Open Science Framework and Google Scholar also provide access to my papers, posters, proposals, and presentations.
 

Contents

 

Mental health technologies

ThermalSensors_NatureDigitalMedicine2019.jpg

JJ Son, JC Clucas, C White, A Krishnakumar, JT Vogelstein, MP Milham, A Klein.
Thermal sensors improve wrist-worn position tracking
Nature Partner Journal Digital Medicine 2, Article number: 15 (2019). doi: doi.org/10.1038/s41746-019-0092-2
LENA_SM_FrontiersPsychiatry2018.jpg

HY Xu, J Stroud, RK Jozanovic, J Clucas, JJ Son, B Koo, J Schwarz, A Klein, R Busman, MP Milham.
Clinical perspective on passive audio vocal measurement in the evaluation of selective mutism
Frontiers in Psychiatry 9:443 (2018). doi: doi.org/10.3389/fpsyt.2018.00443
AssessingWearables_bioRxiv2017_small.png

J Clucas, C White, B Koo, M Milham, A Klein.
Assessing actimeters for inclusion in the Healthy Brain Network
bioRxiv 183772 (2017). doi: doi.org/10.1101/183772
doctor-as-data-scientist_Medium2016_300px.png A Klein, SS Ghosh.
Doctor as data scientist: a high-dimensional view of health.
Medium.
mPower2 SS Ghosh, G Ciccarelli, TF Quatieri, A Klein.
Speaking one's mind: Vocal biomarkers of depression and Parkinson disease.
Journal of the Acoustical Society of America. 139:2193 (2016).
doi: doi.org/10.1121/1.4950530
mPower2 E Chaibub Neto, BM Bot, T Perumal, L Omberg, J Guinney, M Kellen, A Klein, SH Friend, AD Trister.
Personalized hypothesis tests for detecting medication response in Parkinson disease patients using iPhone sensor data.
Pacific Symposium on Biocomputing. 21:273-284 (2016). PMID:26776193.
doi: doi.org/10.1142/9789814749411_0026
mPower B Bot, C Suver, EC Neto, M Kellen, A Klein, C Bare, M Doerr, A Pratap, J Wilbanks, ER Dorsey, SH Friend, AD Trister.
The mPower Study, Parkinson Disease Mobile Data Collected Using ResearchKit.
Scientific Data 3, Article number: 160011 (2016).
doi: doi.org/10.1038/sdata.2016.11
 

Brain image analysis

Mindboggle_bioRxiv2016_Fig7top.png

Y Zhao, A Klein, FX Castellanos, MP Milham.
Brain age prediction: cortical and subcortical shape covariation in the developing human brain.
bioRxiv Mar 7 (2019).
doi: doi.org/10.1101/570333
Mindboggle_bioRxiv2016_Fig7top.png

A Klein, SS Ghosh, FS Bao, J Giard, Y Hame, E Stavsky, N Lee, B Rossa, M Reuter, EC Neto, A Keshavan.
Mindboggling morphometry of human brains.
PLoS Computational Biology 13(3): e1005350 (2017).
doi: doi.org/10.1371/journal.pcbi.1005350
UsefulBrainImaging_DepAnx2017.png

MP Milham, RC Craddock, A Klein.
Clinically useful brain imaging for neuropsychiatry: How can we get there?
Depression and Anxiety 2017:1-10 (2017). doi: doi.org/10.1002/da.22627
pic_pres16 A Klein, S Ghosh.
Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data (NIH proposal).
Research Ideas and Outcomes. 2: e8835 (2016). doi: doi.org/10.3897/rio.2.e8835
pic_pres16 A Klein.
Brain Graph Interface (NIH proposal).
Research Ideas and Outcomes. 2: e8817 (2016). doi: doi.org/10.3897/rio.2.e8817
pic_pres16 A Klein, SP Ellis.
Concurrence Topology: Finding High-Order Dependence in Neuropsychiatric Data (NIH proposal).
Research Ideas and Outcomes. 2: e8815 (2016). doi: doi.org/10.3897/rio.2.e8815

