Journal Articles

Wang H, Nie F, Huang H, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, for the Alzheimer’s Disease Neuroimaging Initiative. Identifying quantitative trait loci via group-sparse multi-task regression and feature selection: An imaging genetics study of the ADNI cohort. Bioinformatics, 2012, in press. doi: 10.1093/bioinformatics/btr649.

Swaminathan S, Shen L, Kim S, Inlow M, West JD, Faber KM, Foroud T, Mayeux R, Saykin AJ, ADNI,  and the NIA-LOAD/NCRAD Family Study Group. Analysis of copy number variation in Alzheimer's disease: the NIA-LOAD/NCRAD family study. Current Alzheimer Research, 2012, in press.

Meda SA, Narayanan B, Liu J, Perrone-Bizzozero NI,Stevens MC,Calhoun VD, Glahn DC, Shen L, Risacher SL, Saykin AJ, Pearlson GD. A large scale multivariate parallel ICA method reveals novel imaging-genetic relationships for Alzheimer ’s disease in the ADNI cohort. Neuroimage, 2012, in press.

Journal Articles

Swaminathan S, Shen L, Risacher SL, Yoder KK, West JD, Kim S, Nho K, Foroud T, Inlow M, Potkin SG, Huentelman MJ, Craig DW, Jagust WJ, Koeppe RA, Mathis CA, Jack CR, Weiner MW, Saykin AJ and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Amyloid pathway-based candidate gene analysis of [11C]PiB-PET in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort.  Brain Imaging and Behavior (in press); doi:10.1007/s11682-011-9136-1.

Hibar D, Stein JL, Kohannim O, Jahanshad N, Saykin AJ, Shen L, Kim S, Pankratz N, Foroud F, Huentelman MJ, Potkin SG, Jack CR, Weiner MW, Toga AW, Thompson PM, and ADNI. Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects. Neuroimage, 56 :1875–1891, 2011. doi:10.1016/j.neuroimage.2011.03.077.

Swaminathan S, Kim S, Shen L, Risacher SL, Foroud T, Pankratz N, Potkin SG, Huentelman MJ, Craig DW, Weiner MW, Saykin AJ, and ADNI. Genomic copy number analysis in Alzheimer's disease and MCI: An ADNI Study. International Journal of Alzheimer’s Disease, vol. 2011, Article ID 729478, 10 pages, 2011. doi:10.4061/2011/729478.

Wang Y, Saykin AJ, Pfeufer J, Lin C, Mosier KM, Shen L, Kim S, Hutchins GD. Region dependent reliability and reproducibility of pulsed arterial spin labeling perfusion imaging at 3T. Neuroimage, 54(2):188-1195, 2011. doi:10.1016/j.neuroimage.2010.08.043

Kim S, Swaminathan S, Shen L, Risacher SL, Nho K, Foroud T, Shaw LM, Trojanowski, JQ, Potkin SG, Huentelman MJ, Craig DW, DeChairo BM, Aisen PS, Petersen RC, Weiner MW, Saykin AJ, ADNI. Genome-wide association study of CSF biomarkers Abeta-42, t-tau, and p-tau181p in the ADNI cohort. Neurology, 76:69-79, 2011. 10.1212/WNL.0b013e318204a397.

Furney SJ, Simmons A, Breen G, Pedroso I, Lunnon K, Proitsi P, Hodges A, Powell J, Wahlund LO, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Spenger C, Lathrop M, Shen L, Kim S, Saykin AJ, Weiner MW, Lovestone S, ADNI, and AddNeuroMed. Genome wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer’s disease. Molecular Psychiatry, Pub Ahead of Print on 11/30/2010 as doi: 10.1038/mp.2010.123.

Book Chapters

Shen L, Kim S, Wan J, West JD, Saykin AJ. Fourier methods for 3D surface modeling and analysis. Emerging Topics in Computer Vision and Its Applications, World Scientific Pub Co Inc, 2011. Book Chapter

Singh RP, Shen L, Zhou FC. The stereology and 3D volume analyses in nervous tissue. Animal Models of Acute Neurological Injuries II: Injury and Mechanistic Assessments. Section 1, Chapter 93.  Humana Press, 2011, in press.

Full Length, Peer Reviewed Conference Papers

Wang H, Nie F, Huang H, Risacher SL, Ding C, Saykin AJ, Shen L. Sparse multi-task regression and feature selection to identify brain imaging predictors for memory performance. ICCV 2011: IEEE Conference on Computer Vision, pages 557-562, November 6-13 2011, Barcelona, Spain.

Nho K, Shen L, Kim S, Risacher SL, Swaminathan S, Saykin AJ. The effect of reference datasets and software tools on genotype imputation. AMIA 2011: The American Medical Informatics Association Annual Symposium, October 22-26, 2011, Washington, DC.

Wang H, Nie F, Huang H, Risacher SL, Saykin AJ, Shen L, ADNI. Identifying AD-sensitive and cognition-relevant imaging biomarkers via joint classification and regression. MICCAI 2011, Lecture Notes in Computer Science (LNCS) 6893:115–123, Springer, Heidelberg, 2011. Selected for a platform talk. [acceptance for oral paper 4.15%, 34/819]

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. Hippocampal surface mapping of genetic risk factors in AD via sparse learning models. MICCAI 2011, Lecture Notes in Computer Science (LNCS) 6892:376-383, Springer, Heidelberg, 2011. [acceptance 30%]

Shen L, Kim S, Qi Y, Inlow M, Swaminathan S, Nho K, Wan J, Risacher S, Shaw L, Trojanowski J, Weiner M, Saykin A, ADNI. Identifying neuroimaging and proteomic biomarkers for MCI and AD via the elastic net. MBIA 2011: Lecture Notes in Computer Science (LNCS) 7012:27-34, Springer, Heidelberg, 2011.

