IBB

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