Sandeep Kambhampati
@SandeepKambham2
Followers
71
Following
20
Media
3
Statuses
15
PhD candidate in Fei Chen's lab @insitubiology (Harvard Bioinformatics & Integrative Genomics program) | AI for imaging + 'omics
Boston, MA
Joined October 2018
Announcing our new preprint! We built SPICE, a framework that combines large-scale experiments and generative AI to design RNA sequences that control cell type-specific gene expression using alternative splicing - a powerful new modality! (1/10) Preprint:
biorxiv.org
Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular...
2
20
92
Huge thanks to all of our co-authors (Luca D’Alessio, Fedor Grab, Stephen Fleming, @immunoliugy, @RuthRaichur, @insitubiology, and the Cellarium ML group) for their contributions!
0
0
2
Check out our Github ( https://t.co/mwi91K7ZUO) and the thread on our preprint for more details: https://t.co/MMYoxilcZz
We’re excited to share our latest computational method, TissueMosaic, for comparative analysis of spatial transcriptomic datasets across conditions! (1/5) https://t.co/uytkq4jRib
1
0
1
TissueMosaic, our method to study how changes in tissue structure across conditions affect cell-intrinsic function, is now out @CellSystemsCP! https://t.co/ctFE33aFPP
2
5
19
Super cool method for spatial transcriptomics data from @uthsavc!
GASTON, our method to learn “topographic maps” of gene expression, is out now @naturemethods! IMO the coolest part is a new model of *spatial gradients in sparse data*. As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇
1
0
3
Super cool work from @rumya_r and @mircoscopy!
1/ Thrilled to share an advancement in gene therapy from my PhD in @NatureComms! We've developed a new approach to reduce immune responses while maintaining efficiency—paving the way for safer, more effective therapies. Big thanks to @zhangf & @mircoscopy! https://t.co/eXZkpgiMXq
0
0
4
Thanks to all of the coauthors: Luca D’Alessio, @ordabayevy, Fedor Grab, and Stephen Fleming for their contributions and the @insitubiology and Cellarium ML groups for their support!
0
0
0
Check out our github ( https://t.co/mwi91K7ZUO) and tutorial ( https://t.co/8zQUyD1xCD) for more details! (5/5)
1
0
1
Users can identify tissue motifs enriched for a particular condition and perform spatial differential expression analysis via a downstream GLM to identify genes associated with condition-enriched motifs. (4/5)
1
0
1
These representations enable downstream tasks such as motif query, clustering, and gene expression regression to identify genes with high mutual information with tissue structure. (3/5)
1
0
2
TissueMosaic trains a CNN via a self-supervised learning framework (DINO) to represent tissue architectural motifs from spatial transcriptomic datasets cast as images. (2/5)
1
0
2
We’re excited to share our latest computational method, TissueMosaic, for comparative analysis of spatial transcriptomic datasets across conditions! (1/5) https://t.co/uytkq4jRib
biorxiv.org
Spatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment....
3
14
51
So excited!!
Thrilled to be opening my lab this fall at the Ragon Institute! Come work with us to build new tools for immunology.
0
0
1
Single-cell or spatial? Our new technology - Slide-tags - allows both in the same experiment, enabling true single-cell multi-modal spatial genomics ➡️ https://t.co/i1m5T4bEme
12
168
582