Peer Reviewed Conference Abstracts

Swaminathan S, Shen L, Kim S, Inlow M, West JD, Foroud T, Faber KM, Mayeux R, Saykin AJ, The NIA-LOAD/NCRAD Family Study Group. Analysis of copy number variation in Alzheimer's disease: the NIA-LOAD/NCRAD Family Study. ICHG 2011: 12th International Congress of Human Genetics. 10/11-15/2011, Montreal, Canada.

Risacher SL, Shen L, West JD, Flashman LA, Wishart HA, Rabin LA, Paré N, Englert JJ, Schwartz ES, Kim S, McDonald BC, Curtain JR, Pixley HS, Santulli RB, Saykin AJ. Longitudinal Structural MRI Changes in Alzheimer's Disease, Mild Cognitive Impairment, and Older Adults with Cognitive Complaints: Relationship to Conversion Status. AAIC 2011: International Conference on Alzheimer's Disease (ICAD), July 16-21, Paris, France.

Kim S, Swaminathan S, Inlow M, Risacher SL, Shen L, Foroud T, Shaw LM, Trojanowski JQ, Soares H, Weiner MW, Saykin AJ, ADNI. Influence of genetic variation on plasma proteomics in AD, MCI and controls: Pairwise gene-protein analysis in the ADNI-1 cohort. AAIC 2011: International Conference on Alzheimer's Disease (ICAD), July 16-21, Paris, France.

Swaminathan S, Risacher SL, Yoder KK, West JD, Shen L, Kim S, Inlow M, Foroud T, Jagust WJ, Koeppe RA, Mathis CA, Shaw LM, Trojanowski JQ, Soares H, Aisen PS, Petersen RC, Weiner MW, Saykin AJ, ADNI. APOE E4 status modulates the association of plasma and cortical AB: Relation of plasma AB and [11C]PiB PET in the ADNI cohort. AAIC 2011: International Conference on Alzheimer's Disease (ICAD), July 16-21, Paris, France.

Hemond CC, Nho K, Shen L, Risacher SL, Kim S, Saykin AJ, Greicius MD, ADNI. Reelin interacts with ApoE to exacerbate Alzheimer's disease endophenotypes. AAIC 2011: International Conference on Alzheimer's Disease (ICAD), July 16-21, Paris, France.

Shen L, Qi Y, Kim S, Nho K, Wan J, Risacher S, Saykin AJ, ADNI. Sparse Bayesian learning for predicting mci conversion to ad and identifying mri biomarkers. OHBM’11: 17th Annual Meeting of the Organization for Human Brain Mapping, June 26-30, 2011, Québec City, Canada.

Wan J, Kim S, Nho K, Risacher S, Swaminathan S, Bertram L, Jack C, Weiner M, Beg F, Wang L, Saykin AJ, Shen L, ADNI. Influence of candidate AlzGene SNPs on hippocampal shape: A study of the ADNI cohort. OHBM’11: 17th Annual Meeting of the Organization for Human Brain Mapping, June 26-30, 2011, Québec City, Canada.

Conroy SK, Nho K, McDonald BC, Risacher SL, Kim S, Shen L, Saykin AJ, ADNI. ESR1 genetic variation differentially influences several aspects of brain morphology by gender in cognitively normal elders: A voxel-based morphometry and SurfStat analysis of the ADNI cohort. OHBM’11: 17th Annual Meeting of the Organization for Human Brain Mapping, June 26-30, 2011, Québec City, Canada.

Hibar D, Stein JL, Kohannim O, Jahanshad N, Saykin AJ, Shen L, Kim S, Pankratz N, Foroud F, Huentelman MJ, Potkin SG, Jack CR, Weiner MW, Toga AW, Thompson PM, and ADNI. Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects. OHBM’11: 17th Annual Meeting of the Organization for Human Brain Mapping, June 26-30, 2011, Québec City, Canada.

Shen L, Ai H, Liang Y, Wan J, Anthony B, Zhou FC, and the CIFASD Consortium. Influence of fetal alcohol on nasal bone development in c57bl/6j mouse models. RSA’11: 34th Annual RSA (Research Society on Alcoholism) Scientific Meeting, June 25-29, 2011, Atlanta, Georgia.

Wan J, Fang S, Vinci-Booher S, Rogers J, Wetherill L, Robinson L, Hoyme E, Molteno C, Foroud T, Jacobson J, Jacobson S, Shen L, and the CIFASD Consortium. Effects of fetal alcohol on 3D facial morphology using surface-based morphometry. RSA’11: 34th Annual RSA (Research Society on Alcoholism) Scientific Meeting, June 25-29, 2011, Atlanta, Georgia.

Journal Articles

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, and ADNI. 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, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.01.042. [preprint]

Shen L, Saykin AJ, Kim S, Firpi H, West J, Risacher SL, McDonald BC, McHugh TL, Wishart HA, Flashman LA. Comparison of manual and automated determination of hippocampal volumes in MCI and older adults with cognitive complaints. Brain Imaging and Behavior, 4:86–95, 2010. http://dx.doi.org/doi:10.1007/s11682-010-9088-x. [preprint]

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. Alzheimer’s Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimer's and Dementia, 6:265–273, 2010. http://dx.doi.org/doi:10.1016/j.jalz.2010.03.013. [PMC]

Risacher SL, Shen L, West JD, Kim S, McDonald BC, Beckett LA, Jack CR Jr, Weiner MW, Saykin AJ, and ADNI. Longitudinal MRI atrophy biomarkers: Relationship to conversion in the ADNI cohort. Neurobiology of Aging, 31(8):1401-1418. Doi:10.1016/j.neurobiolaging.2010.04.029,  NIHMSID: NIHMS203913. [PubMed]

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 A. Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 153B:1060-1069, 2010. http://dx.doi.org/doi:10.1002/ajmg.b.31078.

