Journal Articles

  1. Wen J, Zhao B, Yang Z, Erus G, Skampardoni I, Mamourian E, Cui Y, Hwang G, Bao J, Boquet-Pujadas A, Zhou Z, Veturi Y, Ritchie MD, Shou H, Thompson PM, Shen L, Toga AW, Davatzikos C. (2024) The Genetic Architecture of Multimodal Human Brain Age. Nat Commun, 15:2604. https://doi.org/10.1038/s41467-024-46796-6   
  2. Wang Z, Zhan Q, Tong B, Yang S, Hou B, Huang H, Saykin A, Thompson PM, Davatzikos C, Shen L, for the ADNI. (2024) Distance-weighted Sinkhorn loss for Alzheimer's disease classification. iScience, 27(3): 109212. https://doi.org/10.1016/j.isci.2024.109212  
  3. Duong-Tran D, Kaufmann R, Chen J, Wang X, Garai S, Xu FH, Bao J, Amico E, Kaplan AD, Petri G, Goni J, Zhao Y, Shen L. (2024) Homological landscape of human brain functional sub-circuits. Mathematics, 12(3):455. https://doi.org/10.3390/math12030455
  4. Yang Z, Wen J, Abdulkadir A, Cui Y, Erus G, Mamourian E, Melhem R, Srinivasan D, Govindarajan ST, Chen J, Habes M, Masters CL, Maruff P, Fripp J, Ferrucci L, Albert MS, Johnson SC, Morris JC, LaMontagne P, Marcus DS, Benzinger TLS, Wolk DA, Shen L, Bao J, Resnick SM, Shou H, Nasrallah IM, Davatzikos C. (2024) Gene-SGAN: a method for discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering. Nat Commun, 15(1):354. https://doi.org/10.1038/s41467-023-44271-2 
  5. Wen J, Nasrallah IM, Abdulkadir A, Satterthwaite TD, Yang Z, Erus G, Robert-Fitzgerald T, Singh A, Sotiras A, Boquet-Pujadas A, Mamourian E, Doshi J, Cui Y, Srinivasan D, Chen J, Hwang G, Bergman M, Bao J, Veturi Y, Zhou Z, Yang S, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Gur RC, Gur RE, Koutsouleris N, Wolf DH, Saykin AJ, Ritchie MD, Shen L, Thompson PM, Colliot O, Wittfeld K, Grabe HJ, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Espeland M, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Resnick SM, Fan Y, Habes M, Wolk D, Shou H, Davatzikos C, iSTAGING, the BLSA, the BIOCARD, the PHENOM, the ADNI studies, the AI4AD consortium. (2023) Genomic loci influence patterns of structural covariance in the human brain. Proceedings of the National Academy of Sciences of the United States of America, 2023; 120 (52) e2300842120. https://doi.org/10.1073/pnas.2300842120  
  6. Romano J, Kumar R, Venkatesan M, Graham B, Hao Y, Matsumoto N, Li X, Wang Z, Ritchie M, Shen L, Moore J. (2023) The Alzheimer's Knowledge Base - A knowledge graph for therapeutic discovery in Alzheimer's Disease research. Journal of Medical Internet Research, 2023:07/11/2023:46777 (forthcoming/in press), 10.2196/preprints.46777.
