# BRIAN BEAUMONT AVANTS, Ph.D.

**AI & Machine Learning Executive · Computational Anatomy Pioneer · Founder, Cingulate LLC**

- **Address:** Cingulate LLC, 145 High Street, Portsmouth, NH, USA
- **Phone:** +1 (415) 508-4437 | **Email:** [antsx@antsx.com](mailto:antsx@antsx.com) | **Website:** [stnava.github.io](https://stnava.github.io)
- **GitHub:** [github.com/stnava](https://github.com/stnava) · [github.com/ANTsX](https://github.com/ANTsX) | **LinkedIn:** [linkedin.com/in/brian-avants](https://www.linkedin.com/in/brian-avants)
- **ORCID:** [0000-0002-4212-3362](https://orcid.org/0000-0002-4212-3362) | **PubMed:** [Author Profile](https://pubmed.ncbi.nlm.nih.gov/?term=Avants+B)
- **Google Scholar:** [57,500+ Citations · h-index: 71 · i10-index: 166](https://scholar.google.com/citations?user=t4kkowgAAAAJ&hl=en)

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## EXECUTIVE & SCIENTIFIC SUMMARY

Entrepreneurial AI/ML executive, principal data scientist, and computational imaging leader with over two decades of impact spanning academic medicine, pharmaceutical drug development, clinical trial CROs, and open-source software engineering. Co-creator and lead architect of the **ANTsX ecosystem** (`ANTs`, `ANTsPy`, `ANTsR`, `ANTsPyNet`, `ANTsPyMM`), the international standard for diffeomorphic medical image registration (`SyN`), morphometry, and deep learning phenotyping (**57,500+ citations, h-index 71**). Author of four papers each cited more than 6,000 times (`SyN`, `N4ITK`, BRATS, and the ANTs registration evaluation). Proven executive track record founding **Cingulate LLC**, directing global Machine Learning teams at **Invicro**, and leading translational imaging biomarker strategy for the landmark *Aducanumab/Aduhelm* program at **Biogen**.

| **57,500+ Citations** | **h-index: 71 / i10: 166** | **6x #1 Global Benchmarks** | **Pharma & Venture AI Lead** |
| :---: | :---: | :---: | :---: |
| Foundational imaging & ML methods | 180+ peer-reviewed publications | Klein, EMPIRE10, BRATS, SATA | Cingulate, Invicro, Biogen, UVA, UPenn |

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## ENTREPRENEURIAL, EXECUTIVE & ACADEMIC APPOINTMENTS

### **Founder & Principal Consultant** | Cingulate LLC — *Portsmouth, NH* *(2018 – Present)*
- Founder and managing principal of an independent AI, machine learning, and computational neuroimaging consultancy serving biotechnology, pharmaceutical, defense (DoD/CDMRP), and academic research organizations.
- Architect of novel interpretable representation learning and matrix optimization tools, including **NSA-Flow** (*Non-Negative Stiefel Approximating Flow*, PyTorch) and **SiMLR** (*Similarity-driven Multi-view Linear Reconstruction*, *Nature Computational Science* 2021).
- Lead multi-modal neuroimaging phenotyping, longitudinal subtyping, and normative database engineering for large-scale studies including the **UK Biobank**, **Parkinson's Progression Markers Initiative (PPMI)**, and **LIMBIC-CENC**.

### **Visiting Associate Professor of Radiology and Medical Imaging** | University of Virginia School of Medicine — *Charlottesville, VA* *(2018 – Present)*
- Co-lead multi-view machine learning and quantitative neuroimaging investigations of repetitive low-level blast exposure and traumatic brain injury (TBI) in military Special Operations personnel and breachers (*Journal of Neurotrauma* 2020, 2022, 2024).
- Co-architect of the **Normative Neuroimaging Library** (*J. Neurotrauma* 2024) and **Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows** (2026).

### **Senior Director of Machine Learning** | Invicro (a Konica Minolta Company) — *Boston, MA* *(2018 – 2024)*
- Directed the enterprise Machine Learning group for a premier global imaging CRO, leading clinical trial software development and integrative AI analytics across neurodegenerative, oncology, cardiopulmonary, and multi-species drug development programs.
- Designed and deployed **ANTsPyMM**, automated deep learning quality control, 3D concurrent super-resolution, and multi-modal patient representation learning pipelines (*ICLR* 2023, *Patterns* 2023, *European Journal of Human Genetics* 2024).

### **Visiting Scholar, Institute for Computational and Experimental Research in Mathematics (ICERM)** | Brown University — *Providence, RI* *(Spring 2020)*
- Invited visiting scientist for the semester program *"Model and Dimension Reduction in Uncertain and Dynamic Systems"*; developed mathematical foundations for integrative multi-view machine learning (`SiMLR`).

