Selected Publications


You can find a full publication list at Google Scholar.

Underline: trainees from Mostafavi lab; *: co-first authorship; $: co-senior authorship.

Preprints


Selected Published Articles

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Unlocking gene regulation with sequence-to-function models

Alex Sasse, Maria Chikina$, Sara Mostafavi$. Nature Methods (Comment)

2024
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Quick and effective approximation of in silico saturation mutagenesis experiments with first-order Taylor expansion

Alex Sasse, Maria Chikina$, Sara Mostafavi$. RECOMB-seq

2024
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AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization

Yuan Fang, Kushagra Bansal, Sara Mostafavi, Christophe Benoist, Diane Mathis. Nature

2024
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Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings

Alex Sasse*, Bernard Ng*, Anna Spiro*,Shinya Tasaki, David Bennett, Chris Gaiteri, Phil De Jager, Maria Chinkina$, Sara Mostafavi$. Nature Genetics

2023
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Cell sub-type specific effects of genetic variation in the aging and Alzheimer cortex

Masashi Fujita, Zongmei Gao, Lu Zeng, ..., Sara Mostafavi, David Bennett, Vilas Menon, Philip De Jager. Nature Genetics (Accepted)

2023
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Impact of random 50-base sequences inserted into an intron on splicing in Saccharomyces cerevisiae

Molly Perchlik, Alex Sasse, Sara Mostafavi, Stan Fields, Josh T. Cuperus. RNA

2023
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ExplaiNN: interpretable and transparent neural networks for genomics

Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi, Wyeth W Wasserman. Genome Biology

2023
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In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm

Gherman Novakovsky, Shugo Sasaki, ...Sara Mostafavi, Francis Lynn, Wyeth Wasserman. Stem Cell Reports.

2023
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Cross-Linked Unified Embedding for cross-modality representation learning

Xinming Tu*, Zhi-Jie Cao*, Chen-Rui Xia, Sara Mostafavi$, Ge Gao$. NeurIPS (Oral).

2022
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Obtaining genetics insights from deep learning via explainable artificial intelligence

Gherman Novakovsky*, Nick Dexter*, Maxwell Libbrecht$, Wyeth Wasserman$, Sara Mostafavi$. Nature Reviews Genetics.

2022
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Mosaic loss of chromosome Y in aged human microglia

Michael Vermeulen, Richard Pearse, Tracy Young-Pearse, Sara Mostafavi. Genome Research. Cover article, Oct 2022 issue.

2022
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A practical guide to applying machine learning to infant EEG data

Bernard Ng*, Rebecca Reh, Sara Mostafavi$. Developmental Cognitive Neuroscience.

2022
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CEWAS: Cascading Epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variants

Bernard Ng, William Casazza, ..., Sara Mostafavi. PLOS Genetics.

2021
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Biologically relevant transfer learning improves transcription factor binding prediction

Gherman Novakovsky, Manu Saraswat, Oriol Fornes, Sara Mostafavi, Wyeth Wasserman. Genome Biology.

2021
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Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes

Evgeny Kiner, Elijah Willie, Brinda Vijaykumar, ..,Sara Mostafavi, Diane Mathis, Christophe Benoist. Nature Immunology.

2021
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Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies

Nicasia Beebe-Wang, Safiye Celik, ..., Sara Mostafavi$, Su-In Lee$. Nature Communications.

2021
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Deep learning decodes the principles of differential gene expression

Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Yanling Wang. Nature Machine Intelligence.

2020
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Deep learning of immune cell differentiation

Alexandra (Sasha) Maslova* , Ricardo Ramirez*, ... , Christophe Benoist$, Sara Mostafavi$. PNAS.

2020
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Deconvolving the contributions of cell-type heterogeneity on cortical gene expression

Ellis Patrick, Mariko Taga, Ayla Ergun, ... , Elizabeth Bradshaw$, Sara Mostafavi$. PLOS Computational Biology.

2020
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metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes.

Emma Graham Linck, Philip A. Richmond, ... , Mostafavi S. npj Genomic Medicine.

2020
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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
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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
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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
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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
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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
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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
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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
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Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes

Raj T, Rothamel K, Mostafavi S,..., De Jager PL. Science .

2014
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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
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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
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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
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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
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Predicting node characteristics from molecular networks

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

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

Mostafavi S and Morris Q. Bioinformatics .

2010
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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

Student Theses


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Advancing our understanding of genome regulation via optimization of stem cell differentiation and interpretable deep learning

Gherman Novakovsky.

2022
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Robust methods for identifying cluster structure in single-cell RNA-sequecing data

Elijah Willie.

2020
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Improving the estimation of Y chromosome loss using high-throughput sequencing

Michael Vermeulen.

2020
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Understanding gene regulatory mechanisms of mouse immune cells using a convolutional neural network

Alexandra (Sasha) Maslova.

2020
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Integration of genomic and metabolomic data for the prioritization of rare disease variants.

Emma Graham.

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

Farnush Farhadi Hassan Kiadeh.

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

Louie Dinh.

2017