Shahin Mohammadi

System Biosciences (United States) — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

22h-index4.6kcitations61works35.52yr avg
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Research Topics

Bioinformatics and Genomic Networks(27), Single-cell and spatial transcriptomics(20), Fungal and yeast genetics research(14), Neuroinflammation and Neurodegeneration Mechanisms(9), Gene Regulatory Network Analysis(8)

Publications56 total

Foundation Models Improve Perturbation Response Prediction
2026Open Access
PertSpectra: Interpretable Matrix Factorization for Predicting Functional Impact of Genetic Perturbation Experiments
2025Open Access
Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction
2025· 3 citedOpen Access
Pertspectra: Interpretable matrix factorization for predicting functional impact of genetic perturbation experiments
Faculty of 1000 Research Ltd·2025Open Access
2. SINGLE-CELL MULTI-COHORT TRANSCRIPTOMIC DISSECTION OF BIPOLAR DISORDER
European Neuropsychopharmacology·2024
Single-cell multi-cohort dissection of the schizophrenia transcriptome
Science·2024· 108 citedOpen Access
Single-cell multi-cohort dissection of the schizophrenia transcriptome
2022· 29 citedOpen Access
Single-cell profiling of the human primary motor cortex in ALS and FTLD
2021· 42 citedOpen Access
Single-cell anatomical analysis of human hippocampus and entorhinal cortex uncovers early-stage molecular pathology in Alzheimer’s disease
2021· 21 citedOpen Access
Single-Cell Dissection of Schizophrenia Reveals Neurodevelopmental-Synaptic Link and Transcriptional Resilience Associated Cellular State
Biological Psychiatry·2021· 26 cited
Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders
2021· 15 citedOpen Access
Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic axis and transcriptional resilience
2020· 59 citedOpen Access
A multiresolution framework to characterize single-cell state landscapes
Nature Communications·2020· 65 citedOpen Access
Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation
Neuron·2020· 282 citedOpen Access
Apoptosis Induced by Prednisolone Occurs without Altering the Promoter Methylation of BAX and BCL-2 Genes in Acute Lymphoblastic Leukemia Cells CCRF-CEM
Asian Pacific Journal of Cancer Prevention·2020· 12 citedOpen Access
Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution
Cell Systems·2019· 78 citedOpen Access
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
Nature Communications·2019· 334 citedOpen Access
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
DSpace@MIT (Massachusetts Institute of Technology)·2019Open Access
A multiresolution framework to characterize single-cell state landscapes
2019· 8 citedOpen Access
Author Correction: Single-cell transcriptomic analysis of Alzheimer’s disease
Nature·2019· 61 citedOpen Access
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Frequent Co-authors

Ananth Grama(27), José Dávila-Velderrain(15), Manolis Kellis(15), Shankar Subramaniam(11), Baharak Saberidokht(8), David F. Gleich(5), David A. Bennett(4), Li‐Huei Tsai(4), Sivan Subburaju(4), Makayla Hourihan(4), Giorgos Kollias(4), Zhuyu Peng(3), Fan Gao(3), Madhvi Menon(3), Liang He(3), Xueqiao Jiang(3), Brian P. Hafler(3), W. Brad Ruzicka(3), Daniel Reed Tso(3), Hansruedi Mathys(2)