### **Associate Director, Translational & Advanced Analytics (Imaging Biomarkers)** | Biogen — *Cambridge, MA* *(2016 – 2018)*
- Lead integrative imaging data scientist for the **Aducanumab (Aduhelm)** clinical trial program (Phase 1b PRIME and Phase 3 ENGAGE/EMERGE); performed confirmatory amyloid PET SUVR analyses and created Figure 1 and the cover visualization for the landmark **2016 *Nature* publication**.
- Led longitudinal network-specific rs-fMRI biomarker discovery in amyloid-positive cohorts (*Neurobiology of Aging* 2018) and initiated **ANTsPy** development for deep learning in neuroimaging.

### **Assistant Professor of Radiology** | University of Pennsylvania Perelman School of Medicine (PICSL) — *Philadelphia, PA* *(2012 – 2016)*
- Directed computational neuroimaging, multi-modal MRI/DTI/PET/ASL methodology, and big-data imaging genetics projects; served as Principal Investigator on NIH BD2K K01 Career Development Award and Image Analysis Lead for IARPA KRNS.

### **Research Associate (2008–2012) · Postdoctoral Research Fellow (2006–2008)** | University of Pennsylvania — *Philadelphia, PA* *(2006 – 2012)*
- Developed foundational methods for **Symmetric Diffeomorphic Image Registration (`SyN`)**, **N4ITK** bias correction, **Atropos** multivariate segmentation, **DiReCT** cortical thickness, and **Sparse Canonical Correlation Analysis (`SCCAN`)**.

### **Algorithm Developer, Imaging Department** | Siemens Corporate Research — *Princeton, NJ* *(1999 – 2000)*
- Developed adaptive minimal-path vessel tracking and 3D segmentation algorithms in CTA/CE-MRA volumetric imaging.

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## EDUCATION & POSTDOCTORAL TRAINING

- **2006 – 2008:** **Postdoctoral Fellowship in Radiology**, University of Pennsylvania, Philadelphia, PA.
- **2005:** **Ph.D. in Bioengineering**, University of Pennsylvania, Philadelphia, PA. Dissertation: *Diffeomorphometry for Computational Anatomy*. NIH Institute for Medicine and Engineering Trainee (2002).
- **2002 / 2003:** **M.S. in Computer Science**, University of Pennsylvania, Philadelphia, PA.
- **1998:** **B.A. in Physics and Literature**, New College of Florida, Sarasota, FL (*With High Honors*; National Merit Scholar).

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## RESEARCH DOMAINS & TECHNICAL EXPERTISE

- **Deep Learning & AI:** High-dimensional multi-output regression, 3D segmentation, concurrent super-resolution, longitudinal manifold embedding (Aligned-UMAP), Stiefel manifold flow (`NSA-Flow`), normalizing flows, multi-modal prediction with missing modalities, and interpretable neural architectures.
- **Brain Mapping:** Brain structure, function, perfusion, neuroinflammation, and cognition across development, aging, neurotrauma, and neurodegeneration; multi-view modality integration (`SiMLR`, `SCCAN`); disease subtyping and staging (`subtyper`); reproducible biobank-scale phenotyping.
- **Tech Stack:** C++, Python, PyTorch, TensorFlow/Keras, R, Julia, CMake, ITK, Bash, Git, LaTeX, Docker/Singularity, AWS/HPC cloud architectures.

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## FLAGSHIP SOFTWARE CONTRIBUTIONS & OPEN-SOURCE ECOSYSTEM

*Ecosystem reach (Nov 2026): ANTsX GitHub organization: 13 repositories, 2,900+ stars, 700+ forks; `ANTsPy` 30,000+ PyPI downloads per month; `ANTs`/`SyN` is a core dependency of fMRIPrep, QSIPrep, Nipype, Clinica, and TemplateFlow.*

