%% MY BIB %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%brainnetcnn
@article{kawahara2017brainnetcnn,
  title={BrainNetCNN: convolutional neural networks for brain networks; towards predicting neurodevelopment},
  author={Kawahara, Jeremy and Brown, Colin J and Miller, Steven P and Booth, Brian G and Chau, Vann and Grunau, Ruth E and Zwicker, Jill G and Hamarneh, Ghassan},
  journal={NeuroImage},
  volume={146},
  pages={1038--1049},
  year={2017},
  publisher={Elsevier}
}

%connectome
@article{filippi2018changes,
  title={Changes in functional and structural brain connectome along the Alzheimer’s disease continuum},
  author={Filippi, Massimo and Basaia, Silvia and Canu, Elisa and Imperiale, Francesca and Magnani, Giuseppe and Falautano, Monica and Comi, Giancarlo and Falini, Andrea and Agosta, Federica},
  journal={Molecular psychiatry},
  pages={1},
  year={2018},
  publisher={Nature Publishing Group}
}

%ref11
@article{hampel2008core,
  title={Core candidate neurochemical and imaging biomarkers of Alzheimer’s disease},
  author={Hampel, Harald and B{\"u}rger, Katharina and Teipel, Stefan J and Bokde, Arun LW and Zetterberg, Henrik and Blennow, Kaj},
  journal={Alzheimer's \& Dementia},
  volume={4},
  number={1},
  pages={38--48},
  year={2008},
  publisher={Elsevier}
}

%ref12
@article{kapaki2007cerebrospinal,
  title={Cerebrospinal fluid tau, phospho-tau181 and $\beta$-amyloid1- 42 in idiopathic normal pressure hydrocephalus: a discrimination from Alzheimer's disease},
  author={Kapaki, EN and Paraskevas, GP and Tzerakis, NG and Sfagos, C and Seretis, A and Kararizou, E and Vassilopoulos, D},
  journal={European journal of neurology},
  volume={14},
  number={2},
  pages={168--173},
  year={2007},
  publisher={Wiley Online Library}
}
%desikan
@article{desikan2006automated,
  title={An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest},
  author={Desikan, Rahul S and S{\'e}gonne, Florent and Fischl, Bruce and Quinn, Brian T and Dickerson, Bradford C and Blacker, Deborah and Buckner, Randy L and Dale, Anders M and Maguire, R Paul and Hyman, Bradley T and others},
  journal={Neuroimage},
  volume={31},
  number={3},
  pages={968--980},
  year={2006},
  publisher={Elsevier}
}

@article{li2015robust,
  title={A robust deep model for improved classification of AD/MCI patients},
  author={Li, Feng and Tran, Loc and Thung, Kim-Han and Ji, Shuiwang and Shen, Dinggang and Li, Jiang},
  journal={IEEE journal of biomedical and health informatics},
  volume={19},
  number={5},
  pages={1610--1616},
  year={2015},
  publisher={IEEE}
}

@article{irizarry2004biomarkers,
  title={Biomarkers of Alzheimer disease in plasma},
  author={Irizarry, Michael C},
  journal={NeuroRx},
  volume={1},
  number={2},
  pages={226--234},
  year={2004},
  publisher={Elsevier}
}

@article{blennow2015amyloid,
  title={Amyloid biomarkers in Alzheimer's disease},
  author={Blennow, Kaj and Mattsson, Niklas and Sch{\"o}ll, Michael and Hansson, Oskar and Zetterberg, Henrik},
  journal={Trends in pharmacological sciences},
  volume={36},
  number={5},
  pages={297--309},
  year={2015},
  publisher={Elsevier}
}

@article{patel2011potential,
  title={Potential peripheral biomarkers for the diagnosis of Alzheimer's disease},
  author={Patel, Seema and Shah, Raj J and Coleman, Paul and Sabbagh, Marwan},
  journal={International Journal of Alzheimer’s Disease},
  volume={2011},
  year={2011},
  publisher={Hindawi}
}