Ho AJ, Stein JL, Hua X, Lee S, Hibar DP, Leow AD, Dinov I, Toga A, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen A, Corneveaux J, Stephan DA, Webster J, DeChairo BM, Potkin SG, Jack C, Weiner M, Raji CA, Lopez OL, Becker JT, Thompson PM, and ADNI. Commonly carried allele within FTO, an obesity-associated gene, relates to accelerated brain degeneration in the elderly. PNAS: Proc Natl Acad Sci USA, 107(18):8404-9, 2010 . [PubMed]

Stein JL, Hua X, Lee S, Ho AJ, Leow AD, Toga AW, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Dechairo BM, Potkin SG, Weiner MW, Thompson PM, and ADNI. Voxelwise Genome-Wide Association Study (vGWAS). Neuroimage, 53:1160–1174, 2010. http://dx.doi.org/doi:10.1016/j.neuroimage.2010.02.032.

Stein JL, Hua X, Morra JH, Lee S, Ho AJ, Leow AD, Toga A, Sul J, Kang HM, Eskin E, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen A, Corneveaux J, Stephan DA, Webster J, DeChairo BM, Potkin SG, Jack C, Weiner M, Thompson P, and ADNI. Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. NeuroImage, 51(2):542-554, 2010. http://dx.doi.org/doi:10.1016/j.neuroimage.2010.02.068

Full Length, Peer Reviewed Conference Papers

Nho K, Shen L, Kim S, Risacher SL, West JD, Foroud T, Jack CR, Weiner MW, Saykin AJ, ADNI. Automatic prediction of MCI conversion to probable AD using baseline structural MRI in the ADNI cohort. The American Medical Informatics Association (AMIA) 2010 annual meeting, 542 (5 pages), Washington DC, November 13-17, 2010.

Shen L, Qi Y, Kim S, Nho K, Wan J, Risacher SL, Saykin AJ, ADNI. Sparse bayesian learning for identifying imaging biomarkers in AD prediction. MICCAI 2010: the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, Lecture Notes in Computer Science (LNCS) 6363, pp. 611-618, Springer, Heidelberg, 2010. [acceptance 32%]

Wan J, Shen L, Fang S, McLaughlin J, Autti-Ramo I, Fagerlund A, Riley E, Hoyme HE, Moore ES, Foroud T, CIFASD. A framework for 3D analysis of facial morphology in fetal alcohol syndrome. MIAR 2010: the 5th Int. Workshop on Medical Imaging and Augmented Reality, Lecture Notes in Computer Science (LNCS) 6326, pp. 118-127, Springer, Heidelberg, 2010. Selected for a platform talk. [acceptance for oral presentation 29%]

Peer Reviewed Conference Abstracts

Meda S, Narayanan B, Calhoun V, Liu J, Bizzozero-Peron N, Risacher S, Shen L, Saykin AJ, Pearlson G. Parallel independent component analysis successfully identifies clusters of interacting genes and structural mri brain regions from the large-scale ADNI Alzheimer’s/MCI data set. The ACNP 49th Annual Meeting, Miami Beach, Florida, December 5-9, 2010. Neuropsychopharmacology 35:S347, 2010.

Deters K, Saykin AJ, Swaminathan S, Risacher SL, Nho K, Kim S, Foroud T, Shen L, and ADNI. Association of haplotypes of the MAPT gene with Alzheimer's disease and quantitative neuroimaging phenotypes. 2010 Annual Biomedical Research Conference for Minority Students (ABRCMS), Charlotte, North Carolina, November 10-13, 2010.

Swaminathan S, Shen L, Risacher SL, Kim S, Nho K, West JD, Foroud T, Yoder KK, Potkin SG, Huentelman MJ, Craig DW, Jagust WJ, Mathis CA, Weiner MW, Saykin AJ, ADNI. Amyloid pathway-based candidate gene analysis of [11C]PiB-PET in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. ASHG 2010: American Society of Human Genetics 60th Annual Meeting, Nov 2-6, 2010, Washington DC.

Wan J, Kim S, McCullough K, Kwangsik Nho, Swaminathan S, West JD, Fang S, McHugh T, Flashman LA, Wishart HA, Rabin LA, Rhodes CH, Guerin SJ, Moore JH, Santulli RB, Saykin AJ, Shen L. Association analysis of candidate SNPs on hippocampal volume and shape in mild cognitive impairment and older adults with cognitive complaints. International Conference on Alzheimer's Disease (ICAD), July 10-15, 2010, Honolulu Hawaii. Selected for a platform talk.

Shen L, Ai H, Liang Y, Anthony B, Zhou FC, CIFASD. Effect of fetal alcohol on craniofacial bone development in C57BL/6J mouse models. 33rd Annual RSA (Research Society on Alcoholism) Scientific Meeting, June 26-30, 2010, San Antonio, Texas.

