Perelman School of Medicine at the University of Pennsylvania

Shen Lab

Journal Articles

  1. Shen L, Thompson PM. (2019) Brain imaging genomics: integrated analysis and machine learning. Proceedings of the IEEE, in press.

  2. Du L, Liu K, Yao X, Risacher SL, Han J, Saykin AJ, Guo L, Shen L, for the ADNI. (2019) Multi-task sparse canonical correlation analysis with application to multi-modal brain imaging genetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.

  3. Wang M, Shao W, Hao X, Shen L, Zhang D. (2019) Identify consistent cross-modality imaging genetic patterns via discriminant sparse canonical correlation analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press. https://ieeexplore.ieee.org/document/8854121

  4. Satizabal CL, Adams H, Hibar D, White C, Knol M, Stein J, Scholz M, Sargurupremraj M, Jahanshad N, Roshchupkin G, Smith A, Bis J, Jian X, Luciano M, Hofer E, Teumer A, Lee Svd, Yang J, Yanek L, Lee T, Li S, Hu Y, Koh JY, Eicher J, Desrivières S, Arias-Vasquez A, Chauhan G, Athanasiu ML, Renteria M, Kim S, Höhn D, Armstrong N, Chen Q, Holmes A, Braber Ad, Kloszewska I, Andersson M, Espeseth T, Grimm O, Abramovic L, Alhusaini S, Milaneschi Y, Papmeyer M, Axelsson T, Ehrlich S, Roiz-Santiañez R, Kraemer B, Haberg A, Jones H, Pike GB, Stein D, Stevens AA, Bralten J, Vernooij M, Harris T, Filippi I, Witte AV, Guadalupe T, Wittfeld K, Mosley T, Becker J, Doan NT, Hagenaars S, Saba MY, Cuellar-Partida G, Amin N, Hilal S, Nho K, Mirza-Schreiber N, Arfanakis K, Becker D, Ames D, Goldman A, Lee P, Boomsma D, Lovestone S, Giddaluru S, Hellard SL, Mattheisen M, Bohlken M, Kasperaviciute D, Schmaal L, Lawrie S, Agartz I, Walton E, Tordesillas-Gutierrez D, Davies G, Shin J-H, Ipser J, Vinke L, Hoogman M, Jia T, Burkhardt R, Klein MM, Crivello F, Janowitz D, Carmichael O, Haukvik U, Aribisala B, Schmidt H, Strike L, Cheng C-Y, Risacher S, Puetz B, Fleischman D, Assareh A, Mattay V, Buckner R, Mecocci P, Dale A, Cichon S, Boks M, Matarin M, Penninx B, Calhoun V, Chakravarty M, MARQUAND A, Macare C, Masouleh SK, Oosterlaan J, Amouyel P, Hegenscheid K, Rotter J, Schork A, Liewald D, Zubicaray GD, Wong T, Shen L, Samann P, Brodaty H, Roffman J, Geus Ed, Tsolaki M, Erk S, Eijk Kv, Cavalleri G, Wee Nvd, Mcintosh A, Gollub R, Bulayeva K, Bernard M, Richards J, Himali J, Loeffler M, Rommelse N, Hoffmann W, Westlye LT, Hernandez MV, Hansell N, Erp Tv, Wolf C, Kwok J, Vellas B, Heinz A, Loohuis LO, Delanty N, Ho B-C, Ching C, Shumskaya E, Singh B, Hofman A, Meer DVd, Homuth G, Psaty B, Bastin M, Montgomery G, Foroud T, Reppermund S, Hottenga J, Simmons A, Meyer-Lindenberg A, Cahn W, Whelan C, Donkelaar Mv, Yang Q, Hosten N, Green R, Thalamuthu A, Mohnke S, Pol HH, Lin H, Jack C, Schofield P, Mühleisen T, Maillard P, Potkin S, Wen W, Fletcher E, Toga A, Gruber O, Huentelman M, Smith GD, Launer L, Nyberg L, Jönsson E, Crespo-Facorro B, Koen N, Greve D, Uitterlinden A, Weinberger D, Steen V, Fedko I, Groenewold N, Niessen W, Toro R, Tzourio C, Longstreth W, Ikram MK, Smoller J, Tol M-Jv, Sussmann J, Paus T, Lemaitre H, Schroeter M, Mazoyer B, Andreassen O, Holsboer F, Depondt C, Veltman D, Turner J, Pausova Z, Schumann G, Rooij DV, Djurovic S, Deary I, McMahon K, Müller-Myhsok B, Brouwer R, Soininen H, Pandolfo M, Wassink T, Cheung J, Wolfers T, Martinot J-L, Zwiers M, Nauck M, Melle I, Martin N, Kanai R, Westman E, Kahn R, Sisodiya S, White T, Saremi A, Bokhoven Hv, Brunner H, Völzke H, Wright M, Ent Dvt, Nöthen M, Ophoff R, Buitelaar J, Fernández G, Sachdev P, Rietschel M, Haren Nv, Fisher S, Beiser A, Francks C, Saykin A, Mather K, Romanczuk-Seiferth N, Hartman C, Stefano Ad, Heslenfeld D, Weiner M, Walter H, Hoekstra P, Nyquist P, Franke B, Bennett D, Grabe H, Johnson A, Chen C, Duijn Cv, Lopez O, Fornage M, Wardlaw J, Schmidt R, DeCarli C, Jager PD, Villringer A, Debette S, Gudnason V, Medland S, Shulman J, Thompson P, Seshadri S, Ikram MA. (2019) Genetic architecture of subcortical brain structures in 38,851 individuals. Nature genetics. in press.

  5. Yao X, Risacher SL, Nho K, Saykin AJ, Wang Z, Shen L, for the ADNI. (2019) Targeted genetic analysis of cerebral blood flow imaging phenotypes implicates the INPP5D gene. Neurobiology of Aging, 81: 213-221. https://doi.org/10.1016/j.neurobiolaging.2019.06.003.

  6. Yan J, Deng C, Wang X, Yao X, Shen L, Huang H. (2019) Identifying imaging markers for predicting cognitive assessments using Wasserstein distances based matrix regression. Frontiers in Neuroscience, 13:668, https://doi.org/10.3389/fnins.2019.00668.

  7. Du L, Liu K, Zhu L, Yao X, Risacher SL, Guo L, Saykin AJ, Shen L. (2019) Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: a longitudinal study of the ADNI cohort. Bioinformatics, 35(14):i474-i483. https://doi.org/10.1093/bioinformatics/btz320. [ISMB/ECCB 2019 Issue, acceptance rate 18.9%]

  8. Wang M, Hao X, Huang J, Wang K, Shen L, Xu X, Zhang D, Liu M. (2019) Hierarchical structured sparse learning for schizophrenia identification. Neuroinformatics, https://doi.org/10.1007/s12021-019-09423-0.
  9. Moore JH, Boland MR, Camara PG, Chervitz H, Gonzalez G, Himes BE, Kim D, Mowery DL, Ritchie MD, Shen L, Urbanowicz RJ, Holmes JH. (2019) Preparing next-generation scientists for biomedical big data: Artificial intelligence approaches. Personalized Medicine, 16(3):247-257. https://doi.org/10.2217/pme-2018-0145.

  10. Chasioti D, Yao X, Zhang P, Lerner S, Quinney SK, Ning X, Li L, Shen L. (2018) Mining directional drug interaction effects on myopathy using the FAERS database. IEEE Journal of Biomedical and Health Informatics, in press. https://doi.org/10.1109/JBHI.2018.2874533.

  11. Wang X, Chen H, Yan J, Nho K, Risacher SL, Saykin AJ, Shen L, Huang H, for the ADNI. (2018) Quantitative trait loci identification for brain endophenotypes via new additive model with random networks. Bioinformatics, 34(17):i866-i74. https://doi.org/10.1093/bioinformatics/bty557.

