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Shinya Tasaki

TitleAssistant Professor
InstitutionRush University, Rush Medical College
DepartmentNeurological Sciences
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    Collapse Biography 
    Collapse awards and honors
    2007Research assistant fellowship, Medical Genome Science Program
    2008 - 2009Research assistant fellowship, Global Center of Excellence (G-CoE), Elucidation of Language Structure and Semantics behind Genome and Life Systems
    2014Senior Director's Award (CLK inhibitor), Takeda
    2014Director's Award (TRINTELLIX-antidepressant), Takeda
    2015Director's Award (RSLV132), Takeda

    Collapse Overview 
    Collapse overview
    Shinya Tasaki is a computational biologist at the Rush Alzheimer’s Disease Center and an assistant professor at Rush University Medical Center. His current research activities focus on building healthcare solutions for aging and Alzheimer’s disease by unifying different types of biomedical information. Before joining Rush, he worked in the pharmaceutical industry and experienced a broad range of drug discovery processes, such as target identification, portfolio prioritization, translational and personalized medicine. Data-driven hypotheses feed into collaborations with wet lab biologists and clinicians, and together we verify and refine the predictions to contribute to better healthcare programs.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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. Nat Genet. 2023 Dec; 55(12):2060-2064. PMID: 38036778.
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    2. Seidlitz J, Mallard TT, Vogel JW, Lee YH, Warrier V, Ball G, Hansson O, Hernandez LM, Mandal AS, Wagstyl K, Lombardo MV, Courchesne E, Glessner JT, Satterthwaite TD, Bethlehem RAI, Bernstock JD, Tasaki S, Ng B, Gaiteri C, Smoller JW, Ge T, Gur RE, Gandal MJ, Alexander-Bloch AF. The molecular genetic landscape of human brain size variation. Cell Rep. 2023 Nov 28; 42(11):113439. PMID: 37963017.
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    3. Gaiteri C, Connell DR, Sultan FA, Iatrou A, Ng B, Szymanski BK, Zhang A, Tasaki S. Robust, scalable, and informative clustering for diverse biological networks. Genome Biol. 2023 10 12; 24(1):228. PMID: 37828545.
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    4. Tang S, Buchman AS, Wang Y, Avey D, Xu J, Tasaki S, Bennett DA, Zheng Q, Yang J. Differential gene expression analysis based on linear mixed model corrects false positive inflation for studying quantitative traits. Sci Rep. 2023 10 03; 13(1):16570. PMID: 37789141.
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    5. 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. bioRxiv. 2023 Sep 28. PMID: 36993652.
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    6. Lopes KP, Yu L, Shen X, Qiu Y, Tasaki S, Iatrou A, Beeri MS, Seyfried NT, Menon V, Wang Y, Schneider JA, Cantor H, Bennett DA. Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adults. Alzheimers Dement. 2023 Sep 19. PMID: 37727065.
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    7. Tasaki S, Kim N, Truty T, Zhang A, Buchman AS, Lamar M, Bennett DA. Explainable deep learning approach for extracting cognitive features from hand-drawn images of intersecting pentagons. NPJ Digit Med. 2023 Aug 23; 6(1):157. PMID: 37612472.
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    8. Ng B, Tasaki S, Greathouse KM, Walker CK, Zhang A, Covitz S, Cieslak M, Adamson AB, Andrade JP, Poovey EH, Curtis KA, Muhammad HM, Seidlitz J, Satterthwaite T, Bennett DA, Seyfried NT, Vogel J, Gaiteri C, Herskowitz JH. A Molecular Basis of Human Brain Connectivity. bioRxiv. 2023 Jul 24. PMID: 37546752.
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    9. Parrish RL, Buchman AS, Tasaki S, Wang Y, Avey D, Xu J, De Jager PL, Bennett DA, Epstein MP, Yang J. SR-TWAS: Leveraging Multiple Reference Panels to Improve TWAS Power by Ensemble Machine Learning. medRxiv. 2023 Jun 27. PMID: 37425698.
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    10. Li J, Capuano AW, Agarwal P, Arvanitakis Z, Wang Y, De Jager PL, Schneider JA, Tasaki S, de Paiva Lopes K, Hu FB, Bennett DA, Liang L, Grodstein F. The MIND diet, brain transcriptomic alterations, and dementia. medRxiv. 2023 Jun 13. PMID: 37398494.
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    11. Yao Q, Mascarenhas Dos Santos AC, Zhang H, Ma?as A, Hussaini A, Kim U, Xu C, Basheer S, Tasaki S, Xiang J. Unconventional Source of Neurotoxic Protein Aggregation from Organelle Off-Target Bax?2 in Alzheimer's Disease. Biomolecules. 2023 06 10; 13(6). PMID: 37371550.