Kim S, Swaminathan S, Shen L, Risacher SL, Nho K, Foroud T, Shaw LM, Trojanowski JQ, Potkin SG, Huentelman MJ, Craig DW, DeChairo BM, Weiner MW, Saykin AJ, and ADNI. Genome-wide association study of CSF biomarkers amyloid beta 1-42, tau and tau phosphorylated at threonine 181 in the ADNI cohort. International Conference on Alzheimer's Disease (ICAD), July 10-15, 2010, Honolulu Hawaii. Selected for a platform talk.

Swaminathan S, Kim S, Shen L, Risacher SL, Foroud T, Pankratz N, Potkin SG, Huentelman MJ, Craig DW, Weiner MW, Saykin AJ, and ADNI. Preliminary analysis of copy number variation in the ADNI cohort. International Conference on Alzheimer's Disease (ICAD), July 10-15, 2010, Honolulu Hawaii.

Risacher SL, Saykin AJ, Pepin S, WuDunn D, Magee T, Englert J, Flashman LA, Pixley HA, Wishart HA, Shen L, West JD, McDonald BC, O'Neill DP, Santulli RB, Newman RW. Visual contrast sensitivity as a novel biomarker for neurodegeneration in early Alzheimer's disease, mild cognitive impairment, and older adults with cognitive complaints. International Conference on Alzheimer's Disease (ICAD), July 10-15, 2010, Honolulu Hawaii.

Saykin AJ, Yoder KK, Risacher SL, Magee TR, McDonald BC, Zheng QH, Wang M, Mock BH, Shen L, West JD, Fletcher JW, Farlow MR, Hutchins GD. Neuroinflammation and amyloid deposition: concurrent [11c]PBR28 and [11c]PIB pet in patients with Alzheimer's disease, mild cognitive impairment, and older adults with cognitive complaints. Alzheimer's Imaging Consortium, July 10, 2010, Honolulu, Hawaii. Selected for a platform talk.

Wang Y, West JD, Flashman LA, Wishart HA, Rabin LA, Pare N, Englert J, Santulli RB, Shen L, Arfanakis K, Saykin AJ. Diffusion tensor MRI in preclinical AD: Decreased fractional anisotropy in parahippocampal white matter in MCI and older adults with cognitive complaints. Alzheimer's Imaging Consortium, July 10, 2010, Honolulu, Hawaii.

Yoder KK, Risacher SL, MaGee TR, McDonald BC, Zheng QH, Wang M, Mock BH, West JD, Shen L, Hutchins GD, Saykin AJ. Age-related neuroinflammation in non-demented elderly adults: Preliminary findings with the TSPO ligand [11C]PBR28. The Eighth International Symposium on Functional Neuroreceptor Mapping of the Living Brain (NRM2010), July 22-24, Glasgow, Scotland, UK. Selected for a platform talk.

Ho AJ, Stein JL, Hua X, Lee S, Hibar DP, Toga AW, Saykin AJ, Shen L, Foroud T, Potkin SG, Jack CR, Weiner MW, Raji CA, Lopez OL, Becker JT, Thompson PM. Obesity gene, FTO, is associated with lower brain volumes in 206 healthy elderly subjects. OHBM'10: Organization for Human Brain Mapping, Barcelona, Barcelona, Spain, June 2010.

Stein J, Hua X, Lee S, Ho A, Leow A, Toga A, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman M, Craig D, DeChairo B, Potkin S, Weiner M, Thompson PM. Voxelwise genome-wide association study (vGWAS). OHBM'10: Organization for Human Brain Mapping, Barcelona, Barcelona, Spain, June 2010.

Journal Articles

Shen L, Kim S, Saykin AJ. Fourier method for large scale surface modeling and registration. Computers and Graphics (Special Issue on Shape Modeling International 2009), 33(3):299-311. [PDF, PMC]

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

Risacher SL, Saykin AJ, West JD, Shen L, Firpi HA, McDonald BC, and ADNI. Baseline MRI predictors of conversion from MCI to probable AD in the ADNI cohort. Current Alzheimer Research, 6(4): 347-361, 2009. [PDF]

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

McPeek MA, Shen L, and Farid H. The correlated evolution of 3-dimensional reproductive structures between male and female damselflies. Evolution, 63(1):73-83, 2009. [PDF]

Full Length, Peer Reviewed Conference Papers

Wan J, Shen L, Sheehan KE, Kim S, Roth RM, Ford J, Fang S, Saykin AJ, and Wishart HA. Shape analysis of thalamic atrophy in multiple sclerosis. MIAMS 2009: MICCAI Workshop on "Medical Image Analysis on Multiple Sclerosis", pages 93-104, September 20, 2009, Imperial College London, UK.

Kim S, Shen L, Saykin AJ, and West JD. Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study. EMBC'09: the 31st Annual Int. Conf. of the IEEE Engineering in
Medicine and Biology Society, pages 3849-3852, September 2-6, 2009, Minneapolis, Minnesota.

Li H, Yan M, Henschel R, Shen L. Implementing 3D SPHARM surfaces registration on cell processor. SAAHPC'09: Symposium on Application Accelerators in High Performance Computing. July 28-30, 2009
Urbana, Illinois.

Kim S, Shen L, Saykin AJ, and West JD. Data synthesis and tool development for exploring imaging genomic patterns. CIBCB'09: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 298-305, 3/30-4/2, 2009, Nashville, TN.

Peer Reviewed Conference Abstracts

Sheehan K, Wishart H, Roth R, Shen L, Wan J, MacDonald J, Ford J, Seville J, Oliver B, Kasper L. The relationship of thalamic volume and shape to pain in relapsing-remitting MS. The European Conference on Treatment and Research in MS, Dusseldorf, Germany, Sept 2009.