  12. Yan J, Raja V, Huang Z, Enrico A, Nho K, Fang S, Sporns O, Wu Y, Saykin AJ, Goni J, Shen L. (2018) Brain-wide structural connectivity alterations under the control of Alzheimer risk genes. International Journal of Computational Biology and Drug Design, in press.

  13. Zigon B, Li H, Yao X, Fang S, Hasan MA, Yan J, Moore JH, Saykin AJ, Shen L, for the ADNI. (2018) GPU accelerated browser for neuroimaging genomics. Neuroinformatics, in press. doi: 10.1007/s12021-018-9376-y

  14. Chiang W, Shen L, Li L, Ning X. (2018) Drug-drug interaction prediction based on co-medication patterns and graph matching. International Journal of Computational Biology and Drug Design, in press.

  15. Hao X, Yao X, Risacher SL, Saykin AJ, Yu J, Wang H, Tan L, Shen L, Zhang D, for the ADNI. (2018) Identifying candidate genetic associations with MRI-derived AD-related ROI via tree-guided sparse learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, doi: 10.1109/TCBB.2018.2833487.
  16. Chiang WH, Schleyer T, Shen L, Li L, Ning X. (2018) Pattern discovery from high-order drug-drug interaction relations. Journal of Healthcare Informatics Research, 2(3):272-304.

  17. Cong S, Risacher SL, West JD, Wu YC, Apostolova LG, Tallman EF, Rizkalla M, Salama P, Saykin AJ, Shen L. (2018) Volumetric comparison of hippocampal subfields extracted from 4-minute accelerated versus 8-minute high-resolution t2-weighted 3T MRI scans. Brain Imaging Behav., in press. doi: 10.1007/s11682-017-9819-3.

  18. Liu K, Ye J, Yang Y, Shen L, Jiang H. (2018) A unified model for differential expression analysis of RNA-seq data via l1-penalized linear regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.

  19. Wang X, Yan J, Yao X, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, Huang H, for the ADNI. (2018) Longitudinal genotype-phenotype association study via temporal structure auto-learning predictive model. Journal of Computational Biology, 25(7):809-824, DOI: 10.1089/cmb.2018.0008

  20. Wang X, Zhang P, Chiang C, Wu H, Shen L, Ning X, Zeng D, Wang L, Quinney SK, Feng W, Li L. (2018) Mixture drug-count response model for the high dimensional drug combinatory effect on myopathy. Statistics in Medicine, 37(4):673-86

  21. Chiang C, Zhang P, Wang X, Wang L, Zhang S, Ning X, Shen L, Quinney S, Li L. (2018) Translational high-dimensional drug Interaction discovery and validation using health record databases and pharmacokinetics models. Clinical Pharmacology & Therapeutics, 103(2):287-95.

  22. Yao X, Yan J, Ginda M, Börner K, AJ Saykin, Shen L, for the ADNI. (2017) Mapping longitudinal scientific progress, collaboration and impact of the Alzheimer's disease neuroimaging initiative. PLOS ONE, 2017 Nov 2;12(11):e0186095. doi: 10.1371/journal.pone.0186095. eCollection 2017.
  23. Du L, Liu K, Yao X, Yan J, Risacher SL, Han J, Guo L, Saykin AJ, Shen L, for the ADNI. (2017) Pattern discovery in brain imaging genetics via SCCA modeling with a generic non-convex penalty. Scientific Reports, 2017 Oct 25;7(1):14052. doi: 10.1038/s41598-017-13930-y.

  24. Du L, Liu K, Zhang T, Yao X, Yan J, Risacher SL, Han J, Guo L, Saykin AJ, Shen L, for the Alzheimer’s Disease Neuroimaging Initiative. (2017) A novel SCCA approach via truncated l1-norm and its application to brain imaging genetics. Bioinformatics, 2017 Sep 18. doi: 10.1093/bioinformatics/btx594. [Epub ahead of print]

  25. Li H, Fang S, Contreras JA, West JD, Risacher SL, Wang Y, Sporns O, Saykin AJ, Goni J, Shen L, for the Alzheimer’s Disease Neuroimaging Initiative. (2017) Brain explorer for connectomic analysis. Brain Informatics, 2017 Aug 23, doi: 10.1007/s40708-017-0071-9.

  26. Yao X, Yan J, Liu K, Kim S, Nho K, Risacher SL, Greene CS, Moore JH, Saykin AJ, Shen L, for the ADNI. (2017) Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules. Bioinformatics, 2017 May 29. doi: 10.1093/bioinformatics/btx344.

  27. Cong W, Meng X, Li J, Zhang Q, Chen F, Liu W, Wang Y, Cheng S, Yao X, Yan J, Kim S, Saykin AJ, Liang H, Shen L, for the ADNI. (2017) Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort. BMC Genomics, 18(1):421. doi: 10.1186/s12864-017-3798-z.

  28. Yan J, Risacher S, Shen L, Saykin A. (2017) Network approaches to systems biology analysis of complex disease: Integrative methods for multi-omics data. Briefings in Bioinformatics, doi: 10.1093/bib/bbx066.

  29. Li J, Zhang Q, Chen F, Meng X, Liu W, Chen D, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, Shen L, for the ADNI. (2017) Genome-wide association and interaction studies of CSF T-tau/Aβ42 ratio in ADNI cohort. Neurobiology of Aging. 57:247.e1-247.e8. doi: 10.1016/j.neurobiolaging.2017.05.007.

  30. Nho K, Kim S, Risacher SL, Shen L, Foroud T, Shaw LM, Trojanowski JQ, Aisen PS, Petersen RC, Jack CR, Weiner MW, Green RC, Toga AW, Saykin AJ, for the ADNI (2017) Association Analysis of Rare Variants near the APOE region with cerebrospinal fluid (CSF) biomarkers of Alzheimer’s Disease. BMC Medical Genomics, 10(Suppl 1):29. doi: 10.1186/s12920-017-0267-0.

  31. Hao X, Li C, Yan J, Yao X, Risacher SL, Saykin A, Shen L*, Zhang D*.  (2017) Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis. Bioinformatics, 33:i341–i349, doi: 10.1093/bioinformatics/btx245. *Co-corresponding Authors. [ISMB/ECCB 2017 Issue, acceptance rate 16.5%]

  32. Hao X, Li C, Du L, Yao X, Yan J, Risacher SL, Saykin A, Shen L*, Zhang D*. (2017) Mining outcome-relevant brain imaging genetic associations via three-way sparse canonical correlation analysis in Alzheimer's disease. Scientific Reports, 7:44272. doi: 10.1038/srep44272. *Co-corresponding Authors.

  33. Jon B. Toledo, Matthias Arnold, Kastenmüller G, Chang R, Baillie RA, Han X, Thambisetty M, Tenenbaum JD, Suhre K, Thompson JW, John-Williams LS, MahmoudianDehkordi S, Rotroff DM, Jack JR, Motsinger-Reif A, Risacher SL, Blach C, Lucas JE, Massaro T, Louie G, Zhu H, Dallmann G, Klavins K, Koal T, Kim S, Nho K, Shen L, Casanova R, Varma S, Legido-Quigley C, Moseley MA, Zhu K, Henrion M, Lee SJvd, Harms AC, Demirkan A, Hankemeier T, Duijn CMv, Trojanowski JQ, Shaw LM, Saykin AJ, Weiner MW, Doraiswamy PM, Kaddurah-Daouko R, for the Alzheimer’s Disease Neuroimaging Initiative and the Alzheimer Disease Metabolomics Consortium. Metabolic network failures in Alzheimer’s disease - A biochemical roadmap. Alzheimer's and Dementia, pii: S1552-5260(17)30046-8. doi: 10.1016/j.jalz.2017.01.020.

