Author

Mpathi Nzima

The University of Texas Southwestern Medical Center

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Bioinformatics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Assay:scRNA-seq· 4 Approach:experimental assay· 3 Research Focus:perturbation response prediction· 3 Approach:transformer / foundation model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:deep learning· 1

Frequent Co-Authors

Huan ZhaoiD· 5 shared Gary C. HoniD· 4 shared Chikara TakeuchiiD· 3 shared Maria H. ChahrouriD· 3 shared Minnie Deng· 3 shared Sushama SivakumariD· 3 shared W. Lee KrausiD· 3 shared Anjana SundarrajaniD· 2 shared

Activity by Year

2025-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersGenomics

Huan ZhaoORCID

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Author profile →

5 papers

Recent·Most cited

Systematic CRISPRi perturbation of 1,408 autism risk genes maps multilevel transcriptional convergence in human cortical neurons

Ashlesha Gogate, Wei-Chen Chen, Mpathi Nzima, Chikara Takeuchi, Huan Zhao, Lei Wang, Sushama Sivakumar, Minnie Deng, Kiran J. Kaur, W. Lee Kraus, Nikhil V Munshi, Gary C. Hon, Maria H. Chahrour

This study uses CRISPRi Perturb-seq to analyze 1,408 autism risk genes in human cortical neurons, identifying 215 genes that cause global transcriptomic dysregulation and uncovering shared transcriptional pathways.

bioRxiv · Sep 4, 2026 · PreprintNeuroscience

Perturb-seq resolves physiologic programs and bidirectional regulation of non-canonical NF-κB signaling in epidermal organoids

Galen T Squiers, Benjamin A. Nanes, Maggie M. Balas, Joshua J. Lingo, L H Wang, Huan Zhao, Sabahat Munawar, Mpathi Nzima, Gary C. Hon, Jason C. Klein

The paper uses Perturb-seq in epidermal organoids to study non-canonical NF-κB signaling's role in keratinocyte differentiation.

bioRxiv · Jul 23, 2026 · PreprintGenomics

Regulatory network hubs guide dynamic human lineage specification

Chikara Takeuchi, Sushama Sivakumar, Anjana Sundarrajan, Yihan Wang, Sean C. Goetsch, Huan Zhao, Lei Wang, Mpathi Nzima, Minnie Deng, Kartik N Kulkarni, Lin Xu, Jun Wu, Bruce A. Posner, Maria H. Chahrour, W. Lee Kraus, , Gary C. Hon

The paper identifies dynamic regulatory network hubs in human lineage specification using Perturb-Seq and constructs a deep learning model to predict perturbed TFs in patient transcriptomes.

bioRxiv · Jun 15, 2026 · PreprintGenomics

pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction

Yangqi Su, Dingyu Liu, Vipin K. Menon, Bicna Song, Samuel Boccara, Nan Zhang, Huan Zhao, Jiahui Hazel Zhao, Lei Wang, Nan Hu, Mpathi Nzima, Alon Katz, Bharath Kumar Swargam, Seth A. Ament, Yarui Diao, , Wei Li

The paper introduces pertTF, a transformer-based model for predicting genetic perturbation responses, showing improved performance in expression prediction and cell identity shifts across cellular contexts.

bioRxiv · Mar 16, 2026 · PreprintBioinformatics

Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells

Sushama Sivakumar, Yihan Wang, Sean C. Goetsch, Vrushali Pandit, Lei Wang, Huan Zhao, Anjana Sundarrajan, Daniel A. Armendariz, Chikara Takeuchi, Minnie Deng, Mpathi Nzima, Wei-Chen Chen, ASHLEY E. DEDERICH, Lauretta El Hayek, Taosha Gao, , Nikhil V. Munshi

This study benchmarks and optimizes Perturb-seq in human pluripotent stem cells, identifying shared regulatory networks during cardiomyocyte differentiation.

Stem Cell Reports · Nov 13, 2025Peer-reviewedGenomics