- **ANTs (2008–Present):** Advanced Normalization Tools ([github.com/ANTsX/ANTs](https://github.com/ANTsX/ANTs)): C++ library used globally across academia and industry for medical image registration (`SyN`), segmentation (`Atropos`), and cortical thickness; **Creator & Lead Architect**.
- **ANTsPy & ANTsPyNet (2017–Present):** Python interface and deep learning library ([ANTsPy](https://github.com/ANTsX/ANTsPy), [ANTsPyNet](https://github.com/ANTsX/ANTsPyNet)) providing pre-trained 2D/3D networks for brain extraction, Deep Atropos, HippMapp3r, brain age, lesion segmentation, and super-resolution; **Co-Creator & Architect**.
- **ANTsPyMM (2021–Present):** Multi-modal neuroimaging processing and automated QC framework ([ANTsX/ANTsPyMM](https://github.com/ANTsX/ANTsPyMM)) converting structural T1w, FLAIR, rs-fMRI, DTI, and neuromelanin MRI into standardized Image Derived Phenotypes (IDPs); **Lead Architect**.
- **ANTsR (2012–Present):** R statistical programming extension of ANTs ([ANTsX/ANTsR](https://github.com/ANTsX/ANTsR)) featuring `Eigenanatomy`, `SCCAN`, and `SiMLR`; **Creator & Lead Designer**.
- **NSA-Flow (2025–Present):** PyTorch package ([stnava/nsa_flow](https://github.com/stnava/nsa_flow)) implementing Non-Negative Stiefel Approximating Flow for orthogonalish, sparse, interpretable matrix factorization and representation learning; **Creator**.
- **syntx, pysimlr & curvanato (2025–Present):** Next-generation ANTsX tooling in Python: [`syntx`](https://github.com/stnava/syntx) (symmetric normalization transformations), [`pysimlr`](https://github.com/stnava/pysimlr) (similarity-driven linear and nonlinear multi-view reconstruction), and [`curvanato`](https://github.com/stnava/curvanato) (local curvature quantification for anatomical data); **Creator**.
- **subtyper (2023–Present):** Disease subtyping, staging, and latent space evaluation toolkit ([stnava/subtyper](https://github.com/stnava/subtyper)); **Creator**.
- **ITKv4 (2002–Present):** The Insight ToolKit ([itk.org](https://itk.org)): **Lead Designer** for the v4 deformable image registration framework.
- **Neuroconductor (2016–Present):** R platform for reproducible neuroimaging data science ([neuroconductor.org](https://neuroconductor.org)); **Co-Founder & Contributor**.

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## AWARDS, INTERNATIONAL BENCHMARKS & HONORS

- **2014:** **Best Paper Award** (with Nicholas J. Tustison) at the STACOM 2014 Challenge, MICCAI.
- **2013:** **1st Place, BRATS 2013 Brain Tumor Segmentation Challenge**, MICCAI, Nagoya, Japan (`ANTsR`, with N. Tustison).
- **2013:** **1st Place, SATA Segmentation Challenge**, MICCAI, Nagoya, Japan (`ANTs`, with N. Tustison).
- **2012–2013:** **"Standard Setting" Image Registration Software** selected for the MICCAI 2013 Multi-Atlas Segmentation Challenge (4D cardiac, brain, and multimodality canine leg MR images); all top finishers in MICCAI 2012 multi-atlas segmentation used `ANTs`.
- **2010:** **1st Overall** in the unbiased **EMPIRE10** International Thoracic CT Lung Registration Challenge (*IEEE TMI* 2011).
- **2009:** **1st Rank** in the unbiased **Klein 2009** International Brain MRI Registration Evaluation of 14 nonlinear algorithms (*NeuroImage* 2009).
- **2007:** **Young Investigator Award**, General Medical Computing, MICCAI, Brisbane, Australia.
- **2003:** **Best Poster Award**, SPIE Medical Imaging.
- **1995:** **Future Healthcare Researcher Scholarship**, Humana Health Care.
- **1994:** **National Merit Scholarship**, New College of Florida, Sarasota, FL.