  7. Zhang Q, Chang C, Shen L, Long Q. (2024) Incorporating graph information in bayesian factor analysis with robust and adaptive shrinkage priors. Biometrics, 80(1):ujad014. https://doi.org/10.1093/biomtc/ujad014
  8. Lee B, Wang J, Hall MA,  Kim D, Stites SD, Shen L. (2024) Sex modifies predictive effects of imaging and CSF biomarkers on cognitive and functional outcomes: A study of Alzheimer’s disease. Neurobiology of Aging, 133:67-77. https://doi.org/10.1016/j.neurobiolaging.2023.10.002
  9. Rosewood TJ, Nho K, Risacher SL, Gao S, Shen L, Foroud T, Saykin AJ, on behalf of the Alzheimer’s Disease Neuroimaging I. (2023) Genome-Wide Association Analysis across Endophenotypes in Alzheimer’s Disease: Main Effects and Disease Stage-Specific Interactions. Genes; 2023. https://doi.org/10.3390/genes14112010
  10. Suh EH, Lee G, Jung SH, Wen Z, Bao J, Nho K, Huang H, Davatzikos C, Saykin AJ, Thompson PM, Shen L, Kim D. (2023) An interpretable Alzheimer's disease oligogenic risk score informed by neuroimaging biomarkers improves risk prediction and stratification. Front. Aging Neurosci., 15:1281748. https://doi.org/10.3389/fnagi.2023.1281748
  11. Bao J, Wen J, Wen Z, Cui Y, Yang Z, Erus G, Saykin AJ, Long Q, Davatzikos C, Shen L. (2023) Brain-wide genome-wide colocalization study for integrating genetics, transcriptomics and brain morphometry in Alzheimer’s disease. Neuroimage, 280:120346.  https://doi.org/10.1016/j.neuroimage.2023.120346 
  12. Sha J, Bao J, Liu K, Yang S, Wen Z, Wen J, Cui Y, Tong B, Moore JH, Saykin AJ, Davatzikos C, Long Q, Shen L, for the ADNI. (2023) Preference matrix guided sparse canonical correlation analysis for mining brain imaging genetic associations in Alzheimer's disease. Methods, 218:27-38. https://doi.org/10.1016/j.ymeth.2023.07.007
  13. Mao C, Xu J, Rasmussen L, Li Y, Adekkanattu P, Pacheco J, Bonakdarpour B, Vassar R, Shen L, Jiang G, Wang F, Pathak J, Luo Y. (2023) AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. J Biomed Inform,144:104442. https://doi.org/10.1016/j.jbi.2023.104442
  14. Nam Y, Lucas A, Yun JS, Lee SM, Park JW, Chen Z, Lee B, Ning X, Shen L, Verma A, Kim D. (2023) Development of complemented comprehensive networks for rapid screening of repurposable drugs applicable to new emerging disease outbreaks. J Transl Med. 2023 Jun 26;21(1):415, http://doi.org/10.1186/s12967-023-04223-2
  15. Torgersen J, Akers S, Huo Y, Terry JG, Carr JJ, Ruutiainen AT, Skanderson M, Levin W, Lim JK, Taddei TH, So-Armah K, Bhattacharya D, Rentsch CT, Shen L, Carr R, Shinohara RT, McClain M, Freiberg M, Justice AC, Lo Re V. (2023) Performance of fully automated liver attenuation assessment for measurement of hepatic steatosis within noncontrast computed tomography scans among people with and without HIV. Pharmacoepidemiology and Drug Safety. http://doi.org/10.1002/pds.5648.
  16. Bao J, Chang C, Zhang Q, Saykin AJ, Shen L, Long Q, for the ADNI. (2023) Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis. Briefings in Bioinformatics, 24(2):bbad073. https://doi.org/10.1093/bib/bbad073 
  17. Mai H, Bao J, Thompson PM, Kim D, Shen L. (2022) Identifying genes associated with brain volumetric differences through tissue specific transcriptomic inference from GWAS summary data. BMC Bioinformatics, 23 (Suppl 3), 398 (2022). https://doi.org/10.1186/s12859-022-04947-w
  18. Feng Y, Kim M, Yao X, Liu K, Long Q, Shen L, for the ADNI. (2022) Deep multiview learning to identify imaging-driven subtypes in mild cognitive impairment. BMC Bioinformatics, 23 (Suppl 3), 402 (2022). https://doi.org/10.1186/s12859-022-04946-x 
  19. Wu R, Bao J, Kim M, Saykin AJ, Moore JH, Shen L. (2022) Mining high-level imaging genetic associations via clustering AD candidate variants with similar brain association patterns. Genes, 13(9), 1520; https://doi.org/10.3390/genes13091520
  20. Jin C, Lee B, Shen L, Long Q, for the ADNI. (2022) Integrating multi-omics summary data using a Mendelian randomization framework. Briefings in Bioinformatics, 2022 Sep 12;bbac376. https://doi.org/10.1093/bib/bbac376 
  21. Kim M, Wu R, Yao X, Saykin AJ, Moore JH, Shen L, for the ADNI. (2022) Identifying genetic markers enriched by brain imaging endophenotypes in Alzheimer's disease. BMC Med Genomics, 15, Article 168. https://doi.org/10.1186/s12920-022-01323-8.
