By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference, and batch effect mitigation.

nature.com/articles/s4159…

Check out this new method for embedding point clouds with transformers - tons of potential applications on single-cell/spatial data😊 congrats to all authors!

1/17
Thrilled to announce our Gastroenterology paper, where we tackle the challenging exocrine #pancreas context to achieve unprecedented scRNA-seq definition of cell landscapes in homeostasis, #AcutePancreatitis , and recovery. Led by NissimLab @aneykatie + Woo-Jeong Jeong. 🧵👇

Very much looking forward to this!

🧵1/10 We’re thrilled to share our latest paper, Bicycle, a novel approach for inferring cyclic causal relationships from observational and interventional data! This work addresses a critical gap in understanding complex biological networks.

Excited to share a pre-print from the lab describing our effort to use multiplex single-cell chemical transcriptomics to examine differences in tumor cell response associated with the precise manner by which you target an oncogenic kinase.
biorxiv.org/content/10.110…

Thrilled to unveil a preprint of my postdoc work unveiling powerful new 🐭 models to study lineage plasticity (adeno>NEPC). Much much more to come! The Charles Sawyers Lab dana_peer HHMI NEWS

Next Tuesday at 2024-04-16 18:00 CEST will be another community meeting!

Doron Haviv will talk about about ENVI, a deep learnining based variational inference method to integrate scRNA-seq with spatial data. For more information, check here: github.com/dpeerlab/ENVI

CRC progression is all about plasticity. Brilliant talk by the amazing dana_peer about this visionary project with Karuna Ganesh! Shout out to the team behind the work Andrew Moorman Ellie Benitez Francesco Cambuli Cassandra Burdziak Karuna Ganesh Lab #AACR24 #CRC #plasticity

Join Dr. dana_peer for a plenary session about charting the awesome power of plasticity during #metastasis TODAY at #AACR24 (@AACR) Learn more: bit.ly/3VRRabo

Part of Karuna Ganesh’s conclusion during her research presentation on #colorectalcancer progression: “ #CRC metastases span an expanded range of canonical intestinal and non-canonical states.” Learn more: bit.ly/3VPwJvF #AACR24

1) Super excited that COVET and ENVI by the gifted Doron Haviv finally out in Nature Biotechnology providing a powerful tool to analyze the rapidly accumulating spatial transcriptomics data. See x.com/dana_peer/stat… for the original BioRxiv tweetorial -->

What a PERFFect day to share our new preprint!

With Tsion Abay #BobStickels Meril Takizawa Ronan Chaligne (He/Him) and Ansu Satpathy, we introduce PERFF-seq, a new experimental approach to studying rare cells with scRNA-seq via transcript-specific enrichment. biorxiv.org/content/10.110… 1/n

1/ #Starfysh ⭐️🐟 for spatial transcriptomic+histology analysis and multi-sample integration is out today in Nature Biotechnology🎉 Thanks to reviewer feedback we improved model interpretability (learning anchors and joint representation of multiple samples)
tinyurl.com/5b7m5mv5

New preprint from Lowe Lab showing how the interplay between canonical genomic alterations like SMAD4 loss & tissue resident epigenomic drivers (KLF4, RUNX1) impacts tissue specific metastatic behavior (liver versus lung).
biorxiv.org/content/10.110…
dana_peer Chris Iacobuzio

HHMI Hanna Gray Fellow Francisco J. Sánchez-Rivera & his Koch Institute at MIT lab have developed a framework to scale up prime editing, a powerful tool in the genome editing toolkit. The team hopes their work will help advance cancer & disease research: hhmi.org/news/scaling-p… #HannaGrayFellows

Cell It includes a Commentary from 24 transgender (and/or family of trans) scientists discussing the experiences of sex and gender minorities in STEMM and offering actions to help build a more inclusive academia and produce more accurate and rigorous science: cell.com/cell/fulltext/…

#ICYMI : Deep Learning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data, by Madison Darmofal, Michael Berger, Quaid Morris et al.
bit.ly/3Iz7gyx
Memorial Sloan Kettering Cancer Center

Our outstanding lab manager is moving on to the next stage of her career, creating an exciting opportunity for someone to step into this role immediately. The candidate will have the opportunity to shadow and work closely with her over the next few months for a smooth transition.

when your algorithm is named Calligraphy, naturally you need one of these✍️ thanks Julia Zhao for the awesome gift from Oxford😊