Annika Vannan
@annikavannan.bsky.social
Postdoc @tgenresearch.bsky.social in the Banovich lab
Reposted by Annika Vannan
Great new work led by Aaron Kwok from @davisjmcc.bsky.social’s group. A tool to “denoise” contaminating transcripts from image based spatial data.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Denoising image-based spatial transcriptomics data with DenoIST
Image-based spatial transcriptomics (IST) technologies provide unprecedented resolution of gene expression in tissue sections, but suffer from contamination of cells' gene expression profiles due to i...
www.biorxiv.org
November 15, 2025 at 1:31 PM
Great new work led by Aaron Kwok from @davisjmcc.bsky.social’s group. A tool to “denoise” contaminating transcripts from image based spatial data.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Annika Vannan
Check out @saahimall.bsky.social's #skysplain of our latest work! Very proud of all her hard work on this study and REALLY excited for what she's got planned next!
#bpd #lungdevelopment #genomics #science
#bpd #lungdevelopment #genomics #science
I am so excited to share our most recent work & my first big project as a graduate student! We leveraged spatial transcriptomics to study the cell-cell communication involved in human lung development. Here’s the full study: www.biorxiv.org/content/10.1...
(1/17)
(1/17)
A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity
A molecular understanding of lung organogenesis requires delineation of the timing and regulation of the cellular transitions that ultimately form and support a surface capable of gas exchange. While ...
www.biorxiv.org
June 6, 2025 at 6:49 PM
Check out @saahimall.bsky.social's #skysplain of our latest work! Very proud of all her hard work on this study and REALLY excited for what she's got planned next!
#bpd #lungdevelopment #genomics #science
#bpd #lungdevelopment #genomics #science
Reposted by Annika Vannan
Our work looking at the effects of using autosomal assumptions for calling variation on X and Y. We used simulated data to compare to a ground truth.
Tldr: Accurate ploidy is important for reducing false positives; appropriate alignment reduces false negatives.
www.biorxiv.org/content/10.1...
Tldr: Accurate ploidy is important for reducing false positives; appropriate alignment reduces false negatives.
www.biorxiv.org/content/10.1...
Best practices for improving alignment and variant calling on human sex chromosomes
Sex chromosome complement is the largest karyotypic variation observed in humans. X and Y chromosomes were once a pair of homologous autosomes. Although chromosome X and Y differentiated from one anot...
www.biorxiv.org
May 7, 2025 at 1:28 PM
Our work looking at the effects of using autosomal assumptions for calling variation on X and Y. We used simulated data to compare to a ground truth.
Tldr: Accurate ploidy is important for reducing false positives; appropriate alignment reduces false negatives.
www.biorxiv.org/content/10.1...
Tldr: Accurate ploidy is important for reducing false positives; appropriate alignment reduces false negatives.
www.biorxiv.org/content/10.1...
Reposted by Annika Vannan
America don't let up now. Preserve the NIH funding that lets us train the next generation of scientists and researchers!
Carl Sagan would have said the same! bsky.app/profile/saga...
Carl Sagan would have said the same! bsky.app/profile/saga...
This is from The Tonight Show with Johnny Carson aired on May 20th, 1977.
Carl Sagan says something very important, a strong message that didn't lose any validity since then.
Carl Sagan says something very important, a strong message that didn't lose any validity since then.
April 30, 2025 at 2:52 PM
America don't let up now. Preserve the NIH funding that lets us train the next generation of scientists and researchers!
Carl Sagan would have said the same! bsky.app/profile/saga...
Carl Sagan would have said the same! bsky.app/profile/saga...
Reposted by Annika Vannan
Excited to share our new work exploring strategies to overcome resistance to CAR T cell therapy in solid tumors. Using scRNA-seq, mouse models, and functional studies, our work points to SPP1 signaling in the TME as a critical component of this resistance. www.biorxiv.org/content/10.1...
www.biorxiv.org
April 3, 2025 at 2:16 PM
Excited to share our new work exploring strategies to overcome resistance to CAR T cell therapy in solid tumors. Using scRNA-seq, mouse models, and functional studies, our work points to SPP1 signaling in the TME as a critical component of this resistance. www.biorxiv.org/content/10.1...
Reposted by Annika Vannan
Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses!
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
March 26, 2025 at 6:04 PM
Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses!
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Annika Vannan
Today is World Tuberculosis Day. This year's theme is "We can end TB: Commit, Invest, Deliver."
Our very own @ats-pitb.bsky.social works to help learn more and work to ending this disease!
Our very own @ats-pitb.bsky.social works to help learn more and work to ending this disease!
March 24, 2025 at 3:48 PM
Today is World Tuberculosis Day. This year's theme is "We can end TB: Commit, Invest, Deliver."
Our very own @ats-pitb.bsky.social works to help learn more and work to ending this disease!
Our very own @ats-pitb.bsky.social works to help learn more and work to ending this disease!
Reposted by Annika Vannan
Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!
Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics
Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.
www.nature.com
February 4, 2025 at 2:11 PM
Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!