SP Ellis, A Klein.
"Concurrence Topology:" A New Method for Describing High-Order Statistical Dependence in Data.
31st International Symposium on Computational Geometry (Eindhover, the Netherlands) (2015).
HBM2015_MindboggleADshapes.png A Klein, EC Neto, S Ghosh, ADNI.
Detailed shape analysis of healthy brains and brains with Alzheimer's disease.
Human Brain Mapping 2015 (Honolulu, Hawaii). Abstract
pic_math1 SP Ellis, A Klein.
Describing high-order statistical dependence using “Concurrence Topology,” with application to functional MRI brain data.
Homology, Homotopy and Applications. 16(1): 245-264 (2014).
doi: doi.org/10.4310/HHA.2014.v16.n1.a14
Earlier version on arXiv and poster
Concurrence Topology website
  HBM2014_Mindboggle101shapes.png A Klein, EN Neto, J Giard, F Bao, Y Hame, M Reuter, N Tustison, B Avants, J Tourville, H Dai, N Nichols, S Ghosh.
Shape analysis of 101 healthy human brains.
Human Brain Mapping 2014 (Hamburg, Germany).
ANTs_FS_corticalthickness_NeuroImage2014.png TJ Tustison, PA Cook, A Klein, G Song, SR Das, JT Duda, BM Kandel, N van Strien, JR Stone, JC Gee, BB Avants.
Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements.
NeuroImage. 99:166-179 (2014). doi: doi.org/10.1016/j.neuroimage.2014.05.044
https://binarybottle.com/images/papers/Mindboggle_Neuroinformatics2012.png A Klein, FS Bao, Y Hame, E Stavsky, J Giard, D Haehn, N Nichols, SS Ghosh.
Mindboggle: Automated human brain MRI feature extraction, labeling, morphometry, and online visualization.
Neuroinformatics 2012 (Munich, Germany).
SFN2011_MDDremission.png FS Bao, SS Ghosh, J Giard, RV Parsey, A Klein.
Brain shape analysis for predicting treatment remission in major depressive disorder.
41st Annual Meeting for the Society for Neuroscience (2011).
NOTE: The results did not hold up for a larger sample.
JaneliaFarm2011_small.png A Klein.
Mindboggle: an informatics framework for open research in quantifying the shape of the human brain.
BioImage Informatics II (talk at Janelia Farm) (2011).
Neuroinformatics2011_small.png N Lee, A Klein.
A graph-based database of hierarchical brain features.
Frontiers in Neuroinformatics (Neuroinformatics 2011).
doi: doi.org/10.3389/conf.fninf.2011.08.00139
HBM2011_small.png F Bao, N Lee, Y Hame, K Im, D Riviere, G Li, A Klein.
Automated extraction of nested sulcal features from human brain MRI data.
17th Annual Meeting for the Organization of Human Brain Mapping (2011).
GitHub repository
 