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## GRANTS, SPONSORED RESEARCH & CONSORTIUM LEADERSHIP

- **2018 – Present:** **DoD / CDMRP / LIMBIC-CENC Neurotrauma & Blast Overpressure Research Programs** (with James R. Stone, M.D., Ph.D. & Nicholas J. Tustison, D.Sc., University of Virginia): Multi-view neuroimaging biomarkers (`SiMLR`, `NSA-Flow`), TSPO PET neuroinflammation, and Normative Neuroimaging Library development in Special Operations personnel and combat breachers (Role: **Co-Investigator / Lead ML Consultant**).
- **2018 – 2024:** **Parkinson's Progression Markers Initiative (PPMI) & Multimodal Neurodegeneration Consortia** (Invicro / Michael J. Fox Foundation / NIH CARD Collaborations): Automated multi-modal MRI/PET phenotyping (`ANTsPyMM`), Aligned-UMAP longitudinal subtyping, and missing-modality patient representation learning (Role: **Senior Director of ML / Co-Investigator**).
- **10/2014 – 09/2019:** **The Imaging Genomics of Pediatric Executive Function**, NIH Big Data to Knowledge (BD2K), **K01-ES025432-01** (**Avants, Brian, PI**), $275,000/annual direct costs, 80% effort.
- **08/2015 – 05/2018:** **Multimodal Brain Maturation Indices Modulating Psychopathology and Neurocognition**, NIH **R01-MH107235-01** (Gur, Ruben, PI), $275,000/annual direct costs (Role: **Collaborator**).
- **09/2013 – 08/2018:** **Neuroscience Neuroimaging Center**, NIH **P30-NS045839-07** (Detre, John, M.D., PI), $499,727/annual direct costs (Role: **Collaborator / Technical Core Lead**).
- **2014:** **Knowledge Representation in Neural Systems (KRNS)**, IARPA-BAA-12-05, 50% effort (Role: **Image Analysis Lead**).
- **09/2012 – 07/2013:** **Age, Hearing Loss, and Sentence Comprehension: Neural Correlates**, NIA/NIH **5-R01-AG038490-05** (Grossman, Murray, PI), $291,978/annual direct costs (Role: **Co-PI**).
- **09/2011 – 08/2015:** **Continued Development and Maintenance of ITK-SNAP 3D Image Segmentation Software**, NIH **R01-EB014346-01** (Yushkevich, Paul A., PI), $350,824/annual direct costs (Role: **Collaborator**).
- **09/2010 – 08/2015:** **TDP-43 Proteinopathies in ALS-Dementia**, NIH **P01-AG032953-02** (Lee, Virginia / Grossman, Murray, PI), $729,272/annual direct costs (Role: **Collaborator**).
- **06/2010 – 06/2013:** **Fundamental Refactoring of Deformable Image Registration in ITK with Distributed Computing and GPU Acceleration**, National Library of Medicine **HHSN276201000492P** (Gee, James C., PI), $472,861/annual direct costs (Role: **Co-PI & Architecture Lead**).
- **02/2011 – 01/2012:** **Longitudinal Multi-Modal Neuroimaging of Natural Recovery after Traumatic Brain Injury: A Pilot Study**, Moss Rehab Research Institute / NIH (**Avants, Brian, PI**), $7,764/annual direct costs.
- **08/2007 – 04/2013:** **In Utero Cocaine Exposure: Adolescent & Young Adult Neurocognitive Outcome**, CHOP / NIH **R01-DA14129-08** (Gee, James C., PI), $102,515/annual direct costs (Role: **Collaborator**).
- **06/2010 – 05/2012:** **Parkinson's Disease & Dementia**, NIH **P50-NS053488-04S1** (Trojanowski / Grossman, PI), $132,641/annual direct costs (Role: **Collaborator**).
- **09/2009 – 08/2012:** **Tract-Specific Analysis of Brain White Matter**, NIH **R01-NS065347-02** (Gee, James C., PI), $370,667/annual direct costs (Role: **Collaborator**).
- **09/2009 – 05/2010:** **Pediatric Template of Brain Perfusion**, NIMH/NIH **3-R01-MH080892-01A2S1** (Wang, Jiongjiong, PI) (Role: **Co-PI**).
- **09/2008 – 09/2011:** **Advanced Neuroimage Registration Methods: Effects of Prenatal Cocaine Exposure**, NIH (Gee, James C., PI; **Avants, Brian, Co-PI**), $354,375/annual direct costs.
- **06/2008 – 01/2011:** **The Longitudinal Effect of Neurodegeneration on Language-Network Neuroanatomy and Cognition**, UPenn Institute on Aging (Gee, James C., PI; **Avants, Brian, Co-PI**).
- **04/2007 – 01/2011:** **Long Term Effects of Prenatal Cocaine Exposure**, NIH (Hurt, Hallam, PI) (Role: **Research Scientist**).
- **04/2006 – 03/2010:** **Shape Optimizing Diffeomorphisms for Computational Biology**, NIH / UCLA Center for Computational Biology **R01-EB006266** (Gee, James C., PI; based on B. Avants' Ph.D. thesis).
- **08/2004 – 06/2009:** **Surface-based Cortical Analysis in ITK: Segmentation, Conformal Flattening and Statistics**, NLM-NIH ITK Development Grant (Gee, James C., PI; **Avants, Brian, Co-PI**).
- **09/2002 – 06/2005:** **Bioengineering Training in Cardiovascular Pathophysiology**, Institute for Medicine and Engineering Training Grant, UPenn (Davies, Peter, PI; **Trainee**).

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## EDITORIAL POSITIONS, ADVISORY PANELS & PROFESSIONAL SERVICE

- **2019:** **Brain Injury Biomarker Strategy Panel Contributor**, sponsored by Cohen Veterans Bioscience.
- **2017:** **Topic Editor**, *NeuroImage* Special Issue on Brain Parcellation.
- **2012 – 2015:** **Topic Editor**, *Frontiers in Neuroinformatics*: Research Topic on Neuroinformatics with the Insight ToolKit (ITK).
- **2013 – Present:** **Grant Reviewer**, Alzheimer's Association & Ad Hoc Federal/International Study Sections.
- **2013 – Present:** **Consultant**, American College of Radiology (ACR) Head Injury Institute Information Technology Committee.
- **2010 – Present:** **Insight ToolKit (ITKv4) Development Leader**, NLM/NIH-sponsored industry-academic consortium.
- **2011 – Present:** **Task Force Member**, International Neuroinformatics Coordinating Facility (INCF) Registration and Atlasing Task Force.
- **2006 – Present:** **Member**, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) & Spatial Transformations Informatics Technology Initiative (SIFTI).
- **Peer Review:** *Nature Neuroscience*, *Nature Computational Science*, *Nature Methods*, *Medical Image Analysis*, *NeuroImage*, *IEEE Transactions on Medical Imaging*, *IEEE TPAMI*, *Human Brain Mapping*, *Medical Physics*, *Pediatrics*.
- **Memberships:** Organization for Human Brain Mapping (OHBM); International Society for Magnetic Resonance in Medicine (ISMRM).