Reposted by Annika Vannan
It’s been hard lately to focus on doing my job as a postdoc, which is under daily threat at this point. But we are persisting. Out now: “Dissociating the incubation of appetitive and consummatory behavior in a model of oral cocaine self-administration”. Very thankful to all who helped get this done!
www.biorxiv.org
February 13, 2025 at 10:12 PM
It’s been hard lately to focus on doing my job as a postdoc, which is under daily threat at this point. But we are persisting. Out now: “Dissociating the incubation of appetitive and consummatory behavior in a model of oral cocaine self-administration”. Very thankful to all who helped get this done!
Reposted by Annika Vannan
It's not every day your work is on the cover of a magazine. Congrats to first author and TGen post-doc, @annikavannan.bsky.social, @nebanovich.bsky.social, his team and collaborators on earning the cover of this month's publication of @naturegenet.bsky.social 🧬 🫁 👏 Photo courtesy of Nature Genetics
March 20, 2025 at 1:18 PM
It's not every day your work is on the cover of a magazine. Congrats to first author and TGen post-doc, @annikavannan.bsky.social, @nebanovich.bsky.social, his team and collaborators on earning the cover of this month's publication of @naturegenet.bsky.social 🧬 🫁 👏 Photo courtesy of Nature Genetics
Reposted by Annika Vannan
The March issue of @naturegenet.bsky.social is live!
Featuring:
✅spatial transcriptomics in pulmonary fibrosis
✅clonal hematopoiesis
✅psychiatric disorders across sex
✅PD-L1 succinylation in melanoma
✅human microglia isoform atlas
✅genomic analyses in Citrus
& more
⬇️
www.nature.com/ng/volumes/5...
Featuring:
✅spatial transcriptomics in pulmonary fibrosis
✅clonal hematopoiesis
✅psychiatric disorders across sex
✅PD-L1 succinylation in melanoma
✅human microglia isoform atlas
✅genomic analyses in Citrus
& more
⬇️
www.nature.com/ng/volumes/5...
March 17, 2025 at 5:10 PM
The March issue of @naturegenet.bsky.social is live!
Featuring:
✅spatial transcriptomics in pulmonary fibrosis
✅clonal hematopoiesis
✅psychiatric disorders across sex
✅PD-L1 succinylation in melanoma
✅human microglia isoform atlas
✅genomic analyses in Citrus
& more
⬇️
www.nature.com/ng/volumes/5...
Featuring:
✅spatial transcriptomics in pulmonary fibrosis
✅clonal hematopoiesis
✅psychiatric disorders across sex
✅PD-L1 succinylation in melanoma
✅human microglia isoform atlas
✅genomic analyses in Citrus
& more
⬇️
www.nature.com/ng/volumes/5...
Reposted by Annika Vannan
I am excited to share our most recent work using spatial transcriptomics to uncover dynamic molecular responses to rejection in transplanted human hearts! 1/15
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Dynamic responses to rejection in the transplanted human heart revealed through spatial transcriptomics
Allograft rejection following solid-organ transplantation is a major cause of graft dysfunction and mortality. Current approaches to diagnosis rely on histology, which exhibits wide diagnostic variabi...
www.biorxiv.org
March 7, 2025 at 4:34 PM
I am excited to share our most recent work using spatial transcriptomics to uncover dynamic molecular responses to rejection in transplanted human hearts! 1/15
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Annika Vannan
🎙️ Just published a new episode of Out of the Blue: An AJRCCM Podcast: Progressive Early Interstitial Lung Abnormalities in Persons At-Risk for Familial Pulmonary Fibrosis: A Prospective Cohort Study and Big Things Have Small Beginnings: Clinical Implications of Early Interstitial.... Have a listen:
Progressive Early Interstitial Lung Abnormalities in Persons At-Risk for Familial Pulmonary Fibrosis: A Prospective Cohort Study and Big Things Have Small Beginnings: Clinical Implications of Early Interstitial Lung Disease
Dr. Mohleen Kang chats with Dr. Margaret Salisbury and Dr. Anna...
share.transistor.fm
February 20, 2025 at 10:00 AM
🎙️ Just published a new episode of Out of the Blue: An AJRCCM Podcast: Progressive Early Interstitial Lung Abnormalities in Persons At-Risk for Familial Pulmonary Fibrosis: A Prospective Cohort Study and Big Things Have Small Beginnings: Clinical Implications of Early Interstitial.... Have a listen:
Reposted by Annika Vannan
@nebanovich.bsky.social recently partnered with Illumina to use its newest technology to uncover breakthroughs in spatial transcriptomics. The team was able to explore pulmonary fibrosis at a high resolution and uncover new mechanisms of the disease. More at: www.genengnews.com/topics/omics...
Illumina Unveils Spatial Technology Days Before AGBT Meeting
Illumina announces a new NGS-based spatial technology kit and new software platform, Illumina Connected Multiomics.
www.genengnews.com
February 20, 2025 at 4:48 PM
@nebanovich.bsky.social recently partnered with Illumina to use its newest technology to uncover breakthroughs in spatial transcriptomics. The team was able to explore pulmonary fibrosis at a high resolution and uncover new mechanisms of the disease. More at: www.genengnews.com/topics/omics...