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Li Shen, Ph.D.

Associate Professor, Center for Neuroimaging, Radiology and Imaging Sciences
Associate Director, Center for Computational Biology & Bioinformatics


Education/Training:
Ph.D., Dartmouth College (2004)

Multidimensional Brain Imaging Genomics.
The central theme of my research is to study computational and informatics methods for integrative analysis of multimodal imaging data, high throughput "omics" data, fluid and cognitive biomarker data, and rich biological knowledge such as pathways and networks, with applications to various complex disorders. The goal is twofold: (1) advance computer science and bioinformatics by producing novel algorithms for comprehensive joint analysis of large scale heterogeneous data sets; and (2) improve mechanistic understanding of disease processes and treatment responses for early diagnosis and therapeutics. Keywords describing my research areas include medical image computing, bioinformatics, imaging genomics, machine learning, network science, data intensive computing, visual analytics, and morphometric analysis.

Search for Dr. Shen on PubMed

Recent Publications:

1.      Shen L, Farid H, and McPeek MA (2009) Modeling 3-dimensional morphological structures using spherical harmonics. Evolution. 63(4):1003-1016. PMC2936781.

2.      Shen L, Saykin AJ, Firpi HA, West JD (2009) Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. Hippocampus, 19(6):588-95. PMID19405146.

3.      Shen L, Kim S, Risacher SL, Nho K, Swaminathan S, West JD, Foroud TM, Pankratz ND, Moore JH, Sloan CD, Huentelman MJ, Craig DW, DeChairo BM, Potkin SG, Jack CR, Weiner MW, Saykin AJ, ADNI (2010) Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. NeuroImage, 53:1051–1063. PMC2892122.

4.      Sloan C, Shen L, West J, Wishart H, Flashman L, Rabin L, Santulli R, Guerin S, Rhodes C, Tsongalis G, McAllister T, Ahles T, Lee S, Moore J, Saykin AJ (2010) Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes. Am J Med Genet Part B 153B:1060–1069. PMC3021757.

5.      Saykin AJ, Shen L, Foroud TM, Potkin SG, Swaminathan S, Kim S, Risacher SL, Nho K, Huentelman MJ, Craig DW, Thompson PM, Stein JL, Moore JH, Farrer LA, Green RC, Bertram L, Jack CR, Weiner MW, ADNI (2010) Alzheimer’s Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimer's and Dementia, 6:265–273. PMC2868595.

6.      Wan J, Kim S, Inlow M, Nho K, Swaminathan S, Risacher SL, Fang S, Weiner M, Beg F, Wang L, Saykin AJ, Shen L, ADNI (2011) Hippocampal surface mapping of genetic risk factors in AD via sparse learning models. MICCAI'11: Med Image Comput Comput Assist Interv, Lecture Notes in Computer Science, 6892:376-383. PMC3196668.

7.      Ramanan VK, Shen L, Moore JH, Saykin AJ (2012) Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends in Genetics, 28(7):323–332. PMC3378813.

8.      Wang H, Nie F, Huang H, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, for the ANDI (2012) Identifying quantitative trait loci via group-sparse multi-task regression and feature selection: An imaging genetics study of the ADNI cohort. Bioinformatics, 28(2):229-237. PMID22155867.

9.      Wang H, Nie F, Huang H, Risacher SL, Saykin AJ, Shen L, for the ADNI (2012) Identifying disease sensitive and quantitative trait relevant biomarkers from multi-dimensional heterogeneous imaging genetics data via sparse multi-modal multi-task learning. Bioinformatics, 28(12):i127-i136. PMC3371860.

10.   Wang H, Nie F, Huang H, Yan J, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, for the ADNI (2012) From phenotype to genotype: An association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs. Bioinformatics, 28(18):i619-i625. PMC3436838.

11.   Shen L, Ai H, Liang Y, Ren X, Anthony CB, Goodlett CR, Ward R, Zhou F (2013) Effect of prenatal alcohol exposure on bony craniofacial development: A mouse MicroCT study. Alcohol, 47(5): 405-415. PMID23809873.

12.   Shen L, Thompson PM, Potkin SG, Bertram L, Farrer LA, Foroud TM, Green RC, Hu X, Huentelman MJ, Kim S, Kauwe JSK, Li Q, Liu E, Macciardi F, Moore JH, Munsie L, Nho K, Ramanan VK, Risacher SL, Stone DJ, Swaminathan S, Toga AW, Weiner MW, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (2014) Genetic analysis of quantitative phenotypes in AD and MCI: Imaging, cognition and biomarkers. Brain Imaging and Behavior, 8:183-207. doi:10.1007/s11682-013-9262-z. PMID24092460.

13.   Wan J, Zhang Z, Rao BD, Fang S, Yan J, Saykin AJ, Shen L, for the ADNI (2014) Identifying the neuroanatomical basis of cognitive impairment in Alzheimer's disease by correlation- and nonlinearity-aware sparse Bayesian learning. IEEE Trans. on Medical Imaging, 33(7):1476-1488. PMID24710828.

14.   Yan J, Du L, Kim S, Risacher SL, Huang H, Moore JH, Saykin AJ, Shen L, for the ADNI (2014) Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. Bioinformatics, Vol. 30 ECCB 2014, pages i564–i571. PMID25161248.

15.   Yan J, Li T, Wang H, Huang H, Wan J, Nho K, Kim S, Risacher SL, Saykin AJ, Shen L, for the ADNI (2014) Cortical surface biomarkers for predicting cognitive outcomes using group L21 norm. Neurobiology of Aging, http://dx.doi.org/10.1016/j.neurobiolaging.2014.07.045.

Stark Neurosciences Research Institute | Neuroscience Research Building | 320 West 15th Street | Indianapolis, IN 46202 | Phone: (317) 278-5848 | FAX: (317) 231-0203