CIT168 Parcellation
This app generates a subject-specific parcellation of subcortical areas using the CIT168 parcellation.
Posts by Collection
apps
White matter anatomy segmentation
An automated segmentation of major white matter tracts from an input whole brain tractography. Utilizes a WMQL-like approach to segment streamlines, as documented in Bullock et al. 2019. Makes extensive use of the wmaTools library.
MAIA Rings Plot
This app computes and plots the degree-based ring averages for microperimetry measurements. It makes use of OCT_scripts. It outputs radar plots, along with a table indicating the returned value for each degree of visual eccentricity.
Tract Density Mask
This app creates a streamline density mask (NIfTI format) for each structure labled in a classification structure and saves it to disk. You can then use this data to compare overlap between tracts, the general course taken, or even cortical intersections (e.g. endpoint mappings).
cvmodes
Academic
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Graduate Student Researcher Representative
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Voting member of the Bloomington Faculty Council (BFC), representing graduate student researchers on all matters before the council, including campus-level policy, resolutions, and development planning. Engaged campus and university administrators on specific issues and standing ad hoc committees.
Member, Research Affairs Committee (RAC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Member of the BFC Research Affairs Committee, representing graduate student researchers on campus research-affairs issues — including COVID impacts, conflict-of-interest management, research disclosures, openaccess policy, and non-tenure-track researchers. Worked with the Office of Research Administration, the Office of the Vice Provost for Research, and other campus stakeholders.
Member, Technology Policy Committee
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Member of the BFC Technology Policy Committee, representing graduate student researchers on technology-implementation issues — including virtual conferencing, email and data platforms, and research-data storage and ownership.
Graduate Teaching Assistant
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences
Graduate teaching assistant across four semesters for courses in research methods and statistics, cognitive neuroscience, and social neuroscience. Led discussion sections, held office hours, and supported grading and classroom management.
Chair, Benefits committee
at Indiana University Bloomington (Bloomington, IN),
Indiana University Graduate and Professional Student Government
at Indiana University Bloomington (Bloomington, IN),
Indiana University Graduate and Professional Student Government
Chair of the Benefits Committee in the IU Graduate & Professional Student Government (GPSG) and member of the GPSG executive committee, advocating for graduate and professional students on compensation, benefits, and professional issues. Managed a team of graduate student representatives and engaged university administrators — including the Dean of the University Graduate School — on policy development and specific concerns.
Summer Research Fellow in the Data Science for the Public Good (DSPG) program, serving as participant lead on two projects: ontology/taxonomy development for Army personnel performance assessments, and systematic valuation of open-source development processes. Produced code and qualitative/quantitative analyses, performed data curation and dataset linking, built visualizations, and managed interns. Presented insights to multiple audiences and led delivery under rapid-production timelines.
Neuroscience Representative
at Indiana University Bloomington (Bloomington, IN),
Graduate and Professional Student Government
at Indiana University Bloomington (Bloomington, IN),
Graduate and Professional Student Government
Elected representative for the Program in Neuroscience to the IU Graduate & Professional Student Government, helping shape and develop resolutions as an active member of the organization.
Undergraduate researcher in the Godwin Lab studying stress and anxiety markers in the brain of a model species (zebrafish). Ran experiments, collected and analyzed data, prepared and processed biological samples, maintained subject stocks, and presented results. Contributed to grant development.
Chief Editor of the NCSU undergraduate research journal, evaluating submissions and providing author feedback, and collaborating with faculty in support of the organization.
Undergraduate teaching assistant for GN 311 (Principles of Genetics): led discussion sections, lectured and reviewed, held office hours, and graded assignments and tests.
Vice President, Future Society Club
at North Carolina State University (Raleigh, NC),
Future Society Club
at North Carolina State University (Raleigh, NC),
Future Society Club
As Vice President of the NCSU Future Society Club, I led meetings, scheduled and organized talks, and managed membership. Meeting topics included technology, science, society, and the interplay between these.
SENS Research Foundation Summer Scholar at the Wake Forest Institute for Regenerative Medicine, characterizing and calibrating the process for producing functional thymic organoids for immune-system revitalization. Assisted with sample production, processing, and analysis, and presented project status and findings.
Graduate Teaching Assistant
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
Graduate teaching assistant for philosophy courses in ethics, introduction to philosophy, political philosophy, and classical philosophy. Led discussion sections, held office hours, and supported grading and classroom management.
Psychology Instructor
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Instructor for an intensive introduction to psychology for academically gifted high-school students (Duke TIP), taught at a college-101 level across the standard first-year topic range. Designed the course and syllabus, delivered instruction, assessed performance, and reported progress.
Undergraduate research assistant in the Hopfinger Lab studying memory and emotion effects on attentional control, using EEG and eye-tracking with the attentional-blink paradigm. Supported experimental design, subject recruitment, data collection, and data management under IRB protocols.
Psychology Teaching Assistant
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Teaching assistant for an intensive introductory psychology course for gifted high-school students (Duke TIP); led daily review sessions and supported grading and classroom management.
Nanotechnology Teaching Assistant
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Teaching assistant for an intensive nanotechnology course for gifted highschool students (Duke TIP); led daily review sessions and supported grading and classroom management.
Pre-baccalaureate research assistant studying Fusarium wilt in melons, exploring genetic hallmarks of susceptibility and resilience. Trained in fieldand bench-based research processes; assisted with sample preparation and PCR/gel-electrophoresis workflows.
Publications
| Title | Date | Venue | Link | Citation |
|---|---|---|---|---|
| A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule | 12-01 2024 | Biological Psychiatry: Cognitive Neuroscience and Neuroimaging | Sretavan, K., Braun, H., Liu, Z., Bullock, D., Palnitkar, T., Patriat, R., Chandrasekaran, J., Brenny, S., Johnson, M. D., Widge, A. S., Harel, N., & Heilbronner, S. R. (2024). A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(12), 1249-1261. https://doi.org/10.1016/j.bpsc.2024.07.008 | |
| brainlife.io: A decentralized and open source cloud platform to support neuroscience research | 06-03 2023 | arXiv | Hayashi, S., Caron, B. A., Heinsfeld, A. S., Vinci-Booher, S., McPherson, B., Bullock, D. N., ... & Pestilli, F. (2023). brainlife. io: A decentralized and open source cloud platform to support neuroscience research. ArXiv.Current Research in Neurobiology, revision under review, https://doi.org/10.48550/arXiv.2306.02183 | |
| The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI | 12-30 2022 | Current Research in Neurobiology | Adriana K. Cushnie, Daniel N. Bullock, Ana M. G. Manea, Wei Tang, Jan Zimmermann, Sarah R.Heilbronner, The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI, Current Research in Neurobiology, in press, https://doi.org/10.1016/j.crneur.2022.100072 | |
| Development of white matter tracts between and within the dorsal and ventral streams | 03-10 2022 | Brain Structure and Function | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2022). Development of white matter tracts between and within the dorsal and ventral streams. Brain Structure and Function, 227(4), 1457-1477. | |
| A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century | 02-15 2022 | Cerebral Cortex | Daniel N Bullock, Elena A Hayday, Mark D Grier, Wei Tang, Franco Pestilli, Sarah R Heilbronner, A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century, Cerebral Cortex, Volume 32, Issue 20, 15 October 2022, Pages 4524–4548, https://doi.org/10.1093/cercor/bhab500 | |
| Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints | 01-15 2022 | Cerebral Cortex | Babo-Rebelo, M., Puce, A., Bullock, D., Hugueville, L., Pestilli, F., Adam, C., ... & George, N. (2022). Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints. Cerebral Cortex, 32(2), 342-366. | |
| Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? | 10-22 2021 | NeuroImage | Schilling, K. G., Rheault, F., Petit, L., Hansen, C. B., Nath, V., Yeh, F. C., ... & Descoteaux, M. (2021). Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?. NeuroImage, 243, 118502. | |
| A model of the development of major white matter pathways within and between ventral and dorsal visual streams | 09-27 2021 | Journal of Vision | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2021). A model of the development of major white matter pathways within and between ventral and dorsal visual streams. Journal of Vision, 21(9), 2698-2698. | |
| Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards | 06-01 2021 | Indiana University ProQuest Dissertations Publishing | Bullock, D. (2021). Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards. | |
| Collegiate athlete brain data for white matter mapping and network neuroscience | 02-11 2021 | Scientific Data | Caron, B., Stuck, R., McPherson, B. et al. Collegiate athlete brain data for white matter mapping and network neuroscience. Sci Data 8, 56 (2021). https://doi.org/10.1038/s41597-021-00823-z | |
| The human endogenous attentional control network includes a ventro-temporal cortical node | 01-15 2021 | Nature Communications | Sani, I., Stemmann, H., Caron, B., Bullock, D., Stemmler, T., Fahle, M., ... & Freiwald, W. A. (2021). The human endogenous attentional control network includes a ventro-temporal cortical node. Nature communications, 12(1), 1-16. | |
| Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation | 01-01 2021 | NeuroImage | Bertò, G., Bullock, D., Astolfi, P., Hayashi, S., Zigiotto, L., Annicchiarico, L., ... & Olivetti, E. (2021). Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation. NeuroImage, 224, 117402. | |
| Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations | 10-13 2020 | Scientific reports | Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F. C., Koudoro, S., ... & Garyfallidis, E. (2020). Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific reports, 10(1), 1-18. | |
| Advanced mapping of the human white matter microstructure better separates elite sports participation | 08-25 2020 | PsyArXiv | Caron, B., Bullock, D., Kitchell, L., McPherson, B. C., Kellar, D. A., Cheng, H., ... & Pestilli, F. (2020). Advanced mapping of the human white matter microstructure better separates elite sports participation. PsyArXiv. | |
| Associative white matter connecting the dorsal and ventral posterior human cortex | 07-24 2019 | Brain Structure and Function | Bullock, D., Takemura, H., Caiafa, C.F. et al. Associative white matter connecting the dorsal and ventral posterior human cortex. Brain Struct Funct 224, 2631–2660 (2019). https://doi.org/10.1007/s00429-019-01907-8 | |
| The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services | 05-23 2019 | Scientific data | Avesani, P., McPherson, B., Hayashi, S., Caiafa, C. F., Henschel, R., Garyfallidis, E., ... & Pestilli, F. (2019). The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Scientific data, 6(1), 1-13. | |
| Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation | 04-08 2019 | 2019 IEEE 16th International Symposium on Biomedical Imaging | Bertò, G., Avesani, P., Pestilli, F., Bullock, D., Caron, B., & Olivetti, E. (2019, April). Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation. In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) (pp. 135-138). IEEE. | |
| Shape analysis of white matter tracts via the Laplace-Beltrami spectrum | 09-20 2018 | International Workshop on Shape in Medical Imaging | Kitchell, L., Bullock, D., Hayashi, S., & Pestilli, F. (2018, September). Shape analysis of white matter tracts via the Laplace-Beltrami spectrum. In International Workshop on Shape in Medical Imaging (pp. 195-206). Springer, Cham. | |
| Oryza sativa (japonica cultivar-group) clone dan18 putative D-type cyclin gene, partial cds. | 06-18 2004 | NIH NCBI GenBank | N/A |
Presentations and Posters
| Title | Year | Venue | Type | Authors |
|---|---|---|---|---|
| TRX: A community-oriented tractography file format | 2022 | Organization for Human Brain Mapping | Presentation | Francois Rheault, Valérie Hayot-Sassonb, Robert E. Smith, Christopher Rordend, Jacques-Donald Tourniere, Eleftherios Garyfallidis, Fang-Cheng Yehh, Christopher J. Markiewicz, Matthew Brett, Ben Jeurissenk, Paul A. Taylor, D. Baran Aydogan, Derek A. Pisner, Serge Koudorof, Soichi Hayashi, Daniel Haehn, Steve Pieper, Daniel Bullock, Emanuele Olivetti, Jean-Christophe Houde, Marc-Alexandre Côté, Flavio Dell’Acqua, Alexander Leemansy, Maxime Descoteaux, Bennett Landman, Franco Pestilli, Ariel Rokem |
| The relationship between the microstructure of vertical white matter pathways and behavior in early elementary school children | 2019 | Cognitive Development Society Biennial Conference | Presentation | Sophia Vinci-Booher, Daniel Bullock, Bradley Caron, Brent McPherson, Karen H. James, Franco Pestilli |
| Making network neuroscience more findable, accessible, interoperable, and reusable via brainlife.io | 2019 | Organization for Human Brain Mapping | Poster | Brent McPherson, Daniel Bullock, Bradley Caron, Lindsey Kitchell, Soichi Hayashi, Josh Faskowitz, Olaf Sporns, Richard Betzel, Paolo Avesani, Franco Pestilli |
| Orchestrating Cloud Networks for Discoverable, Accessible, Interoperable, and Reusable Neuroscience | 2019 | Organization for Human Brain Mapping | Poster | Soichi Hayashi, Lindsey Kitchell, Brent McPherson, Bradley Caron, Daniel Bullock, Paolo Avesani, Robert Henschel, Eleftherios Garyfallidis, Lei Wang, Ivo Dinov, Franco Pestilli |
| Segmentation of White Matter Bundles as Anatomically-Informed Multiple Linear Assignment Problems | 2019 | Organization for Human Brain Mapping | Poster | Giulia Bertó, Paolo Avesani, Franco Pestilli, Daniel Bullock, Bradley Caron, Emanuele Olivetti |
| Microstructural Differences in Both the White- and Gray-matter Tissue Distinguish Athletes Groups | 2019 | Organization for Human Brain Mapping | Poster | Bradley Caron, Lindsey Kitchell, Brent McPherson, Daniel Bullock, Soichi Hayashi, Derek Keller, Hu Cheng, Sharlene Newman, Nicholas Port, Franco Pestilli |
| White Matter Mapping on brainlife.io: A Findable, Accessible, Interoperable, Reusable Implementation | 2019 | Organization for Human Brain Mapping | Poster | Daniel Bullock, Soichi Hayashi, Lindsey Kitchell, Brent McPherson, Bradley Caron, Franco Pestilli |
| Advanced White Matter Mapping in the Subconcussive Brain | 2018 | AAN Sports Concussion Conference, Big Ten-Ivy League TBI Research Consortium Summit | Poster | Bradley Caron, Derek Keller, Lindsey Kitchell, Brent McPherson, Daniel Bullock, Soichi Hayashi, Hu Cheng, Sharlene Newman, Nicholas Port, Franco Pestilli |
| White Matter Tracts as Classification Features for Machine Learning | 2018 | Midwest Cognitive Science Conference | Poster | Lindsey Kitchell, Daniel Bullock, Soichi Hayashis, Franco Pestilli |
| Clarifying the anatomical organization and cortical projections of multiple major white matter tracts associating the human temporal and parietal lobes | 2018 | Society for Neuroscience | Poster | Daniel Bullock, Hiromasa Takemura, Cesar F. Caiafa, Lindsey Kitchell, Brent McPherson, Bradley Caron, Franco Pestilli |
| Shape Analysis of White Matter Tracts via the Laplace-Beltrami Spectrum | 2018 | Shape in Medical Imaging Workshop at MICCAI | Poster | Lindsey Kitchell, Daniel Bullock, Soichi Hayashi, Franco Pestilli |
| Multidimensional Encoding of Structural Brain Connectomes: Building Quantitative Biological Networks with Preserved Edge Properties to Study the Visual White Matter and Brain Aging | 2017 | Network Science, Society for Neuroscience | Presentation | Franco Pestilli, Brent McPherson, Daniel Bullock, Andrea Avena-Koenigsberger, Joey Contreras, Cesar Caiafa, Olaf Sporns, Andrew Saykin |
| Evidence for a Direct White Matter Tract Between Human Parietal and Inferotemporal Cortex | 2016 | Association for Psychological Science | Poster | Daniel Bullock, Julian Moehlen, Brent McPherson, Cesar Caiafa, Hiromasa Takemura, Franco Pestilli |
| The Posterior Associative White Matter Network Connecting Temporal and Parietal Human Brain Lobes | 2016 | Society for Neuroscience | Poster | Daniel Bullock, Hiromasa Takemura, Cesar F. Caiafa, Franco Pestilli |
| Localization of Differential Neuron Activity in Zebrafish with Distinct Stress Dispositions using c-fos Activity | 2014 | State of North Carolina Undergraduate Research and Creativity Symposium, NC State Summer Undergraduate Research Symposium, NCSU Spring Biology Capstone Symposium | Poster | Daniel Bullock, Ryan Wong, John Godwin |
| Towards Engineered Thymic Tissue | 2013 | Wake Forest Institute for Regenerative Medicine Research Day | Poster and Presentation | Daniel Bullock, Sookwon Ryu, Ashis Mondal, James Yoo, John Jackson |
Awards, Fellowships and Grants
| Title and Source | Type | Duration | Link |
|---|---|---|---|
| AAAS Science and Technology Policy Fellow at National Science Foundation (NSF) via Association For the Advancement of Science (AAAS) | Fellowship | 8 / 2022 to 8 / 2024 | |