Saykin AJ, Shen L, Risacher SL, Kim S, Nho K, West JD, Forond TM, and the ADNI. Genetic predictors of 12 month change in MRI hippocampal volume in the Alzheimer’s Disease Neuroimaging Initiative cohort: Analysis of leading candidates from the AlzGene database. International Conference on Alzheimer's Disease (ICAD), July 11-16, 2009, Vienna, Austria. Selected for a platform talk.

Risacher SL, Saykin AJ, Shen L, West JD, Kim S, McDonald BC, and the ADNI. Volumetric, cortical thickness, and grey matter density changes on MRI over 12 months: Relationship to conversion status in the ADNI cohort. International Conference on Alzheimer's Disease (ICAD), July 11-16, 2009, Vienna, Austria.

Shen L, Kim S, West JD, Saykin AJ. Building an imaging genomic browsing system for examining genetic effects on brain. OHBM’09: 15th Annual Meeting of Organization for Human Brain Mapping, Neuroimage, 7(Sup. 1):S32, June 18 - 23, 2009, San Francisco, CA. Selected for a platform talk.

Barkay G, Dzemidzic M, Shen L, Saykin AJ, French AD, Vanam R, and Anand A. Brain morphological abnormalities in unmedicated bipolar disorder and major depression: an automated segmentation analysis. Society of Biological Psychiatry: 64th Annual Scientific Convention, May 14-16, 2009, Vancover, Canada.

Shen L, Firpi HA, Saykin AJ, West JW. Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. MICCAI 2008 Workshop on the Computational Anatomy and Physiology of the Hippocampus, NYC, Sep 6, 2008.

Shen L and Makedon FS. Mining 3D shape data for morphometric pattern discovery. Book chapter in Encyclopedia of Data Warehousing and Mining, 2nd Edition, John Wang eds., Idea Group Inc (IGI), 2008.

McPeek MA, Shen L, Torrey JZ, and Farid H. The tempo and mode of 3-dimensional morphological evolution in male reproductive structures. American Naturalist, 171(5):E158-E178, 2008. [PDF]

Huang H, Shen L, Ford JC, Wang Y, and Xu Y. Computational issues in biomedical nanometrics and nano-materials. Journal of Nano Research, Inaugural Issue, Vol. 1:50-58, 2008.

Shen L, Saykin AJ, Firpi HA, West JD, McHugh TL, Wishart HA, Flashman LA, Wessels AM, McDonald BC, Cannon A. Comparison of manual and automated determination of hippocampal volumes in MCI and older adults with cognitive complaints. Alzheimer's & Dementia, Vol. 4, Iss. 4, Suppl 2:T29-30, 2008.

Saykin AJ, West JD, Shen L, Firpi HA, Wessels AM, Cannon A, Risacher S, McDonald BC, and the Alzheimer's Disease Neuroimaging Initiative. Hippocampal and Distributed Gray Matter Abnormalities in MCI and Early AD in the ADNI Baseline 1.5T MRI Scans: Cross-Sectional Analysis and Relation to Verbal Learning. Alzheimer's & Dementia, Vol. 4, Iss. 4, Suppl 2:T59, 2008.

Huang H, and Shen L. Three dimensional model for cardiac bioelectricity simulation: cell to organ. Simulation: Transactions of the Society for Modeling and Simulation International, 83(4): 321-327, 2007.

Huang H, Shen L, Zhang R, Makedon FS, Saykin AJ, and Pearlman JD. A novel surface registration algorithm in medical modeling applications. IEEE Transactions on Information Technology in Biomedicine, 11(4): 474-482, 2007.

Chung MK, Dalton KM, Shen L, Robbins SM, Evans AC, and Davidson RJ. Weighted fourier series representation and its application to quantifying amount of gray matter. IEEE Transactions on Medical Imaging, Special Issue on Computational Neuroanatomy (invited paper), 26(4): 566-581, 2007.

McHugh TL, Saykin AJ, Wishart HA, Flashman LA, Cleavinger HB, Rabin LA, Mamourian AC, and Shen L. Hippocampal volume and shape analysis in an older adult population. The Clinical Neuropsychologist (special technology issue), 21(1): 131-146, 2007.

Shen L, Saykin AJ, Chung MK, and Huang H. Morphometric analysis of hippocampal shape in mild cognitive impairment: an imaging genetics study. IEEE 7th International Symposium on Bioinformatics and BioEngineering, pages 211-217, Boston, MA, October 14-17, 2007. [acceptance for full paper 12%]

 Huang H, and Shen L. Surface harmonics for shape modeling. ICIP 2007: 14th IEEE International Conference on Image Processing, Volume 2:553-556, San Antonio, Texas, September 16-19, 2007.

Shen L, Huang H, Makedon FS, and Saykin AJ. Efficient registration of 3D SPHARM surfaces. CRV 2007: Fourth Canadian Conference on Computer and Robot Vision, Montreal, QC, pages 81-88, May 28-30, 2007. [acceptance for oral 24%]

Xu Y, Ford JC, Makedon FS, Popa D, Huang H, Shen L. In-home localization for home care of Alzheimer's disease patients using wireless sensor networks. International workshop on Pervasive Technologies for the support of Alzheimer's Disease and Related Disorders Sufferers, Thessaloniki, February 24, 2007.

Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, and Pearlman JD. Cardiac motion analysis to improve pacing site selection in CRT. Journal of Academic Radiology, Elsevier Science, 13(9):1124-1134, September 2006.

Shen L, and Makedon FS. Spherical mapping for processing of 3-D closed surfaces. Image and Vision Computing, 24(7): 743-761, 2006.