  34. Thompson PM, Andreassen OA, Arias-Vasquez A, Bearden CE, Boedhoe PS, Brouwer RM, Buckner RL, Buitelaar JK, Bulayeva KB, Cannon DM, Cohen RA, Conrod PJ, Dale AM, Deary IJ, Dennis EL, de Reus MA, Desrivieres S, Dima D, Donohoe G, Fisher SE, Fouche JP, Francks C, Frangou S, Franke B, Ganjgahi H, Garavan H, Glahn DC, Grabe HJ, Guadalupe T, Gutman BA, Hashimoto R, Hibar DP, Holland D, Hoogman M, Pol HE, Hosten N, Jahanshad N, Kelly S, Kochunov P, Kremen WS, Lee PH, Mackey S, Martin NG, Mazoyer B, McDonald C, Medland SE, Morey RA, Nichols TE, Paus T, Pausova Z, Schmaal L, Schumann G, Shen L, Sisodiya SM, Smit DJ, Smoller JW, Stein DJ, Stein JL, Toro R, Turner JA, van den Heuvel MP, van den Heuvel OL, van Erp TG, van Rooij D, Veltman DJ, Walter H, Wang Y, Wardlaw JM, Whelan CD, Wright MJ, Ye J, Consortium E. ENIGMA and the individual: Predicting factors that affect the brain in 35 countries worldwide. NeuroImage. 2017 Jan 15;145(Pt B):389-408, 10.1016/j.neuroimage.2015.11.057.

  35. Hibar DP, Adams HHH, Jahanshad N, Chauhan G, Stein JL, Hofer E, Renteria ME, Bis JC, Arias-Vasquez A, Ikram MK, Desrivières S, Vernooij MW, Abramovic L, Alhusaini S, Amin N, Andersson M, Arfanakis KA, Aribisala BS, Armstrong NJ, Athanasiu L, Axelsson T, Beecham AH, Beiser A, Bernard M, Blanton SH, Bohlken MM, Boks MP, Bralten J, Brickman AM, Carmichael O, Chakravarty MM, Chen Q, Ching CRK, Chouraki V, Cuellar-Partida G, Crivello F, Braber AD, Doan NT, Ehrlich S, Giddaluru S, Goldman AL, Gottesman RF, Grimm O, Griswold ME, Guadalupe T, Gutman BA, Hass J, Haukvik UK, Hoehn D, Holmes AJ, Hoogman M, Janowitz D, Jia T, Jørgensen KN, Karbalai N, Kasperaviciute D, Kim S, Klein M, Kraemer B, Lee PH, Liewald DCM, Lopez LM, Luciano M, Macare C, Marquand A, Matarin M, Mather KA, Mattheisen M, McKay DR, Milaneschi Y, Maniega SM, Nho K, Nugent AC, Nyquist P, Loohuis LMO, Oosterlaan J, Papmeyer M, Pirpamer L, ̈tz BP, Ramasamy A, Richards JS, Risacher SL, ̃ez RR-S, Rommelse N, Ropele S, Rose EJ, Royle NA, Rundek T, Sämann PG, Saremi A, Satizabal CL, Schmaal L, Schork AJ, Shen L, Shin J, Shumskaya E, Smith AV, Strike LT, Teumer A, Tordesillas-Gutierrez D, Toro R, Trabzuni D, Trompet S, Vaidya D, Grond JVd, Lee SJVd, Meer DVd, Donkelaar MMJV, Eijk KRV, Erp TGMV, Rooij DV, Walton E, Westlye LT, Whelan CD, Windham BG, Winkler AM, Wittfeld K, Woldehawariat G, Wolf C, Wolfers T, Yanek LR, Yang J, Zijdenbos A, Zwiers MP, Agartz I, Almasy L, Ames D, Amouyel P, Andreassen OA, Arepalli S, Assareh AA, Barral S, Bastin ME, Becker DM, Becker JT, Bennett DA, Blangero J, Bokhoven Hv, Boomsma DI, Brodaty H, Brouwer RM, Brunner HG, Buckner RL, Buitelaar JK, Bulayeva KB, Cahn W, Calhoun VD, Cannon DM, Cavalleri GL, Cheng C-Y, Cichon S, Cookson MR, Corvin A, Crespo-Facorro B, Curran JE, Czisch M, Dale AM, Davies GE, Craen AJMD, Geus EJCD, Jager PLD, Zubicaray GID, Deary IJ, Debette Sp, DeCarli C, Delanty N, Depondt C, DeStefano A, Dillman A, Djurovic S, Donohoe G, Drevets WC, Duggirala R, Dyer TD, Enzinger C, Erk S, Espeseth T, Fedko IO, ́ndez GnF, Ferrucci L, Fisher SE, Fleischman DA, Ford I, Fornage M, Foroud TM, Fox PT, Francks C, Fukunaga M, Gibbs JR, Glahn DC, Gollub RL, ̈ring HHHG, Green RC, Gruber O, Gudnason V, Guelfi S, Håberg AK, Hansell NK, Hardy J, Hartman CA, Hashimoto R, Hegenscheid K, Heinz A, Hellard SL, Hernandez DG, Heslenfeld DJ, Ho B-C, Hoekstra PJ, Hoffmann W, Hofman A, Holsboer F, Homuth G, Hosten N, Hottenga J-J, Huentelman M, Pol HEH, Ikeda M, Jack CR, Jenkinson M, Johnson R, ̈nsson EGJ, Jukema JW, Kahn RS, Kanai R, Kloszewska I, Knopman DS, Kochunov P, Kwok JB, Lawrie SM, Lemaître H, Liu X, Longo DL, Lopez OL, Lovestone S, Martinez O, Martinot J-L, Mattay VS, McDonald C, McIntosh AM, McMahon FJ, McMahon KL, Mecocci P, Melle I, Meyer-Lindenberg A, Mohnke S, Montgomery GW, Morris DW, Mosley TH, Mühleisen TW, ̈ller-Myhsok BM, Nalls MA, Nauck M, Nichols TE, Niessen WJ, ̈then MMN, Nyberg L, Ohi K, Olvera RL, Ophoff RA, Pandolfo M, Paus T, Pausova Z, Penninx BWJH, Pike GB, Potkin SG, Psaty BM, Reppermund S, Rietschel M, Roffman JL, Romanczuk-Seiferth N, Rotter JI, Ryten M, Sacco RL, Sachdev PS, Saykin AJ, Schmidt R, Schmidt H, Schofield PR, Sigursson S, Simmons A, Singleton A, Sisodiya SM, Smith C, Smoller JW, Soininen H, Steen VM, Stott DJ, Sussmann JE, Thalamuthu A, Toga AW, Traynor B, Troncoso J, Tsolaki M, Tzourio C, Uitterlinden AG, Hernández MCV, Brug MVd, Lugt AVd, Wee NJAVd, Haren NEMV, Ent DVt, Tol M-JV, Vardarajan BN, Vellas B, Veltman DJ, ̈lzke HV, Walter H, Wardlaw JM, Wassink TH, Weale ME, Weinberger DR, Weiner MW, Wen W, Westman E, White T, Wong TY, Wright CB, Zielke RH, Zonderman AB, Martin NG, Duijn CMV, Wright MJ, Longstreth WT, Schumann G, Grabe HJ, Franke B, Launer LJ, Medland SE, Seshadri S, Thompson PM, Ikram MA. (2017) Novel genetic loci associated with hippocampal volume. Nature Communication, 8:13624. doi: 10.1038/ncomms13624