  22. Baik JY, Kim M, Bao J, Long Q, Shen L, for the ADNI. (2022) Identifying Alzheimer’s genes via brain transcriptome mapping. BMC Med Genomics, 15, Article 116. https://doi.org/10.1186/s12920-022-01260-6 
  23. Lee B, Yao X, Shen L, for the ADNI. (2022) Integrative analysis of summary data from GWAS and eQTL studies implicates genes differentially expressed in Alzheimer’s disease. BMC Genomics, 23, Article 414. https://doi.org/10.1186/s12864-022-08584-8.
  24. Zarzar TG, Lee B, Coughlin R, Kim D, Shen L, Hall MA. (2022) Sex differences in the metabolome of Alzheimer's disease progression. Frontiers in Radiology, Artificial Intelligence in Radiology. https://www.frontiersin.org/articles/10.3389/fradi.2022.782864  
  25. Lee B, Yao X, Shen L, for the ADNI. (2022) Genome-wide association study of quantitative biomarkers identifies a novel locus for Alzheimer’s disease at 12p12.1. BMC Genomics, 23(1):85. https://doi.org/10.1186/s12864-021-08269-8.
  26. Wen J, Fu CHY, Tosun D, Veturi Y, Yang Z, Abdulkadir A, Mamourian E, Srinivasan D, Bao J, Erus G, Shou H, Habes M, Doshi J, Varol E, Mackin SR, Sotiras A, Fan Y, Saykin AJ, Sheline YI, Shen L, Ritchie MD, Wolk DA, Albert M, Resnick SM, Davatzikos C. (2022) Characterizing heterogeneity in neuroimaging, cognition, clinical symptoms, and genetics among patients with late-life depression. JAMA Psychiatry, 2022;79(5):464-474. https://doi.org/10.1001/jamapsychiatry.2022.0020
  27. Cong S, Yao X, Xie L, Yan J, Shen L. (2022) Genetic influence underlying brain connectivity phenotype: A study on two age-specific cohorts. Frontiers in Genetics, section Statistical Genetics and Methodology, 12:782953. https://www.frontiersin.org/articles/10.3389/fgene.2021.782953 
  28. Kim M, Min EJ, Liu K, Yan J, Saykin AJ, Moore JH, Long Q, Shen L. (2022) Multi-task learning based structured sparse canonical correlation analysis for brain imaging genetics. Med Image Anal. 2022 2022/02/01/;76:102297, https://doi.org/10.1016/j.media.2021.102297. 
  29. Yang P, Zhao C, Yang Q, Wei Z, Xiao X, Shen L, Wang T, Lei B, Peng Z. (2022) Diagnosis of obsessive-compulsive disorder via spatial similarity-aware learning and fused deep polynomial network. Med Image Anal. 2022 2022/01/01/;75:102244, https://doi.org/10.1016/j.media.2021.102244.
  30. Gutman BA, van Erp TGM, Alpert K, Ching CRK, Isaev D, Ragothaman A, Jahanshad N, Saremi A, Zavaliangos-Petropulu A, Glahn DC, Shen L, Cong S, Alnaes D, Andreassen OA, Doan NT, Westlye LT, Kochunov P, Satterthwaite TD, Wolf DH, Huang AJ, Kessler C, Weideman A, Nguyen D, Mueller BA, Faziola L, Potkin SG, Preda A, Mathalon DH, Bustillo J, Calhoun V, Ford JM, Walton E, Ehrlich S, Ducci G, Banaj N, Piras F, Piras F, Spalletta G, Canales-Rodriguez EJ, Fuentes-Claramonte P, Pomarol-Clotet E, Radua J, Salvador R, Sarro S, Dickie EW, Voineskos A, Tordesillas-Gutierrez D, Crespo-Facorro B, Setien-Suero E, van Son JM, Borgwardt S, Schonborn-Harrisberger F, Morris D, Donohoe G, Holleran L, Cannon D, McDonald C, Corvin A, Gill M, Filho GB, Rosa PGP, Serpa MH, Zanetti MV, Lebedeva I, Kaleda V, Tomyshev A, Crow T, James A, Cervenka S, Sellgren CM, Fatouros-Bergman H, Agartz I, Howells F, Stein DJ, Temmingh H, Uhlmann A, de Zubicaray GI, McMahon KL, Wright M, Cobia D, Csernansky JG, Thompson PM, Turner JA, Wang L. (2022) A meta-analysis of deep brain structural shape and asymmetry abnormalities in 2,833 individuals with schizophrenia compared with 3,929 healthy volunteers via the ENIGMA Consortium. Human brain mapping. 2022 Jan;43(1):352-72, https://doi.org/10.1002/hbm.25625. 
