : doi.org/doi:10.18129... #genomics
Characterizing efficient feature selection for single-cell expression analysis
Abstract. Unsupervised feature selection is a critical step for efficient and accurate analysis of single-cell RNA-seq data. Previous benchmarks used two d
doi.org
July 1, 2025 at 8:56 PM
Benchmarking study of single-cell feature selection finds deviance to be an effective criterion: doi.org/10.1093/bib/... . Try it yourself with our ( @kstreet.bsky.social @stephaniehicks.bsky.social @davi1893.bsky.social ) scry package @bioconductor.bsky.social : doi.org/doi:10.18129... #genomics
Reposted by Stephanie Hicks
Big thanks to everyone who made #GBCC2025 a fantastic week of science, collaboration, and community!
Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬
@galaxyproject.bsky.social @bioconductor.bsky.social
Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬
@galaxyproject.bsky.social @bioconductor.bsky.social
July 1, 2025 at 1:14 PM
Big thanks to everyone who made #GBCC2025 a fantastic week of science, collaboration, and community!
Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬
@galaxyproject.bsky.social @bioconductor.bsky.social
Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬
@galaxyproject.bsky.social @bioconductor.bsky.social
Very excited to see this important work out led by the talented @mictott.bsky.social @boyiguo.bsky.social @jhubiostat.bsky.social! 🧪🧬🖥️
🚨 New paper published in @natmethods.nature.com!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
nature.com
June 6, 2025 at 5:34 PM
Very excited to see this important work out led by the talented @mictott.bsky.social @boyiguo.bsky.social @jhubiostat.bsky.social! 🧪🧬🖥️
Looking forward to visit Icahn School of Medicine at Mount Sinai tomorrow morning. If you are around NYC and are interested in single cell / spatial genomics, the talk starts at 10am. Hope you see you there! 🧪🧬🖥️
events.mountsinaihealth.org/event/geneti...
events.mountsinaihealth.org/event/geneti...
Genetics and Genomic Sciences External Seminar Series | Stephanie Hicks, MA, PhD
events.mountsinaihealth.org
June 3, 2025 at 4:52 PM
Looking forward to visit Icahn School of Medicine at Mount Sinai tomorrow morning. If you are around NYC and are interested in single cell / spatial genomics, the talk starts at 10am. Hope you see you there! 🧪🧬🖥️
events.mountsinaihealth.org/event/geneti...
events.mountsinaihealth.org/event/geneti...
Reposted by Stephanie Hicks
Kinnary Shah is a fourth-year PhD candidate and co-president of the Biostats Student Org. Learn more about Kinnary and two of her ongoing research projects, one with the @lieberinstitute.bsky.social, and one with @stephaniehicks.bsky.social, on our website:
publichealth.jhu.edu/departments/...
publichealth.jhu.edu/departments/...
May 28, 2025 at 4:17 PM
Kinnary Shah is a fourth-year PhD candidate and co-president of the Biostats Student Org. Learn more about Kinnary and two of her ongoing research projects, one with the @lieberinstitute.bsky.social, and one with @stephaniehicks.bsky.social, on our website:
publichealth.jhu.edu/departments/...
publichealth.jhu.edu/departments/...
New paper out in @genomeresearch.bsky.social on using contrastive self-supervised learning for spatial domain detection with multi-omics data! Huge congratulations to Jianing Yao and coauthors Jinglun Yu, Brian Caffo Stephanie Page & @martinowk.bsky.social! 🧬 🖥️ 🧪
doi.org/10.1101/gr.2...
doi.org/10.1101/gr.2...
May 21, 2025 at 1:14 PM
New paper out in @genomeresearch.bsky.social on using contrastive self-supervised learning for spatial domain detection with multi-omics data! Huge congratulations to Jianing Yao and coauthors Jinglun Yu, Brian Caffo Stephanie Page & @martinowk.bsky.social! 🧬 🖥️ 🧪
doi.org/10.1101/gr.2...
doi.org/10.1101/gr.2...