Shen L, Zheng W, Gao L, Huang H, Makedon FS, and Pearlman JD. Spatio-temporal modeling of lung images for cancer detection.  Oncology Reports, Special Issue on Computational Analysis and Decision Support Systems in Oncology, 15:1085-1090, 2006.

Huang H, Shen L, Ford JC, Gao L, and Pearlman JD. Early lung cancer detection based on registered perfusion MRI. Oncology Reports, Special Issue on Computational Analysis and Decision Support Systems in Oncology, 15:1081-1084, 2006.

Shen L, Saykin AJ, Chung MK, Huang H, Ford JC, Makedon FS, McHugh TL, and Rhodes CH. Morphometric analysis of genetic variation in hippocampal shape in mild cognitive impairment: Role of an IL-6 promoter polymorphism. CSB 2006: LSS Computational Systems Bioinformatics Conference, Stanford University, CA, August 14-18, 2006.

Chung MK, Shen L, Dalton KM, and Davidson RJ. Multi-scale voxel-based morphometry via weighted spherical harmonic representation. MIAR 2006: International Workshop on Medical Imaging and Augmented Reality, LNCS 4091, pages 36-43, Shanghai, China, August 17-18, 2006.

Shen L and Chung MK. Large-scale modeling of parametric surfaces using spherical harmonics. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

Huang H, Zhang L, Samaras D, Shen L, Makedon FS, and Pearlman JD. Hemispherical harmonic surface description and applications to medical image analysis. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

Huang H, Shen L, Makedon FS, and Pearlman JD. A Spatio-temporal modeling method for shape representation. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

Moolani V, Balasubramanian R, Shen L, and Tandon A. Shape analysis and spatio-temporal tracking of mesoscale eddies in Miami isopycnic coordinate ocean model. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

Shen L, Huang H, Ford JC, Lu C, Gao L, Zheng W, Makedon FS, and Pearlman JD. Spatio-temporal analysis tool for modeling pulmonary nodules in MR images.  SPIE Medical Imaging 2006: Visualization, Image-Guided Procedures, and Display, Proc. of SPIE Vol 6141:740-749, San Diego, CA, February 2006.

Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Fast surface alignment for cardiac spatiotemporal modeling. SPIE Medical Imaging 2006: Image Processing, Proc. of SPIE Vol 6144:1002-1009, San Diego, California, February 2006.

Zheng W, Wang Z, Shen L, Makedon FS, and Pearlman JD. Measuring blood delivery to solitary pulmonary nodule by perfusion magnetic resonance imaging.  SPIE Medical Imaging 2006: Physiology, Function, and Structure from Medical Images, Proc. of SPIE Vol 6143, 614332 (9 pages), San Diego, CA, February 2006.

Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Surface alignment of 3D spherical harmonic models: Application to cardiac MRI analysis. MICCAI 2005: 8th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3749, pages 67-74, Palm Springs, California, USA, Oct 26-29, 2005.

Huang H, Shen L, Zhang R, Makedon FS, Pearlman JD. A prediction framework for cardiac resynchronization therapy via 4D cardiac motion analysis. MICCAI 2005: 8th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3749, pages 704-711, Palm Springs, California, USA, Oct 26-29, 2005.

Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Clustering based cardiac resynchronization therapy prediction using open source toolkit PRTools. ISC/NA-MIC Open-Source Workshop at MICCAI 2005: 8th Int. Conf. on Medical Image Computing and Computer Assisted Intervention, Palm Springs, California, USA, Oct 26-29, 2005.

Shen L, Zheng W, Gao L, Huang H, Makedon FS, and Pearlman JD. Modeling time-intensity profiles for pulmonary nodules in MR images.  EMBS 2005: The 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 1359-1362, Shanghai, China, September 1-4, 2005.

Huang H, Zhang R, Fei Xiong, Makedon FS, Shen L, Hettleman B, Pearlman JD. K-means+ method for improving gene selection for classification of microarray Data. Poster at CSB 2005: IEEE Computational Systems Bioinformatics Conference, pages 110-111, Stanford, California, Aug 8-11, 2005.

Shen L, Saykin AJ, McHugh TL, West JD, Rabin LA, Wishart HA, Chung MK, Makedon FS. Morphometric analysis of 3D surfaces: Application to hippocampal shape in mild cognitive impairment. CVPRIP 2005: 6th Int. Conf. on Computer Vision, Pattern Recognition and Image Processing, pages 699-702, Salt Lake City, Utah, July 21-26, 2005.

Shen L, Saykin AJ, McHugh TL, West JD, Rabin LA, Wishart HA, Chung MK, Makedon FS. Morphometric MRI study of hippocampal shape in MCI using spherical harmonics. Alzheimer's Association International Conference on Prevention of Dementia: Early diagnosis and intervention, P-120, Washington, D.C., June 18-21, 2005.

Huang H, Shen L, Makedon FS, Sheng Zhang, Greenberg M, Gao L, and Pearlman JD. A clustering-based approach for prediction of cardiac resynchronization therapy. 20th ACM Symposium on Applied Computing, pages 260-266, Santa Fe, NM, March 13-17, 2005.

Shen L, Gao L, Zhuang Z, DeMuinck E, Huang H, Makedon FS, and Pearlman JD. An interactive 3D visualization and manipulation tool for effective assessment of angiogenesis and arteriogenesis using computed tomographic angiography. SPIE Medical Imaging 2005, Proc. of SPIE Vol 5744: 848-858, San Diego, CA, 12-17 February 2005.

