Yann Le Guen, Ph.D.

Assistant Director, Computational Biology
Dr. Le Guen joined Stanford University in 2019 and the QSU in 2022, with a computational biology background analyzing a variety of omics data. 
Dr. Le Guen graduated in 2015 from both Telecom Paris and the Imperial College London, respectively with an MSc in Computer Science and an MSc in Biomedical Engineering. Then, he pursued a PhD thesis in imaging genetics at Neurospin (Paris-Saclay University) analyzing MR images and genomics data to decipher the genetic causes underlying the well-characterized brain asymmetries which support the human language processing. He received his PhD in 2018 at the University Paris-Saclay and joined the Greicius lab where he is contributing to improve our understanding of the genetics causes of neurodegenerative diseases including Alzheimer’s and Parkinson’s diseases. While at Stanford University, he was awarded a highly selective European fellowship (Marie Skłodowska-Curie Actions, 2019 call) for the following proposal “A multimodal approach to accelerate drug discovery and development in Alzheimer’s disease”. The project aimed at integrating genomics data (whole-genome sequencing, transcriptomics, proteomics and other omics data) with deep phenotyping of Alzheimer' disease cases and cognitively unimpaired individuals (clinical characterization, blood and CSF biomarkers, as well as PET/MRI).


Clinical area of interest
Aging, Neurology, Neuroimaging and others
Methodology area of interest
Analysis of omics data including whole-genome and whole-exome sequencing, bulk and single-cell RNA sequencing (transcriptomics), proteomics, etc..
Selected Publications :

Le Guen Y*, Luo G*, Ambati A*, Damotte V*, Jansen I, Yu E, et al. Protective association of HLA-DRB1*04 subtypes in neurodegenerative diseases implicates acetylated Tau PHF6 sequences.



Le Guen Y, Belloy ME, Eger SJ, Chen A, Kennedy G, Thornton TA, Farrer LA, Napolioni V, He Z, Greicius MD. 2021. APOE Missense Variant R145C is Associated with Increased Alzheimer’s Disease Risk in African Ancestry Individuals with the APOE Ε3/Ε4 Genotype (SSRN Scholarly Paper No. ID 3975348). Rochester, NY: Social Science Research Network. 



Le Guen Y, Belloy ME, Grenier-Boley B, de Rojas I, Castillo A, Jansen I, et al. Rare APOE missense variant R251G counterbalances the Alzheimer’s disease risk associated with APOE-ε4. JAMA Neurology. Published online May 31st, 2022. 



Kassani PH, Lu F, Le Guen Y, He Z. 2021. Deep neural networks with controlled variable selection for the identification of putative causal genetic variants. arXiv:210914719 [cs, stat]. 


 Belloy ME, Eger SJ, Le Guen Y, Damotte V, Ahmad S, Ikram MA, et al. 2022. Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping. Alzheimer’s Research & Therapy. 14:22.


Eger SJ*, Le Guen Y*, Khan RR, Hall JN, Kennedy G, Zaharchuk G, et al. 2022. Confirming Pathogenicity of the F386L PSEN1 Variant in a South Asian Family With Early-Onset Alzheimer Disease. Neurology Genetics. 8.


He Z*, Le Guen Y*, Liu L, Lee J, Ma S, Yang AC, et al. 2021. Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics. The American Journal of Human Genetics. 108:2336–2353.


Le Guen Y, Belloy ME, Napolioni V, Eger SJ, Kennedy G, Tao R, et al. 2021. A novel age-informed approach for genetic association analysis in Alzheimer’s disease. Alzheimer’s Research & Therapy. 13:72.


Le Guen Y, Napolioni V, Belloy ME, Yu E, Krohn L, Ruskey JA, et al. 2021. Common X-Chromosome Variants Are Associated with Parkinson Disease Risk. Annals of Neurology. 90:22-34.


He Z, Liu L, Wang C, Le Guen Y, Lee J, Gogarten S, et al. 2021. Identification of putative causal loci in whole-genome sequencing data via knockoff statistics. Nature Communications. 12:3152.


Belloy ME, Eger SJ, Le Guen Y, Napolioni V, Deters KD, Yang H-S, et al. 2021. KLVS heterozygosity reduces brain amyloid in asymptomatic at-risk APOE4 carriers. Neurobiology of Aging. 101:123–129.


Karkar S, Dandine-Roulland C, Mangin JF, Le Guen Y, Philippe C, Deleuze JF, et al. 2021. Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects. European Journal of Human Genetics. 29:1424–1437.


Belloy ME*, Napolioni V*, Han SS, Le Guen Y, Greicius MD. 2020. Association of Klotho-VS Heterozygosity with Risk of Alzheimer Disease in Individuals Who Carry APOE4. JAMA Neurology 77:849–862.


Le Guen Y, Leroy F, Philippe I, IMAGEN Consortium, Mangin JF, Dehaene-Lambertz G, Frouin V, 2020. A DACT1 enhancer modulates brain asymmetric temporal regions involved in language processing. Cerebral Cortex. 30:5322-5332. 


Mangin JF, Le Guen Y, Labra N, Grigis A, Frouin V, Guevara M, Fischer C, Rivière D, Hopkins WD, Régis J, Sun ZY. 2019. “Plis de passage” Deserve a Role in Models of the Cortical Folding Process. Brain Topography. 32:1035–1048.


Le Guen Y, Philippe C, Riviere D, Lemaitre H, Grigis A, Fischer C, Dehaene-Lambertz G, Mangin JF, Frouin V. 2019. eQTL of KCNK2 regionally influences the brain sulcal widening: evidence from 15,597 UK Biobank participants with neuroimaging data. Brain Structure & Function. 224:847–857.


Lubba CH, Le Guen Y, Jarvis S, Jones NS, Cork SC, Eftekhar A, Schultz SR. 2019. PyPNS: Multiscale Simulation of a Peripheral Nerve in Python. Neuroinformatics. 17: 63-81.


Le Guen Y, Amalric M, Pinel P, Pallier C, Frouin V. 2018. Shared genetic aetiology between cognitive performance and brain activations in language and math tasks. Scientific Reports. 8:17624. 


Le Guen Y, Auzias G, Leroy F, Noulhiane, M, Dehaene-Lambertz G, Duchesnay E, Mangin JF, Coulon O, Frouin V. 2018. Genetic Influence on the Sulcal Pits: On the Origin of the First Cortical Folds. Cerebral Cortex. 28:1922–1933. 


Le Guen Y, Leroy F, Auzias G, Riviere D, Grigis A, Mangin JF, Coulon O, Dehaene-Lambertz G, Frouin V. 2018. The chaotic morphology of the left superior temporal sulcus is genetically constrained. Neuroimage. 174:297–307.