@article{henriksen2014future,
  title={The future of blood-based biomarkers for Alzheimer's disease},
  author={Henriksen, Kim and O’Bryant, Sid E and Hampel, Harald and Trojanowski, John Q and Montine, Thomas J and Jeromin, Andreas and Blennow, Kaj and L{\"o}nneborg, Anders and Wyss-Coray, Tony and Soares, Holly and others},
  journal={Alzheimer's \& Dementia},
  volume={10},
  number={1},
  pages={115--131},
  year={2014},
  publisher={Elsevier}
}
@article{weintraub2012neuropsychological,
  title={The neuropsychological profile of Alzheimer disease},
  author={Weintraub, Sandra and Wicklund, Alissa H and Salmon, David P},
  journal={Cold Spring Harbor perspectives in medicine},
  volume={2},
  number={4},
  pages={a006171},
  year={2012},
  publisher={Cold Spring Harbor Laboratory Press}
}
@article{moradi2015machine,
  title={Machine learning framework for early MRI-based Alzheimer's conversion prediction in MCI subjects},
  author={Moradi, Elaheh and Pepe, Antonietta and Gaser, Christian and Huttunen, Heikki and Tohka, Jussi and Alzheimer's Disease Neuroimaging Initiative and others},
  journal={Neuroimage},
  volume={104},
  pages={398--412},
  year={2015},
  publisher={Elsevier}
}
@article{liu2018applications,
  title={Applications of deep learning to MRI images: A survey},
  author={Liu, Jin and Pan, Yi and Li, Min and Chen, Ziyue and Tang, Lu and Lu, Chengqian and Wang, Jianxin},
  journal={Big Data Mining and Analytics},
  volume={1},
  number={1},
  pages={1--18},
  year={2018},
  publisher={TUP}
}
@article{litjens2017survey,
  title={A survey on deep learning in medical image analysis},
  author={Litjens, Geert and Kooi, Thijs and Bejnordi, Babak Ehteshami and Setio, Arnaud Arindra Adiyoso and Ciompi, Francesco and Ghafoorian, Mohsen and Van Der Laak, Jeroen Awm and Van Ginneken, Bram and S{\'a}nchez, Clara I},
  journal={Medical image analysis},
  volume={42},
  pages={60--88},
  year={2017},
  publisher={Elsevier}
}
@article{jo2019deep,
  title={Deep Learning in Alzheimer's disease: Diagnostic Classification and Prognostic Prediction using Neuroimaging Data},
  author={Jo, Taeho and Nho, Kwangsik and Saykin, Andrew J},
  journal={arXiv preprint arXiv:1905.00931},
  year={2019}
}
@article{lee2019predicting,
  title={Predicting Alzheimer’s disease progression using multi-modal deep learning approach},
  author={Lee, Garam and Nho, Kwangsik and Kang, Byungkon and Sohn, Kyung-Ah and Kim, Dokyoon},
  journal={Scientific reports},
  volume={9},
  number={1},
  pages={1952},
  year={2019},
  publisher={Nature Publishing Group}
}
@article{li2019deep,
  title={A deep learning model for early prediction of Alzheimer's disease dementia based on hippocampal MRI},
  author={Li, Hongming and Habes, Mohamad and Wolk, David A and Fan, Yong},
  journal={arXiv preprint arXiv:1904.07282},
  year={2019}
}
@inproceedings{liu2014early,
  title={Early diagnosis of Alzheimer's disease with deep learning},
  author={Liu, Siqi and Liu, Sidong and Cai, Weidong and Pujol, Sonia and Kikinis, Ron and Feng, Dagan},
  booktitle={2014 IEEE 11th international symposium on biomedical imaging (ISBI)},
  pages={1015--1018},
  year={2014},
  organization={IEEE}
}
@article{thambisetty2010blood,
  title={Blood-based biomarkers of Alzheimer’s disease: challenging but feasible},
  author={Thambisetty, Madhav and Lovestone, Simon},
  journal={Biomarkers in medicine},
  volume={4},
  number={1},
  pages={65--79},
  year={2010},
  publisher={Future Medicine}
}
@article{jacobs1995neuropsychological,
  title={Neuropsychological detection and characterization of preclinical Alzheimer's disease},
  author={Jacobs, Diane M and Sano, Mary and Dooneief, George and Marder, Karen and Bell, Karen L and Stern, Yaakov},
  journal={Neurology},
  volume={45},
  number={5},
  pages={957--962},
  year={1995},
  publisher={AAN Enterprises}
}
@article{tierney2005neuropsychological,
  title={Neuropsychological tests accurately predict incident Alzheimer disease after 5 and 10 years},
  author={Tierney, Mary C and Yao, Christie and Kiss, Alex and McDowell, Ian},
  journal={Neurology},
  volume={64},
  number={11},
  pages={1853--1859},
  year={2005},
  publisher={AAN Enterprises}
}
@article{mckhann1984clinical,
  title={Clinical diagnosis of Alzheimer's disease: Report of the NINCDS-ADRDA Work Group* under the auspices of Department of Health and Human Services Task Force on Alzheimer's Disease},
  author={McKhann, Guy and Drachman, David and Folstein, Marshall and Katzman, Robert and Price, Donald and Stadlan, Emanuel M},
  journal={Neurology},
  volume={34},
  number={7},
  pages={939--939},
  year={1984},
  publisher={AAN Enterprises}
}

