Cathrine Sant (Petersen) (@cathrine_sant) 's Twitter Profile
Cathrine Sant (Petersen)

@cathrine_sant

Postdoc @GladstoneInst · Methods development for single-cell data analysis & applications to Alzheimer's

ID: 1325889937

linkhttp://CHOIRclustering.com calendar_today04-04-2013 01:46:44

309 Tweet

1,1K Followers

579 Following

Pall Melsted (@pmelsted) 's Twitter Profile Photo

In this preprint biorxiv.org/content/10.110… with @sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N

Prof. Melissa E. Murray 📸🔬 (@drneurochic) 's Twitter Profile Photo

Moving opening at #Tau2024 by Linde Jacobs on MAPT families fighting for a future. She and her sisters have already inspired work in my lab on MAPT mutation carriers and I hope her families' galvanizing story inspires more research curemaptftd.org/team/linde-jac…

Moving opening at #Tau2024 by Linde Jacobs on MAPT families fighting for a future. She and her sisters have already inspired work in my lab on MAPT mutation carriers and I hope her families' galvanizing story inspires more research

curemaptftd.org/team/linde-jac…
Can  Ergen (@_canergen) 's Twitter Profile Photo

The authors highlight that UMAP/tSNE preserve neighborhoods and conclude: "If used properly, 2D (tSNE/UMAP) embeddings will continue to help charting the world of single-cell biology." Dmitry Kobak Jan Lause 🟦 @janlause.bsky.social🦉 biorxiv.org/content/10.110…

Cathrine Sant (Petersen) (@cathrine_sant) 's Twitter Profile Photo

Happening today!! Watch me try to describe my thesis work on clustering single-cell data in under 3 minutes! Live stream at graduate.ucsf.edu/watch-grad-sla…

Happening today!! Watch me try to describe my thesis work on clustering single-cell data in under 3 minutes! Live stream at graduate.ucsf.edu/watch-grad-sla…
Jan Lause 🟦 @janlause.bsky.social🦉 (@janlause) 's Twitter Profile Photo

tSNE/UMAP preserve neighbors in a "soft" sense: Yes, tSNE recalls only ~30% of neighbors exactly. But ~60-80% of the 10 nearest tSNE neighbors are among the 100 nearest true neighbors! So even if some tSNE neighbors are not next-door neighbors, most are "from the same block".

tSNE/UMAP preserve neighbors in a "soft" sense:

Yes, tSNE recalls only ~30% of neighbors exactly. 

But ~60-80% of the 10 nearest tSNE neighbors are  among the 100 nearest true neighbors! So even if some tSNE neighbors are not next-door neighbors, most are "from the same block".
Bo Wang (@bowang87) 's Twitter Profile Photo

This study reveals something fascinating: Different packages (e.g., in terms of versions and programming languages) of the same algorithms/pipelines can lead to varied results in downstream analysis. Here are my thoughts: Firstly, this should not be used to critique Seurat and

Lea T. Grinberg, M.D, Ph.D (@grinberg_t) 's Twitter Profile Photo

Why do some with #Alzheimer's pathology have more language or visual issues than memory problems? In a new paper led by Stefanie Piña & Renaud LaJoie, we explore if more copathology explains #AtypicalAlzheimer. tinyurl.com/mu8dtzts See comments 👇 UCSF MAC Global Brain Health Institute Atypical Alzheimer's Disease PIA

Why do some with #Alzheimer's pathology have more language or visual issues than memory problems? In a new paper led by <a href="/halsty/">Stefanie Piña</a> &amp; Renaud LaJoie, we explore if more copathology explains #AtypicalAlzheimer. tinyurl.com/mu8dtzts See comments 👇 <a href="/UCSFmac/">UCSF MAC</a> <a href="/GBHI_Fellows/">Global Brain Health Institute</a> <a href="/AtypicalPIA/">Atypical Alzheimer's Disease PIA</a>
Lea T. Grinberg, M.D, Ph.D (@grinberg_t) 's Twitter Profile Photo

ISTAART Grinberg Lab UCSF LAC-CD This paper adds to our studies anchored by solid neuropath data. Previously, we showed atypical AD = more regional tau burden related to symptoms. tinyurl.com/3yb6fy3e We conclude that selective vulnerability is key to deciphering atypical AD. See comments 👇 @cathrinepet

<a href="/ISTAART/">ISTAART</a> <a href="/GrinbergLabUCSF/">Grinberg Lab UCSF</a> <a href="/LACCD9/">LAC-CD</a> This paper adds to our studies anchored by solid neuropath data. Previously, we showed atypical AD = more regional tau burden related to symptoms. tinyurl.com/3yb6fy3e We conclude that selective vulnerability is key to deciphering atypical AD. See comments 👇 @cathrinepet
Ryan Corces (@doctorcorces) 's Twitter Profile Photo

One of the last stories from my postdoc work with Howard Chang and William J. Greenleaf is out today Science Magazine led by Laksshman Sundaram. scATAC-seq of 8 different tumor types from TCGA. science.org/doi/10.1126/sc…

Gladstone Institutes (@gladstoneinst) 's Twitter Profile Photo

Gladstone scientists developed a computational approach that accurately distinguishes cells of different identities or characteristics in complex biological samples used in diverse areas of biomedical and discovery research. Nature Genetics UC San Francisco bit.ly/3FXBBZI

Cathrine Sant (Petersen) (@cathrine_sant) 's Twitter Profile Photo

CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type! nature.com/articles/s4158…

Ryan Corces (@doctorcorces) 's Twitter Profile Photo

CHOIR is officially published Nature Genetics. No more arbitrary decisions in clustering. Add this to your single-cell toolbox - it will save you so much heart ache. And now it can scale to millions of cells. Compliments of the very talented Cathrine Sant (Petersen).

RNA-Seq Blog (@rnaseqblog) 's Twitter Profile Photo

CHOIR adds statistical muscle to single-cell #RNAsequencing, helping scientists at Gladstone Institutes cluster cells more accurately and uncover real biological patterns—not just noise. rna-seqblog.com/choir-improves…

Gladstone Institutes (@gladstoneinst) 's Twitter Profile Photo

Gladstone scientists have developed a computational approach that accurately distinguishes cells of different identities or characteristics in complex biological samples used in diverse areas of biomedical and discovery research. Cathrine Sant (Petersen) Ryan Corces Nature Genetics

Gladstone Institutes (@gladstoneinst) 's Twitter Profile Photo

Congratulations to Ryan Corces and the entire Gladstone team that hosted last week’s 2025 FunGen-AD meeting. The annual program examines genetic risk factors for Alzheimer’s disease, with the goal of finding new targets for preventing, diagnosing, and treating disease.

Congratulations to <a href="/doctorcorces/">Ryan Corces</a> and the entire Gladstone team that hosted last week’s 2025 FunGen-AD meeting. The annual program examines genetic risk factors for Alzheimer’s disease, with the goal of finding new targets for preventing, diagnosing, and treating disease.