  31. Ye Z, Mo C, Liu S, Hatch KS, Gao S, Ma Y, Hong LE, Thompson PM, Jahanshad N, Acheson A, Garavan H, Shen L, Nichols TE, Kochunov P, Chen S, Ma T. (2021) White Matter Integrity and Nicotine Dependence: Evaluating Vertical and Horizontal Pleiotropy. Front Neurosci. 2021;15:738037, https://doi.org/10.3389/fnins.2021.738037. 
  32. Nayor M, Shen L, Hunninghake GM, Kochunov P, Barr RG, Bluemke DA, Broeckel U, Caravan P, Cheng S, de Vries PS, Hoffmann U, Kolossvary M, Li H, Luo J, McNally EM, Thanassoulis G, Arnett DK, Vasan RS. (2021) Progress and Research Priorities in Imaging Genomics for Heart and Lung Disease: Summary of an NHLBI Workshop. Circ Cardiovasc Imaging. 2021 Aug;14(8):e012943, https://doi.org/10.1161/circimaging.121.012943.
  33. Kim M, Bao J, Liu K, Park BY, Park H, Baik JY, Shen L. (2021) A structural enriched functional network: An application to predict brain cognitive performance. Med Image Anal. 2021 Jul;71:102026, https://doi.org/10.1016/j.media.2021.102026.
  34. Lu L, Elbeleidy S, Baker L, Wang H, Shen L, Heng H. (2021) Improved Prediction of Cognitive Outcomes via Globally Aligned Imaging Biomarker Enrichments Over Progressions. IEEE Trans Biomed Eng. 2021 Nov;68(11):3336-46, https://doi.org/10.1109/tbme.2021.3070875.
  35. McKinley TO, Gaski GE, Zamora R, Shen L, Sun Q, Namas RA, Billiar TR, Vodovotz Y. (2021) Early dynamic orchestration of immunologic mediators identifies multiply injured patients who are tolerant or sensitive to hemorrhage. J Trauma Acute Care Surg. 2021 Mar 1;90(3):441-50, https://doi.org/10.1097/TA.0000000000002998. 
  36. Li J, Bian C, Chen D, Meng X, Luo H, Liang H, Shen L, for the ADNI. (2020) Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study. BMC Bioinformatics, 21(21):535, https://doi.org/10.1186/s12859-020-03877-9.
  37. Meng X, Li J, Zhang Q, Chen F, Bian C, Yao X, Yan J, Xu Z, Risacher SL, Saykin AJ, Liang H, Shen L, for the ADNI. (2020) Multivariate genome wide association and network analysis of subcortical imaging phenotypes in Alzheimer's disease. BMC Genomics, 21(11):896, https://doi.org/10.1186/s12864-020-07282-7.
  38. Peng B, Yao X, Risacher SL, Saykin AJ, Shen L, Ning X, for the ADNI (2020) Cognitive biomarker prioritization in Alzheimer's disease using brain morphometric data. BMC Med Inform Decis Mak. 2020 Dec 2;20(1):319, https://doi.org/10.1186/s12911-020-01339-z. 