Huang H, Shen L, Ford JC, Makedon FS, Zhang R, Gao L, and Pearlman JD. Functional analysis of cardiac MR images using SPHARM modeling. SPIE Medical Imaging 2005, Proc. of SPIE Vol 5747:1384-1391, San Diego, CA, 12-17 February 2005.

Shen L, Ford JC, Makedon FS, and Saykin AJ. A surface-based approach for classification of 3D neuroanatomic structures. Intelligent Data Analysis, An International Journal, 8(6):519-542, 2004.

Huang H, Makedon FS, Pearlman JD, Ford JC, Shen L, Wang Y, and Gao L. Efficient similarity retrieval framework for temporal shape sequences: A case study in cardiac MR images. Proc. 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 3250-3253, San Francisco, California, September 1, 2004.

Wang Y, Makedon FS, Ford JC, Shen L, and Goldin D. Generating fuzzy semantic metadata describing spatial relations from images using the R-histogram. The 4th ACM/IEEE-CS Joint Conference on Digital Libraries, pages 202-211, Tucson, Arizona, June 7-11, 2004.

Steinberg T, Ford JC, Ouyang Y, Shen L, Wang Y, Zheng W, and Makedon FS. Tracking resource usage using heterogeneous feature spaces with local exceptions. EDBT'04 Workshop: Clustering Information over the Web, Heraklion-Crete, Greece, March 14th, 2004.

Shen L and Makedon FS. Spherical parameterization for 3D surface analysis in volumetric images. IEEE Conference on ITCC'04: International Conference on Information Technology, pages 643-649, Las Vegas, NV, April 5-7, 2004.

Makedon FS, Ye S, Sheng Zhang, Ford JC, Shen L, Kapidakis S. Data brokers: Building collections through automated negotiation. SETN'04: The 3rd Hellenic Conference on Artificial Intelligence, LNCS 3025, pages 13-22, Samos, Greece, 5-8 May 2004.

Huang H, Shen L, Makedon FS, Gao L, and Pearlman JD. Three-dimensional analysis of cardiac magnetic resonance imaging using spherical harmonics model. ACC'04: Annual Scientific Session of the American College of Cardiology, New Orleans, March 7-10, 2004.

Shen L, Makedon FS, and Saykin AJ. Shape-based discriminative analysis of combined bilateral hippocampi using multiple object alignment. Medical Imaging 2004: Image Processing, SPIE Proceedings 5370, pages 274-282, San Diego, California, 14-19 February 2004.

Shen L, Ford JC, Makedon FS, Wang Y, Steinberg T, Ye S, and Saykin AJ. Morphometric analysis of brain structures for improved discrimination. MICCAI'03: Medical Image Computing and Computer Assisted Intervention, LNCS 2879, pages 513-520, Montreal, Quebec, Canada, November 15-18, 2003.

Makedon FS, Tzika AA, Astrakas L, Pearlman JD, Wang Y, Steinberg T, Shen L, Chambers K, and Ford JC. Fusing information for tracking tumors. The 8th World Congress on Advances in Oncology and 6th International Symposium on Molecular Medicine, Hersonissos, Crete, Greece, October 16-18, 2003.

Shen L, Ford JC, Makedon FS, and Saykin AJ. Effective classification of 3D closed sur-faces: Application to modeling neuroanatomical structures. CVPRIP’03: International Conference on Computer Vision, Pattern Recognition and Image Processing, pages 708-711, Cary, NC, September 26-30, 2003.

Steinberg T, Wang Y, Makedon FS, Shen L, Saykin AJ, and Wishart HA. A spatio-temporal multi-modal data management and analysis environment for tracking MS lesions. SSDBM'03: the 15th Int. Conference on Scientific and Statistical Database Management, pages 245-246, Cambridge, MA, July 9-11, 2003.

Shen L, Ford JC, Makedon FS, Flashman LA, and Saykin AJ. Surface-based morphometric analysis for hippocampal shape in schizophrenia. Neuroimage, 19(2):e1966-e1970, Human Brain Mapping 2003, New York, USA, June 18-22, 2003.

Ye S, Makedon FS, Steinberg T, Shen L, Wang Y, Zhao Y, and Ford JC. SCENS: a system for the mediated sharing of sensitive data. JCDL'03: The 3rd ACM/IEEE-CS Joint Conference on Digital Libraries, pages 263-265, Houston, TX, May 27-31, 2003.

Saykin AJ, Flashman LA, T. McHugh, C. Pietras, McAllister TW, A. C. Mamourian, R. Vidaver, Shen L, Ford JC, Wang L, and Makedon FS. Principal components analysis of hippocampal shape in schizophrenia. Schizophrenia Research, 60(1):206, March 29 - April 2, 2003.

Makedon FS, Wang Y, Steinberg T, Wishart HA, Saykin AJ, Ford JC, Ye S, and Shen L. A system framework for the integration and analysis of multi-modal spatio-temporal data streams: A case study in MS lesion analysis. The First International IEEE EMBS Neural Engineering Conference, pages 495-498, Capri Island, Italy, March 20-22, 2003.

Shen L, Ford JC, Makedon FS, and Saykin AJ. Hippocampal shape analysis: Surface-based representation and classification. Medical Imaging 2003: Image Processing, SPIE Proceedings 5032, pages 253-264, San Diego, CA, February 15-20, 2003.

Ford JC, Shen L, Makedon FS, Flashman LA, and Saykin AJ. A combined structural-functional classification of schizophrenia using hippocampal volume plus fMRI activation. EMBS-BMES'02: The 2nd Joint Meeting of the IEEE Engineering in Medicine and Biology Society and the Biomedical Engineering Society, volume 1, pages 48-49, Houston, Texas, October 23-26, 2002.