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## MENTORSHIP, ADVISING & MAJOR RESEARCH COLLABORATIONS

- **2018 – Present:** **Industry & Consortium Mentorship (Invicro, Cingulate LLC, UVA):** Mentored machine learning scientists, postdoctoral fellows, and Ph.D. interns across deep learning, multimodal representation learning, and longitudinal clinical trial modeling (including collaborations with Anant Dadu, Zhenbang Wu, Brandon Theodorou, and Taylor Gosselin).
- **Summer 2017:** **Industry Internship Advisor to Nicholas Cullen** (Biogen Biomarkers Group): Deep learning and multivariate neuroimaging in Alzheimer's Disease; co-created `ANTsPy` and co-authored Springer Protocols chapter on deep learning brain segmentation.
- **2014 – 2016:** **Faculty Technical Advisor to Dr. Dorian Pustina** (UPenn Postdoctoral Scientist, with Dr. H. Branch Coslett): Automated stroke lesion segmentation (`LINDA`) and multivariate lesion-symptom mapping (`SCCAN`); *subsequently Director of Experimental Neuroimaging at CHDI Foundation*.
- **2012 – 2017:** **Ph.D. Co-Advisor to Dr. Efstathios (Stathis) Gennatas** (UPenn Neuroscience): Developmental brain morphometry across childhood to young adulthood (*J. Neurosci.* 2017); *subsequently faculty/scientist at UCSF*.
- **2010 – 2015:** **Ph.D. Advisor to Dr. Benjamin M. Kandel** (UPenn Bioengineering): Eigenanatomy, sparse linear regression, and ASL perfusion decomposition (Oral presentation at IPMI 2013).
- **2010 – 2015:** **Ph.D. Co-Advisor to Dr. Paramveer S. Dhillon** (UPenn Computer Science, with Prof. Lyle Ungar): Prior-based Eigenanatomy and functional parcellation (Oral presentation at PRNI 2013; *subsequently MIT postdoc and faculty at University of Michigan*).
- **2012 – 2013:** **Organizer, UPenn Provost's Interdisciplinary Seminar Series on Multi-Modality Brain Mapping** (*Brainomics*): Hosted David Van Essen (Human Connectome Project), Mert Sabuncu, and Moriah Thomason.

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## PEER-REVIEWED JOURNAL PUBLICATIONS & RECENT PREPRINTS (1999 – 2026)