@article{doecke2012blood,
  title={Blood-based protein biomarkers for diagnosis of Alzheimer disease},
  author={Doecke, James D and Laws, Simon M and Faux, Noel G and Wilson, William and Burnham, Samantha C and Lam, Chiou-Peng and Mondal, Alinda and Bedo, Justin and Bush, Ashley I and Brown, Belinda and others},
  journal={Archives of neurology},
  volume={69},
  number={10},
  pages={1318--1325},
  year={2012},
  publisher={American Medical Association}
}

@article{mayeux2011blood,
  title={Blood-based biomarkers for Alzheimer's disease: plasma A$\beta$40 and A$\beta$42, and genetic variants},
  author={Mayeux, Richard and Schupf, Nicole},
  journal={Neurobiology of aging},
  volume={32},
  pages={S10--S19},
  year={2011},
  publisher={Elsevier}
}

@article{gomar2011utility,
  title={Utility of combinations of biomarkers, cognitive markers, and risk factors to predict conversion from mild cognitive impairment to Alzheimer disease in patients in the Alzheimer's disease neuroimaging initiative},
  author={Gomar, Jesus J and Bobes-Bascaran, Maria T and Conejero-Goldberg, Concepcion and Davies, Peter and Goldberg, Terry E and Alzheimer's Disease Neuroimaging Initiative and others},
  journal={Archives of general psychiatry},
  volume={68},
  number={9},
  pages={961--969},
  year={2011},
  publisher={American Medical Association}
}
@article{gomez2019challenge,
  title={The Challenge of Defining Alzheimer Disease Based on Biomarkers in the Absence of Symptoms},
  author={Gomez-Isla, Teresa and Frosch, Matthew P},
  journal={JAMA neurology},
  year={2019}
}
@article{mattsson2009csf,
  title={CSF biomarkers and incipient Alzheimer disease in patients with mild cognitive impairment},
  author={Mattsson, Niklas and Zetterberg, Henrik and Hansson, Oskar and Andreasen, Niels and Parnetti, Lucilla and Jonsson, Michael and Herukka, Sanna-Kaisa and van der Flier, Wiesje M and Blankenstein, Marinus A and Ewers, Michael and others},
  journal={Jama},
  volume={302},
  number={4},
  pages={385--393},
  year={2009},
  publisher={American Medical Association}
}

@article{st2018surface,
  title={Surface-enhanced tractography (SET)},
  author={St-Onge, Etienne and Daducci, Alessandro and Girard, Gabriel and Descoteaux, Maxime},
  journal={NeuroImage},
  volume={169},
  pages={524--539},
  year={2018},
  publisher={Elsevier}
}