Neuroinformatics and brain image processing

NIH_BigData_GranteeMeeting2015_NCANDA_ROYGBIV_200px.png BN Nichols, JB Poline, RA Poldrack, A Klein, D Kwon, W Chu, KM Pohl.
Implementing Semantics-Driven Data Exchange in Brain Science: The NCANDA Case Study.
Big Data to Knowledge All Hands Grantee Meeting (2015).
National Institutes of Health, Bethesda, MD.
pic_pres16 DB Keator, J Poline, BN Nichols, SS Ghosh, C Maumet, KJ Gorgolewski, T Auer, C Craddock, G Chen, G Flandin, YO Halchenko, M Hanke, C Haselgrove, K Helmer, M Jenkinson, A Klein, L Lanyon, D Marcus, D Margulies, F Michel, TE Nichols, RA Poldrack, R Reynolds, Z Saad, T Schmah, J Steffener, JA Turner, JD Van Horn, S Das, DN Kennedy.
Standardizing Metadata in Brain Imaging.
Front. Neurosci. Conference Abstract: Neuroinformatics 2015.
doi: doi.org/10.3389/conf.fnins.2015.91.00004
Online presentation by David Keator.
pic_pres16 DB Keator, SS Ghosh, C Maumet, G Flandin, BN Nichols, TE Nichols, GA Burns, R Bruehl, C Craddock, B Federick, K Gorgolewski, YO Halchenko, M Hanke, C Haselgrove, K Helmer, A Klein, D Marcus, M Milham, F Michel, R Poldrack, J Steffener, Y Schwartz, RM Stoner, JA Turner, DN Kennedy, J Poline.
Developing and using the data models for neuroimaging: the NIDASH Working Group.
Front. Neuroinform. Conference Abstract: Neuroinformatics 2014.
doi: doi.org/10.3389/conf.fninf.2014.18.00030
BIDS-Apps_bioRxiv2016.png KJ Gorgolewski, F Alfaro-Almagro, T Auer, P Bellec, M Capota, M Mallar Chakravarty, NW Churchill, RC Craddock, GA Devenyi, A Eklund, O Esteban, G Flandin, SS Ghosh, JS Guntupalli, M Jenkinson, A Keshavan, G Kiar, PR Raamana, D Raffelt, CJ Steele, P-O Quirion, RE Smith, SC Strother, G Varoquaux, T Yarkoni, Y Wang, RA Poldrack.
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
PLOS Computational Biology 13(3): e1005209 (2016). doi: 10.1371/journal.pcbi.1005209
pic_pres16 S Ghosh, A Keshavan, J Salvatore, A Klein.
BIPS: A Framework for Curating and Executing Brain Imaging Pipelines.
Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics (2014).
doi: doi.org/10.3389/conf.fninf.2014.08.00053
ANTSevaluation_NeuroImage2010.png BB Avants, NJ Tustison, G Song, PA Cook, A Klein, JC Gee.
A reproducible evaluation of ANTs similarity metric performance in brain image registration.
NeuroImage. 54(3): 2033-2044 (2011). PMCID: PMC3065962.
ESMRMB2011_small.png D Peruzzo, A Bertoldo, R Parsey, A Klein.
Automatic detection of corrupted volumes in DTI data.
28th Annual Meeting for the European Society for Magnetic Resonance in Medicine and Biology (2011).
Atropos_HBM2010.png B Avants, A Klein, N Tustison, J Woo, JC Gee.
Evaluation of open-access, automated brain extraction methods on multi-site multi-disorder data.
16th Annual Meeting for the Organization of Human Brain Mapping (2010).
Synapse website
SurfaceVolumeEval_NeuroImage_2009.jpg A Klein, SS Ghosh, B Avants, BTT Yeo, B Fischl, B Ardekani, JC Gee, JJ Mann, RV Parsey.
Evaluation of volume-based and surface-based brain image registration methods.
NeuroImage. 51: 214-220 (2010). PMCID: PMC2862732.
Synapse website
HBM2009_evaluation_surfaceVSvolume.png A Klein, SS Ghosh, B Avants, B Fischl, T Yeo, JJ Mann, RV Parsey.
An evaluation of volume- and surface-based nonlinear registration of human brain MRI data.
15th Annual Meeting for the Organization of Human Brain Mapping (2009).
EvaluationData_NeuroImage2009_half.png A Klein, J Andersson, BA Ardekani, J Ashburner, B Avants, M-C Chiang, GE Christensen, DL Collins, J Gee, P Hellier, JH Song, M Jenkinson, C Lepage, D Rueckert, P Thompson, T Vercauteren, RP Woods, JJ Mann, RV Parsey.
Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.
NeuroImage. 46(3): 786-802 (2009). PMCID: PMC2747506
Synapse website
coregistration_SPIE_2009.png C DeLorenzo, A Klein, A Mikhno, N Gray, F Zanderigo, JJ Mann, RV Parsey.
A new method for assessing PET-MRI coregistration.
Proc. SPIE - Medical Imaging. 7259, 72592W (2009).
 