  39. Cong S*, Yao X*, Huang Z, Risacher SL, Nho K, Saykin AJ, Shen L, for the ADNI. (2020) Volumetric GWAS of medial temporal lobe structures identifies an ERC1 locus using ADNI high-resolution T2-weighted MRI data. Neurobiology of Aging, 95:81-93. (* Equal Contribution) https://doi.org/10.1016/j.neurobiolaging.2020.07.005
  40. Moore JH, Barnett I, Boland MR, Chen Y, Demiris G, Gonzalez-Hernandez G, Herman DS, Himes BE, Hubbard RA, Kim D, Morris JS, Mowery DL, Ritchie MD, Shen L, Urbanowicz R, Holmes JH. (2020) Ideas for how informaticians can get involved with COVID-19 research. BioData mining. 2020;13:3. https://doi.org/10.1186/s13040-020-00213-y
  41. Du L, Liu F, Liu K, Yao X, Risacher SL, Han J, Saykin AJ, Shen L, for the ADNI. (2020) Associating multi-modal brain imaging phenotypes and genetic risk factors via a dirty multi-task learning method. IEEE Trans. on Medical Imaging, 39(11):3416-3428. https://doi.org/10.1109/TMI.2020.2995510
  42. Du L, Liu F, Liu K, Yao X, Risacher SL, Han J, Guo L, Saykin AJ, Shen L, for the ADNI. (2020) Identifying diagnosis-specific genotype-phenotype associations via joint multi-task sparse canonical correlation analysis and classification. Bioinformatics (ISMB 2020 Issue), 36:i371-i379. [19.4% acceptance rate]
  43. Grasby KL, Jahanshad N, Painter JN, Colodro-Conde L, Bralten J, Hibar DP, Lind PA, Pizzagalli F, Ching CRK, McMahon MAB, Shatokhina N, Zsembik LCP, Thomopoulos SI, Zhu AH, Strike LT, Agartz I, Alhusaini S, Almeida MAA, Alnæs D, Amlien IK, Andersson M, Ard T, Armstrong NJ, Ashley-Koch A, Atkins JR, Bernard M, Brouwer RM, Buimer EEL, Bülow R, Bürger C, Cannon DM, Chakravarty M, Chen Q, Cheung JW, Couvy-Duchesne B, Dale AM, Dalvie S, de Araujo TK, de Zubicaray GI, de Zwarte SMC, den Braber A, Doan NT, Dohm K, Ehrlich S, Engelbrecht H-R, Erk S, Fan CC, Fedko IO, Foley SF, Ford JM, Fukunaga M, Garrett ME, Ge T, Giddaluru S, Goldman AL, Green MJ, Groenewold NA, Grotegerd D, Gurholt TP, Gutman BA, Hansell NK, Harris MA, Harrison MB, Haswell CC, Hauser M, Herms S, Heslenfeld DJ, Ho NF, Hoehn D, Hoffmann P, Holleran L, Hoogman M, Hottenga J-J, Ikeda M, Janowitz D, Jansen IE, Jia T, Jockwitz C, Kanai R, Karama S, Kasperaviciute D, Kaufmann T, Kelly S, Kikuchi M, Klein M, Knapp M, Knodt AR, Krämer B, Lam M, Lancaster TM, Lee PH, Lett TA, Lewis LB, Lopes-Cendes I, Luciano M, Macciardi F, Marquand AF, Mathias SR, Melzer TR, Milaneschi Y, Mirza-Schreiber N, Moreira JCV, Mühleisen TW, Müller-Myhsok B, Najt P, Nakahara S, Nho K, Olde Loohuis LM, Orfanos DP, Pearson JF, Pitcher TL, Pütz B, Quidé Y, Ragothaman A, Rashid FM, Reay WR, Redlich R, Reinbold CS, Repple J, Richard G, Riedel BC, Risacher SL, Rocha CS, Mota NR, Salminen L, Saremi A, Saykin AJ, Schlag F, Schmaal L, Schofield PR, Secolin R, Shapland CY, Shen L, Shin J, Shumskaya E, Sønderby IE, Sprooten E, Tansey KE, Teumer A, Thalamuthu A, Tordesillas-Gutiérrez D, Turner JA, Uhlmann A, Vallerga CL, van der Meer D, van Donkelaar MMJ, van Eijk L, van Erp TGM, van Haren NEM, van Rooij D, van Tol M-J, Veldink JH, Verhoef E, Walton E, Wang M, Wang Y, Wardlaw JM, Wen W, Westlye LT, Whelan CD, Witt SH, Wittfeld K, Wolf C, Wolfers T, Wu JQ, Yasuda CL, Zaremba D, Zhang Z, Zwiers MP, Artiges E, Assareh AA, Ayesa-Arriola R, Belger A, Brandt CL, Brown GG, Cichon S, Curran JE, Davies GE, Degenhardt F, Dennis MF, Dietsche B, Djurovic S, Doherty CP, Espiritu R, Garijo D, Gil Y, Gowland PA, Green RC, Häusler AN, Heindel W, Ho B-C, Hoffmann WU, Holsboer F, Homuth G, Hosten N, Jack CR, Jang M, Jansen A, Kimbrel NA, Kolskår K, Koops S, Krug A, Lim KO, Luykx JJ, Mathalon DH, Mather KA, Mattay VS, Matthews S, Mayoral Van Son J, McEwen SC, Melle I, Morris DW, Mueller BA, Nauck M, Nordvik JE, Nöthen MM, O’Leary DS, Opel N, Martinot M-LP, Pike GB, Preda A, Quinlan EB, Rasser PE, Ratnakar V, Reppermund S, Steen VM, Tooney PA, Torres FR, Veltman DJ, Voyvodic JT, Whelan R, White T, Yamamori H, Adams HHH, Bis JC, Debette S, Decarli C, Fornage M, Gudnason V, Hofer E, Ikram MA, Launer L, Longstreth WT, Lopez OL, Mazoyer B, Mosley TH, Roshchupkin GV, Satizabal CL, Schmidt R, Seshadri S, Yang Q, Alvim MKM, Ames D, Anderson TJ, Andreassen OA, Arias-Vasquez A, Bastin ME, Baune BT, Beckham JC, Blangero J, Boomsma DI, Brodaty H, Brunner HG, Buckner RL, Buitelaar JK, Bustillo JR, Cahn W, Cairns MJ, Calhoun V, Carr VJ, Caseras X, Caspers S, Cavalleri GL, Cendes F, Corvin A, Crespo-Facorro B, Dalrymple-Alford JC, Dannlowski U, de Geus EJC, Deary IJ, Delanty N, Depondt C, Desrivières S, Donohoe G, Espeseth T, Fernández G, Fisher SE, Flor H, Forstner AJ, Francks C, Franke B, Glahn DC, Gollub RL, Grabe HJ, Gruber O, Håberg AK, Hariri AR, Hartman CA, Hashimoto R, Heinz A, Henskens FA, Hillegers MHJ, Hoekstra PJ, Holmes AJ, Hong LE, Hopkins