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Sara Mostafavi, Ph.D. - Publications

Affiliations: 
2011 Computer Science University of Toronto, Toronto, ON, Canada 
Area:
Computational biology
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sasse A, Ng B, Spiro AE, Tasaki S, Bennett DA, Gaiteri C, De Jager PL, Chikina M, Mostafavi S. Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings. Nature Genetics. PMID 38036778 DOI: 10.1038/s41588-023-01524-6  0.307
2021 Ng B, Casazza W, Kim NH, Wang C, Farhadi F, Tasaki S, Bennett DA, De Jager PL, Gaiteri C, Mostafavi S. Cascading epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variants. Plos Genetics. 17: e1009918. PMID 34807913 DOI: 10.1371/journal.pgen.1009918  0.354
2020 Graham Linck EJ, Richmond PA, Tarailo-Graovac M, Engelke U, Kluijtmans LAJ, Coene KLM, Wevers RA, Wasserman W, van Karnebeek CDM, Mostafavi S. metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes. Npj Genomic Medicine. 5: 25. PMID 33579969 DOI: 10.1038/s41525-020-0132-5  0.34
2020 Wright GEB, Caron NS, Ng B, Casal L, Casazza W, Xu X, Ooi J, Pouladi MA, Mostafavi S, Ross CJD, Hayden MR. Gene expression profiles complement the analysis of genomic modifiers of the clinical onset of Huntington disease. Human Molecular Genetics. PMID 32898862 DOI: 10.1093/Hmg/Ddaa184  0.464
2020 Patrick E, Taga M, Ergun A, Ng B, Casazza W, Cimpean M, Yung C, Schneider JA, Bennett DA, Gaiteri C, De Jager PL, Bradshaw EM, Mostafavi S. Deconvolving the contributions of cell-type heterogeneity on cortical gene expression. Plos Computational Biology. 16: e1008120. PMID 32804935 DOI: 10.1371/Journal.Pcbi.1008120  0.354
2020 Tasaki S, Gaiteri C, Mostafavi S, Wang Y. Deep learning decodes the principles of differential gene expression. Nature Machine Intelligence. 2: 376-386. PMID 32671330 DOI: 10.1038/S42256-020-0201-6  0.425
2020 Richmond PA, van der Kloet F, Vaz FM, Lin D, Uzozie A, Graham E, Kobor M, Mostafavi S, Moerland PD, Lange PF, van Kampen AHC, Wasserman WW, Engelen M, Kemp S, van Karnebeek CDM. Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy. Frontiers in Cell and Developmental Biology. 8: 520. PMID 32671069 DOI: 10.3389/Fcell.2020.00520  0.338
2020 Wan YW, Al-Ouran R, Mangleburg CG, Perumal TM, Lee TV, Allison K, Swarup V, Funk CC, Gaiteri C, Allen M, Wang M, Neuner SM, Kaczorowski CC, Philip VM, Howell GR, ... ... Mostafavi S, et al. Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models. Cell Reports. 32: 107908. PMID 32668255 DOI: 10.1016/J.Celrep.2020.107908  0.354
2020 Graham Linck EJ, Richmond PA, Tarailo-Graovac M, Engelke U, Kluijtmans LAJ, Coene KLM, Wevers RA, Wasserman W, van Karnebeek CDM, Mostafavi S. metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes. Npj Genomic Medicine. 5: 25. PMID 32637154 DOI: 10.1038/S41525-020-0132-5  0.442
2020 Yang HS, White CC, Klein HU, Yu L, Gaiteri C, Ma Y, Felsky D, Mostafavi S, Petyuk VA, Sperling RA, Ertekin-Taner N, Schneider JA, Bennett DA, De Jager PL. Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology. Neuron. PMID 32526197 DOI: 10.1016/J.Neuron.2020.05.010  0.43
2019 Aristizabal MJ, Anreiter I, Halldorsdottir T, Odgers CL, McDade TW, Goldenberg A, Mostafavi S, Kobor MS, Binder EB, Sokolowski MB, O'Donnell KJ. Biological embedding of experience: A primer on epigenetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 31624126 DOI: 10.1073/Pnas.1820838116  0.339
2019 Ng B, Casazza W, Patrick E, Tasaki S, Novakovsky G, Felsky D, Ma Y, Bennett DA, Gaiteri C, De Jager PL, Mostafavi S. Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain. American Journal of Human Genetics. PMID 31447098 DOI: 10.1016/J.Ajhg.2019.07.016  0.437
2019 Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, ... ... Mostafavi S, et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell. PMID 30686579 DOI: 10.1016/J.Cell.2018.12.036  0.353