@article{theaud2020tractoflow,
  title={TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow \& Singularity},
  author={Theaud, Guillaume and Houde, Jean-Christophe and Bor{\'e}, Arnaud and Rheault, Fran{\c{c}}ois and Morency, Felix and Descoteaux, Maxime},
  journal={NeuroImage},
  pages={116889},
  year={2020},
  issn={1053-8119},
  publisher={Elsevier}
}

@article{zetterberg2008biomarkers,
  title={Biomarkers reflecting different facets of Alzheimer’s disease},
  author={Zetterberg, H},
  journal={European journal of neurology},
  volume={15},
  number={11},
  pages={1143--1144},
  year={2008},
  publisher={Wiley Online Library}
}

@article{abrol2019deep,
  title={Deep Residual Learning for Neuroimaging: An application to Predict Progression to Alzheimer's Disease},
  author={Abrol, Anees and Bhattarai, Manish and Fedorov, Alex and Du, Yuhui and Plis, Sergey and Calhoun, Vince},
  journal={bioRxiv},
  pages={470252},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{iwatsubo2011alzheimer,
  title={Alzheimer's disease neuroimaging initiative (ADNI)},
  author={Iwatsubo, T},
  journal={Nihon rinsho. Japanese journal of clinical medicine},
  volume={69},
  pages={570--574},
  year={2011}
}

@article{prescott2014alzheimer,
  title={The Alzheimer structural connectome: changes in cortical network topology with increased amyloid plaque burden},
  author={Prescott, Jeffrey W and Guidon, Arnaud and Doraiswamy, P Murali and Roy Choudhury, Kingshuk and Liu, Chunlei and Petrella, Jeffrey R and Alzheimer’s Disease Neuroimaging Initiative},
  journal={Radiology},
  volume={273},
  number={1},
  pages={175--184},
  year={2014},
  publisher={Radiological Society of North America}
}

@article{ye2019connectome,
  title={Connectome-wide network analysis of white matter connectivity in Alzheimer's disease},
  author={Ye, Chenfei and Mori, Susumu and Chan, Piu and Ma, Ting},
  journal={NeuroImage: Clinical},
  volume={22},
  pages={101690},
  year={2019},
  publisher={Elsevier}
}

@article{refHyper,
  title={HpBandSter},
  author={HpBandSter},
  journal={https://automl.github.io/HpBandSter/build/html/index.html},
  year={2018}
}

@article{falkner2018bohb,
  title={BOHB: Robust and efficient hyperparameter optimization at scale},
  author={Falkner, Stefan and Klein, Aaron and Hutter, Frank},
  journal={arXiv preprint arXiv:1807.01774},
  year={2018}
}
% FreeSurfer
@article{dale1999cortical,
  title={Cortical surface-based analysis: I. Segmentation and surface reconstruction},
  author={Dale, Anders M and Fischl, Bruce and Sereno, Martin I},
  journal={Neuroimage},
  volume={9},
  number={2},
  pages={179--194},
  year={1999},
  publisher={Elsevier}
}

%parcelation
@article{destrieux2009sulcal,
  title={A sulcal depth-based anatomical parcellation of the cerebral cortex.},
  author={Destrieux, C and Fischl, B and Dale, AM and Halgren, E},
  journal={NeuroImage},
  volume={47},
  pages={S151},
  year={2009},
  publisher={Academic Press}
}

@article{hagmann2008mapping,
  title={Mapping the structural core of human cerebral cortex},
  author={Hagmann, Patric and Cammoun, Leila and Gigandet, Xavier and Meuli, Reto and Honey, Christopher J and Wedeen, Van J and Sporns, Olaf},
  journal={PLoS biology},
  volume={6},
  number={7},
  pages={e159},
  year={2008},
  publisher={Public Library of Science}
}