1. Tustison, N. J.; **Avants, B. B.**; Cook, P. A.; Gee, J. C.; Stone, J. R. (2026). *Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows*. **bioRxiv / PubMed** (PMID: 42146611).
2. Pustina, D.; Bogale, H.; Das, S.; **Avants, B.**; Sathe, S.; Sampaio, C.; Wood, A. (2026). *Geometric properties of caudate and putamen mark the progression of Huntington's disease*. **Imaging Neuroscience**, 4, IMAG.a.1351.
3. Theodorou, B.; Dadu, A.; **Avants, B.**; Nalls, M.; Sun, J.; Faghri, F. (2026). *Realistic PET image synthesis from MRI for automated inference of brain atrophy and Alzheimer's*. **iScience**, 29(5), 115747.
4. **Avants, B. B.**, et al. (2025). *Non-Negative Stiefel Approximating Flow: Orthogonalish Matrix Optimization for Interpretable Embeddings*. **arXiv**:2511.06425.
5. **Avants, B. B.**; Tustison, N. J.; Stone, J. R. (2025). *Joint representations from multi-view MRI-based learning support cognitive and functional performance domains*. **medRxiv**.
6. Tustison, N. J.; Yassa, M. A.; Rizvi, B.; Cook, P. A.; Holbrook, A. J.; Sathishkumar, M. T.; Tustison, M. G.; Gee, J. C.; Stone, J. R.; **Avants, B. B.** (2024). *ANTsX neuroimaging-derived structural phenotypes of UK Biobank*. **Scientific Reports**, 14(1), 8848.
7. Stone, J. R.; **Avants, B. B.**; Tustison, N. J.; Gill, J.; Wilde, E. A.; Neumann, K. D.; Gladney, L. A.; Kilgore, M. O.; Bowling, F.; Wilson, C. M. (2024). *Neurological effects of repeated blast exposure in Special Operations personnel*. **Journal of Neurotrauma**, 41(7–8), 942–956.
8. Tustison, N.; **Avants, B.**; Whitlow, C. T.; Lancashire, L.; Bhatt, S. D.; Haas, M. (2024). *Normative Neuroimaging Library: Designing a Comprehensive and Demographically Diverse Dataset of Healthy Controls to Support Traumatic Brain Injury Diagnostic and Therapeutic Development*. **Journal of Neurotrauma**, 41(23–24), 2497–2512.
9. Yang, Z.; Wen, J.; Erus, G.; **Avants, B. B.**, et al. (2024). *Brain aging patterns in a large and diverse cohort of 49,482 individuals*. **Nature Medicine**, 30, 3015–3026.
10. **Avants, B. B.**; Fonville, L.; Hampton, O.; Reardon, A.; Stenger, A.; Wang, X.; Tustison, N. J.; Stone, J. R.; Cook, P. A.; Marebwa, B.; Chahine, L. M. (2024). *Magnetic Resonance Imaging Data Phenotypes for the Parkinson's Progression Markers Initiative*. **medRxiv**.
11. Dennis, E. L.; Rowland, J.; Esopenko, C.; Tustison, N.; Newsome, M.; **Avants, B.**; Gill, J.; Hinds, S.; Kenney, K.; Lindsey, H. (2024). *Brain volume changes following blast-related mild TBI in service members and veterans: a LIMBIC-CENC study*. **medRxiv**, 2024.02.27.24303460.
12. Polfus, L.; Shirazi, H. M.; Reardon, A.; Varga, M.; Tchourbanov, A.; Gosselin, T.; Dadu, A.; **Avants, B.**; Faghri, F.; Nalls, M.; Hesterman, J. (2024). *Genetic and brain imaging phenotype joint prediction of longitudinal Parkinson's Disease subtypes*. **European Journal of Human Genetics**, 32, 653.
13. Wu, Z.; Dadu, A.; Tustison, N.; **Avants, B.**; Nalls, M.; Sun, J.; Faghri, F. (2023). *Multimodal Patient Representation Learning with Missing Modalities and Labels*. **The Twelfth International Conference on Learning Representations (ICLR)**.
14. Dadu, A.; Satone, V. K.; Kaur, R.; Koretsky, M. J.; Iwaki, H.; Qi, Y. A.; Ramos, D. M.; **Avants, B.**; Hesterman, J.; Gunn, R.; Nalls, M.; Faghri, F. (2023). *Application of Aligned-UMAP to longitudinal biomedical studies*. **Patterns** (Cell Press), 4(6), 100741.
15. **Avants, B.**; Tustison, N. J.; McMillan, C. T.; Gosselin, T.; Gunn, R.; Hesterman, J. (2023). *Concurrent 3D super resolution on intensity and segmentation maps improves detection of structural effects in neurodegenerative disease*. **medRxiv**, 2023.02.02.23285376.
16. Elhamod, M.; Diamond, K. M.; Maga, A. M.; Bakis, Y.; Bart Jr, H. L.; Mabee, P.; Dahdul, W.; Leipzig, J.; Greenberg, J.; **Avants, B.** (2022). *Hierarchy-guided neural network for species classification*. **Methods in Ecology and Evolution**, 13(3), 642–652.
17. **Avants, B. B.**; Tustison, N. J. (2022). *Mapping the Spatial Distribution of Lesions in Stroke: Effect of Diffeomorphic Registration Strategy in the ATLAS Dataset*. In **Lesion-to-Symptom Mapping: Principles and Tools** (pp. 79–94), Springer.
18. Stone, J.; **Avants, B.**; Tustison, N.; Gill, J.; Wilde, E.; Neumann, K.; Gladney, L.; Kilgore, M.; Modica, L. T.; Bowling, F. (2022). *Increased Neuroinflammation in special operators with a history of blast overpressure exposure*. **Journal of Neurotrauma**, 39(11–12), A27–A28.