Reposted by Stephanie Hicks
New article is out! Sleep deprivation is bad for the brain transcriptome, but how quickly can a little sleep reverse this effect? A team effort and fun collaboration with @stephaniehicks.bsky.social (a thread) pubmed.ncbi.nlm.nih.gov/40315180/
a cartoon character from the movie monsters inc is asking is it hard to stay awake ? nap time .
ALT: a cartoon character from the movie monsters inc is asking is it hard to stay awake ? nap time .
media.tenor.com
May 6, 2025 at 4:51 PM
New article is out! Sleep deprivation is bad for the brain transcriptome, but how quickly can a little sleep reverse this effect? A team effort and fun collaboration with @stephaniehicks.bsky.social (a thread) pubmed.ncbi.nlm.nih.gov/40315180/
Reposted by Stephanie Hicks
Congratulations to Malone Center affiliate member @stephaniehicks.bsky.social on this distinction from @amstatnews.bsky.social!
Stephanie Hicks named fellow of the American Statistical Association
Hicks was recognized for her professional contributions, leadership, and commitment to the field of statistics.
malonecenter.jhu.edu
May 8, 2025 at 2:10 PM
Congratulations to Malone Center affiliate member @stephaniehicks.bsky.social on this distinction from @amstatnews.bsky.social!
Reposted by Stephanie Hicks
. @stephaniehicks.bsky.social giving a master class on spatial genomics analysis - normalization and qc are essential to reveal the underlying biology! #bog25
May 8, 2025 at 5:54 PM
. @stephaniehicks.bsky.social giving a master class on spatial genomics analysis - normalization and qc are essential to reveal the underlying biology! #bog25
I really enjoyed this article: The synaptic hypothesis of schizophrenia version III: a master mechanism! 🧪🧠 #neuroskyence
www.nature.com/articles/s41...
h/t @boyiguo.bsky.social
www.nature.com/articles/s41...
h/t @boyiguo.bsky.social
The synaptic hypothesis of schizophrenia version III: a master mechanism - Molecular Psychiatry
Molecular Psychiatry - The synaptic hypothesis of schizophrenia version III: a master mechanism
www.nature.com
April 24, 2025 at 12:08 PM
I really enjoyed this article: The synaptic hypothesis of schizophrenia version III: a master mechanism! 🧪🧠 #neuroskyence
www.nature.com/articles/s41...
h/t @boyiguo.bsky.social
www.nature.com/articles/s41...
h/t @boyiguo.bsky.social
Reposted by Stephanie Hicks
We are thrilled to announce that @dattascientist.bsky.social and @stephaniehicks.bsky.social have been elected Fellows of the American Statistical Association! 🎉 This prestigious honor recognizes outstanding contributions to statistical science. Congrats Abhi & Stephanie! 👏 @amstatnews.bsky.social
April 22, 2025 at 1:18 PM
We are thrilled to announce that @dattascientist.bsky.social and @stephaniehicks.bsky.social have been elected Fellows of the American Statistical Association! 🎉 This prestigious honor recognizes outstanding contributions to statistical science. Congrats Abhi & Stephanie! 👏 @amstatnews.bsky.social
Reposted by Stephanie Hicks
April is #Autism Awareness Month. This is a month to accept, understand and love those in the Autism Spectrum. Above all accepting that someone is different and respecting their differences is the most important thing we can do. Here are some facts to help understand (a thread):
April 21, 2025 at 5:39 PM
April is #Autism Awareness Month. This is a month to accept, understand and love those in the Autism Spectrum. Above all accepting that someone is different and respecting their differences is the most important thing we can do. Here are some facts to help understand (a thread):
Rafa has come out swinging this morning 😂
April 11, 2025 at 1:26 PM
Rafa has come out swinging this morning 😂
Always excited to have @rafalab.bsky.social visit Hopkins! He’s talk about statistical challenges in single single and spatial omics. 🧪🧬🖥️
April 11, 2025 at 1:13 PM
Always excited to have @rafalab.bsky.social visit Hopkins! He’s talk about statistical challenges in single single and spatial omics. 🧪🧬🖥️