SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching von Dittenhafer-Reed, Kristin E., Richards, Alicia L., Fan, Jing, Smallegan, Michael J., Fotuhi Siahpirani, Alireza, Kemmerer, Zachary A., Prolla, Tomas A., Roy, Sushmita, Coon, Joshua J., Denu, John M.

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A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions von Fotuhi Siahpirani, Alireza, Ay, Ferhat, Roy, Sushmita

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Machine Learning Techniques for Predicting Drug-Related Side Effects: A Scoping Review von Toni, Esmaeel, Ayatollahi, Haleh, Abbaszadeh, Reza, Fotuhi Siahpirani, Alireza

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Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data von McCalla, Sunnie Grace, Fotuhi Siahpirani, Alireza, Li, Jiaxin, Pyne, Saptarshi, Stone, Matthew, Periyasamy, Viswesh, Shin, Junha, Roy, Sushmita

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Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits von Wheeler, Heather E., Ploch, Sally, Barbeira, Alvaro N., Bonazzola, Rodrigo, Andaleon, Angela, Fotuhi Siahpirani, Alireza, Saha, Ashis, Battle, Alexis, Roy, Sushmita, Im, Hae Kyung

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Network-based approaches for analysis of complex biological systems von Chasman, Deborah, Fotuhi Siahpirani, Alireza, Roy, Sushmita

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Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets von Zhang, Shilu, Pyne, Saptarshi, Pietrzak, Stefan, Halberg, Spencer, McCalla, Sunnie Grace, Siahpirani, Alireza Fotuhi, Sridharan, Rupa, Roy, Sushmita

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Adverse Drug Reactions in Children with Congenital Heart Disease: A Scoping Review von Toni, Esmaeel, Ayatollahi, Haleh, Abbaszadeh, Reza, Fotuhi Siahpirani, Alireza

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Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency von Tran, Khoa A., Pietrzak, Stefan J., Zaidan, Nur Zafirah, Siahpirani, Alireza Fotuhi, McCalla, Sunnie Grace, Zhou, Amber S., Iyer, Gopal, Roy, Sushmita, Sridharan, Rupa

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Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder von Huang, Kunling, Wu, Yuchang, Shin, Junha, Zheng, Ye, Siahpirani, Alireza Fotuhi, Lin, Yupei, Ni, Zheng, Chen, Jiawen, You, Jing, Keles, Sunduz, Wang, Daifeng, Roy, Sushmita, Lu, Qiongshi

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Risk Factors Associated With Drug-Related Side Effects in Children: A Scoping Review von Toni, Esmaeel, Ayatollahi, Haleh, Abbaszadeh, Reza, Fotuhi Siahpirani, Alireza

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Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development von Chasman, Deborah, Iyer, Nisha, Fotuhi Siahpirani, Alireza, Estevez Silva, Maria, Lippmann, Ethan, McIntosh, Brian, Probasco, Mitchell D., Jiang, Peng, Stewart, Ron, Thomson, James A., Ashton, Randolph S., Roy, Sushmita

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A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components von Knaack, Sara A., Siahpirani, Alireza Fotuhi, Roy, Sushmita

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Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks von Siahpirani, Alireza Fotuhi, Chasman, Deborah, Roy, Sushmita

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A predictive modeling approach for cell line-specific long-range regulatory interactions von Roy, Sushmita, Siahpirani, Alireza Fotuhi, Chasman, Deborah, Knaack, Sara, Ay, Ferhat, Stewart, Ron, Wilson, Michael, Sridharan, Rupa

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Dynamic regulatory module networks for inference of cell type-specific transcriptional networks von Siahpirani, Alireza Fotuhi, Knaack, Sara, Chasman, Deborah, Seirup, Morten, Sridharan, Rupa, Stewart, Ron, Thomson, James, Roy, Sushmita

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Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets von Zhang, Shilu, Pyne, Saptarshi, Pietrzak, Stefan, Halberg, Spencer, McCalla, Sunnie Grace, Siahpirani, Alireza Fotuhi, Sridharan, Rupa, Roy, Sushmita

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Dynamic positioning based on voronoi cells (DPVC) von HESAMADDIN TORABI DASHTI, AGHAEEPOUR, Nima, ASADI, Sahar, BASTANI, Meysam, DELAFKAR, Zahra, FATEMEH MIRI DISFANI, SERVEH MAM GHADERI, KAMALI, Shahin, PASHAMI, Sepideh, ALIREZA FOTUHI SIAHPIRANI

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Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy von Sinha, Divya, Steyer, Benjamin, Shahi, Pawan K., Mueller, Katherine P., Valiauga, Rasa, Edwards, Kimberly L., Bacig, Cole, Steltzer, Stephanie S., Srinivasan, Sandhya, Abdeen, Amr, Cory, Evan, Periyasamy, Viswesh, Siahpirani, Alireza Fotuhi, Stone, Edwin M., Tucker, Budd A., Roy, Sushmita, Pattnaik, Bikash R., Saha, Krishanu, Gamm, David M.

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Supervised and unsupervised machine learning approaches for prediction and geographical discrimination of Iranian saffron ecotypes based on flower-related and phytochemical attribu... von Alavi-Siney, Seid Mohammad, Saba, Jalal, Siahpirani, Alireza Fotuhi, Nasiri, Jaber

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