  36. Adams HHH, Hibar DP, Chouraki V, Stein JL, Nyquist PA, Renteria ME, Trompet S, Arias-Vasquez A, Seshadri S, Desrivieres S, Beecham AH, Jahanshad N, Wittfeld K, Van der Lee SJ, Abramovic L, Alhusaini S, Amin N, Andersson M, Arfanakis K, Aribisala BS, Armstrong NJ, Athanasiu L, Axelsson T, Beiser A, Bernard M, Bis JC, Blanken LME, Blanton SH, Bohlken MM, Boks MP, Bralten J, Brickman AM, Carmichael O, Chakravarty MM, Chauhan G, Chen Q, Ching CRK, Cuellar-Partida G, Braber AD, Doan NT, Ehrlich S, Filippi I, Ge T, Giddaluru S, Goldman AL, Gottesman RF, Greven CU, Grimm O, Griswold ME, Guadalupe T, Hass J, Haukvik UK, Hilal S, Hofer E, Hoehn D, Holmes AJ, Hoogman M, Janowitz D, Jia T, Kasperaviciute D, Kim S, Klein M, Kraemer B, Lee PH, Liao J, Liewald DCM, Lopez LM, Luciano M, Macare C, Marquand A, Matarin M, Mather KA, Mattheisen M, Mazoyer B, McKay DR, McWhirter R, Milaneschi Y, Mirza-Schreiber N, Muetzel RL, Maniega SM, Nho K, Nugent AC, Loohuis LMO, Oosterlaan J, Papmeyer M, Pappa I, Pirpamer L, Pudas S, Putz B, Rajan KB, Ramasamy A, Richards JS, Risacher SL, Roiz-Santianez R, Rommelse N, Rose EJ, Royle NA, Rundek T, Samann PG, Satizabal CL, Schmaal L, Schork AJ, Shen L, Shin J, Shumskaya E, Smith AV, Sprooten E, Strike LT, Teumer A, Thomson R, Tordesillas-Gutierrez D, Toro R, Trabzuni D, Vaidya D, Van der Grond J, Van der Meer D, Van Donkelaar MMJ, Van Eijk KR, Van Erp TGM, Van Rooij D, Walton E, Westlye LT, Whelan CD, Windham BG, Winkler AM, Woldehawariat G, Wolf C, Wolfers T, Xu B, Yanek LR, Yang J, Zijdenbos A, Zwiers MP, Agartz I, Aggarwal NT, Almasy L, Ames D, Amouyel P, Andreassen OA, Arepalli S, Assareh AA, Barral S, Bastin ME, Becker DM, Becker JT, Bennett DA, Blangero J, van Bokhoven H, Boomsma DI, Brodaty H, Brouwer RM, Brunner HG, Buckner RL, Buitelaar JK, Bulayeva KB, Cahn W, Calhoun VD, Cannon DM, Cavalleri GL, Chen C, Cheng C-Y, Cichon S, Cookson MR, Corvin A, Crespo-Facorro B, Curran JE, Czisch M, Dale AM, Davies GE, De Geus EJC, De Jager PL, de Zubicaray GI, Delanty N, Depondt C, DeStefano AL, Dillman A, Djurovic S, Donohoe G, Drevets WC, Duggirala R, Dyer TD, Erk S, Espeseth T, Evans DA, Fedko IO, Fernandez G, Ferrucci L, Fisher SE, Fleischman DA, Ford I, Foroud TM, Fox PT, Francks C, Fukunaga M, Gibbs JR, Glahn DC, Gollub RL, Goring HHH, Grabe HJ, Green RC, Gruber O, Gudnason V, Guelfi S, Hansell NK, Hardy J, Hartman CA, Hashimoto R, Hegenscheid K, Heinz A, Le Hellard S, Hernandez DG, Heslenfeld DJ, Ho B-C, Hoekstra PJ, Hoffmann W, Hofman A, Holsboer F, Homuth G, Hosten N, Hottenga J-J, Pol HEH, Ikeda M, Ikram MK, Jr CRJ, Jenkinson M, Johnson R, Jonsson EG, Jukema JW, Kahn RS, Kanai R, Kloszewska I, Knopman DS, Kochunov P, Kwok JB, Lawrie SM, Lemaitre H, Liu X, Longo DL, Jr WTL, Lopez OL, Lovestone S, Martinez O, Martinot J-L, Mattay VS, McDonald C, McIntosh AM, McMahon KL, McMahon FJ, Mecocci P, Melle I, Meyer-Lindenberg A, Mohnke S, Montgomery GW, Morris DW, Mosley TH, Muhleisen TW, Muller-Myhsok B, Nalls MA, Nauck M, Nichols TE, Niessen WJ, Nothen MM, Nyberg L, Ohi K, Olvera RL, Ophoff RA, Pandolfo M, Paus T, Pausova Z, Penninx BWJH, Pike GB, Potkin SG, Psaty BM, Reppermund S, Rietschel M, Roffman JL, Romanczuk-Seiferth N, Rotter JI, Ryten M, Sacco RL, Sachdev PS, Saykin AJ, Schmidt R, Schofield PR, Sigurdsson S, Simmons A, Singleton A, Sisodiya SM, Smith C, Smoller JW, Soininen H, Srikanth V, Steen VM, Stott DJ, Sussmann JE, Thalamuthu A, Tiemeier H, Toga AW, Traynor BJ, Troncoso J, Turner JA, Tzourio C, Uitterlinden AG, Hernandez MCV, Van der Brug M, Van der Lugt A, Van der Wee NJA, Van Duijn CM, Van Haren NEM, Van t Ent D, Van Tol M-J, Vardarajan BN, Veltman DJ, Vernooij MW, Volzke H, Walter H, Wardlaw JM, Wassink TH, Weale ME, Weinberger DR, Weiner MW, Wen W, Westman E, White T, Wong TY, Wright CB, Zielke HR, Zonderman AB, Deary IJ, DeCarli C, Schmidt H, Martin NG, De Craen AJM, Wright MJ, Launer LJ, Schumann G, Fornage M, Franke B, Debette S, Medland SE, Ikram MA, Thompson PM. (2016) Novel genetic loci underlying human intracranial volume identified through genome-wide association. Nature Neuroscience 2016 Dec;19(12):1569-82, 10.1038/nn.4398.

  37. Frost HR, Shen L, Saykin AJ, Williams SM, Moore JH, for the ADNI. (2016) Identifying significant gene-environment interactions using a combination of screening-testing and hierarchical false discovery rate control. Genetic Epidemiology, 40(7):544-557. 

  38. Hao X, Yao X, Yan J, Risacher SL, Saykin AJ, Zhang D, Shen L, for the Alzheimer's Disease Neuroimaging Initiative. (2016) Identifying multimodal intermediate phenotypes between genetic risk factors and disease status in Alzheimer’s disease. Neuroinformatics. 14(4):439-52. 

  39. Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the Alzheimer's Disease Neuroimaging Initiative. (2016) Two-dimensional enrichment analysis for mining high-level imaging genetic associations. Brain Informatics. http://dx.doi.org/10.1007/s40708-016-0052-4, pp 1-11, first online: 13 May 2016.

  40. Du L, Huang H, Yan J, Kim S, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the Alzheimer's Disease Neuroimaging Initiative. (2016) Structured Sparse CCA for Brain Imaging Genetics via Graph OSCAR. BMC Syst Biol. 10 Suppl 3:68.

  41. Song A, Yan J, Kim S, Risacher SL, Wong AK, Saykin AJ, Shen L, Greene CS, for the Alzheimer's Disease Neuroimaging Initiative. (2016) Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. BioData mining. 9:3, 10.1186/s13040-016-0082-8. 

  42. Du L, Huang H, Yan J, Kim S, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the Alzheimer's Disease Neuroimaging Initiative. (2016) Structured Sparse Canonical Correlation Analysis for Brain Imaging Genetics: An Improved GraphNet Method. Bioinformatics. 32 (10):1544-1551. 10.1093/bioinformatics/btw033.

  43. Birch SM, Lenox MW, Kornegay JN, Shen L, Ai H, Ren X, Goodlett CR, Cudd TA, Washburn SE. (2015) Computed tomography assessment of peripubertal craniofacial morphology in a sheep model of binge alcohol drinking in the first trimester. Alcohol. 2015 Nov;49(7):675-89, 10.1016/j.alcohol.2015.08.007.

