Student Theses


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Integration of genomic and metabolomic data for the prioritization of rare disease variants.

Emma Graham.

2018
MSc thesis
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Molecular interpretation of genome-wide association studies using multiomics analysis.

Farnush Farhadi Hassan Kiadeh.

2018
MSc thesis
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Estimating cell type proportions in human cord blood samples from DNAm arrays.

Louie Dinh.

2017
MSc thesis

Publications


You can find a full publication list at Google Scholar.


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Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain.

Bernard Ng, William Casazza, ... , Mostafavi S. The American Journal of Human Genetics.

2019
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Somatic mosaicism of sex chromosomes in the blood and brain.

Emma Graham, Mike Vermeulen, Badri Vardarjan, ... , Tracy Young-Pearse*,Mostafavi S*. Brain Research.

2019
PubMed
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The cis-Regulatory Atlas of the Mouse Immune System.

Yoshida H, Lereau C, ..., Mostafavi S*, Buenrostro J*, Benoist C*. Cell.

2019
PubMed
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A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

Mostafavi S*, Gaiteri C*, ..., Bennett D*, De Jager P*. Nature Neuroscience.

2018
PubMed
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Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review

Graham E, ...,Van Karnebeek CBD*, Mostafavi S*. Journal of Inherited Metabolic Disease.

2018
PubMed
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An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.

Ng B, White C, Klein HU, ..., Mostafavi S*, De Jager P*. Nature Neuroscience.

2017
PubMed
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Allele-specific expression reveals interactions between genetic variation and environment

Knowles D,Davis JR, Edgington H, ..., Mostafavi S, Montgomery SB*, Battle AJ*. Nature Methods.

2017
PubMed
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Network pharmacology of Jak inhibitors

Moodley D, Yoshida H, Mostafavi S, ..., Mathis D, Benoist C. PNAS.

2016
PubMed
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Genetic variants in Alzheimer disease - molecular and brain network approaches

Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA. Nature Review Neurology.

2016
PubMed
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Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation

Clifford RL, Jones MJ, Maclsaac JL, McEwan LM, Goodman SJ, Mostafavi S, Kobor MS, Carlsten C. Journal of Allergy & Clinical Immunology .

2016
PubMed
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Impact of the X Chromosome and sex on regulatory variation

Kukurba K, Parsana P, ..., Mostafavi S, Battle A*, Montgomery SB*. Genome Research .

2016
PubMed
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Parsing the interferon transcriptional network and its disease associations

Mostafavi S*, Yoshida H*, Moodley D, ..., Mathis D, Benoist C, and the ImmGen Consortium. Cell .

2016
PubMed
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Sharing and Specificity of Co-expression Networks across 35 Human Tissues

Pierson E, the GTEx Consortium, Koller D, Battle A*, Mostafavi S*. PLOS Computational Biology .

2015
PubMed
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Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes

Raj T, Rothamel K, Mostafavi S,..., Benoist C*, Stranger BE*, De Jager PL*. Science .

2014
PubMed
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Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

Battle A, Mostafavi S, Zhu X,..., Koller D. Genome Research .

2014
PubMed
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Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge

Mostafavi S, Battle A, Zhu X,..., Koller D. PLOS ONE .

2013
PubMed
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Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing

Mostafavi S, Battle A, Zhu X,..., Levinson DF. Molecular Psychiatry.

2013
PubMed
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Using prior biological knowledge when constructing gene regulatory networks

Mostafavi S, and Koller, D. ICML workshop on Machine Learning in Genomics and Genetics .

2012
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Labeling nodes using three degrees of propagation

Mostafavi S, Goldenberg A, Morris Q. PLOS ONE .

2012
PubMed
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Predicting node characteristics from molecular networks

Mostafavi S, Goldenberg A, Morris Q. Methods in Molecular Biology .

2011
PubMed
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Fast integration of heterogeneous data sources for predicting gene function with limited annotation.

Mostafavi S and Morris Q. Bioinformatics .

2010
PubMed
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Using the Gene Ontology hierarchy when predicting gene function

Mostafavi S and Morris Q. Uncertainty in Artificial Intelligence (UAI) .

2009
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GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. Genome Biology .

2008
PubMed