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Uddalok Jana

@uddalok.bsky.social
14 followers 25 following 0 posts

PhD student @ University of Louisville

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Reposted by Uddalok Jana
Sina Majidian @sinamajidian.bsky.social · 08/04/2026
Nature Language Model: Deciphering the Language of Nature for Scientific Discovery arxiv.org/abs/2502.07527 Design a heme-binding protein sequence. ⟨protein⟩MSAAEGAVVFSEEKEALVLK· · · ⟨/protein⟩ Generate a molecule with four hydrogen bond donors. ⟨mol⟩C(C[C@@H](C(=O)O)N)CN=C(N)N⟨/mol⟩
NatureLM is a GPT-style generative model trained on a diverse range of data, including small molecule compounds, proteins, DNA, RNA, materi- als, and both general and scientific texts, amounting to a total of 143 billion tokensFig. 2: The scaling effect in NatureLM is obvious. The chart depicts the overall ranking of models with varying sizes, where a better rank is represented by the “outsider” bar. The 8x7B model achieves top performance in 19 tasks, while the 8B model excels in 3 tasks. 18 categories exhibited performance improvements with increasing model size (i.e., 8x7B demonstrated the best performance, followed by 8B, and then 1B), highlighting the potential of large foundation models for scientific applications.
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Reposted by Uddalok Jana
Andreas Lossius @lossiusandreas.bsky.social · 22/09/2025
New BCR reconstruction tool for scRNA-seq: assembles full heavy & light chains and annotates constant regions. Check it out: www.biorxiv.org/content/10.1... #scRNAseq #immunology
biorxiv.org
GATHeR: Graph-based Accurate Tool for Immunoglobulin HEavy- and Light-chain Reconstruction
Recovering full-length, paired B-cell receptor (BCR) sequences from scRNA-seq reads remains difficult, especially in naive and memory B cells where immunoglobulin transcripts are sparse. Current metho...
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Reposted by Uddalok Jana
Corey Watson @cdubsig.bsky.social · 02/06/2025
Turns out...just like in the antibody heavy chain repertoire, germline variants in the immunoglobulin lambda and kappa loci influence the composition of light chain B cell receptors! Way to go Eric @e-engelbrecht1.bsky.social !!!! www.biorxiv.org/content/10.1...
biorxiv.org
Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire
Variation in antibody (Ab) responses contributes to disease outcomes and therapeutic responsiveness, the determinants of which remain incompletely understood. This study demonstrates that polymorphism...
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Reposted by Uddalok Jana
Corey Watson @cdubsig.bsky.social · 06/03/2025
Very proud of this collective effort to enhance understanding of immunoglobulin diversity in rhesus macaque @guryaari.bsky.social @williamlees.bsky.social www.biorxiv.org/content/10.1... --> NEW and IMPROVED germline sets for this important animal model...explore here: vdjbase.org/reference_bo...
biorxiv.org
A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques
Rhesus macaques (RMs) are a vital model for studying human disease and invaluable to pre-clinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies ...
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