  44. Weiss TL, Zieselman A, Hill DP, Diamond SG, Shen L, Saykin AJ, Moore JH, Alzheimer's Disease Neuroimaging I. (2015) The role of visualization and 3-D printing in biological data mining. BioData mining, 8:22. doi: 10.1186/s13040-015-0056-2 

  45. Ramanan VK, Risacher SL, Nho K, Kim S, Shen L, McDonald BC, Yoder KK, Hutchins GD, West JD, Tallman EF, Gao S, Foroud TM, Farlow MR, De Jager PL, Bennett DA, Aisen PS, Petersen RC, Jack CR, Toga AW, Green RC, Jagust WJ, Weiner MW, Saykin AJ, for the Alzheimer’s Disease Neuroimaging Initiative (ADNI). (2015) GWAS of longitudinal amyloid accumulation on [18F]-florbetapir PET in Alzheimer’s disease implicates microglial activation gene IL1RAP. BRAIN, 2015 Oct;138(Pt 10):3076-88, 10.1093/brain/awv231.

  46. Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Cedarbaum J, Green RC, Harvey D, Jack CR, Jagust W, Luthman J, Morris JC, Petersen RC, Saykin AJ, Shaw L, Shen L, Schwarz A, Toga AW, Trojanowski JQ, Alzheimer's Disease Neuroimaging I. (2015) 2014 Update of the Alzheimer's Disease Neuroimaging Initiative: A review of papers published since its inception. Alzheimer's & dementia: the journal of the Alzheimer's Association, 11(6):e1-e120. doi: 10.1016/j.jalz.2014.11.001

  47. Du L, Chakraborty A, Chiang CW, Cheng L, Quinney SK, Wu HY, Zhang P, Li L, and Shen L. (2015) Graphic mining of high-order drug interactions and their directional effects on myopathy using electronic medical records. CPT: Pharmacometrics & Systems Pharmacology, 4(8):481-488.

  48. Zhang P, Du L, Wang L, Liu M, Cheng L, Chiang CW, Wu HY, Quinney SK, Shen L and Li L. (2015) A mixture dose-response model for identifying high-dimensional drug interaction effects on myopathy using electronic medical record databases. CPT: Pharmacometrics & Systems Pharmacology, 4(8):474-480.

  49. Saykin AJ, Shen L, Yao X, Kim S, Nho K, Risacher SL, Ramanan VK, Foroud TM, Faber KM, Sarwar N, Munsie LM, Hu X, Soares HD, Potkin SG, Thompson PM, Kauwe JS, Kaddurah-Daouk R, Green RC,  Toga AW, Weiner MW, for the Alzheimer’s Disease neuroimaging Initiative. (2015) Genetic Studies of Quantitative MCI and AD Phenotypes in ADNI: Progress, Opportunities, and Plans. Alzheimers Dement., 11(7):792–814.

  50. Risacher SL, Kim S, Nho K, Foroud T, Shen L, Petersen RC, Jack CR, Beckett LA, Aisen PS, Koeppe RA, Jagust WJ, Shaw LM, Trojanowski JQ, Weiner MW, Saykin AJ, for the ADNI (2015) APOE effect on Alzheimer's biomarkers in older adults with significant memory concern. Alzheimers Dement., pii: S1552-5260(15)00124-7. doi: 10.1016/j.jalz.2015.03.003.

  51. Li J, Zhang Q, Chen F, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, and Shen L (2015) Genetic interactions explain variance in cingulate amyloid burden: An AV-45 PET genome-wide association and interaction study in the ADNI cohort. BioMed Research International, Article ID 647389, 11 pages.

  52. Yan J, Kim S, Nho K, Chen R, Risacher SL, Moore JH, Saykin AJ, Shen L, and for the ADNI. (2015) Hippocampal Transcriptome-Guided Genetic Analysis of Correlated Episodic Memory Phenotypes in Alzheimer's Disease. Frontiers in Genetics, 6, doi: 10.3389/fgene.2015.00117

  53. Nho K, Kim S, Risacher SL, Shen L, Corneveaux JJ, Swaminathan S, Lin H, Ramanan VK, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Jr., Weiner MW, Baldwin CT, Lunetta KL, Farrer LA, Study M, Furney SJ, Lovestone S, Simmons A, Mecocci P, Vellas B, Tsolaki M, Kloszewska I, Soininen H, AddNeuroMed C, McDonald BC, Farlow MR, Ghetti B, Indiana M, Aging S, Huentelman MJ, Saykin AJ, Alzheimer's Disease Neuroimaging I. (2015) Protective variant for hippocampal atrophy identified by whole exome sequencing. Annals of neurology, 77(3):547-52.

  54. Hibar DP, Stein JL, Renteria ME, Arias-Vasquez A, Desrivieres S, Jahanshad N, Toro R, Wittfeld K, Abramovic L, Andersson M, Aribisala BS, Armstrong NJ, Bernard M, Bohlken MM, Boks MP, Bralten J, Brown AA, Mallar Chakravarty M, Chen Q, Ching CR, Cuellar-Partida G, den Braber A, Giddaluru S, Goldman AL, Grimm O, Guadalupe T, Hass J, Woldehawariat G, Holmes AJ, Hoogman M, Janowitz D, Jia T, Kim S, Klein M, Kraemer B, Lee PH, Olde Loohuis LM, Luciano M, Macare C, Mather KA, Mattheisen M, Milaneschi Y, Nho K, Papmeyer M, Ramasamy A, Risacher SL, Roiz-Santianez R, Rose EJ, Salami A, Samann PG, Schmaal L, Schork AJ, Shin J, Strike LT, Teumer A, van Donkelaar MM, van Eijk KR, Walters RK, Westlye LT, Whelan CD, Winkler AM, Zwiers MP, Alhusaini S, Athanasiu L, Ehrlich S, Hakobjan MM, Hartberg CB, Haukvik UK, Heister AJ, Hoehn D, Kasperaviciute D, Liewald DC, Lopez LM, Makkinje RR, Matarin M, Naber MA, Reese McKay D, Needham M, Nugent AC, Putz B, Royle NA, Shen L, Sprooten E, Trabzuni D, van der Marel SS, van Hulzen KJ, Walton E, Wolf C, Almasy L, Ames D, Arepalli S, Assareh AA, Bastin ME, Brodaty H, Bulayeva KB, Carless MA, Cichon S, Corvin A, Curran JE, Czisch M, de Zubicaray GI, Dillman A, Duggirala R, Dyer TD, Erk S, Fedko IO, Ferrucci L, Foroud TM, Fox PT, Fukunaga M, Raphael Gibbs J, Goring HH, Green RC, Guelfi S, Hansell NK, Hartman CA, Hegenscheid K, Heinz A, Hernandez DG, Heslenfeld DJ, Hoekstra PJ, Holsboer F, Homuth G, Hottenga JJ, Ikeda M, Jack CR, Jr., Jenkinson M, Johnson R, Kanai R, Keil M, Kent JW, Jr., Kochunov P, Kwok JB, Lawrie SM, Liu X, Longo DL, McMahon KL, Meisenzahl E, Melle I, Mohnke S, Montgomery GW, Mostert JC, Muhleisen TW, Nalls MA, Nichols TE, Nilsson LG, Nothen MM, Ohi K, Olvera RL, Perez-Iglesias R, Bruce Pike G, Potkin SG, Reinvang I, Reppermund S, Rietschel M, Romanczuk-Seiferth N, Rosen GD, Rujescu D, Schnell K, Schofield PR, Smith C, Steen VM, Sussmann JE, Thalamuthu A, Toga AW, Traynor BJ, Troncoso J, Turner JA, Valdes Hernandez MC, van 't Ent D, van der Brug M, van der Wee NJ, van Tol MJ, Veltman DJ, Wassink TH, Westman E, Zielke RH, Zonderman AB, Ashbrook DG, Hager R, Lu L, McMahon FJ, Morris DW, Williams RW, Brunner HG, Buckner RL, Buitelaar JK, Cahn W, Calhoun VD, Cavalleri GL, Crespo-Facorro B, Dale AM, Davies GE, Delanty N, Depondt C, Djurovic S, Drevets WC, Espeseth T, Gollub RL, Ho BC, Hoffmann W, Hosten N, Kahn RS, Le Hellard S, Meyer-Lindenberg A, Muller-Myhsok B, Nauck M, Nyberg L, Pandolfo M, Penninx BW, Roffman JL, Sisodiya SM, Smoller JW, van Bokhoven H, van Haren NE, Volzke H, Walter H, Weiner MW, Wen W, White T, Agartz I, Andreassen OA, Blangero J, Boomsma DI, Brouwer RM, Cannon DM, Cookson MR, de Geus EJ, Deary IJ, Donohoe G, Fernandez G, Fisher SE, Francks C, Glahn DC, Grabe HJ, Gruber O, Hardy J, Hashimoto R, Hulshoff Pol HE, Jonsson EG, Kloszewska I, Lovestone S, Mattay VS, Mecocci P, McDonald C, McIntosh AM, Ophoff RA, Paus T, Pausova Z, Ryten M, Sachdev PS, Saykin AJ, Simmons A, Singleton A, Soininen H, Wardlaw JM, Weale ME, Weinberger DR, Adams HH, Launer LJ, Seiler S, Schmidt R, Chauhan G, Satizabal CL, Becker JT, Yanek L, van der Lee SJ, Ebling M, Fischl B, Longstreth WT, Jr., Greve D, Schmidt H, Nyquist P, Vinke LN, van Duijn CM, Xue L, Mazoyer B, Bis JC, Gudnason V, Seshadri S, Ikram MA, Alzheimer's Disease Neuroimaging I, Consortium C, Epigen, Imagen, Sys, Martin NG, Wright MJ, Schumann G, Franke B, Thompson PM, Medland SE. (2015) Common genetic variants influence human subcortical brain structures. Nature, doi: 10.1038/nature14101.