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    12. Yu L, Petyuk VA, Lopes KP, Tasaki S, Menon V, Wang Y, Schneider JA, De Jager PL, Bennett DA. Associations of VGF with Neuropathologies and Cognitive Health in Older Adults. Ann Neurol. 2023 08; 94(2):232-244. PMID: 37177846.
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    13. Tasaki S, Kim N, Truty T, Zhang A, Buchman AS, Lamar M, Bennett DA. Interpretable deep learning approach for extracting cognitive features from hand-drawn images of intersecting pentagons in older adults. bioRxiv. 2023 Apr 19. PMID: 37131841.
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    14. Buchman AS, Yu L, Klein HU, Zammit AR, Oveisgharan S, Grodstein F, Tasaki S, Levey AI, Seyfried NT, Bennett DA. Proteome-Wide Discovery of Cortical Proteins That May Provide Motor Resilience to Offset the Negative Effects of Pathologies in Older Adults. J Gerontol A Biol Sci Med Sci. 2023 03 01; 78(3):494-503. PMID: 35512265.
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    15. Oveisgharan S, Yang J, Yu L, Burba D, Bang W, Tasaki S, Grodstein F, Wang Y, Zhao J, De Jager PL, Schneider JA, Bennett DA. Estrogen Receptor Genes, Cognitive Decline, and Alzheimer Disease. Neurology. 2023 04 04; 100(14):e1474-e1487. PMID: 36697247.
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    16. Tasaki S, Xu J, Avey DR, Johnson L, Petyuk VA, Dawe RJ, Bennett DA, Wang Y, Gaiteri C. Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks. Nat Commun. 2022 02 03; 13(1):655. PMID: 35115553.
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    17. 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 Genet. 2021 11; 17(11):e1009918. PMID: 34807913.
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    18. Lagomarsino VN, Pearse RV, Liu L, Hsieh YC, Fernandez MA, Vinton EA, Paull D, Felsky D, Tasaki S, Gaiteri C, Vardarajan B, Lee H, Muratore CR, Benoit CR, Chou V, Fancher SB, He A, Merchant JP, Duong DM, Martinez H, Zhou M, Bah F, Vicent MA, Stricker JMS, Xu J, Dammer EB, Levey AI, Chibnik LB, Menon V, Seyfried NT, De Jager PL, Noggle S, Selkoe DJ, Bennett DA, Young-Pearse TL. Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donors. Neuron. 2021 11 03; 109(21):3402-3420.e9. PMID: 34473944.
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    19. Buchman AS, Yu L, Oveisgharan S, Petyuk VA, Tasaki S, Gaiteri C, Wilson RS, Grodstein F, Schneider JA, Klein HU, De Jager PL, Bennett DA. Cortical proteins may provide motor resilience in older adults. Sci Rep. 2021 05 28; 11(1):11311. PMID: 34050212.
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    20. Yu L, Tasaki S, Schneider JA, Arfanakis K, Duong DM, Wingo AP, Wingo TS, Kearns N, Thatcher GRJ, Seyfried NT, Levey AI, De Jager PL, Bennett DA. Cortical Proteins Associated With Cognitive Resilience in Community-Dwelling Older Persons. JAMA Psychiatry. 2020 11 01; 77(11):1172-1180. PMID: 32609320.
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    21. Tasaki S, Gaiteri C, Mostafavi S, Wang Y. Deep learning decodes the principles of differential gene expression. Nat Mach Intell. 2020 Jul; 2(7):376-386. PMID: 32671330.
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    22. Inamo J, Suzuki K, Takeshita M, Kassai Y, Takiguchi M, Kurisu R, Okuzono Y, Tasaki S, Yoshimura A, Takeuchi T. Identification of novel genes associated with dysregulation of B cells in patients with primary Sj?gren's syndrome. Arthritis Res Ther. 2020 06 22; 22(1):153. PMID: 32571405.
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    23. Kaneshwaran K, Olah M, Tasaki S, Yu L, Bradshaw EM, Schneider JA, Buchman AS, Bennett DA, De Jager PL, Lim ASP. Sleep fragmentation, microglial aging, and cognitive impairment in adults with and without Alzheimer's dementia. Sci Adv. 2019 12; 5(12):eaax7331. PMID: 31844665.
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    24. Tasaki S, Gaiteri C, Petyuk VA, Blizinsky KD, De Jager PL, Buchman AS, Bennett DA. Genetic risk for Alzheimer's dementia predicts motor deficits through multi-omic systems in older adults. Transl Psychiatry. 2019 10 03; 9(1):241. PMID: 31582723.
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    25. 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. Am J Hum Genet. 2019 09 05; 105(3):562-572. PMID: 31447098.
