Current Research
Current Research
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CIPHUS: Probabilistic inference of cell differentiation maps from lineage trees
CIPHUS: Probabilistic inference of cell differentiation maps from lineage trees
During development, cells differentiate through a hierarchy of increasingly restricted cell types, which can be denoted as cell differentiation map. Here we introduce a probabalistic framework to evaluate cell differentiation maps using CIPHUS, that infers an optimal differentiation map from single-cell lineage tracing data.
Clustering-based Lineage Inference from CRISPR–Cas9 Barcodes under a Maximum Likelihood Framework
Clustering-based Lineage Inference from CRISPR–Cas9 Barcodes under a Maximum Likelihood Framework
Despite major experimental advances, accurately reconstructing lineage relationships from observed data remains challenging. To address the challenges in lineage reconstruction from noisy and sparse single-cell lineage tracing data, we propose a clustering-based lineage inference under a maximum likelihood framework from CRISPR--Cas9 barcodes
Publications
Publications
Musale Krushna Pavan*, Anirudh Nanduri*, Kushagra Pandey, Hamim Zafar
*equally contributed
Simran Singh*, Musale Krushna Pavan*, Luiz F. Barella*, Jayesh Telang, Ajita Shree, Shruti Agarwal, Ayush Goel, Saahiba Thaleshwari, Jürgen Wess, Hamim Zafar, Sai Prasad Pydi *equally contributed
Molecular Metabolism 2026
Faster Amylin Aggregation on Fibrillar Collagen I Hastens Diabetic Progression through β-Cell Death and Loss of Function
Faster Amylin Aggregation on Fibrillar Collagen I Hastens Diabetic Progression through β-Cell Death and Loss of Function
Md Asrafuddoza Hazari, Gautam Kannan, Subrata Dasgupta, Musale Krushna Pavan, Akash Kumar Jha, Farhin Sultana, Soumya Ranjan Pujahari, Simran Singh, Sarbajeet Dutta, Sai Prasad Pydi, Sankhadeep Dutta, Hamim Zafar, Prasenjit Bhaumik, Ashutosh Kumar, and Shamik Sen
Journal of the American Chemical Society (JACS) 2025 147 (19), 15985-16006
Mirazul Islam, Yilin Yang, Alan Simmons, Vishal Shah, Musale Krushna Pavan, Yanwen Xu, Naila Tasneem, Zhengyi Chen, Linh Trinh, Paola Molina, Marisol Ramirez, Iannish Sadien, Jinzhuang Dou, Ken Chen, Mark Magnuson, Jeffrey Rathmell, Ian Macara, Douglas Winton, Qi Liu, Hamim Zafar, Reza Kalhor, George Church, Martha Shrubsole, Robert Coffey
Nature volume 634, pages1187–1195 (2024)
Ajita Shree*, Musale Krushna Pavan* & Hamim Zafar*equally contributed
Nature Communications 14 (1), 7781 (2023)
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