Alireza Fotuhi - مركز تحقيقات بيوشيمی و بيوفيزيك
Dr. Alireza Fotuhi Siahpirani
| Alireza Fotuhi Siahpirani, Ph.D. Assistant Professor E-mail: a.fotuhi@ut.ac.ir
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Personal Records | Education | |||
Last name: Fotuhi Siahpirani First name: Alireza Date of birth: Position: Assistant Professor of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran. Contact Info Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran. P.O.Box: 13145-1384. E-mail: a.fotuhi@ut.ac.ir Web page: ibb.ut.ac.ir/fotuhi Office: Tel: Fax: (+98)-21-66404680 | Ph.D. in Computer Sciences, UW-Madison, Madison, WI, USA (2011-2019) M.Sc. in Computer Science, University of Tehran, Tehran, Iran. (2006-2009) B.Sc. in Computer Science, University of Tehran, Tehran, Iran. (2001-2006) |
Research Interests
• Bioinformatics & Computational Biology
• Machine Learning
Publications
Siahpirani AF, Knaack S, Chasman D, et al. (2022)
"Dynamic regulatory module networks for inference of cell type-specific transcriptional networks."
Genome Res. https://doi.org/10.1101/gr.276542.121
Huang K, Wu Y, Shin J, et al. (2021)
"Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder."
PLOS Genetics https://doi.org/10.1371/journal.pgen.1009309
Sinha D, Steyer B, Shahi P, et al. (2020)
"Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy."
The American Journal of Human Genetics https://doi.org/10.1016/j.ajhg.2020.06.011
Wheeler HE, Ploch S, Barbeira AN, et al. (2019)
"Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits."
Genet. Epidemiol https://doi.org/10.1002/gepi.22205
Chasman D, Iyer N, Siahpirani AF, et al. (2019)
"Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development."
Cell Systems https://doi.org/10.1016/j.cels.2019.05.012
Tran KA, Pietrzak SJ, Zaidan NZ, et al. (2019)
"Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency."
Cell Reports https://doi.org/10.1016/j.celrep.2019.04.056
Siahpirani AF, Roy S, (2017) "A prior-based integrative framework for functional transcriptional regulatory network inference." Nucleic Acids Research
https://doi.org/10.1093/nar/gkw963
Siahpirani AF, Ay F, Roy S. (2016)
"A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions."
Genome Biol https://doi.org/10.1186/s13059-016-0962-8
Marx, H., Minogue, C., Jayaraman, D. et al. (2016)
"A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti."
Nat Biotechnol https://doi.org/10.1038/nbt.3681
Chasman D, Siahpirani AF, Roy S, (2016)
"Network-based approaches for analysis of complex biological systems."
Current Opinion in Biotechnology https://doi.org/10.1016/j.copbio.2016.04.007
Roy S, Siahpirani AF, Chasman D, et al. (2015)
"A predictive modeling approach for cell line-specific long-range regulatory interactions."
Nucleic Acids Research https://doi.org/10.1093/nar/gkv865
Larrainzar E, Riely BK, Kim SC, et al. (2015)
"Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals."
Plant Physiology https://doi.org/10.1104/pp.15.00350
Dittenhafer-Reed KE, Richards AL, Fan J, et al. (2015)
"SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching."
Cell Metabolism https://doi.org/10.1016/j.cmet.2015.03.007
Course Titles
• Algorithms in Bioinformatics
• Machine Learning
• Discrete Mathematics