Brain anatomical labeling

Mindboggle101_FIBIM2012.png A Klein, J Tourville.
101 labeled brain images and a consistent human cortical labeling protocol.
Frontiers in Brain Imaging Methods. 6:171 (2012). doi: doi.org/10.3389/fnins.2012.00171
Supplementary website and Open Science Framework repository
Neuroinformatics2012_Mindboggle101.png J Tourville, A Klein.
101 labeled brains and a new human cortical labeling protocol.
Neuroinformatics 2012 (Munich, Germany).
ISBI2011_deeplearning3.png N Lee, AF Laine, A Klein.
Towards a deep learning approach to brain parcellation.
IEEE International Symposium on Biomedical Imaging: From Nano to Macro (2011):321-324.
doi: doi.org/10.1109/ISBI.2011.5872414
SFN2010_OptimalColormaps.png A Klein, A Worth, J Tourville, B Landman, T Dal Canton, SS Ghosh, D Shattuck.
An interactive tool for constructing optimal brain colormaps.
40th Annual Meeting for the Society for Neuroscience (2010).
Website: https://binarybottle.github.io/braincolor/colormaps/
HBM2010_OpenLabels.png A Klein, T Dal Canton, SS Ghosh, B Landman, J Lee, A Worth.
Open labels: online feedback for a public resource of manually labeled brain images.
16th Annual Meeting for the Organization of Human Brain Mapping (2010).
Mindboggle_BMCMedicalImaging_2005.png A Klein, B Mensh, S Ghosh, J Tourville, J Hirsch.
Mindboggle: Automated brain labeling with multiple atlases.
BMC Medical Imaging. 5:7 (2005). PMCID: PMC1283974
Mindboggle_NeuroImage_2005.png A Klein, J Hirsch.
Mindboggle: A scatterbrained approach to automate brain labeling.
NeuroImage. 24(2): 261-280 (2005). PMID: 15627570
Thesis: Automated brain labeling with Mindboggle
HBM2003c.png A Klein.
Activity patterns in the brain: breaking up the problem into pieces.
International Conference on Complex Systems (2004) talk.
hbm2003b.png A Klein, J Hirsch.
Mindboggle: new developments in automated brain labeling.
9th Annual Meeting for the Organization of Human Brain Mapping (2003).
hbm2002.png A Klein, J Hirsch.
Fully-automated nonlinear labeling of human brain activity.
8th Annual Meeting for the Organization of Human Brain Mapping (2002).
hbm2001.png A Klein, J Hirsch.
Automatic labeling of brain anatomy and fMRI brain activity.
7th Annual Meeting for the Organization of Human Brain Mapping (2001).
 

Open science

BeTheChange_bioRxiv2018_300px.png

M Milham, A Klein.
Be the change you seek in science
PsyArXiv Preprints. Sept. 21, 2018. Web. doi: doi.org/10.31234/osf.io/gry2j
ImpactOfDataSharing_bioRxiv2017_300px.png

MP Milham, RC Craddock, JJ Son, M Fleischmann, J Clucas, H Xu, B Koo, A Krishnakumar, BB Biswal, FX Castellanos, S Colcombe, A Di Martino, X-N Zuo, A Klein.
Assessment of the impact of shared brain imaging data on the scientific literature
Nature Communications. 9, Article number: 2818 (2018).
doi: doi.org/10.1038/s41467-018-04976-1
Editorial: Data sharing and the future of science.

MP Milham, A Klein, C Craddock.
Opinion: Share your data
The Scientist (2017).
HBNbiobank2017.png