| Neuroimaging NIH Postdoctoral Training Fellowship (T32) at University of Minnesota via National Institute of Biomedical Imaging and Bioengineering (NIBIB) | Fellowship | 1 / 2022 to 8 / 2022 | |
| Data Science for the Public Good (DSPG) Young Scholars program at University of Virginia Biocomplexity Institute via Data Science for the Public Good (DSPG) | Fellowship | 6 / 2020 to 8 / 2020 | |
| Clinical Translational NIMH Predoctoral Training Fellowship (T32) at Indiana University Bloomington, Department of Psychological and Brain Sciences, Clinical Science Program via National Institute of Mental Health (NIMH) | Fellowship | 8 / 2018 to 5 / 2020 | |
| UW eScience Institute Neurohackacademy Summer Scholar at University of Washington eScience Institute via NeuroHackAcademy | Fellowship | 8 / 2019 to 9 / 2019 | |
| Center for Information and Neural Networks (CiNet) Training Fellowship at Center for Information and Neural Networks (CiNet) via National Institute of Information and Communications Technology (NICT) | Fellowship | 12 / 2016 to 1 / 2017 | |
| Psychological and Brain Sciences departmental fellowship at Indiana University Bloomington via Department of Psychological and Brain Sciences | Fellowship | 8 / 2015 to 5 / 2017 | |
| SENS Research Foundation Summer Scholar at Wake Forest Institute for Regenerative Medicine via Sens Research Foundation | Fellowship | 6 / 2013 to 8 / 2013 | |
| Wake Forest Institute for Regenerative Medicine Summer Scholar at Wake Forest University School of Medicine via Wake Forest Institute for Regenerative Medicine | Fellowship | 6 / 2013 to 8 / 2013 | |
| NCSU Undergraduate Research Grant at North Carolina State University via Office of Undergraduate Research | Grant | 1 / 2013 to 6 / 2013, & 1 / 2014 to 6 / 2014 |
Arpah
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Federal
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
Technical skills: Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Platform Design
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Technical skills: Python, Linux, Git, XML, JSON, Big Data, Data Scraping, Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Jupyter Notebooks, Open-Source Software
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Technical skills: Python, Linux, Git, Docker, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, Containerization, Open-Source Development, Open-Source Software, High Performance Computing (HPC), Data Visualization, Testing and Debugging, Coordinated/Collaborative Testing and Debugging, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Technical skills: Python, Matlab, JSON, Markdown, Linux, Git, Neuroimaging Software Packages, Brain Imaging Data Structure (BIDS), Neuroimaging, Neuroimaging Data Structures, Neuroimaging Data Processing, 3-D Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Docker, Containerization, High Performance Computing (HPC), Continuous Integration and Continuous Delivery/Deployment (CI/CD), Testing and Debugging, Collaborative Development, Data Visualization, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Technical skills: Python, Matlab, Linux, Git, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Structures, Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, High Performance Computing (HPC), Data Visualization, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Full
Whether conducting research, developing software, working with data, or advancing policy, my work aims to improve the efficiency and impact of the collective activities of the broader scientific community. Across the entire spectrum of scientific endeavors--all the way from bench work to policy and even philosophical conceptualization--I strive to foster the virtuous cycle of insight formation, validation, and extension. In our modern era of research these priorities demand a critical focus on all levels of the socio-technical processes associated with how we produce, interact, store, share, and use data. My work is dedicated to the advancement of these processes, and the development of tools and practices that support the scientific community in these endeavors.
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
Technical skills: Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Platform Design
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Technical skills: Python, Linux, Git, XML, JSON, Big Data, Data Scraping, Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Jupyter Notebooks, Open-Source Software
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Technical skills: Python, Linux, Git, Docker, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, Containerization, Open-Source Development, Open-Source Software, High Performance Computing (HPC), Data Visualization, Testing and Debugging, Coordinated/Collaborative Testing and Debugging, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Technical skills: Python, Matlab, JSON, Markdown, Linux, Git, Neuroimaging Software Packages, Brain Imaging Data Structure (BIDS), Neuroimaging, Neuroimaging Data Structures, Neuroimaging Data Processing, 3-D Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Docker, Containerization, High Performance Computing (HPC), Continuous Integration and Continuous Delivery/Deployment (CI/CD), Testing and Debugging, Collaborative Development, Data Visualization, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Technical skills: Python, Matlab, Linux, Git, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Structures, Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, High Performance Computing (HPC), Data Visualization, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Graduate Student Researcher Representative
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Voting member of the Bloomington Faculty Council (BFC), representing graduate student researchers on all matters before the council, including campus-level policy, resolutions, and development planning. Engaged campus and university administrators on specific issues and standing ad hoc committees.
Non-technical skills: Advocacy, Constituency Engagement, Constituency Representation, Rapport Building, Institutional Advocacy, Institutional Engagement, University Policy, University Development Strategy, Public Speaking
Member, Research Affairs Committee (RAC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Member of the BFC Research Affairs Committee, representing graduate student researchers on campus research-affairs issues — including COVID impacts, conflict-of-interest management, research disclosures, openaccess policy, and non-tenure-track researchers. Worked with the Office of Research Administration, the Office of the Vice Provost for Research, and other campus stakeholders.
Non-technical skills: Constituency Representation, Rapport Building, Institutional Advocacy, Institutional Engagement, Research Policy, Research Ethics, Research Staffing, Conflict of Interest Management, Institutional Research Policy, Open Access Policy
Member, Technology Policy Committee
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
at Indiana University Bloomington (Bloomington, IN),
Bloomington Faculty Council (BFC)
Member of the BFC Technology Policy Committee, representing graduate student researchers on technology-implementation issues — including virtual conferencing, email and data platforms, and research-data storage and ownership.
Non-technical skills: Advocacy, Technology Policy Development, Research Data Policy, Institutional Engagement
Graduate Teaching Assistant
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences
Graduate teaching assistant across four semesters for courses in research methods and statistics, cognitive neuroscience, and social neuroscience. Led discussion sections, held office hours, and supported grading and classroom management.
Non-technical skills: Performance Assessment, Classroom Management, Discussion Section Coordination, Individualized Instruction, Feedback Provision
Chair, Benefits committee
at Indiana University Bloomington (Bloomington, IN),
Indiana University Graduate and Professional Student Government
at Indiana University Bloomington (Bloomington, IN),
Indiana University Graduate and Professional Student Government
Chair of the Benefits Committee in the IU Graduate & Professional Student Government (GPSG) and member of the GPSG executive committee, advocating for graduate and professional students on compensation, benefits, and professional issues. Managed a team of graduate student representatives and engaged university administrators — including the Dean of the University Graduate School — on policy development and specific concerns.
Non-technical skills: Leadership, Committee Management, Advocacy, Team Management, Human Resources and Benefits Policy, Stakeholder Engagement, Institutional Engagement
Summer Research Fellow in the Data Science for the Public Good (DSPG) program, serving as participant lead on two projects: ontology/taxonomy development for Army personnel performance assessments, and systematic valuation of open-source development processes. Produced code and qualitative/quantitative analyses, performed data curation and dataset linking, built visualizations, and managed interns. Presented insights to multiple audiences and led delivery under rapid-production timelines.
