Publications

Faster Amylin Aggregation on Fibrillar Collagen I Hastens Diabetic Progression through β-Cell Death and Loss of Function

Md Asrafuddoza Hazari, ... Musale Krushna Pavan, ... Hamim Zafar, Ashutosh Kumar, Shamik Sen

Journal of the American Chemical Society (2025). doi: https://doi.org/10.1021/jacs.4c15698

multiHIVE: Hierarchical Multimodal Deep Generative Model for Single-cell Multiomics Integration

Anirudh Nanduri, Krushna Pavan Musale, Kushagra Pandey, Hamim Zafar^

bioRxiv (2025). doi: https://doi.org/10.1101/2025.01.28.635222

A Temporal Single-Cell Multi-Omics Atlas of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression

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

bioRxiv (2025). doi: https://doi.org/10.1101/2025.05.29.656754

Intratumor Heterogeneity Through the Lens of Gene Regulatory Networks

Narein Rao, Nicolae Sapoval, Hamim Zafar, Luay Nakhleh

bioRxiv (2025). doi: https://doi.org/10.1101/2025.04.01.646625

Charting spatial ligand-target activity using Renoir

Narein Rao, Tanush Kumar, Rhea Pai, Archita Mishra, Florent Ginhoux, Jerry Chan, Ankur Sharma, Hamim Zafar

bioRxiv (2024). doi: https://www.researchsquare.com/article/rs-5331951/v1 

Cell-Type-Specific Regulation of TOR-Mediated Microtubule Acetylation Predicts Yki Loss-Induced Squamous Cell Carcinoma in Drosophila

Rachita Bhattacharya, Shruti Agarwal, Hamim Zafar, Pradip Sinha, Nitin Mohan

bioRxiv (2024). doi: https://doi.org/10.1101/2024.08.08.607173 

Stiffness-dependent MSC homing and their differentiation to CAFs: Implications in breast cancer invasion

Neha Saxena, Soura Chakraborty, Sarbajeet Dutta, Garvit Bhardwaj, Nupur Karnik, Omshree Shetty, Sameer Jadhav, Hamim Zafar, Shamik Sen

Journal of Cell Science (2023) jcs. 261145. doi: https://doi.org/10.1242/jcs.261145

Thrombospondin 2 is a key determinant of fibrogenesis in NAFLD

Takefumi Kimura, Takanobu Iwadare, Shun-ichi Wakabayashi, Seema Kuldeep, Tomoyuki Nakajima, Tomoo Yamazaki, Daiki Aomura, Hamim Zafar, Mai Iwaya, Takeshi Uehara, Sai P Pydi, Naoki Tanaka, Takeji Umemura

Liver international (2023). doi: https://doi.org/10.1111/liv.15792

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Mohammadamin Edrisi, Monica Valecha, Sunkara Chowdary, Sergio Robledo, Huw Ogilvie, David Posada, Hamim Zafar*, Luay Nakhleh*

Bioinformatics 38 (Supplement_1), i195–i202. 

doi: https://doi.org/10.1093/bioinformatics/btac254

Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET

Kushagra Pandey, Hamim Zafar^

Nucleic Acids Research 50 (15). doi: https://doi.org/10.1093/nar/gkac412

TruthBot: An Automated Conversational Tool for Intent Learning, Curated Information Presenting, and Fake News Alerting

Ankur Gupta, Yash Varun, Prarthana Das, Nithya Muttineni, Parth Srivastava, Hamim Zafar, Tanmoy Chakraborty, Swaprava Nath

arXiv preprint arXiv:2102.00509

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Hamim Zafar, Chieh Lin, Ziv Bar-Joseph

Nature Communications 11, 3055 (2020) doi: https://doi.org/10.1038/s41467-020-16821-5

Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models”

Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh

Genome Biology volume 20, Article number: 95 (2019) doi: https://doi.org/10.1186/s13059-019-1692-5

A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference

Mohammadamin Edrisi, Hamim Zafar, Luay Nakhleh

19th International Workshop on Algorithms in Bioinformatics (WABI 2019)

Matrilysin/MMP-7 cleavage of perlecan/HSPG2 complexed with semaphorin 3A supports FAK-mediated stromal invasion by prostate cancer cells

Brian J Grindel, Jerahme R Martinez, Tristen V Tellman, Daniel A Harrington, Hamim Zafar, Luay Nakhleh, Leland W Chung, Mary C Farach-Carson

Scientific Reports volume 8, Article number: 7262 (2018) doi : https://doi.org/10.1038/s41598-018-25435-3

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh

Genome biology 2017/12 doi : https://doi.org/10.1186/s13059-017-1311-2

Interplay between perlecan/HSPG2 and matrilysin/MMP-7 in the prostate cancer tumor microenvironment directs metastatic programming through focal adhesion kinase and FoxM1

Brian J Grindel, Jerahme Martinez, Hamim Zafar, Luay K Nakhleh, Leland WK Chung, Mary C Farach-Carson

Cancer Res (2016) 76 (14_Supplement): 1563. doi : https://doi.org/10.1158/1538-7445.AM2016-1563