2018 Tasaki S, Gaiteri C, Mostafavi S, De Jager PL, Bennett DA. The Molecular and Neuropathological Consequences of Genetic Risk for Alzheimer's Dementia. Frontiers in Neuroscience. 12: 699. PMID 30349450 DOI: 10.3389/Fnins.2018.00699  0.303
2018 Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, Wang YC, Ng B, Gupta I, Haroutunian V, Schadt EE, Young-Pearse T, Mostafavi S, Zhang B, Sklar P, et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility. Nature Genetics. PMID 30297968 DOI: 10.1038/S41588-018-0238-1  0.374
2018 Tasaki S, Gaiteri C, Mostafavi S, Yu L, Wang Y, De Jager PL, Bennett DA. Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. Frontiers in Genetics. 9: 294. PMID 30140277 DOI: 10.3389/Fgene.2018.00294  0.419
2018 Gaiteri C, Dawe R, Mostafavi S, Blizinsky KD, Tasaki S, Komashko V, Yu L, Wang Y, Schneider JA, Arfanakis K, De Jager PL, Bennett DA. Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristics. Brain Imaging and Behavior. PMID 29934819 DOI: 10.1007/S11682-018-9910-4  0.398
2018 Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA. Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia. Annals of Neurology. PMID 29908079 DOI: 10.1002/Ana.25266  0.403
2018 Mostafavi S, Gaiteri C, Sullivan SE, White CC, Tasaki S, Xu J, Taga M, Klein HU, Patrick E, Komashko V, McCabe C, Smith R, Bradshaw EM, Root DE, Regev A, et al. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nature Neuroscience. 21: 811-819. PMID 29802388 DOI: 10.1038/S41593-018-0154-9  0.349
2018 Graham E, Lee J, Price M, Tarailo-Graovac M, Matthews A, Engelke U, Tang J, Kluijtmans LAJ, Wevers RA, Wasserman WW, van Karnebeek CDM, Mostafavi S. Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review. Journal of Inherited Metabolic Disease. PMID 29721916 DOI: 10.1007/S10545-018-0139-6  0.323
2017 Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nature Biotechnology. PMID 29227470 DOI: 10.1038/Nbt.4042  0.322
2017 Ng B, White CC, Klein HU, Sieberts SK, McCabe C, Patrick E, Xu J, Yu L, Gaiteri C, Bennett DA, Mostafavi S, De Jager PL. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nature Neuroscience. PMID 28869584 DOI: 10.1038/Nn.4632  0.358
2017 Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A. Allele-specific expression reveals interactions between genetic variation and environment. Nature Methods. PMID 28530654 DOI: 10.1038/Nmeth.4298  0.338
2016 Moodley D, Yoshida H, Mostafavi S, Asinovski N, Ortiz-Lopez A, Symanowicz P, Telliez JB, Hegen M, Clark JD, Mathis D, Benoist C. Network pharmacology of JAK inhibitors. Proceedings of the National Academy of Sciences of the United States of America. PMID 27516546 DOI: 10.1073/Pnas.1610253113  0.348
2016 Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA. Genetic variants in Alzheimer disease - molecular and brain network approaches. Nature Reviews. Neurology. PMID 27282653 DOI: 10.1038/Nrneurol.2016.84  0.331
2016 Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, ... ... Mostafavi S, et al. Impact of the X Chromosome and sex on regulatory variation. Genome Research. PMID 27197214 DOI: 10.1101/Gr.197897.115  0.355
2016 Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, et al. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell. 164: 564-578. PMID 26824662 DOI: 10.1016/J.Cell.2015.12.032  0.364
2015 Pierson E, Koller D, Battle A, Mostafavi S, Ardlie KG, Getz G, Wright FA, Kellis M, Volpi S, Dermitzakis ET. Sharing and Specificity of Co-expression Networks across 35 Human Tissues. Plos Computational Biology. 11: e1004220. PMID 25970446 DOI: 10.1371/Journal.Pcbi.1004220  0.407
2015 Holm A, Lin L, Faraco J, Mostafavi S, Battle A, Zhu X, Levinson DF, Han F, Gammeltoft S, Jennum P, Mignot E, Kornum BR. EIF3G is associated with narcolepsy across ethnicities. European Journal of Human Genetics : Ejhg. PMID 25669430 DOI: 10.1038/Ejhg.2015.4  0.339
2014 Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. Journal of Immunology (Baltimore, Md. : 1950). 193: 4485-96. PMID 25267973 DOI: 10.4049/Jimmunol.1401280  0.425