  55. Ramanan VK, Nho K, Shen L, Risacher SL, Kim S, McDonald BC, Farlow MR, Foroud TM, Gao S, Soininen H, Kloszewska I, Mecocci P, Tsolaki M, Vellas B, Lovestone S, Aisen PS, Petersen RC, Jack CR, Shaw LM, Trojanowski JQ, Weiner MW, Green RC, Toga AW, De Jager PL, Yu L, Bennett DA Saykin AJ, for the ADNI. (2015) FASTKD2 is associated with memory and hippocampal structure in older adults. Molecular Psychiatry, 20(10):1197-204, doi:10.1038/mp.2014.142.

  56. Yan J, Li T, Wang H, Huang H, Wan J, Nho K, Kim S, Risacher SL, Saykin AJ, Shen L, for the ADNI. (2015) Cortical surface biomarkers for predicting cognitive outcomes using group L21 norm. Neurobiology of Aging, 36:Suppl 1:S185-93.

  57. Huang F, Oldfield CJ, Xue B, Hsu WL, Meng J, Liu X, Shen L, Romero P, Uversky VN, and Dunker AK (2014) Improving Protein Order-Disorder Classification Using Charge-Hydropathy Plots. BMC Bioinformatics, 15:Suppl 17:S4.

  58. Zieselman AL, Fisher JM, Hu T, Andrews PC, Greene CS, Shen L, Saykin AJ, Moore JH. (2014) Computational genetics analysis of grey matter density in Alzheimer's disease. BioData mining, 7:17. 

  59. 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. [ECCB 2014 Issue, acceptance rate 14.8%]

  60. 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.

  61. Thompson PM, Stein JL, Medland SE, Hibar DP, Vasquez AA, Renteria ME, Toro R, Jahanshad N, Schumann G, Franke B, Wright MJ, Martin NG, Agartz I, Alda M, Alhusaini S, Almasy L, Almeida J, Alpert K, Andreasen NC, Andreassen OA, Apostolova LG, Appel K, Armstrong NJ, Aribisala B, Bastin ME, Bauer M, Bearden CE, Bergmann O, Binder EB, Blangero J, Bockholt HJ, Boen E, Bois C, Boomsma DI, Booth T, Bowman IJ, Bralten J, Brouwer RM, Brunner HG, Brohawn DG, Buckner RL, Buitelaar J, Bulayeva K, Bustillo JR, Calhoun VD, Cannon DM, Cantor RM, Carless MA, Caseras X, Cavalleri GL, Chakravarty MM, Chang KD, Ching CR, Christoforou A, Cichon S, Clark VP, Conrod P, Coppola G, Crespo-Facorro B, Curran JE, Czisch M, Deary IJ, de Geus EJ, den Braber A, Delvecchio G, Depondt C, de Haan L, de Zubicaray GI, Dima D, Dimitrova R, Djurovic S, Dong H, Donohoe G, Duggirala R, Dyer TD, Ehrlich S, Ekman CJ, Elvsashagen T, Emsell L, Erk S, Espeseth T, Fagerness J, Fears S, Fedko I, Fernandez G, Fisher SE, Foroud T, Fox PT, Francks C, Frangou S, Frey EM, Frodl T, Frouin V, Garavan H, Giddaluru S, Glahn DC, Godlewska B, Goldstein RZ, Gollub RL, Grabe HJ, Grimm O, Gruber O, Guadalupe T, Gur RE, Gur RC, Goring HH, Hagenaars S, Hajek T, Hall GB, Hall J, Hardy J, Hartman CA, Hass J, Hatton SN, Haukvik UK, Hegenscheid K, Heinz A, Hickie IB, Ho BC, Hoehn D, Hoekstra PJ, Hollinshead M, Holmes AJ, Homuth G, Hoogman M, Hong LE, Hosten N, Hottenga JJ, Hulshoff Pol HE, Hwang KS, Jack CR, Jr., Jenkinson M, Johnston C, Jonsson EG, Kahn RS, Kasperaviciute D, Kelly S, Kim S, Kochunov P, Koenders L, Kramer B, Kwok JB, Lagopoulos J, Laje G, Landen M, Landman BA, Lauriello J, Lawrie SM, Lee PH, Le Hellard S, Lemaitre H, Leonardo CD, Li CS, Liberg B, Liewald DC, Liu X, Lopez LM, Loth E, Lourdusamy A, Luciano M, Macciardi F, Machielsen MW, Macqueen GM, Malt UF, Mandl R, Manoach DS, Martinot JL, Matarin M, Mather KA, Mattheisen M, Mattingsdal M, Meyer-Lindenberg A, McDonald C, McIntosh AM, McMahon FJ, McMahon KL, Meisenzahl E, Melle I, Milaneschi Y, Mohnke S, Montgomery GW, Morris DW, Moses EK, Mueller BA, Munoz Maniega S, Muhleisen TW, Muller-Myhsok B, Mwangi B, Nauck M, Nho K, Nichols TE, Nilsson LG, Nugent AC, Nyberg L, Olvera RL, Oosterlaan J, Ophoff RA, Pandolfo M, Papalampropoulou-Tsiridou M, Papmeyer M, Paus T, Pausova Z, Pearlson GD, Penninx BW, Peterson CP, Pfennig A, Phillips M, Pike GB, Poline JB, Potkin SG, Putz B, Ramasamy A, Rasmussen J, Rietschel M, Rijpkema M, Risacher SL, Roffman JL, Roiz-Santianez R, Romanczuk-Seiferth N, Rose EJ, Royle NA, Rujescu D, Ryten M, Sachdev PS, Salami A, Satterthwaite TD, Savitz J, Saykin AJ, Scanlon C, Schmaal L, Schnack HG, Schork AJ, Schulz SC, Schur R, Seidman L, Shen L, Shoemaker JM, Simmons A, Sisodiya SM, Smith C, Smoller JW, Soares JC, Sponheim SR, Sprooten E, Starr JM, Steen VM, Strakowski S, Strike L, Sussmann J, Samann PG, Teumer A, Toga AW, Tordesillas-Gutierrez D, Trabzuni D, Trost S, Turner J, Van den Heuvel M, van der Wee NJ, van Eijk K, van Erp TG, van Haren NE, van 't Ent D, van Tol MJ, Valdes Hernandez MC, Veltman DJ, Versace A, Volzke H, Walker R, Walter H, Wang L, Wardlaw JM, Weale ME, Weiner MW, Wen W, Westlye LT, Whalley HC, Whelan CD, White T, Winkler AM, Wittfeld K, Woldehawariat G, Wolf C, Zilles D, Zwiers MP, Thalamuthu A, Schofield PR, Freimer NB, Lawrence NS, Drevets W (2014) The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging Behav., 8:153-182. doi:10.1007/s11682-013-9269-5.