% ADDED by MAX:
@article{livingston2017dementia,
  title={Dementia prevention, intervention, and care},
  author={Livingston, Gill and Sommerlad, Andrew and Orgeta, Vasiliki and Costafreda, Sergi G and Huntley, Jonathan and Ames, David and Ballard, Clive and Banerjee, Sube and Burns, Alistair and Cohen-Mansfield, Jiska and others},
  journal={The Lancet},
  volume={390},
  number={10113},
  pages={2673--2734},
  year={2017},
  publisher={Elsevier}
}
@article{contreras2015structural,
  title={The structural and functional connectome and prediction of risk for cognitive impairment in older adults},
  author={Contreras, Joey A and Go{\~n}i, Joaqu{\'\i}n and Risacher, Shannon L and Sporns, Olaf and Saykin, Andrew J},
  journal={Current behavioral neuroscience reports},
  volume={2},
  number={4},
  pages={234--245},
  year={2015},
  publisher={Springer}
}
@article{vemuri2010role,
  title={Role of structural MRI in Alzheimer's disease},
  author={Vemuri, Prashanthi and Jack, Clifford R},
  journal={Alzheimer's research \& therapy},
  volume={2},
  number={4},
  pages={23},
  year={2010},
  publisher={BioMed Central}
}
@article{engelborghs2013clinical,
  title={Clinical indications for analysis of Alzheimer's disease CSF biomarkers},
  author={Engelborghs, S},
  journal={Revue neurologique},
  volume={169},
  number={10},
  pages={709--714},
  year={2013},
  publisher={Elsevier}
}
@article{biju2017alzheimer,
  title={Alzheimer’s detection based on segmentation of MRI image},
  author={Biju, KS and Alfa, SS and Lal, Kavya and Antony, Alvia and Akhil, M Kurup},
  journal={Procedia computer science},
  volume={115},
  pages={474--481},
  year={2017},
  publisher={Elsevier}
}
@article{cummings2019rights,
  title={The “rights” of precision drug development for Alzheimer’s disease},
  author={Cummings, Jeffrey and Feldman, Howard H and Scheltens, Philip},
  journal={Alzheimer's research \& therapy},
  volume={11},
  number={1},
  pages={1--14},
  year={2019},
  publisher={BioMed Central}
}
@article{qureshi2019evaluation,
  title={Evaluation of functional decline in alzheimer’s dementia using 3d deep learning and group ica for rs-fmri measurements},
  author={Qureshi, Muhammad Naveed Iqbal and Ryu, Seungjun and Song, Joonyoung and Lee, Kun Ho and Lee, Boreom},
  journal={Frontiers in aging neuroscience},
  volume={11},
  pages={8},
  year={2019},
  publisher={Frontiers}
}
@article{weller2018current,
  title={Current understanding of Alzheimer’s disease diagnosis and treatment},
  author={Weller, Jason and Budson, Andrew},
  journal={F1000Research},
  volume={7},
  year={2018},
  publisher={Faculty of 1000 Ltd}
}
@article{li2017hyperband,
  title={Hyperband: A novel bandit-based approach to hyperparameter optimization},
  author={Li, Lisha and Jamieson, Kevin and DeSalvo, Giulia and Rostamizadeh, Afshin and Talwalkar, Ameet},
  journal={The Journal of Machine Learning Research},
  volume={18},
  number={1},
  pages={6765--6816},
  year={2017},
  publisher={JMLR. org}
}
@article{jhoo2010discrimination,
  title={Discrimination of normal aging, MCI and AD with multimodal imaging measures on the medial temporal lobe},
  author={Jhoo, Jin Hyeong and Lee, Dong Young and Choo, Il Han and Seo, Eun Hyun and Oh, Jungsu S and Lee, Jae Sung and Lee, Dong Soo and Kim, Shin Gyeom and Youn, Jong Chul and Kim, Ki Woong and others},
  journal={Psychiatry Research: Neuroimaging},
  volume={183},
  number={3},
  pages={237--243},
  year={2010},
  publisher={Elsevier}
}
@article{choo2010posterior,
  title={Posterior cingulate cortex atrophy and regional cingulum disruption in mild cognitive impairment and Alzheimer's disease},
  author={Choo, IL Han and Lee, Dong Young and Oh, Jungsu S and Lee, Jae Sung and Lee, Dong Soo and Song, In Chan and Youn, Jong Choul and Kim, Shin Gyeom and Kim, Ki Woong and Jhoo, Jin Hyeong and others},
  journal={Neurobiology of aging},
  volume={31},
  number={5},
  pages={772--779},
  year={2010},
  publisher={Elsevier}
}
@article{pennanen2004hippocampus,
  title={Hippocampus and entorhinal cortex in mild cognitive impairment and early AD},
  author={Pennanen, Corina and Kivipelto, Miia and Tuomainen, Susanna and Hartikainen, P{\"a}ivi and H{\"a}nninen, Tuomo and Laakso, Mikko P and Hallikainen, Merja and Vanhanen, Matti and Nissinen, Aulikki and Helkala, Eeva-Liisa and others},
  journal={Neurobiology of aging},
  volume={25},
  number={3},
  pages={303--310},
  year={2004},
  publisher={Elsevier}
}

