Alireza Fotuhi Siahpirani

1. Adverse Drug Reactions in Children with Congenital Heart Disease: A Scoping Review

Toni Esmaeel, Ayatollahi Haleh, Abbaszadeh Reza, Fotuhi Siahpirani Alireza (2024)., Paediatric Drugs, 26(5), 519-553.

2. Machine Learning Techniques for Predicting Drug-Related Side Effects: A Scoping Review

Toni Esmaeel, Ayatollahi Haleh, Abbaszadeh Reza, Fotuhi Siahpirani Alireza (2024)., Pharmaceuticals, 17(6), 795.

1. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

Zhang Shilu, Pyne Saptarshi, Pietrzak Stefan, Halberg Spencer, McCalla Sunnie Grace, Fotuhi Siahpirani Alireza, Sridharan Rupa, Roy Sushmita (2023)., Nature Communications, 14(1).

2. ISSR-assisted spatial genetic structure, population admixture, and biodiversity estimates across locally adopted saffron ecotypes from 18 different provenances of Iran

Mohammad Alavi Siney Seid, Saba Jalal, Fotuhi Siahpirani Alireza, Nasiri Jaber (2023)., Journal of Applied Research on Medicinal and Aromatic Plants, 35(1), 100467.

3. Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data

McCalla Sunnie Grace, Fotuhi Siahpirani Alireza, Lii Jiaxin, Pyne Saptarshi, Stone Matthew, Periyasamy Viswesh, Shin Junha, Roy Sushmita (2023)., G3-Genes Genomes Genetics, 13(3).

1. Dynamic regulatory module networks for inference of cell type–specific transcriptional networks

Fotuhi Siahpirani Alireza, Knaack Sara, Chasman Deborah, Seirup Morten, Sridharan Rupa, Stewart Ron, Thomson James, Roy Sushmita (2022)., GENOME RESEARCH, 32(7), 1367-1384.

1. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder

Huang Kunling, Wuu Yuchang, Shin Junha, Zheng Yee, Fotuhi Siahpirani Alireza, Lin Yupei, Nii Zheng, Chen Jiawen, You Jing, Keles Sunduz, Wang Daifeng, Roy Sushmita, Luu Qiongshi (2021)., PLoS Genetics, 17(2), e1009309.

1. Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy

Sinha Divya, Steyer Benjamin, Shahi Pawan, Mueller Katherine, Valiauga Rasa, Edwards Kimberly, Bacig Cole, Steltzer Stephanie, Srinivasan Sandhya, Abdeen Amr, Cory Evan, Periyasamy Viswesh, Fotuhi Siahpirani Alireza, Stone Edwin, Tucker Budd, Roy Sushmita, Pattnaik Bikash, Saha Krishanu, Gamm David (2020)., AMERICAN JOURNAL OF HUMAN GENETICS, 107(2), 278-292.

1. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency

Tran Khoa, Pietrzak Stefan, Zaidan Nur Zafirah, Fotuhi Siahpirani Alireza, McCalla Sunnie Grace, Zhou Amber, Iyer Gopal, Roy Sushmita, Sridharan Rupa (2019)., Cell Reports, 27(6), 1726-1741.e5.

2. Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits

Wheeler Heather, Ploch Sally, Barbeira Alvaro, Bonazzola Rodrigo, Andaleon Angela, Fotuhi Siahpirani Alireza, Saha Ashis, Battle Alexis, Roy Sushmita, Imm Hae Kyung (2019)., GENETIC EPIDEMIOLOGY, 43(1).

1. Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks

Fotuhi Siahpirani Alireza, Chasman Deborah, Roy Sushmita (2018)., Methods in molecular biology (Clifton, N.J.), 1883(1), 161-194.

1. A prior-based integrative framework for functional transcriptional regulatory network inference

Fotuhi Siahpirani Alireza, Roy Sushmita (2016)., NUCLEIC ACIDS RESEARCH, 45(4), gkw963.

2. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti

Marx Harald, Minogue Catherine, Jayaraman Dhileepkumar, Richards Alicia, Kwiecien Nicholas, Fotuhi Siahpirani Alireza, Rajasekar Shanmugam, Maeda Junko, Garcia Kevin, Del Valle-Echevarria Angel, Volkening Jeremy, Westphall Michael, Roy Sushmita, Sussman Michael, Ane Jean-Michel, Coon Joshua (2016)., NATURE BIOTECHNOLOGY, 34(11), 1198-1205.

3. Network-based approaches for analysis of complex biological systems

Chasman Deborah, Fotuhi Siahpirani Alireza, Roy Sushmita (2016)., CURRENT OPINION IN BIOTECHNOLOGY, 39(1), 157-166.

4. A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

Fotuhi Siahpirani Alireza, Ayy Ferhat, Roy Sushmita (2016)., GENOME BIOLOGY, 17(1).

1. A predictive modeling approach for cell line-specific long-range regulatory interactions

Roy Sushmita, Fotuhi Siahpirani Alireza, Chasman Deborah, Knaack Sara, Ayy Ferhat, Stewart Ron, Wilson Michael, Sridharan Rupa (2015)., NUCLEIC ACIDS RESEARCH, 43(18), 8694-8712.

2. Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

Larrainzar Estibaliz, Riely Brendan, Kim Sang Cheol, Carrasquilla-Garcia Noelia, Yuu Hee-Ju, Hwang Hyun-Ju, Ohh Mijin, Kim Goon Bo, Surendrarao Anandkumar, Chasman Deborah, Fotuhi Siahpirani Alireza, Penmetsa Ramachandra, Lee Gang-Seob, Kim Namshin, Roy Sushmita, Mun Jeong-Hwan, Cook Douglas (2015)., PLANT PHYSIOLOGY, 169(1), 233-265.

3. SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching

Dittenhafer-Reed Kristin, Richards Alicia, Fan Jing, Smallegan Michael, Fotuhi Siahpirani Alireza, Kemmerer Zachary, Prolla Tomas, Roy Sushmita, Coon Joshua, Denu John (2015)., Cell Metabolism, 21(4), 637-646.

1. A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components

Knaack Sara, Fotuhi Siahpirani Alireza, Roy Sushmita (2014)., Cancer Informatics, 13s5(1), CIN.S14058.