  62. 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.

  63. Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Green RC, Harvey D, Jack CR, Jagust W, Liu E, Morris JC, Petersen RC, Saykin AJ, Schmidt ME, Shaw L, Shen L, Siuciak JA, Soares H, Toga AW, Trojanowski JQ (2013) The Alzheimer's Disease Neuroimaging Initiative: A review of papers published since its inception. Alzheimers Dement., 9(5):e111-94. doi: 10.1016/j.jalz.2013.05.1769.

  64. Wang J, Ren X, Shen L, Yanni S, Leffler J, and Birch E (2013) Development of refractive error in individual children with regressed retinopathy of prematurity. Invest Ophthalmol Vis Sci, 54(9):6018-24. doi: 10.1167/iovs.13-11765.

  65. Kim S, Swaminathan S, Inlow M, Risacher SL, Nho K, Shen L, Foroud TM, Petersen RC, Aisen PS, Soares H, Toledo JB, Shaw LM, Trojanowski JQ, Weiner MW, McDonald BC, Farlow MR, Ghetti B, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (ADNI) (2013) Influence of genetic variation on plasma protein levels in older adults using a multi-analyte panel. PLoS One, 8(7): e70269. doi:10.1371/journal.pone.0070269.

  66. 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.

  67. Li T, Xie Z, Wu J, Yan J, Shen L (2013) Interactive object extraction by merging regions with k-global maximal similarity. Neurocomputing, 120: 610-623.

  68. Yoder K, Nho K, Risacher SL, Kim S, Shen L, Saykin AJ (2013) Influence of TSPO genotype on [11C]PBR28 standardized uptake values. Journal of Nuclear Medicine, 54(8):1320-2. doi:10.2967/jnumed.112.118885.

  69. Risacher SL, Kim S, Shen L, Nho K, Foroud TM, Green RC, Petersen RC, Jack CR, Aisen PS, Koeppe RA, Jagust WJ, Shaw LM, Trojanowski JQ, Weiner MW, Saykin AJ, for the ADNI (2013) The role of Apolipoprotein E (APOE) genotype in early mild cognitive impairment (E-MCI). Front Aging Neurosci, 5: 11. doi: 10.3389/fnagi.2013.00011.

  70. Nho K, Corneveaux JJ, Kim S, Lin H, Risacher SL, Shen L, Swaminathan S, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta K, Farrer LA, for the Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study, Furney SJ, Lovestone SL, Simmons AS, Mecocci PM, Vellas B, Magda VB, Tsolaki M, Kloszewska I, Soininen H, for the AddNeuroMed Consortium, McDonald BC, Farlow MR, for the Indiana Memory and Aging Study, Huentelman MJ, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (2013) Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in Mild Cognitive Impairment. Mol Psychiatry, 18(7), 781-787.

  71. Nho K, Corneveaux JJ, Kim S, Lin H, Risacher SL, Shen L, Swaminathan S, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta K, Farrer LA, for the Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study, Furney SJ, Lovestone SL, Simmons AS, Mecocci PM, Vellas B, Magda VB, Tsolaki M, Kloszewska I, Soininen H, for the AddNeuroMed Consortium, McDonald BC, Farlow MR, for the Indiana Memory and Aging Study, Huentelman MJ, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (2013) Identification of functional variants from whole-exome sequencing, combined with neuroimaging genetics. Mol Psychiatry, 18(7), 739.

  72. Ramanan VK, Risacher SL, Nho K, Kim S, Swaminathan S, Shen L, Foroud TM, Hakonarson H, Huentelman MJ, Aisen PS, Petersen RC, Green RC, Jack CR, Koeppe RA, Jagust WJ, Weiner MW, Saykin AJ, for the Alzheimer’s Disease Neuroimaging Initiative (2013) APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir 1 PET genome-wide association study. Mol Psychiatry, doi: 10.1038/mp.2013.19.

  73. 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, for the Alzheimer's Disease Neuroimaging Initiative (2013) Association of plasma and cortical beta-amyloid is modulated by APOE e4 status. Alzheimer's & Dementia, pii: S1552-5260(13)00039-3, http://dx.doi.org/10.1016/j.jalz.2013.01.007.

  74. Shen L (2012) Principles of computational modeling in neuroscience (book review). Briefings in Bioinformatics, 13(3): 390-392, doi:10.1093/bib/bbs003. 

  75. Luo XJ, Li M, Huang L, Nho K, Deng M, Chen Q, Weinberger DR, Vasquez AA, Rijpkema M, Mattay VS, Saykin AJ, Shen L, Fernández G, Franke B, Chen JC, Chen XN, Wang JK, Xiao X, Qi XB, Xiang K, Peng YM, Cao XY, Li Y, Shi XD, for the Alzheimer's Disease Neuroimaging Initiative, Gan L, and Su B (2012) The interleukin 3 gene (IL3) contributes to human brain volume variation by regulating proliferation and survival of neural progenitors. PLoS One, 7(11): e50375. doi:10.1371/journal.pone.0050375.

  76. Swaminathan S, Huentelman MJ, Corneveaux JJ, Myers AJ, Faber KM, Foroud T, Mayeux R, Shen L, Kim S, Turk M, Hardy J, Reiman EM, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the NIA-LOAD/NCRAD Family Study Group (2012) Analysis of copy number variation in Alzheimer's Disease in a cohort of clinically characterized and neuropathologically verified individuals. PLoS One, 7(12): e50640. doi:10.1371/journal.pone.0050640.

  77. Nho K, Risacher SL, Crane PK, DeCarli C, Glymour MM, Habeck C, Kim S, Lee GJ, Mormino E, Mukherjee S, Shen L, West JD, Saykin AJ, and the Alzheimer's Disease Neuroimaging Initiative (2012) Voxel and surface-based topography of memory and executive deficits in mild cognitive impairment and Alzheimer's disease. Brain Imaging and Behavior, 6(4):551-67.

  78. Ramanan VK, Kim S, Holohan K, Shen L, Nho K, Risacher SL, Foroud TM, Mukherjee S, Crane PK, Aisen PS, Petersen RC, Weiner MW, Saykin AJ, for the Alzheimer's Disease Neuroimaging Initiative (2012) Genome-wide pathway analysis of memory impairment in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort implicates gene candidates, pathways, and networks. Brain Imaging and Behavior, 6(4):634-48.

  79. 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. [ECCB 2012 Issue, acceptance rate 14%]

  80. Melville S, Buros J, Parrado A, Vardarajan B, Shen L, Risacher SL, Kim S, Jun G, DeCarli C, Lunetta KL, Baldwin CT, Saykin AJ, Farrer LA (2012) Multiple loci influencing hippocampal degeneration identified by genome scan. Annals of Neurology, 72(1):65-75. doi: 10.1002/ana.23644.