Technical skills: Software Development, Web Development, Data Science, Data Curation, Dataset Quality Assessment, Data Visualization, Python, Git, SQL
Non-technical skills: Presentation Development and Delivery, Project Management, Team Management, Mentorship, Report Development, Stakeholder Engagement, Problem Scoping
Non-technical skills: Presentation Development and Delivery, Project Management, Team Management, Mentorship, Report Development, Stakeholder Engagement, Problem Scoping
Neuroscience Representative
at Indiana University Bloomington (Bloomington, IN),
Graduate and Professional Student Government
at Indiana University Bloomington (Bloomington, IN),
Graduate and Professional Student Government
Elected representative for the Program in Neuroscience to the IU Graduate & Professional Student Government, helping shape and develop resolutions as an active member of the organization.
Non-technical skills: Representation, Resolution Development, Public Speaking, Robert's Rules of Order
Undergraduate researcher in the Godwin Lab studying stress and anxiety markers in the brain of a model species (zebrafish). Ran experiments, collected and analyzed data, prepared and processed biological samples, maintained subject stocks, and presented results. Contributed to grant development.
Technical skills: Behavioral Testing, Movement Tracking Analysis, Cryosectioning, Microscopy, In-situ Hybridization (ISH), DNA/RNA Extraction, Protocol Optimization, Movement Tracking Data Processing, Subject Monitoring and Maintenance
Non-technical skills: Grant Writing, Science Communication, Research Review, Article Summary and Discussion, Resource Monitoring and Management
Non-technical skills: Grant Writing, Science Communication, Research Review, Article Summary and Discussion, Resource Monitoring and Management
Chief Editor of the NCSU undergraduate research journal, evaluating submissions and providing author feedback, and collaborating with faculty in support of the organization.
Non-technical skills: Research Article Review, Feedback Provision, Manuscript Revision
Undergraduate teaching assistant for GN 311 (Principles of Genetics): led discussion sections, lectured and reviewed, held office hours, and graded assignments and tests.
Non-technical skills: Grading, Classroom Management, Discussion Section Coordination, Individualized Instruction
Vice President, Future Society Club
at North Carolina State University (Raleigh, NC),
Future Society Club
at North Carolina State University (Raleigh, NC),
Future Society Club
As Vice President of the NCSU Future Society Club, I led meetings, scheduled and organized talks, and managed membership. Meeting topics included technology, science, society, and the interplay between these.
Non-technical skills: Leadership, Event Coordination, Membership Management, Discussion Facilitation, Organizational Continuity and Preservation
SENS Research Foundation Summer Scholar at the Wake Forest Institute for Regenerative Medicine, characterizing and calibrating the process for producing functional thymic organoids for immune-system revitalization. Assisted with sample production, processing, and analysis, and presented project status and findings.
Technical skills: Tissue Extraction, Tissue Culture, Cell Culturing, Cryosectioning, Advanced Microscopy, Immunofluorescence, PCR, Gel Electrophoresis
Non-technical skills: Team Research, Team Science, Biomedical Industry Research and Development, Research Review, Report Development, Multi-stakeholder Reporting and Communication, Resource Monitoring and Management
Non-technical skills: Team Research, Team Science, Biomedical Industry Research and Development, Research Review, Report Development, Multi-stakeholder Reporting and Communication, Resource Monitoring and Management
Graduate Teaching Assistant
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
Graduate teaching assistant for philosophy courses in ethics, introduction to philosophy, political philosophy, and classical philosophy. Led discussion sections, held office hours, and supported grading and classroom management.
Non-technical skills: Performance Assessment, Classroom Management, Discussion Section Coordination, Individualized Instruction, Feedback Provision
Psychology Instructor
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Instructor for an intensive introduction to psychology for academically gifted high-school students (Duke TIP), taught at a college-101 level across the standard first-year topic range. Designed the course and syllabus, delivered instruction, assessed performance, and reported progress.
Non-technical skills: Course Design, Syllabus Formation, Instruction, Performance Assessment, Progress Reporting, Classroom Management
Undergraduate research assistant in the Hopfinger Lab studying memory and emotion effects on attentional control, using EEG and eye-tracking with the attentional-blink paradigm. Supported experimental design, subject recruitment, data collection, and data management under IRB protocols.
Technical skills: Experimental Design, Subject Recruitment, Behavioral Testing, EEG, Eye Tracking, Data Management, Data Science, Data Curation
Non-technical skills: Research Ethics, Science Communication, IRB Protocols
Non-technical skills: Research Ethics, Science Communication, IRB Protocols
Psychology Teaching Assistant
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Teaching assistant for an intensive introductory psychology course for gifted high-school students (Duke TIP); led daily review sessions and supported grading and classroom management.
Non-technical skills: Grading, Classroom Management, Review session Leadership
Nanotechnology Teaching Assistant
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
at Duke University Talent Identification Program (Durham, NC),
Duke University Talent Identification Program
Teaching assistant for an intensive nanotechnology course for gifted highschool students (Duke TIP); led daily review sessions and supported grading and classroom management.
Non-technical skills: Grading, Classroom Management, Review session Leadership
Pre-baccalaureate research assistant studying Fusarium wilt in melons, exploring genetic hallmarks of susceptibility and resilience. Trained in fieldand bench-based research processes; assisted with sample preparation and PCR/gel-electrophoresis workflows.
Technical skills: PCR, Gel Electrophoresis, Sample Preparation
Non-technical skills: Manuscript Development, Research Article Review
Non-technical skills: Manuscript Development, Research Article Review
Publications
| Title | Date | Venue | Link | Citation |
|---|---|---|---|---|
| A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule | 12-01 2024 | Biological Psychiatry: Cognitive Neuroscience and Neuroimaging | Sretavan, K., Braun, H., Liu, Z., Bullock, D., Palnitkar, T., Patriat, R., Chandrasekaran, J., Brenny, S., Johnson, M. D., Widge, A. S., Harel, N., & Heilbronner, S. R. (2024). A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(12), 1249-1261. https://doi.org/10.1016/j.bpsc.2024.07.008 | |
| brainlife.io: A decentralized and open source cloud platform to support neuroscience research | 06-03 2023 | arXiv | Hayashi, S., Caron, B. A., Heinsfeld, A. S., Vinci-Booher, S., McPherson, B., Bullock, D. N., ... & Pestilli, F. (2023). brainlife. io: A decentralized and open source cloud platform to support neuroscience research. ArXiv.Current Research in Neurobiology, revision under review, https://doi.org/10.48550/arXiv.2306.02183 | |
| The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI | 12-30 2022 | Current Research in Neurobiology | Adriana K. Cushnie, Daniel N. Bullock, Ana M. G. Manea, Wei Tang, Jan Zimmermann, Sarah R.Heilbronner, The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI, Current Research in Neurobiology, in press, https://doi.org/10.1016/j.crneur.2022.100072 | |
| Development of white matter tracts between and within the dorsal and ventral streams | 03-10 2022 | Brain Structure and Function | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2022). Development of white matter tracts between and within the dorsal and ventral streams. Brain Structure and Function, 227(4), 1457-1477. | |
| A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century | 02-15 2022 | Cerebral Cortex | Daniel N Bullock, Elena A Hayday, Mark D Grier, Wei Tang, Franco Pestilli, Sarah R Heilbronner, A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century, Cerebral Cortex, Volume 32, Issue 20, 15 October 2022, Pages 4524–4548, https://doi.org/10.1093/cercor/bhab500 | |
| Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints | 01-15 2022 | Cerebral Cortex | Babo-Rebelo, M., Puce, A., Bullock, D., Hugueville, L., Pestilli, F., Adam, C., ... & George, N. (2022). Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints. Cerebral Cortex, 32(2), 342-366. | |
| Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? | 10-22 2021 | NeuroImage | Schilling, K. G., Rheault, F., Petit, L., Hansen, C. B., Nath, V., Yeh, F. C., ... & Descoteaux, M. (2021). Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?. NeuroImage, 243, 118502. | |
| A model of the development of major white matter pathways within and between ventral and dorsal visual streams | 09-27 2021 | Journal of Vision | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2021). A model of the development of major white matter pathways within and between ventral and dorsal visual streams. Journal of Vision, 21(9), 2698-2698. | |
| Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards | 06-01 2021 | Indiana University ProQuest Dissertations Publishing | Bullock, D. (2021). Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards. | |
| Collegiate athlete brain data for white matter mapping and network neuroscience | 02-11 2021 | Scientific Data | Caron, B., Stuck, R., McPherson, B. et al. Collegiate athlete brain data for white matter mapping and network neuroscience. Sci Data 8, 56 (2021). https://doi.org/10.1038/s41597-021-00823-z | |
| The human endogenous attentional control network includes a ventro-temporal cortical node | 01-15 2021 | Nature Communications | Sani, I., Stemmann, H., Caron, B., Bullock, D., Stemmler, T., Fahle, M., ... & Freiwald, W. A. (2021). The human endogenous attentional control network includes a ventro-temporal cortical node. Nature communications, 12(1), 1-16. | |
| Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation | 01-01 2021 | NeuroImage | Bertò, G., Bullock, D., Astolfi, P., Hayashi, S., Zigiotto, L., Annicchiarico, L., ... & Olivetti, E. (2021). Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation. NeuroImage, 224, 117402. | |
| Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations | 10-13 2020 | Scientific reports | Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F. C., Koudoro, S., ... & Garyfallidis, E. (2020). Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific reports, 10(1), 1-18. | |
| Advanced mapping of the human white matter microstructure better separates elite sports participation | 08-25 2020 | PsyArXiv | Caron, B., Bullock, D., Kitchell, L., McPherson, B. C., Kellar, D. A., Cheng, H., ... & Pestilli, F. (2020). Advanced mapping of the human white matter microstructure better separates elite sports participation. PsyArXiv. | |
| Associative white matter connecting the dorsal and ventral posterior human cortex | 07-24 2019 | Brain Structure and Function | Bullock, D., Takemura, H., Caiafa, C.F. et al. Associative white matter connecting the dorsal and ventral posterior human cortex. Brain Struct Funct 224, 2631–2660 (2019). https://doi.org/10.1007/s00429-019-01907-8 | |
| The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services | 05-23 2019 | Scientific data | Avesani, P., McPherson, B., Hayashi, S., Caiafa, C. F., Henschel, R., Garyfallidis, E., ... & Pestilli, F. (2019). The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Scientific data, 6(1), 1-13. | |
| Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation | 04-08 2019 | 2019 IEEE 16th International Symposium on Biomedical Imaging | Bertò, G., Avesani, P., Pestilli, F., Bullock, D., Caron, B., & Olivetti, E. (2019, April). Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation. In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) (pp. 135-138). IEEE. | |
| Shape analysis of white matter tracts via the Laplace-Beltrami spectrum | 09-20 2018 | International Workshop on Shape in Medical Imaging | Kitchell, L., Bullock, D., Hayashi, S., & Pestilli, F. (2018, September). Shape analysis of white matter tracts via the Laplace-Beltrami spectrum. In International Workshop on Shape in Medical Imaging (pp. 195-206). Springer, Cham. | |
| Oryza sativa (japonica cultivar-group) clone dan18 putative D-type cyclin gene, partial cds. | 06-18 2004 | NIH NCBI GenBank | N/A |
Presentations and Posters
| Title | Year | Venue | Type | Authors |
|---|---|---|---|---|
| TRX: A community-oriented tractography file format | 2022 | Organization for Human Brain Mapping | Presentation | Francois Rheault, Valérie Hayot-Sassonb, Robert E. Smith, Christopher Rordend, Jacques-Donald Tourniere, Eleftherios Garyfallidis, Fang-Cheng Yehh, Christopher J. Markiewicz, Matthew Brett, Ben Jeurissenk, Paul A. Taylor, D. Baran Aydogan, Derek A. Pisner, Serge Koudorof, Soichi Hayashi, Daniel Haehn, Steve Pieper, Daniel Bullock, Emanuele Olivetti, Jean-Christophe Houde, Marc-Alexandre Côté, Flavio Dell’Acqua, Alexander Leemansy, Maxime Descoteaux, Bennett Landman, Franco Pestilli, Ariel Rokem |
| The relationship between the microstructure of vertical white matter pathways and behavior in early elementary school children | 2019 | Cognitive Development Society Biennial Conference | Presentation | Sophia Vinci-Booher, Daniel Bullock, Bradley Caron, Brent McPherson, Karen H. James, Franco Pestilli |
| Making network neuroscience more findable, accessible, interoperable, and reusable via brainlife.io | 2019 | Organization for Human Brain Mapping | Poster | Brent McPherson, Daniel Bullock, Bradley Caron, Lindsey Kitchell, Soichi Hayashi, Josh Faskowitz, Olaf Sporns, Richard Betzel, Paolo Avesani, Franco Pestilli |
| Orchestrating Cloud Networks for Discoverable, Accessible, Interoperable, and Reusable Neuroscience | 2019 | Organization for Human Brain Mapping | Poster | Soichi Hayashi, Lindsey Kitchell, Brent McPherson, Bradley Caron, Daniel Bullock, Paolo Avesani, Robert Henschel, Eleftherios Garyfallidis, Lei Wang, Ivo Dinov, Franco Pestilli |
| Segmentation of White Matter Bundles as Anatomically-Informed Multiple Linear Assignment Problems | 2019 | Organization for Human Brain Mapping | Poster | Giulia Bertó, Paolo Avesani, Franco Pestilli, Daniel Bullock, Bradley Caron, Emanuele Olivetti |
| Microstructural Differences in Both the White- and Gray-matter Tissue Distinguish Athletes Groups | 2019 | Organization for Human Brain Mapping | Poster | Bradley Caron, Lindsey Kitchell, Brent McPherson, Daniel Bullock, Soichi Hayashi, Derek Keller, Hu Cheng, Sharlene Newman, Nicholas Port, Franco Pestilli |
| White Matter Mapping on brainlife.io: A Findable, Accessible, Interoperable, Reusable Implementation | 2019 | Organization for Human Brain Mapping | Poster | Daniel Bullock, Soichi Hayashi, Lindsey Kitchell, Brent McPherson, Bradley Caron, Franco Pestilli |
| Advanced White Matter Mapping in the Subconcussive Brain | 2018 | AAN Sports Concussion Conference, Big Ten-Ivy League TBI Research Consortium Summit | Poster | Bradley Caron, Derek Keller, Lindsey Kitchell, Brent McPherson, Daniel Bullock, Soichi Hayashi, Hu Cheng, Sharlene Newman, Nicholas Port, Franco Pestilli |
| White Matter Tracts as Classification Features for Machine Learning | 2018 | Midwest Cognitive Science Conference | Poster | Lindsey Kitchell, Daniel Bullock, Soichi Hayashis, Franco Pestilli |
| Clarifying the anatomical organization and cortical projections of multiple major white matter tracts associating the human temporal and parietal lobes | 2018 | Society for Neuroscience | Poster | Daniel Bullock, Hiromasa Takemura, Cesar F. Caiafa, Lindsey Kitchell, Brent McPherson, Bradley Caron, Franco Pestilli |
| Shape Analysis of White Matter Tracts via the Laplace-Beltrami Spectrum | 2018 | Shape in Medical Imaging Workshop at MICCAI | Poster | Lindsey Kitchell, Daniel Bullock, Soichi Hayashi, Franco Pestilli |
| Multidimensional Encoding of Structural Brain Connectomes: Building Quantitative Biological Networks with Preserved Edge Properties to Study the Visual White Matter and Brain Aging | 2017 | Network Science, Society for Neuroscience | Presentation | Franco Pestilli, Brent McPherson, Daniel Bullock, Andrea Avena-Koenigsberger, Joey Contreras, Cesar Caiafa, Olaf Sporns, Andrew Saykin |
| Evidence for a Direct White Matter Tract Between Human Parietal and Inferotemporal Cortex | 2016 | Association for Psychological Science | Poster | Daniel Bullock, Julian Moehlen, Brent McPherson, Cesar Caiafa, Hiromasa Takemura, Franco Pestilli |
| The Posterior Associative White Matter Network Connecting Temporal and Parietal Human Brain Lobes | 2016 | Society for Neuroscience | Poster | Daniel Bullock, Hiromasa Takemura, Cesar F. Caiafa, Franco Pestilli |
| Localization of Differential Neuron Activity in Zebrafish with Distinct Stress Dispositions using c-fos Activity | 2014 | State of North Carolina Undergraduate Research and Creativity Symposium, NC State Summer Undergraduate Research Symposium, NCSU Spring Biology Capstone Symposium | Poster | Daniel Bullock, Ryan Wong, John Godwin |