WD, Hulshoff Pol HE, Jernigan TL, Jönsson EG, Kahn RS, Kennedy MA, Kircher TTJ, Kochunov P, Kwok JBJ, Le Hellard S, Loughland CM, Martin NG, Martinot J-L, McDonald C, McMahon KL, Meyer-Lindenberg A, Michie PT, Morey RA, Mowry B, Nyberg L, Oosterlaan J, Ophoff RA, Pantelis C, Paus T, Pausova Z, Penninx BWJH, Polderman TJC, Posthuma D, Rietschel M, Roffman JL, Rowland LM, Sachdev PS, Sämann PG, Schall U, Schumann G, Scott RJ, Sim K, Sisodiya SM, Smoller JW, Sommer IE, St Pourcain B, Stein DJ, Toga AW, Trollor JN, Van der Wee NJA, van ’t Ent D, Völzke H, Walter H, Weber B, Weinberger DR, Wright MJ, Zhou J, Stein JL, Thompson PM, Medland SE. The genetic architecture of the human cerebral cortex. (2020) Science. 2020;367(6484):eaay6690. https://doi.org/10.1126/science.aay6690
  44. Yao X, Tsang T, Qing Sun, Quinney S, Zhang P, Ning X, Li L, Shen L. (2020) Mining and visualizing high-order directional drug interaction effects using the FAERS database. BMC Medical Informatics and Decision Making, 20(Suppl 2):50. https://doi.org/10.1186/s12911-020-1053-z
  45. Zhu A, Zeng D, Shen L, Ning X, Li L, Zhang P. (2020) A super-combo-drug test (SupCD-T) to detect adverse drug events and drug interactions from electronic health records in the era of polypharmacy. Statistics in Medicine, 39(10):1458-1472. https://doi.org/10.1002/sim.8490
  46. Du L, Liu K, Yao X, Risacher SL, Han J, Saykin AJ, Guo L, Shen L, for the ADNI. (2020) Detecting genetic associations with brain imaging phenotypes in Alzheimer's disease via a novel structured SCCA approach. Medical Image Analysis, 61:101656. https://doi.org/10.1016/j.media.2020.101656
  47. Hao X, Bao Y, Guo Y, Yu M, Zhang D, Risacher SL, Saykin AJ, Yao X, Shen L, for the ADNI. (2020) Multi-modal neuroimaging feature selection with consistent metric constraint for diagnosis of Alzheimer's disease. Medical Image Analysis, 60:101625. https://doi.org/10.1016/j.media.2019.101625
  48. Shen L, Thompson PM. (2020) Brain imaging genomics: integrated analysis and machine learning. Proceedings of the IEEE, 108(1):125-162. https://doi.org/10.1109/JPROC.2019.2947272 
  49. Yao X, Cong S, Yan J, Risacher SL, Saykin AJ, Moore JH, Shen L, UK Brain Expression Consortium, for the Alzheimer’s Disease Neuroimaging Initiative. (2019) Regional Imaging Genetic Enrichment Analysis. Bioinformatics, 36(8):2554-2560. https://doi.org/10.1093/bioinformatics/btz948  
  50. Liu M, Li F, Yan H, Wang K, Ma Y, Shen L, Xu M, for the ADNI. (2019) A multi-model deep convolutional neural network for automatic hippocampus segmentation and classification in Alzheimer's disease. Neuroimage, 208:116459. https://doi.org/10.1016/j.neuroimage.2019.116459
  51. Brand L, Nichols K, Wang H, Shen L, Huang H, for the ADNI. (2019) Joint multi-modal longitudinal regression and classification for Alzheimer’s disease prediction. IEEE Trans. on Medical Imaging, 39(6):1845-1855. https://doi.org/10.1109/TMI.2019.2958943 
  52. Li J, Chen F, Zhang Q, Meng X, Yao X, Risacher SL, Yan J, Saykin AJ, Liang H, Shen L, for the ADNI. (2019) Genome-wide network-assisted association and enrichment study of amyloid imaging phenotype in Alzheimer’s disease. Current Alzheimer Research, 16(13):1163-1174. https://doi.org/10.2174/1567205016666191121142558 
  53. Liu K, Shen L, Hui J. (2019) Joint between-sample normalization and differential expression detection through l0-regularized regression. BMC Bioinformatics, 20(Suppl 16):593. https://doi.org/10.1186/s12859-019-3070-4 
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  89. 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. 
  90. 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. 
  91. 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.
  92. 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.
  93. 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. 
  94. 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.
  95. 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.
  96. 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 
  97. 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.
  98. 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
  99. 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.
  100. 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.
  101. 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.
  102. 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.
  103. 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.
  104. 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
  105. 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.
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  108. 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.
  109. 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.