Makedon FS, Ford JC, Shen L, Steinberg T, Saykin AJ, Wishart HA, and Kapidakis S. MetaDL: A digital library of metadata for sensitive or complex research data. ECDL'02: European Conference on Digital Libraries, LNCS 2458, pages 374-389, Rome, Italy, September 16-18, 2002.

Saykin AJ, Wishart HA, Flashman LA, McAllister TW, T. McHugh, Ford JC, Shen L, Steinberg T, and Makedon FS. Structure/function relationships in brain disorders: Strategies for mining volume, shape, lesion and bold fMRI activation data. Society for Biological Psychiatry Meeting, Philadelphia, PA, May 16-18, 2002.

Ford JC, Makedon FS, Shen L, Steinberg T, Saykin AJ, and Wishart HA. Evaluation metrics for user-centered ranking of content in metaDLs. The 4th DELOS Workshop on Evaluation of Digital Libraries: Testbeds, Measurements, and Metrics, Budapest, Hungary, May 6-7, 2002.

Shen L, Cheng L, Teng F, Makedon FS, Ford JC, Steinberg T, and Saykin AJ. A multimedia system for tracing and studying regions-of-interest in brain images. MTAC'01: IEEE Multimedia Technology and Application Conference, pages 238-245, Irvine, CA, November 7-9, 2001.

Cheng L, Shen L, Makedon FS, Donnelly AM, Flashman LA, and Saykin AJ. On the development of a training and research system for tracing human brain structures. SCI'01: The 5th World Multi-Conference on Systemics, Cybernetics and Informatics, Volumn VIII, pages 151-155, Orlando, FL, July 22-25, 2001.

Ford JC, Makedon FS, Megalooikonomou V, Shen L, Steinberg T, and Saykin AJ. Spatial comparison of fMRI activation maps for data mining. Neuroimage, 13(6):s1302, Human Brain Mapping, Brighton, UK, June 10-14, 2001.

Cheng L, Shen L, Makedon FS, Donnelly AM, Flashman LA, and Saykin AJ. TROI: a training and research system for tracing regions of interest in brain images. Neuroimage, 13(6):s1298, Human Brain Mapping 2001, Brighton, UK, June 10-14, 2001.

Saykin AJ, Flashman LA, Shen L, Ashburner J, Sparling M, Donnelly AM, Makedon FS, Isecke D, Ford JC, Megalooikonomou V, and McAllister TW. Hippocampal shape in schizophrenia: A deformation-based morphometric analysis. Neuroimage, 13(6):s1096, Human Brain Mapping, Brighton, UK, June  2001.

Megalooikonomou V, Ford JC, Shen L, Makedon FS, and Saykin AJ. Data mining in brain imaging. Statistical Methods in Medical Research, 9(4):359-394, 2000.

Shen L, Shen H, Cheng L, and Pritchard P. Fast association discovery in derivative transaction collections. Knowledge and Information Systems, An International Journal, 2(2):147-160, May 2000.

Shen L, Cheng L, Ford JC, Makedon FS, Megalooikonomou V, and Steinberg T. Mining the most interesting web access associations. WebNet'00: World Conference on the WWW and Internet, pages 489-494, San Antonio, TX, Oct. 30 - Nov. 4, 2000.

Steinberg T, Shen L, Cheng L, and Makedon FS. Tracking human expression actions in lectures. ED-MEDIA'00: World Conference on Educational Multimedia, Hypermedia & Telecommunication, pages 1090-1095, Montreal, Quebec, Canada, June 26 - July 1, 2000.

Shen L, Shen H, and Cheng L. New algorithms for efficient mining of association rules. Information Sciences, 118(1-4):251-268, September, 1999.

Steinberg T, Cheng L, Shen L, Makedon FS, Owen C, and Ottmann T. A model for authoring for retrieval (AFR): Retrieval on parallel data streams of recorded lecture information. Multimedia Storage and Archiving Systems IV, SPIE Photonics EAST, pages 423-430, Boston, MA, September 19-22, 1999.

Shen L, Shen H, and Cheng L. New algorithms for efficient mining of association rules. IEEE Frontiers'99: The 7th Symposium on the Frontiers of Massively Parallel Computation, pages 234-241, Annapolis, Maryland, February 21-25, 1999.

Shen L, Shen H, Pritchard P, and Topor R. Finding the N largest itemsets. ICDM'98: International Conference on Data Mining, pages 211-222, Rio de Janeiro, RJ, Brazil, September 2-4, 1998.

Shen L and Shen H. Mining flexible multiple-level association rules in all concept hierarchies. DEXA'98: The 9th International Conference on Database and Expert Systems Applications, LNCS 1460, pages 786-795, Vienna, Austria, August 24-28, 1998.

Sun Y, Lin K, and Shen L. The design and implementation of a program development system based on rewriting methods. ACM SIGPLAN Notices, 32(2):27-34, February 1997.

Shen L, and Sun Y. Needed parallel-outermost reduction strategy. Journal of Software (in Chinese), 8(10):760-767, October 1997.

Shen L, Lin K, and Sun Y. Parallel-outermost pattern matching. Journal of Software (in Chinese), 7(Supplement):329-337, 1996.

Lin K, Shen L, Lu C, and Sun Y. The design and implementation of function-specification mixed programming language. Journal of Shanghai Jiaotong University (in Chinese), 30(6):100-106, 1996.