| Towards Engineered Thymic Tissue | 2013 | Wake Forest Institute for Regenerative Medicine Research Day | Poster and Presentation | Daniel Bullock, Sookwon Ryu, Ashis Mondal, James Yoo, John Jackson |
Awards, Fellowships and Grants
| Title and Source | Type | Duration | Link |
|---|---|---|---|
| AAAS Science and Technology Policy Fellow at National Science Foundation (NSF) via Association For the Advancement of Science (AAAS) | Fellowship | 8 / 2022 to 8 / 2024 | |
| Neuroimaging NIH Postdoctoral Training Fellowship (T32) at University of Minnesota via National Institute of Biomedical Imaging and Bioengineering (NIBIB) | Fellowship | 1 / 2022 to 8 / 2022 | |
| Data Science for the Public Good (DSPG) Young Scholars program at University of Virginia Biocomplexity Institute via Data Science for the Public Good (DSPG) | Fellowship | 6 / 2020 to 8 / 2020 | |
| Clinical Translational NIMH Predoctoral Training Fellowship (T32) at Indiana University Bloomington, Department of Psychological and Brain Sciences, Clinical Science Program via National Institute of Mental Health (NIMH) | Fellowship | 8 / 2018 to 5 / 2020 | |
| UW eScience Institute Neurohackacademy Summer Scholar at University of Washington eScience Institute via NeuroHackAcademy | Fellowship | 8 / 2019 to 9 / 2019 | |
| Center for Information and Neural Networks (CiNet) Training Fellowship at Center for Information and Neural Networks (CiNet) via National Institute of Information and Communications Technology (NICT) | Fellowship | 12 / 2016 to 1 / 2017 | |
| Psychological and Brain Sciences departmental fellowship at Indiana University Bloomington via Department of Psychological and Brain Sciences | Fellowship | 8 / 2015 to 5 / 2017 | |
| SENS Research Foundation Summer Scholar at Wake Forest Institute for Regenerative Medicine via Sens Research Foundation | Fellowship | 6 / 2013 to 8 / 2013 | |
| Wake Forest Institute for Regenerative Medicine Summer Scholar at Wake Forest University School of Medicine via Wake Forest Institute for Regenerative Medicine | Fellowship | 6 / 2013 to 8 / 2013 | |
| NCSU Undergraduate Research Grant at North Carolina State University via Office of Undergraduate Research | Grant | 1 / 2013 to 6 / 2013, & 1 / 2014 to 6 / 2014 |
Industry_general
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
Technical skills: Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Platform Design
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Technical skills: Python, Linux, Git, XML, JSON, Big Data, Data Scraping, Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Jupyter Notebooks, Open-Source Software
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Technical skills: Python, Linux, Git, Docker, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, Containerization, Open-Source Development, Open-Source Software, High Performance Computing (HPC), Data Visualization, Testing and Debugging, Coordinated/Collaborative Testing and Debugging, Statistical Analysis, Advanced Statistical Analysis
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Technical skills: Python, Matlab, JSON, Markdown, Linux, Git, Neuroimaging Software Packages, Brain Imaging Data Structure (BIDS), Neuroimaging, Neuroimaging Data Structures, Neuroimaging Data Processing, 3-D Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Docker, Containerization, High Performance Computing (HPC), Continuous Integration and Continuous Delivery/Deployment (CI/CD), Testing and Debugging, Collaborative Development, Data Visualization, Advanced Statistical Analysis
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Technical skills: Python, Matlab, Linux, Git, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Structures, Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, High Performance Computing (HPC), Data Visualization, Statistical Analysis, Advanced Statistical Analysis
Industry_research
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
Technical skills: Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Platform Design
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Technical skills: Python, Linux, Git, XML, JSON, Big Data, Data Scraping, Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Jupyter Notebooks, Open-Source Software
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Technical skills: Python, Linux, Git, Docker, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, Containerization, Open-Source Development, Open-Source Software, High Performance Computing (HPC), Data Visualization, Testing and Debugging, Coordinated/Collaborative Testing and Debugging, Statistical Analysis, Advanced Statistical Analysis
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Technical skills: Python, Matlab, JSON, Markdown, Linux, Git, Neuroimaging Software Packages, Brain Imaging Data Structure (BIDS), Neuroimaging, Neuroimaging Data Structures, Neuroimaging Data Processing, 3-D Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Docker, Containerization, High Performance Computing (HPC), Continuous Integration and Continuous Delivery/Deployment (CI/CD), Testing and Debugging, Collaborative Development, Data Visualization, Advanced Statistical Analysis
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Technical skills: Python, Matlab, Linux, Git, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Structures, Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, High Performance Computing (HPC), Data Visualization, Statistical Analysis, Advanced Statistical Analysis
Publications
| Title | Date | Venue | Link | Citation |
|---|---|---|---|---|
| A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule | 12-01 2024 | Biological Psychiatry: Cognitive Neuroscience and Neuroimaging | Sretavan, K., Braun, H., Liu, Z., Bullock, D., Palnitkar, T., Patriat, R., Chandrasekaran, J., Brenny, S., Johnson, M. D., Widge, A. S., Harel, N., & Heilbronner, S. R. (2024). A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(12), 1249-1261. https://doi.org/10.1016/j.bpsc.2024.07.008 | |
| brainlife.io: A decentralized and open source cloud platform to support neuroscience research | 06-03 2023 | arXiv | Hayashi, S., Caron, B. A., Heinsfeld, A. S., Vinci-Booher, S., McPherson, B., Bullock, D. N., ... & Pestilli, F. (2023). brainlife. io: A decentralized and open source cloud platform to support neuroscience research. ArXiv.Current Research in Neurobiology, revision under review, https://doi.org/10.48550/arXiv.2306.02183 | |
| The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI | 12-30 2022 | Current Research in Neurobiology | Adriana K. Cushnie, Daniel N. Bullock, Ana M. G. Manea, Wei Tang, Jan Zimmermann, Sarah R.Heilbronner, The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI, Current Research in Neurobiology, in press, https://doi.org/10.1016/j.crneur.2022.100072 | |
| Development of white matter tracts between and within the dorsal and ventral streams | 03-10 2022 | Brain Structure and Function | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2022). Development of white matter tracts between and within the dorsal and ventral streams. Brain Structure and Function, 227(4), 1457-1477. | |
| A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century | 02-15 2022 | Cerebral Cortex | Daniel N Bullock, Elena A Hayday, Mark D Grier, Wei Tang, Franco Pestilli, Sarah R Heilbronner, A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century, Cerebral Cortex, Volume 32, Issue 20, 15 October 2022, Pages 4524–4548, https://doi.org/10.1093/cercor/bhab500 | |
| Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints | 01-15 2022 | Cerebral Cortex | Babo-Rebelo, M., Puce, A., Bullock, D., Hugueville, L., Pestilli, F., Adam, C., ... & George, N. (2022). Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints. Cerebral Cortex, 32(2), 342-366. | |
| Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? | 10-22 2021 | NeuroImage | Schilling, K. G., Rheault, F., Petit, L., Hansen, C. B., Nath, V., Yeh, F. C., ... & Descoteaux, M. (2021). Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?. NeuroImage, 243, 118502. | |
| A model of the development of major white matter pathways within and between ventral and dorsal visual streams | 09-27 2021 | Journal of Vision | Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2021). A model of the development of major white matter pathways within and between ventral and dorsal visual streams. Journal of Vision, 21(9), 2698-2698. | |
| Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards | 06-01 2021 | Indiana University ProQuest Dissertations Publishing | Bullock, D. (2021). Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards. | |