  110. 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. 
  111. 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%]
  112. 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.
  113. 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.
  114. 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.
  115. 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.
  116. 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.
  117. 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.
  118. 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.
  119. 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.
  120. 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.
  121. 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.
  122. 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.
  123. 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.
  124. 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.
  125. 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.
  126. Shen L (2012) Principles of computational modeling in neuroscience (book review). Briefings in Bioinformatics, 13(3): 390-392, doi:10.1093/bib/bbs003. 
  127. 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.
  128. 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.
  129. 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.
  130. 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.
  131. 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%]
  132. 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.
  133. 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. 
  134. 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%]
  135. 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.
  136. 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.
  137. 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.
  138. 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.
  139. 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.
  140. 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. 
  141. 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. 
  142. 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, AddNeuroMed (2011) Genome wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer’s disease. Molecular Psychiatry, 16(11):1130-8.
  143. 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.
  144. 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.
  145. 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.
  146. 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.
  147. 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. 
  148. 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.
  149. 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.
  150. 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.
  151. 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.
  152. 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.
  153. 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.
  154. 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%]
  155. Shen L, Farid H, McPeek MA (2009) Modeling 3-dimensional morphological structures using spherical harmonics. Evolution, 63(4):1003-1016.
  156. 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.
  157. 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.
  158. 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.
  159. 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.
  160. 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.
  161. 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.
  162. 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.
  163. 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.
  164. 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.
  165. Shen L, Makedon FS. (2006) Spherical mapping for processing of 3-D closed surfaces. Image and Vision Computing, 24(7):743-761.
  166. 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.
  167. 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.
  168. 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.
  169. 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.
  170. Shen L, Shen H, Cheng L, Pritchard P (2000) Fast association discovery in derivative transaction collections. Knowledge and Information Systems, 2(2):147-160.
  171. Shen L, Shen H, Cheng L (1999) New algorithms for efficient mining of association rules. Information Sciences, 118(1-4):251-268.
  172. 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.
  173. Shen L, Sun Y (1997) Needed parallel-outermost reduction strategy. Journal of Software (in Chinese), 8(10):760-767.
  174. Shen L, Lin K, Sun Y (1996) Parallel-outermost pattern matching. Journal of Software (in Chinese), 7(Supplement):329-337.
  175. 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.