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    26. Buchman AS, Yu L, Petyuk VA, Gaiteri C, Tasaki S, Blizinsky KD, Schneider JA, De Jager PL, Bennett DA. Cognition may link cortical IGFBP5 levels with motor function in older adults. PLoS One. 2019; 14(8):e0220968. PMID: 31404102.
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    27. 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 Behav. 2019 Aug; 13(4):963-972. PMID: 29934819.
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    28. Arakawa Y, Yokoyama K, Tasaki S, Kato J, Nakashima K, Takeyama M, Nakatani A, Suzuki M. Transgenic mice overexpressing miR-137 in the brain show schizophrenia-associated behavioral deficits and transcriptome profiles. PLoS One. 2019; 14(7):e0220389. PMID: 31361772.
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    29. Yu L, Petyuk VA, Tasaki S, Boyle PA, Gaiteri C, Schneider JA, De Jager PL, Bennett DA. Association of Cortical ?-Amyloid Protein in the Absence of Insoluble Deposits With Alzheimer Disease. JAMA Neurol. 2019 07 01; 76(7):818-826. PMID: 31009033.
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    30. Tasaki S, Gaiteri C, Mostafavi S, De Jager PL, Bennett DA. The Molecular and Neuropathological Consequences of Genetic Risk for Alzheimer's Dementia. Front Neurosci. 2018; 12:699. PMID: 30349450.
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    31. Lim ASP, Gaiteri C, Yu L, Sohail S, Swardfager W, Tasaki S, Schneider JA, Paquet C, Stuss DT, Masellis M, Black SE, Hugon J, Buchman AS, Barnes LL, Bennett DA, De Jager PL. Seasonal plasticity of cognition and related biological measures in adults with and without Alzheimer disease: Analysis of multiple cohorts. PLoS Med. 2018 09; 15(9):e1002647. PMID: 30180184.
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    32. 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. Front Genet. 2018; 9:294. PMID: 30140277.
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    33. Tasaki S, Suzuki K, Kassai Y, Takeshita M, Murota A, Kondo Y, Ando T, Nakayama Y, Okuzono Y, Takiguchi M, Kurisu R, Miyazaki T, Yoshimoto K, Yasuoka H, Yamaoka K, Morita R, Yoshimura A, Toyoshiba H, Takeuchi T. Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission. Nat Commun. 2018 07 16; 9(1):2755. PMID: 30013029.
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    34. 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, Yu L, Chibnik LB, Schneider JA, Young-Pearse TL, Bennett DA, De Jager PL. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nat Neurosci. 2018 06; 21(6):811-819. PMID: 29802388.
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    35. Tasaki S, Suzuki K, Nishikawa A, Kassai Y, Takiguchi M, Kurisu R, Okuzono Y, Miyazaki T, Takeshita M, Yoshimoto K, Yasuoka H, Yamaoka K, Ikeura K, Tsunoda K, Morita R, Yoshimura A, Toyoshiba H, Takeuchi T. Multiomic disease signatures converge to cytotoxic CD8 T cells in primary Sj?gren's syndrome. Ann Rheum Dis. 2017 Aug; 76(8):1458-1466. PMID: 28522454.
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    36. Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S. CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. Nat Commun. 2017 02 23; 8(1):7. PMID: 28232751.
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    37. Tasaki S, Sauerwine B, Hoff B, Toyoshiba H, Gaiteri C, Chaibub Neto E. Bayesian network reconstruction using systems genetics data: comparison of MCMC methods. Genetics. 2015 Apr; 199(4):973-89. PMID: 25631319.
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    38. Kozuka-Hata H, Tasaki S, Oyama M. Phosphoproteomics-based systems analysis of signal transduction networks. Front Physiol. 2011; 2:113. PMID: 22291655.
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    39. Kurotaki N, Tasaki S, Mishima H, Ono S, Imamura A, Kikuchi T, Nishida N, Tokunaga K, Yoshiura K, Ozawa H. Identification of novel schizophrenia loci by homozygosity mapping using DNA microarray analysis. PLoS One. 2011; 6(5):e20589. PMID: 21655227.
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    40. Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, Oyama M. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS One. 2010 Nov 10; 5(11):e13926. PMID: 21085658.
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    41. Ono S, Imamura A, Tasaki S, Kurotaki N, Ozawa H, Yoshiura K, Okazaki Y. Failure to confirm CNVs as of aetiological significance in twin pairs discordant for schizophrenia. Twin Res Hum Genet. 2010 Oct; 13(5):455-60. PMID: 20874467.
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    42. Oyama M, Kozuka-Hata H, Tasaki S, Semba K, Hattori S, Sugano S, Inoue J, Yamamoto T. Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networks. Mol Cell Proteomics. 2009 Feb; 8(2):226-31. PMID: 18815124.
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    43. Tasaki S, Nagasaki M, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform. 2006; 17(2):226-38. PMID: 17503395.
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