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IEEE/ACM Transactions on Computational Biology and Bioinformatics|December 25, 2015
Gene Regulatory Network Inference from Perturbed Time-Series Expression Data via Ordered Dynamical Expansion of Non-Steady State ActorsMahdi Zamanighomi, Mostafa Zamanian, Michael Kimber, et al.Nucleic Acids Research|May 5, 2017
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression dataMahdi Zamanighomi, Zhixiang Lin, Yong Wang, et al.Genome Biology|July 14, 2019
GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screensMahdi Zamanighomi, Sidharth S Jain, Takahiro Ito, et al.Nature Communications|June 22, 2018
Unsupervised clustering and epigenetic classification of single cellsMahdi Zamanighomi, Zhixiang Lin, Timothy Daley, et al.Proceedings of the National Academy of Sciences of the United States of America|July 11, 2018
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizationsZhana Duren, Xi Chen, Mahdi Zamanighomi, et al.Proceedings of the National Academy of Sciences of the United States of America|December 9, 2016
Simultaneous dimension reduction and adjustment for confounding variationZhixiang Lin, Can Yang, Ying Zhu, et al.Journal of the Neurological Sciences|September 6, 2015
Kinematic analysis of the gait of adult sheep during treadmill locomotion: Parameter values, allowable total error, and potential for use in evaluating spinal cord injurySina Safayi, Nick D Jeffery, Sara K Shivapour, et al.Nature Communications|May 5, 2022
Comparative optimization of combinatorial CRISPR screensRuitong Li, Olaf Klingbeil, Davide Monducci, et al.Nature Communications|November 13, 2025
A large-scale human toxicogenomics resource for drug-induced liver injury predictionVolker Bergen, Konstantia Kodella, Sreenath Srikrishnan, et al.Science (New York, N.Y.)|October 23, 2025
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypesBenjamin DeMeo, Charlotte Nesbitt, Samuel A Miller, et al.Pageof 2