LM Alexander, J Escalera, L Ai, C Andreotti, K Febre, A Mangone, NV Potler, N Langer, A Alexander, M Kovacs, S Litke, B O'Hagan, B Bronstein, A Bui, M Bushey, V Castagna, N Camacho, E Chan, D Citera, J Clucas, S Cohen, M Eaves, B Fradera, N Grant-Villegas, G Green, C Gregory, E Hart, S Harris, C Lord, D Kahn, K Kabotyanski, K Kleinman, B Koo, E Kramer, A Margolis, KR Merikangas, J Milham, G Minniti, R Neuhaus, A Nussbaum, Y Osman, LC Parra, KR Pugh, A Racanello, A Restrepo, T Saltzman, B Septimus, R Tobe, R Waltz, A Williams, A Yeo, FX Castellanos, A Klein, T Paus, BL Leventhal, RC Craddock, HS Koplewicz, MP Milham.
An open resource for transdiagnostic research in pediatric mental health and learning disorders
Scientific Data. 4, Article number: 170181 (2017). doi: doi.org/10.1038/sdata.2017.181
CloudWorkshop H Muller, J Kalpathy-Cramer, A Hanbury, K Farahani, R Sergeev, JH Paik, A Klein, A Criminisi, A Trister, T Norman, D Kennedy, G Srinivasa, A Mamonov, N Preuss.
Report on the Cloud-Based Evaluation Approaches Workshop 2015.
ACM SIGIR Forum. 50(1):35-41 (2015). Workshop Website
pic_pres16 A Klein.
A game for crowdsourcing the segmentation of BigBrain data (NIH proposal).
Research Ideas and Outcomes. 2: e8816 (2016). doi: doi.org/10.3897/rio.2.e8816
pic_pres16 A Klein.
Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease (NIH proposal).
Research Ideas and Outcomes. 2: e8848 (2016). doi: doi.org/10.3897/rio.2.e8848
SageChallenge_AlzheimersAndDementia2016_small_crop.jpg GI Allen, N Amoroso, C Anghel, V Balagurusamy, CJ Bare, D Beaton, R Bellotti, DA Bennett, K Boehme, PC Boutros, L Caberlotto, C Caloian, F Campbell, E Chaibub Neto, Y-C Chang, B Chen, C-Y Chen, T-Y Chien, T Clark, S Das, C Davatzikos, J Deng, D Dillenberger, RJB Dobson, Q Dong, J Doshi, D Duma, R Errico, G Erus, E Everett, DW Fardo, SH Friend, H Fröhlich, J Gan, P St George-Hyslop, SS Ghosh, E Glaab, RC Green, Y Guan, M-Y Hong, C Huang, J Hwang, J Ibrahim, P Inglese, Q Jiang, Y Katsumata, JSK Kauwe, A Klein, D Kong, R Krause, E Lalonde, M Lauria, E Lee X Lin, Z Liu, J Livingstone, BA Logsdon, S Lovestone, T-W Ma, A Malhotra, LM Mangravite, TJ Maxwell, E Merrill, J Nagorksi, A Namasivayam, M Narayan, M Naz, SJ Newhouse, TC Norman, RN Nurtdinov, Y-J Oyang, Y Pawitan, S Peng, MA Peters, SR Piccolo, P Praveen, C Priami, VY Sabelnykova, P Senger, X Shen, A Simmons, A Sotiras, G Stolovitzky, S Tangaro, A Tateo, Y-A Tung, NJ Tustison, S Varol, G Vradenburg, MW Weiner, G Xiao, L Xie, Y Xie, J Xu, H Yang, X Zhan, Y Zhou, F Zhu, H Zhu, S Zhu, Alzheimer's Disease Neuroimaging Initiative.
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.
Alzheimer's & Dementia 12(6): 645-653 (2016). PMID: 27079753.
doi: doi.org/10.1016/j.jalz.2016.02.006
Alzheimer's Disease Challenge website
pic_opensci2 NJ Tustison, HJ Johnson, T Rohlfing, A Klein, SS Ghosh, L Ibanez, B Avants.
Instrumentation bias in the use and evaluation of scientific software: Recommendations for reproducible practices in the computational sciences.
Frontiers in Brain Imaging Methods. 7:162 (2013). doi: doi.org/10.3389/fnins.2013.00162
pic_opensci1 SS Ghosh, A Klein, B Avants, J Millman.
Learning from open source software projects to improve scientific review.
Frontiers in Computational Neuroscience. 6:18 (2012).
doi: doi.org/10.3389/fncom.2012.00018
 