2014 Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science (New York, N.Y.). 344: 519-23. PMID 24786080 DOI: 10.1126/Science.1249547  0.324
2014 Davies MN, Krause L, Bell JT, Gao F, Ward KJ, Wu H, Lu H, Liu Y, Tsai PC, Collier DA, Murphy T, Dempster E, Mill J, Battle A, ... Mostafavi S, et al. Hypermethylation in the ZBTB20 gene is associated with major depressive disorder. Genome Biology. 15: R56. PMID 24694013 DOI: 10.1186/Gb-2014-15-4-R56  0.304
2014 Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB. Transcriptome analysis reveals differential splicing events in IPF lung tissue. Plos One. 9: e92111. PMID 24647608 DOI: 10.1371/Journal.Pone.0092111  0.394
2014 Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, et al. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular Psychiatry. 19: 1267-74. PMID 24296977 DOI: 10.1038/Mp.2013.161  0.431
2014 Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Research. 24: 14-24. PMID 24092820 DOI: 10.1101/Gr.155192.113  0.425
2014 Raj T, Replogle JM, Ryan K, Chibnik L, Ye J, Mostafavi S, Lee M, Rothamel K, McCabe C, Korff AV, Bradshaw EM, Evans D, Bennett D, Benoist C, Stranger B, et al. Expression Qtl Analysis From Primary Immune Cells Identifies Novel Regulatory Effects Underlying Alzheimer'S Disease Susceptibility Alzheimers & Dementia. 10: 216. DOI: 10.1016/J.Jalz.2014.04.290  0.314
2013 Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D. Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge. Plos One. 8: e68141. PMID 23874524 DOI: 10.1371/Journal.Pone.0068141  0.322
2013 Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, ... ... Mostafavi S, et al. The Genotype-Tissue Expression (GTEx) project Nature Genetics. 45: 580-585. PMID 23715323 DOI: 10.1038/Ng.2653  0.353
2012 Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of propagation. Plos One. 7: e51947. PMID 23284828 DOI: 10.1371/Journal.Pone.0051947  0.556
2012 Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics. 12: 1687-96. PMID 22589215 DOI: 10.1002/Pmic.201100607  0.63
2011 Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics (Oxford, England). 27: 3166-72. PMID 21965819 DOI: 10.1093/Bioinformatics/Btr533  0.721
2011 Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods in Molecular Biology (Clifton, N.J.). 781: 399-414. PMID 21877293 DOI: 10.1007/978-1-61779-276-2_20  0.604
2011 Schimmer BP, Tsao J, Cordova M, Mostafavi S, Morris Q, Scheys JO. Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells. Molecular and Cellular Endocrinology. 336: 85-91. PMID 21111771 DOI: 10.1016/J.Mce.2010.11.024  0.563
2010 Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research. 38: W214-20. PMID 20576703 DOI: 10.1093/Nar/Gkq537  0.621
2010 Mostafavi S, Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (Oxford, England). 26: 1759-65. PMID 20507895 DOI: 10.1093/Bioinformatics/Btq262  0.609
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/Science.1180823  0.609
2010 Knott S, Mostafavi S, Mousavi P. A neural network based modeling and validation approach for identifying gene regulatory networks Neurocomputing. 73: 2419-2429. DOI: 10.1016/J.Neucom.2010.04.018  0.319
2009 Mostafavi S, Morris Q. Using the Gene Ontology hierarchy when predicting gene function Proceedings of the 25th Conference On Uncertainty in Artificial Intelligence, Uai 2009. 419-427.  0.579
2008 Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biology. 9: S4. PMID 18613948 DOI: 10.1186/Gb-2008-9-S1-S4  0.593
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/Gb-2008-9-S1-S2  0.603
2007 Otaegui D, Mostafavi S, Bernard CC, Lopez de Munain A, Mousavi P, Oksenberg JR, Baranzini SE. Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosis. Journal of Immunology (Baltimore, Md. : 1950). 179: 4074-82. PMID 17785846 DOI: 10.4049/Jimmunol.179.6.4074  0.335
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