| Collegiate athlete brain data for white matter mapping and network neuroscience | 02-11 2021 | Scientific Data | Caron, B., Stuck, R., McPherson, B. et al. Collegiate athlete brain data for white matter mapping and network neuroscience. Sci Data 8, 56 (2021). https://doi.org/10.1038/s41597-021-00823-z | |
| The human endogenous attentional control network includes a ventro-temporal cortical node | 01-15 2021 | Nature Communications | Sani, I., Stemmann, H., Caron, B., Bullock, D., Stemmler, T., Fahle, M., ... & Freiwald, W. A. (2021). The human endogenous attentional control network includes a ventro-temporal cortical node. Nature communications, 12(1), 1-16. | |
| Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation | 01-01 2021 | NeuroImage | Bertò, G., Bullock, D., Astolfi, P., Hayashi, S., Zigiotto, L., Annicchiarico, L., ... & Olivetti, E. (2021). Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation. NeuroImage, 224, 117402. | |
| Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations | 10-13 2020 | Scientific reports | Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F. C., Koudoro, S., ... & Garyfallidis, E. (2020). Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific reports, 10(1), 1-18. | |
| Advanced mapping of the human white matter microstructure better separates elite sports participation | 08-25 2020 | PsyArXiv | Caron, B., Bullock, D., Kitchell, L., McPherson, B. C., Kellar, D. A., Cheng, H., ... & Pestilli, F. (2020). Advanced mapping of the human white matter microstructure better separates elite sports participation. PsyArXiv. | |
| Associative white matter connecting the dorsal and ventral posterior human cortex | 07-24 2019 | Brain Structure and Function | Bullock, D., Takemura, H., Caiafa, C.F. et al. Associative white matter connecting the dorsal and ventral posterior human cortex. Brain Struct Funct 224, 2631–2660 (2019). https://doi.org/10.1007/s00429-019-01907-8 | |
| The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services | 05-23 2019 | Scientific data | Avesani, P., McPherson, B., Hayashi, S., Caiafa, C. F., Henschel, R., Garyfallidis, E., ... & Pestilli, F. (2019). The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Scientific data, 6(1), 1-13. | |
| Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation | 04-08 2019 | 2019 IEEE 16th International Symposium on Biomedical Imaging | Bertò, G., Avesani, P., Pestilli, F., Bullock, D., Caron, B., & Olivetti, E. (2019, April). Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation. In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) (pp. 135-138). IEEE. | |
| Shape analysis of white matter tracts via the Laplace-Beltrami spectrum | 09-20 2018 | International Workshop on Shape in Medical Imaging | Kitchell, L., Bullock, D., Hayashi, S., & Pestilli, F. (2018, September). Shape analysis of white matter tracts via the Laplace-Beltrami spectrum. In International Workshop on Shape in Medical Imaging (pp. 195-206). Springer, Cham. | |
| Oryza sativa (japonica cultivar-group) clone dan18 putative D-type cyclin gene, partial cds. | 06-18 2004 | NIH NCBI GenBank | N/A |
Onepager
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Policy
Education
Ph.D., Psychology, Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
at Indiana University Bloomington (Bloomington, IN),
Department of Psychological and Brain Sciences, Program in Neuroscience
6 / 2015 to 6 / 2021
B.S., Biology
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
at North Carolina State University (Raleigh, NC),
Department of Biological Sciences
Minor(s): Math, Genetics
8 / 2005 to 5 / 2006, &
8 / 2012 to 5 / 2015
8 / 2012 to 5 / 2015
Graduate Program, Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
at University of Cincinnati (Cincinnati, OH),
Department of Philosophy
8 / 2009 to 5 / 2011
B.A., Psychology, Philosophy
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
at University of North Carolina at Chapel Hill (Chapel Hill, NC),
Department of Psychology and Neuroscience
Minor(s): Cognitive Science
8 / 2006 to 5 / 2009
Experience
Primary Science & Engineering Technical Advisor (SETA) overseeing a portfolio of ARPA-H (80M lifetime budget). Provide technical guidance to performer teams and ARPA-H staff, engage internal and external stakeholders, review incoming proposals, and track milestone progress. Scope and design new ARPA-H programs — developed the initial structure and vision for the Systematic Targeting Of MicroPlastics (STOMP) program and served as primary architect of the major technical requirements (TA-2) for the Imaging Data Exchange (INDEX) program.
Technical skills: Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Platform Design
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
Non-technical skills: Problem Scoping, Project Management, Documentation, Literature Review, Budget Oversight, Program Management, Proposal Review, Report Development
AAAS Science & Technology Policy Fellow in NSF's Office of Advanced Cyberinfrastructure (OAC), supporting open-science and cyberinfrastructure policy. Contributed to the Pathways to Open Source Ecosystems (POSE) program (panels, program-description revision, triage) and to NSF Public Access efforts; member of the NSF team coordinating the multi-agency National AI Research Resource (NAIRR) Pilot, developing data-related practices and policies. For the OSTP Subcommittee on Open Science's Open Science Infrastructure (OSI) Working Group, analyzed openly available federal-agency data and authored the findings in a report on agency investments in open-science infrastructure.
Technical skills: Python, Linux, Git, XML, JSON, Big Data, Data Scraping, Dataset Quality Assessment, Data Science, Data Visualization, Figure Generation, Jupyter Notebooks, Open-Source Software
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Grant Management, Program Management, Grant Review, Literature Review, Science Policy, Data Policy, Policy Drafting, Report Development, Interagency Working Groups
Postdoctoral researcher in computational neuroanatomy developing automated segmentation methods for the brain's major white-matter tracts from tractography, using cross-species and literature-based anatomy. Visualized tractography and segmentation results, quantified tract properties, and developed, documented, and maintained code repositories for replicability. Resulting tools enabled cross-referencing of non-humanprimate 'ground-truth' connectivity against imaging-based human connectivity, and served as anatomy models supporting development of deep brain stimulation (DBS) techniques and technologies.
Technical skills: Python, Linux, Git, Docker, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, Containerization, Open-Source Development, Open-Source Software, High Performance Computing (HPC), Data Visualization, Testing and Debugging, Coordinated/Collaborative Testing and Debugging, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Non-technical skills: Problem Scoping, Project Management, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Mentorship
Application developer for the brainlife.io platform, producing and maintaining containerized brain-data processing applications that drastically simplified use of advanced processing and analysis techniques. Contributed testing, monitoring, and feedback on service deployment and coordination; created novel data-processing and visualization code and adapted existing resources. Led scoping, creation, and maintenance of specific data formats/standards.
Technical skills: Python, Matlab, JSON, Markdown, Linux, Git, Neuroimaging Software Packages, Brain Imaging Data Structure (BIDS), Neuroimaging, Neuroimaging Data Structures, Neuroimaging Data Processing, 3-D Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Docker, Containerization, High Performance Computing (HPC), Continuous Integration and Continuous Delivery/Deployment (CI/CD), Testing and Debugging, Collaborative Development, Data Visualization, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Non-technical skills: Problem Scoping, Project Management, Task Specialization, Multi-endeavor Balancing and Prioritization, Documentation, Stakeholder Engagement, Rapid Iteration Production, Long-Term Product/Project Maintenance, Soliciting and Incorporating Client Feedback, Progress Reporting
Graduate researcher in computational neuroanatomy developing and implementing automated segmentation methods for major white-matter tracts from tractography, enabling personalized models of brain anatomy and connectivity. Visualized segmentation results and quantified tract properties. Developed tractography quality-assurance methods.