Art, design, and visualization

A Klein.
The Insect's Final Dream. Chicken in a Snowstorm Press (2017).
Exhibited in:
Insect Dreams (collaborative edition in permanent collection).
Kohler Art Library, Madison, WI (2018).
and:
Eating Insects Athens Art Exhibition, Athens, GA (2018).
HBM2015_ROYGBIV_small.jpeg

A Keshavan, A Klein, B Cipollini.
Interactive online brain shape visualization.
Research Ideas and Outcomes 3: e12358 (2017).
doi: doi.org/10.3897/rio.3.e12358
mPower2 A Klein.
CTHRU: A composition-based taxonomy of information graphics.
Medium (Jun 1, 2016).
pic_pres16 A Klein.
Data-Visual Relationships to Subject Performance and Eye Movements (NSF proposal).
Research Ideas and Outcomes. 2: e8814 (2016). doi: doi.org/10.3897/rio.2.e8814
pic_pres16 A Klein.
Visual Parkinson's Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India (NIH proposal).
Research Ideas and Outcomes. 2: e8834 (2016). doi: doi.org/10.3897/rio.2.e8834
A Klein, BA Klein.
Insects Incorporated: Database of Cultural Entomology (2016). https://culturalentomology.org/
Neuroinformatics2012_Mindboggle.png A Klein, N Nichols, D Haehn.
Mindboggle 2 interface: online visualization of extracted brain features with XTK.
Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics (2014).
doi: doi.org/10.3389/conf.fninf.2014.08.00086
5-Semper_Book-color-128-958.pdf Ellora Cave Temple photographs on page 958, architecture textbook:
AJ Ignacio (translator and editor)
Semper: El estilo. Buenos Aires: Azpiazu Ediciones (2013).
A Klein, KA Klein.
Hugo Bristol and the Night Sky. Chicken in a Snowstorm Press (2013).
pic_infovis1 A Klein, W Bevington.
“Information visualization” entry in: Erlhoff Michael, Marshall Tim, eds.
Design Dictionary: Perspectives on Design Terminology. Basel, Boston, Berlin: Birkhauser Verlag (2008).
pic_optics2 A Klein.
Relating vector ray-tracing equations for holograms of arbitrary shape and thickness.
Journal of the Optical Society of America A. 25(4): 979-983 (2008).
BA Klein, A Klein.
Congo Rainforest permanent exhibit. Bronx Zoo, Bronx, NY (1999).
pic_optics1 MA Klug, A Klein, W Plesniak, A Kropp, B Chen.
Optics for full-parallax holographic stereograms.
Proc. SPIE. 3011 (78) “Practical Holography XI” (1997).
doi: doi.org/10.1117/12.271340
Thesis: Dispersion Compensation for Reflection Holography
 

Bees

pic_bees5 BA Klein, M Stiegler, A Klein, Tautz J.
Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.
PLoS ONE. 9(7): e102316 (2014). doi: doi.org/10.1371/journal.pone.0102316
Harvard Dataverse
pic_bees4 BA Klein, L Rath, A Klein, SS Ghosh, G Galizia, C Kleineidam.
Neural imaging of honey bees sensing odors during sleep. SLEEP. 36:A57 (2013).
pic_bees3 A Klein, SS Ghosh, BA Klein, L Rath, G Galizia, C Kleineidam.
Applying human brain image processing methods to honeybee calcium image data.
Neuroinformatics 2012 (Munich, Germany).
pic_bees2 BA Klein, A Klein, MK Wray, UG Mueller, TD Seeley.
Sleep Deprivation impairs precision of waggle dance signaling in honey bees.
Proceedings of the National Academy of Sciences. 107(52): 22705-22709 (2010).
doi: doi.org/10.1073/pnas.1009439108
Nature News, New Scientist, Wired,...
pic_bees1 BA Klein, KM Olzsowy, A Klein, KM Saunders, TD Seeley.
Caste-dependent sleep of worker honey bees.
Journal of Experimental Biology. 211: 3028-3040 (2008). doi:10.1242/jeb.017426
Media coverage: Deutsches Bienen Journal, Dec. 2008.