19. **Avants, B. B.**; Tustison, N. J.; Stone, J. R. (2021). *Similarity-driven multi-view embeddings from high-dimensional biomedical data*. **Nature Computational Science**, 1(2), 143–152.
20. Tustison, N. J.; Cook, P. A.; Holbrook, A. J.; Johnson, H. J.; Muschelli, J.; Devenyi, G. A.; Duda, J. T.; Das, S. R.; Cullen, N. C.; Gillen, D. L.; Yassa, M. A.; Stone, J. R.; Gee, J. C.; **Avants, B. B.** (2021). *The ANTsX ecosystem for quantitative biological and medical imaging*. **Scientific Reports**, 11(1), 9068.
21. Tustison, N. J.; Altes, T. A.; Qing, K.; He, M.; Miller, G. W.; **Avants, B. B.**; Shim, Y. M.; Gee, J. C.; Mugler III, J. P.; Mata, J. F. (2021). *Image-versus histogram-based considerations in semantic segmentation of pulmonary hyperpolarized gas images*. **Magnetic Resonance in Medicine**, 86(5), 2822–2836.
22. Diamond, K. M.; **Avants, B. B.**; Maga, A. M. (2021). *Machine learning-based segmentation and landmarking of 2D fish images*. **Integrative and Comparative Biology**, 61, E1100–E1101.
23. Stone, J. R.; **Avants, B. B.**; Tustison, N. J.; Wassermann, E. M.; Gill, J.; Polejaeva, E.; Dell, K. C.; Carr, W.; Yarnell, A. M.; LoPresti, M. L. (2020). *Functional and structural neuroimaging correlates of repetitive low-level blast exposure in career breachers*. **Journal of Neurotrauma**, 37(23), 2468–2481.
24. Tustison, N. J.; Holbrook, A. J.; **Avants, B. B.**; Roberts, J. M.; Cook, P. A.; Reagh, Z. M.; Duda, J. T.; Stone, J. R.; Gillen, D. L.; Yassa, M. A. (2019). *Longitudinal Mapping of Cortical Thickness Measurements: An ANTs Longitudinal Cortical Thickness Pipeline*. **NeuroImage**, 199, 523–536.
25. **Avants, B. B.**; Hutchison, R. M.; Mikulskis, A.; Salinas-Valenzuela, C.; Hargreaves, R.; Beaver, J.; Chiao, P.; ADNI (2018). *Amyloid beta–positive subjects exhibit longitudinal network-specific reductions in spontaneous brain activity*. **Neurobiology of Aging**, 74, 191–201.
26. Chiao, P.; Bedell, B. J.; **Avants, B. B.**; Zijdenbos, A. P.; Grand'Maison, M.; O'Neill, P.; O'Gorman, J.; Chen, T.; Koeppe, R. (2018). *Impact of Reference/Target Region Selection on Amyloid PET Standard Uptake Value Ratios in the Phase 1b PRIME Study of Aducanumab*. **Journal of Nuclear Medicine**, 60(1), 100–106.
27. Muschelli, J.; Fortin, J. P.; Gherman, A.; **Avants, B. B.**; Whitcher, B.; Caffo, B.; Crainiceanu, C. (2018). *Neuroconductor: An R platform for medical imaging analysis*. **Biostatistics**, 20(2), 218–239.
28. Pustina, D.; **Avants, B. B.**; Faseyitan, O. K.; Medaglia, J. D.; Coslett, H. B. (2018). *Improved accuracy of lesion to symptom mapping with multivariate sparse canonical correlations*. **Neuropsychologia**, 115, 154–166.
29. Pustina, D.; Coslett, H. B.; Ungar, L.; Faseyitan, O. K.; Medaglia, J. D.; **Avants, B. B.**; Schwartz, M. F. (2017). *Enhanced estimations of post-stroke aphasia severity using stacked multimodal predictions*. **Human Brain Mapping**, 38(11), 5603–5615.
30. Maga, A. M.; Tustison, N. J.; **Avants, B. B.** (2017). *A population level atlas of Mus musculus craniofacial skeleton and automated image-based shape analysis*. **Journal of Anatomy**, 231(3), 433–443.
31. Gennatas, E. D.; **Avants, B. B.**; Wolf, D. H.; Satterthwaite, T. D.; Ruparel, K.; Ciric, R.; Hakonarson, H.; Gur, R. E.; Gur, R. C. (2017). *Age-related effects and sex differences in gray matter density, volume, mass, and cortical thickness from childhood to young adulthood*. **Journal of Neuroscience**, 37(20), 5065–5073.
32. Xie, L.; Pluta, J. B.; Das, S. R.; Wisse, L. E. M.; Wang, H.; Mancuso, L.; Kliot, D.; **Avants, B. B.**; Ding, S.; Manjón, J. V.; Yushkevich, P. A. (2017). *Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability*. **NeuroImage**, 144, 183–202.
33. Olm, C. A.; Kandel, B. M.; **Avants, B. B.**; Detre, J. A.; Gee, J. C.; Grossman, M.; McMillan, C. T. (2016). *Arterial spin labeling perfusion predicts longitudinal decline in semantic variant primary progressive aphasia*. **Journal of Neurology**, 263(10), 1927–1938.
34. Kandel, B. M.; **Avants, B. B.**; Gee, J. C.; McMillan, C. T.; Erus, G.; Doshi, J.; Davatzikos, C.; Wolk, D. A. (2016). *White matter hyperintensities are more highly associated with preclinical Alzheimer's disease than imaging and cognitive markers of neurodegeneration*. **Alzheimer's & Dementia: DADM**, 4, 18–27.
35. Legant, W. R.; Shao, L.; Grimm, J. B.; Brown, T. A.; Milkie, D. E.; **Avants, B. B.**; Lavis, L. D.; Betzig, E. (2016). *High-density three-dimensional localization microscopy across large volumes*. **Nature Methods**, 13(4), 359–365.
