| SIRT3 mediates multi-tissue coupling for metabolic fuel switching KE Dittenhafer-Reed, AL Richards, J Fan, MJ Smallegan, AF Siahpirani, ... Cell metabolism 21 (4), 637-646, 2015 | 189 | 2015 |
| Deep sequencing of the Medicago truncatula root transcriptome reveals a massive and early interaction between nodulation factor and ethylene signals E Larrainzar, BK Riely, SC Kim, N Carrasquilla-Garcia, HJ Yu, HJ Hwang, ... Plant Physiology 169 (1), 233-265, 2015 | 154 | 2015 |
| A predictive modeling approach for cell line-specific long-range regulatory interactions S Roy, AF Siahpirani, D Chasman, S Knaack, F Ay, R Stewart, M Wilson, ... Nucleic acids research 43 (18), 8694-8712, 2015 | 136 | 2015 |
| A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti H Marx, CE Minogue, D Jayaraman, AL Richards, NW Kwiecien, ... Nature biotechnology 34 (11), 1198-1205, 2016 | 129 | 2016 |
| Network-based approaches for analysis of complex biological systems D Chasman, AF Siahpirani, S Roy Current opinion in biotechnology 39, 157-166, 2016 | 89 | 2016 |
| A prior-based integrative framework for functional transcriptional regulatory network inference AF Siahpirani, S Roy Nucleic acids research 45 (4), e21-e21, 2017 | 74 | 2017 |
| Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency KA Tran, SJ Pietrzak, NZ Zaidan, AF Siahpirani, SG McCalla, AS Zhou, ... Cell reports 27 (6), 1726-1741. e5, 2019 | 53 | 2019 |
| Human iPSC modeling reveals mutation-specific responses to gene therapy in a genotypically diverse dominant maculopathy D Sinha, B Steyer, PK Shahi, KP Mueller, R Valiauga, KL Edwards, ... The American Journal of Human Genetics 107 (2), 278-292, 2020 | 43 | 2020 |
| A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions A Fotuhi Siahpirani, F Ay, S Roy Genome biology 17 (1), 114, 2016 | 33 | 2016 |
| Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets S Zhang, S Pyne, S Pietrzak, S Halberg, SG McCalla, AF Siahpirani, ... Nature Communications 14 (1), 1-25, 2023 | 31 | 2023 |
| A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components SA Knaack, AF Siahpirani, S Roy Cancer informatics 13, CIN. S14058, 2014 | 25 | 2014 |
| Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits HE Wheeler, S Ploch, AN Barbeira, R Bonazzola, A Andaleon, ... Genetic epidemiology 43 (6), 596-608, 2019 | 22 | 2019 |
| Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development D Chasman, N Iyer, AF Siahpirani, ME Silva, E Lippmann, B McIntosh, ... Cell systems 9 (2), 167-186. e12, 2019 | 21 | 2019 |
| Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder K Huang, Y Wu, J Shin, Y Zheng, AF Siahpirani, Y Lin, Z Ni, J Chen, J You, ... PLoS genetics 17 (2), e1009309, 2021 | 17 | 2021 |
| Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data SG McCalla, AF Siahpirani, J Li, S Pyne, M Stone, V Periyasamy, J Shin, ... G3 Genes| Genomes| Genetics, 2023 | 14 | 2023 |
| The inconvenience of data of convenience: computational research beyond post-mortem analyses CA Azencott, T Aittokallio, S Roy, T Norman, S Friend, G Stolovitzky, ... Nature methods 14 (10), 937-938, 2017 | 13 | 2017 |
| Integrative approaches for inference of genome-scale gene regulatory networks AF Siahpirani, D Chasman, S Roy Gene Regulatory Networks: Methods and Protocols, 161-194, 2019 | 9 | 2019 |
| Dynamic regulatory module networks for inference of cell type–specific transcriptional networks AF Siahpirani, S Knaack, D Chasman, M Seirup, R Sridharan, R Stewart, ... Genome Research 32 (7), 1367-1384, 2022 | 4 | 2022 |
| Supervised and unsupervised machine learning approaches for prediction and geographical discrimination of Iranian saffron ecotypes based on flower-related and phytochemical … SM Alavi-Siney, J Saba, AF Siahpirani, J Nasiri Information Processing in Agriculture, 2023 | 1 | 2023 |
| ISSR-assisted spatial genetic structure, population admixture, and biodiversity estimates across locally adopted saffron ecotypes from 18 different provenances of Iran SM Alavi-Siney, J Saba, AF Siahpirani, J Nasiri Journal of Applied Research on Medicinal and Aromatic Plants, 100467, 2023 | 1 | 2023 |