@article{abrol2020deep,
  title={Deep residual learning for neuroimaging: An application to predict progression to alzheimer’s disease},
  author={Abrol, Anees and Bhattarai, Manish and Fedorov, Alex and Du, Yuhui and Plis, Sergey and Calhoun, Vince and Alzheimer’s Disease Neuroimaging Initiative and others},
  journal={Journal of Neuroscience Methods},
  pages={108701},
  year={2020},
  publisher={Elsevier}
}

@article{lisowska2019joint,
  title={Joint pairing and structured mapping of convolutional brain morphological multiplexes for early dementia diagnosis},
  author={Lisowska, Anna and Rekik, Islem and AbbVie, Alzheimer's Association and Alzheimer's Drug Discovery Foundation and Araclon Biotech and Bio-Clinica, Inc. and Biogen and Bristol-Myers Squibb Company and CereSpir, Inc. and Cogstate and others},
  journal={Brain connectivity},
  volume={9},
  number={1},
  pages={22--36},
  year={2019},
  publisher={Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…}
}
@article{liu2019auto,
  title={Auto-encoding graph-valued data with applications to brain connectomes},
  author={Liu, Meimei and Zhang, Zhengwu and Dunson, David B},
  journal={arXiv preprint arXiv:1911.02728},
  year={2019}
}
@article{hojjati2017predicting,
  title={Predicting conversion from MCI to AD using resting-state fMRI, graph theoretical approach and SVM},
  author={Hojjati, Seyed Hani and Ebrahimzadeh, Ata and Khazaee, Ali and Babajani-Feremi, Abbas and Alzheimer’s Disease Neuroimaging Initiative and others},
  journal={Journal of neuroscience methods},
  volume={282},
  pages={69--80},
  year={2017},
  publisher={Elsevier}
}
@article{bronstein2017geometric,
  title={Geometric deep learning: going beyond euclidean data},
  author={Bronstein, Michael M and Bruna, Joan and LeCun, Yann and Szlam, Arthur and Vandergheynst, Pierre},
  journal={IEEE Signal Processing Magazine},
  volume={34},
  number={4},
  pages={18--42},
  year={2017},
  publisher={IEEE}
}
@article{jeurissen2019diffusion,
  title={Diffusion MRI fiber tractography of the brain},
  author={Jeurissen, Ben and Descoteaux, Maxime and Mori, Susumu and Leemans, Alexander},
  journal={NMR in Biomedicine},
  volume={32},
  number={4},
  pages={e3785},
  year={2019},
  publisher={Wiley Online Library}
}
@article{girard2014towards,
  title={Towards quantitative connectivity analysis: reducing tractography biases},
  author={Girard, Gabriel and Whittingstall, Kevin and Deriche, Rachid and Descoteaux, Maxime},
  journal={Neuroimage},
  volume={98},
  pages={266--278},
  year={2014},
  publisher={Elsevier}
}


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