36. Pustina, D.; Coslett, H. B.; Turkeltaub, P. E.; Tustison, N. J.; Schwartz, M. F.; **Avants, B. B.** (2016). *Automated segmentation of chronic stroke lesions using LINDA: Lesion identification with neighborhood data analysis*. **Human Brain Mapping**, 37(4), 1405–1421.
37. Betancourt, L. M.; **Avants, B. B.**; Farah, M. J.; Brodsky, N. L.; Wu, J.; Ashtari, M.; Hurt, H. (2016). *Effect of socioeconomic status (SES) disparity on neural development in female African-American infants at age 1 month*. **Developmental Science**, 19(6), 947–956.
38. **Avants, B. B.**; Hackman, D. A.; Betancourt, L. M.; Lawson, G. M.; Hurt, H.; Farah, M. J. (2016). *Relation of Childhood Home Environment to Cortical Thickness in Late Adolescence: Specificity of Experience and Timing*. **PLOS ONE**, 10(10), e0138217.
39. **Avants, B. B.**; Johnson, H. J.; Tustison, N. J. (2015). *Neuroinformatics and the Insight ToolKit*. **Frontiers in Neuroinformatics**, 9, 5.
40. Pustina, D.; **Avants, B. B.**; Sperling, M.; Gorniak, R.; He, X.; Doucet, G.; Barnett, P.; Mintzer, S.; Sharan, A.; Tracy, J. (2015). *Predicting the laterality of temporal lobe epilepsy from PET, MRI, and DTI: A multimodal study*. **NeuroImage: Clinical**, 9, 20–31.
41. **Avants, B. B.**; Duda, J. T.; Kilroy, E.; Krasileva, K.; Jann, K.; Kandel, B. T.; Tustison, N. J.; Yan, L.; Jog, M.; Smith, R.; Wang, Y.; Dapretto, M.; Wang, D. J. J. (2015). *The pediatric template of brain perfusion*. **Scientific Data**, 2, 150003.
42. Kandel, B. M.; Wang, D. J. J.; Gee, J. C.; **Avants, B. B.** (2015). *Eigenanatomy: sparse dimensionality reduction for multi-modal medical image analysis*. **Methods**, 73, 43–53.
43. **Avants, B. B.**; Tustison, N. J.; Stauffer, M.; Song, G.; Wu, B.; Gee, J. C. (2014). *The Insight ToolKit image registration framework*. **Frontiers in Neuroinformatics**, 8, 44.
44. **Avants, B. B.**; Libon, D. J.; Rascovsky, K.; Boller, A.; McMillan, C. T.; Massimo, L.; Coslett, H. B.; Chatterjee, A.; Gross, R. G.; Grossman, M. (2014). *Sparse canonical correlation analysis relates network-level atrophy to multivariate cognitive measures in a neurodegenerative population*. **NeuroImage**, 84, 698–711.
45. Tustison, N. J.; Cook, P. A.; Klein, A.; Song, G.; Das, S. R.; Duda, J. T.; Kandel, B. M.; van Strien, N.; Stone, J. R.; Gee, J. C.; **Avants, B. B.** (2014). *Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements*. **NeuroImage**, 99, 166–179.
46. **Avants, B. B.**; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A.; Gee, J. C. (2011). *A reproducible evaluation of ANTs similarity metric performance in brain image registration*. **NeuroImage**, 54(3), 2033–2044.
47. **Avants, B. B.**; Tustison, N. J.; Wu, J.; Cook, P. A.; Gee, J. C. (2011). *An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data*. **Neuroinformatics**, 9(4), 381–400.
48. Murphy, K., ..., Tustison, N.; **Avants, B.**; Gee, J. C., ..., Pluim, J. P. W. (2011). *Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge*. **IEEE Transactions on Medical Imaging**, 30(11), 1901–1920.
49. Tustison, N. J.; **Avants, B. B.**; Cook, P. A.; Zheng, Y.; Egan, A.; Yushkevich, P. A.; Gee, J. C. (2010). *N4ITK: Improved N3 bias correction*. **IEEE Transactions on Medical Imaging**, 29(6), 1310–1320.
50. **Avants, B. B.**; Cook, P. A.; Ungar, L.; Gee, J. C.; Grossman, M. (2010). *Dementia induces correlated reductions in white matter integrity and cortical thickness: A multivariate neuroimaging study with sparse canonical correlation analysis*. **NeuroImage**, 50(3), 1004–1016.
51. Klein, A.; Andersson, J.; Ardekani, B. A.; Ashburner, J.; **Avants, B.**, et al. (2009). *Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration*. **NeuroImage**, 46(3), 786–802.
52. Das, S. R.; **Avants, B. B.**; Grossman, M.; Gee, J. C. (2009). *Registration based cortical thickness measurement*. **NeuroImage**, 45(3), 867–879.
53. **Avants, B. B.**; Epstein, C. L.; Grossman, M.; Gee, J. C. (2008). *Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain*. **Medical Image Analysis**, 12(1), 26–41.
54. **Avants, B. B.**; Schoenemann, P. T.; Gee, J. C. (2006). *Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex*. **Medical Image Analysis**, 10(3), 397–412.
55. **Avants, B.**; Gee, J. (2004). *Geodesic estimation for large deformation anatomical shape averaging and interpolation*. **NeuroImage**, 23(1), S139–S150.

*(Full 140+ journal article list and 25+ conference proceedings available in the PDF and interactive Web CV editions).*