  81. Stein JL, Medland SE, Vasquez AA, Hibar DP, Senstad RE, Winkler AM, Toro R, Appel K, Bartecek R, Bergmann O, Bernard M, Brown AA, Cannon DM, Chakravarty MM, Christoforou A, Domin M, Grimm O, Hollinshead M, Holmes AJ, Homuth G, Hottenga JJ, Langan C, Lopez LM, Hansell NK, Hwang KS, Kim S, Laje G, Lee PH, Liu X, Loth E, Lourdusamy A, Mattingsdal M, Mohnke S, Maniega SM, Nho K, Nugent AC, O'Brien C, Papmeyer M, Putz B, Ramasamy A, Rasmussen J, Rijpkema M, Risacher SL, Roddey JC, Rose EJ, Ryten M, Shen L, Sprooten E, Strengman E, Teumer A, Trabzuni D, Turner J, van Eijk K, van Erp TG, van Tol MJ, Wittfeld K, Wolf C, Woudstra S, Aleman A, Alhusaini S, Almasy L, Binder EB, Brohawn DG, Cantor RM, Carless MA, Corvin A, Czisch M, Curran JE, Davies G, de Almeida MA, Delanty N, Depondt C, Duggirala R, Dyer TD, Erk S, Fagerness J, Fox PT, Freimer NB, Gill M, Goring HH, Hagler DJ, Hoehn D, Holsboer F, Hoogman M, Hosten N, Jahanshad N, Johnson MP, Kasperaviciute D, Kent JW, Jr., Kochunov P, Lancaster JL, Lawrie SM, Liewald DC, Mandl R, Matarin M, Mattheisen M, Meisenzahl E, Melle I, Moses EK, Muhleisen TW, Nauck M, Nothen MM, Olvera RL, Pandolfo M, Pike GB, Puls R, Reinvang I, Renteria ME, Rietschel M, Roffman JL, Royle NA, Rujescu D, Savitz J, Schnack HG, Schnell K, Seiferth N, Smith C, Steen VM, Valdes Hernandez MC, Van den Heuvel M, van der Wee NJ, Van Haren NE, Veltman JA, Volzke H, Walker R, Westlye LT, Whelan CD, Agartz I, Boomsma DI, Cavalleri GL, Dale AM, Djurovic S, Drevets WC, Hagoort P, Hall J, Heinz A, Jack CR, Jr., Foroud TM, Le Hellard S, Macciardi F, Montgomery GW, Poline JB, Porteous DJ, Sisodiya SM, Starr JM, Sussmann J, Toga AW, Veltman DJ, Walter H, Weiner MW, Bis JC, Ikram MA, Smith AV, Gudnason V, Tzourio C, Vernooij MW, Launer LJ, Decarli C, Seshadri S, Andreassen OA, Apostolova LG, Bastin ME, Blangero J, Brunner HG, Buckner RL, Cichon S, Coppola G, de Zubicaray GI, Deary IJ, Donohoe G, de Geus EJ, Espeseth T, Fernandez G, Glahn DC, Grabe HJ, Hardy J, Hulshoff Pol HE, Jenkinson M, Kahn RS, McDonald C, McIntosh AM, McMahon FJ, McMahon KL, Meyer-Lindenberg A, Morris DW, Muller-Myhsok B, Nichols TE, Ophoff RA, Paus T, Pausova Z, Penninx BW, Potkin SG, Samann PG, Saykin AJ, Schumann G, Smoller JW, Wardlaw JM, Weale ME, Martin NG, Franke B, Wright MJ, Thompson PM (2012) Identification of common variants associated with human hippocampal and intracranial volumes. Nat Genet. 44: 552–561. doi:10.1038/ng.2250. 

  82. 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. [ISMB 2012 Issue, acceptance rate 13%]

  83. Ramanan VK, Shen L, Moore JH, Saykin AJ (2012) Pathway analysis of genomic data: concepts, methods, prospects for future development. Trends in Genetics, 28(7):323–332. doi:10.1016/j.tig.2012.03.004.

  84. 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 (2012) Analysis of copy number variation in Alzheimer's disease: the NIA-LOAD/NCRAD family study. Current Alzheimer Research, 9:801-814.

  85. Wang H, Nie F, Huang H, Kim S, Nho K, Risacher SL, Saykin AJ, Shen L, for the ADNI (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.

  86. Meda SA, Narayanan B, Liu J, Perrone-Bizzozero NI,Stevens MC,Calhoun VD, Glahn DC, Shen L, Risacher SL, Saykin AJ, Pearlson GD (2012) A large scale multivariate parallel ICA method reveals novel imaging-genetic relationships for Alzheimer’s disease in the ADNI cohort. Neuroimage, 60(3):1608–1621.

  87. 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, ADNI (2011) Amyloid pathway-based candidate gene analysis of [11C]PiB-PET in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Brain Imaging Behav, 6(1):1-15.

  88. 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, ADNI (2011) Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects. Neuroimage, 56:1875-1891. 

  89. Swaminathan S, Kim S, Shen L, Risacher SL, Foroud T, Pankratz N, Potkin SG, Huentelman MJ, Craig DW, Weiner MW, Saykin AJ, ADNI (2011) Genomic copy number analysis in Alzheimer's disease and MCI: An ADNI Study. Int J Alzheimer’s Dis, 2011:729478, 10 pages. 
    Furney SJ, Simmons A, Breen G, Pedroso I, Lunnon K, Proitsi P, Hodges A, Powell J, Wahlund LO,

  90. 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, AddNeuroMed (2011) Genome wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer’s disease. Molecular Psychiatry, 16(11):1130-8.

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

  92. 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 (2011) Genome-wide association study of CSF biomarkers Abeta-42, t-tau, p-tau181p in the ADNI cohort. Neurology, 76:69-79.

  93. 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.

  94. Shen L, Saykin AJ, Kim S, Firpi H, West J, Risacher SL, McDonald BC, McHugh TL, Wishart HA, Flashman LA (2010) Comparison of manual and automated determination of hippocampal volumes in MCI and older adults with cognitive complaints. Brain Imaging and Behavior, 4:86–95.

  95. Risacher SL, Shen L, West JD, Kim S, McDonald BC, Beckett LA, Jack CR Jr, Weiner MW, Saykin AJ, ADNI (2010) Longitudinal MRI atrophy biomarkers: Relationship to conversion in the ADNI cohort. Neurobiology of Aging, 31(8):1401-1418. 

  96. 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, plans. Alzheimers Dement, 6:265–273.

  97. 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 (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 B Neuropsychiatr Genet, 153B:1060-1069.

  98. 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, ADNI (2010) Commonly carried allele within FTO, an obesity-associated gene, relates to accelerated brain degeneration in the elderly. Proc Natl Acad Sci USA, 107(18):8404-9.

  99. 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, ADNI (2010) Voxelwise Genome-Wide Association Study (vGWAS). Neuroimage, 53:1160–1174.

  100. 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, ADNI (2010) Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. NeuroImage, 51(2):542-554.

  101. 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.

  102. Shen L, Kim S, Saykin AJ (2009) Fourier method for large scale surface modeling and registration. Computers and Graphics, 33(3):299-311. [SMI 2009 Issue, acceptance rate 25%]

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

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

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

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

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

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

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

  110. Chung MK, Dalton KM, Shen L, Robbins SM, Evans AC, Davidson RJ (2007) Weighted Fourier series representation and its application to quantifying amount of gray matter. IEEE Trans. on Medical Imaging, 26(4):566-581.

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

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

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

  114. Shen L, Zheng W, Gao L, Huang H, Makedon FS, Pearlman JD. (2006) Spatio-temporal modeling of lung images for cancer detection. Oncology Reports, 15 Spec no.:1085-1090.

  115. Huang H, Shen L, Ford JC, Gao L, Pearlman JD (2006) Early lung cancer detection based on registered perfusion MRI. Oncology Reports, 15 Spec no.:1081-1084.

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

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

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

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

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

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

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

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