Technical skills: Python, Matlab, Linux, Git, Neuroimaging, Neuroanatomy, Neuroscience, Brain Imaging Data Structure (BIDS), Neuroimaging Data Structures, Neuroimaging Data Processing, Medical Image Processing, Bash and Shell Scripting, Big Data, Dataset Quality Assessment, Data Science, Jupyter Notebooks, High Performance Computing (HPC), Data Visualization, Statistical Analysis, Advanced Statistical Analysis
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Non-technical skills: Problem Scoping, Project Management, Multi-endeavor Balancing and Prioritization, Project Schedule Development and Coordination, Documentation, Science Communication, Manuscript Production, Manuscript Editing, Public Speaking, Presentation Development and Delivery, Research Methods, Research Design, Mentorship
Awards, Fellowships and Grants
| Title and Source | Type | Duration | Link |
|---|---|---|---|
| AAAS Science and Technology Policy Fellow at National Science Foundation (NSF) via Association For the Advancement of Science (AAAS) | Fellowship | 8 / 2022 to 8 / 2024 | |
| Neuroimaging NIH Postdoctoral Training Fellowship (T32) at University of Minnesota via National Institute of Biomedical Imaging and Bioengineering (NIBIB) | Fellowship | 1 / 2022 to 8 / 2022 | |
| Data Science for the Public Good (DSPG) Young Scholars program at University of Virginia Biocomplexity Institute via Data Science for the Public Good (DSPG) | Fellowship | 6 / 2020 to 8 / 2020 | |
| Clinical Translational NIMH Predoctoral Training Fellowship (T32) at Indiana University Bloomington, Department of Psychological and Brain Sciences, Clinical Science Program via National Institute of Mental Health (NIMH) | Fellowship | 8 / 2018 to 5 / 2020 | |
| UW eScience Institute Neurohackacademy Summer Scholar at University of Washington eScience Institute via NeuroHackAcademy | Fellowship | 8 / 2019 to 9 / 2019 | |
| Center for Information and Neural Networks (CiNet) Training Fellowship at Center for Information and Neural Networks (CiNet) via National Institute of Information and Communications Technology (NICT) | Fellowship | 12 / 2016 to 1 / 2017 | |
| Psychological and Brain Sciences departmental fellowship at Indiana University Bloomington via Department of Psychological and Brain Sciences | Fellowship | 8 / 2015 to 5 / 2017 | |
| SENS Research Foundation Summer Scholar at Wake Forest Institute for Regenerative Medicine via Sens Research Foundation | Fellowship | 6 / 2013 to 8 / 2013 | |
| Wake Forest Institute for Regenerative Medicine Summer Scholar at Wake Forest University School of Medicine via Wake Forest Institute for Regenerative Medicine | Fellowship | 6 / 2013 to 8 / 2013 | |
| NCSU Undergraduate Research Grant at North Carolina State University via Office of Undergraduate Research | Grant | 1 / 2013 to 6 / 2013, & 1 / 2014 to 6 / 2014 |
portfolio
Qualifying Exams Paper Compilation
A collection of three papers that I wrote in the summer of 2018 for my PhD program’s qualifying examinations
White Matter Anatomy Database (WMAD)
An interactive database and framework for cataloging accounts of white matter tracts and their anatomy throughout the literature.
Interactive White Matter Segmentation
A user-friendly, binder-enabled jupyter notebook for performing anatomy-based segmentations.
White Matter Segmentation Education (WiMSE)
A website/collection of jupyter notebooks designed to provide a comprehensive exploration of concepts related to white matter segmentation.
OCT & MAIA Scripts
A collection of code and scripts for processing, analyzing and visualizing data from Optical Coherence Tomography (OCT) and Macular Integrity Assessment (MAIA), at both the individual and group levels.
CiteAs on requirements.txt
GitHub action for using the CiteAs API to generate a software citation ACKNOWLEDGEMENTS.md document automatically from a requirements.txt file.
White Matter Anatomy Tools (wmaTools)
Matlab-based toolkit for the segmentation and analysis of streamline tractography.
White Matter Anatomy Python Tools (wma_pyTools)
Pythonic refactoring of wma_Tools toolkit for the segmentation and analysis of streamline tractography.
Track the Anterior Limb of the Internal Capsule
A dockerized, brainlife.io application to track the anterior limb of the internal capsule using ensemble tractography.
White Matter Anatomy Segmentation (wmaSeg)
Brainlife.io application for classifying streamlines into known anatomical tracts.
publications
Oryza sativa (japonica cultivar-group) clone dan18 putative D-type cyclin gene, partial cds.
Published in NIH NCBI GenBank, 2004
A mutated sequence from oryza sativa, from the 2004 NCSU SCIBLS program
Recommended citation: N/A https://www.ncbi.nlm.nih.gov/nuccore/AY660000.1
Shape analysis of white matter tracts via the Laplace-Beltrami spectrum
Published in International Workshop on Shape in Medical Imaging, 2018
In this paper, we propose to use the Laplace-Beltrami (LB) spectrum as a descriptor of the shape of white matter tracts.
Recommended citation: Kitchell, L., Bullock, D., Hayashi, S., & Pestilli, F. (2018, September). Shape analysis of white matter tracts via the Laplace-Beltrami spectrum. In International Workshop on Shape in Medical Imaging (pp. 195-206). Springer, Cham. https://par.nsf.gov/servlets/purl/10073355
Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation
Published in 2019 IEEE 16th International Symposium on Biomedical Imaging, 2019
…we extend a state-of-the-art example-based method based on the Linear Assignment Problem (LAP) by including prior anatomical information within the optimization process.
Recommended citation: Bertò, G., Avesani, P., Pestilli, F., Bullock, D., Caron, B., & Olivetti, E. (2019, April). Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation. In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) (pp. 135-138). IEEE. https://arxiv.org/pdf/1907.07077
The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services
Published in Scientific data, 2019
The Open Diffusion Data Derivatives (O3D) repository.
Recommended citation: Avesani, P., McPherson, B., Hayashi, S., Caiafa, C. F., Henschel, R., Garyfallidis, E., ... & Pestilli, F. (2019). The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Scientific data, 6(1), 1-13. https://osf.io/y82n7/download
Associative white matter connecting the dorsal and ventral posterior human cortex
Published in Brain Structure and Function, 2019
The addition of these dorso-ventral connective tracts to our standard picture of white matter architecture results in a more complicated pattern of white matter connectivity than previously considered. 
Recommended citation: Bullock, D., Takemura, H., Caiafa, C.F. et al. Associative white matter connecting the dorsal and ventral posterior human cortex. Brain Struct Funct 224, 2631–2660 (2019). https://doi.org/10.1007/s00429-019-01907-8 https://par.nsf.gov/servlets/purl/10111131
Advanced mapping of the human white matter microstructure better separates elite sports participation
Published in PsyArXiv, 2020
…we examined the baseline differences in collegiate athletic participants by using two models of the diffusion-weighted magnetic resonance imaging signal (the Diffusion Tensor and NODDI model)… For both models, athletes were found to have consistently higher measures of microstructure than controls.
Recommended citation: Caron, B., Bullock, D., Kitchell, L., McPherson, B. C., Kellar, D. A., Cheng, H., ... & Pestilli, F. (2020). Advanced mapping of the human white matter microstructure better separates elite sports participation. PsyArXiv. https://psyarxiv.com/fvk5r/download?format=pdf
Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations
Published in Scientific reports, 2020
BUndle ANalytics (BUAN) is a fast, robust, and flexible computational framework for real-world tractometric studies. 
Recommended citation: Chandio, B. Q., Risacher, S. L., Pestilli, F., Bullock, D., Yeh, F. C., Koudoro, S., ... & Garyfallidis, E. (2020). Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. Scientific reports, 10(1), 1-18. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7555507/pdf/41598_2020_Article_74054.pdf
Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation
Published in NeuroImage, 2021
In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into a simple linear model. 
Recommended citation: Bertò, G., Bullock, D., Astolfi, P., Hayashi, S., Zigiotto, L., Annicchiarico, L., ... & Olivetti, E. (2021). Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation. NeuroImage, 224, 117402. https://www.researchgate.net/profile/Giulia-Berto/publication/339216328_Classifyber_a_robust_streamline-based_linear_classifier_for_white_matter_bundle_segmentation/links/5e47e70f458515072d9f1b79/Classifyber-a-robust-streamline-based-linear-classifier-for-white-matter-bundle-segmentation.pdf
The human endogenous attentional control network includes a ventro-temporal cortical node
Published in Nature Communications, 2021
By combining a demanding behavioral paradigm with functional neuroimaging and diffusion tractography, we show that like fronto-parietal attentional areas, the human posterior inferotemporal cortex exhibits significant attentional modulatory activity.
Recommended citation: Sani, I., Stemmann, H., Caron, B., Bullock, D., Stemmler, T., Fahle, M., ... & Freiwald, W. A. (2021). The human endogenous attentional control network includes a ventro-temporal cortical node. Nature communications, 12(1), 1-16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810878/pdf/41467_2020_Article_20583.pdf
Collegiate athlete brain data for white matter mapping and network neuroscience
Published in Scientific Data, 2021
We describe a dataset of processed data with associated reproducible preprocessing pipeline collected from two collegiate athlete groups and one non-athlete group.
Recommended citation: Caron, B., Stuck, R., McPherson, B. et al. Collegiate athlete brain data for white matter mapping and network neuroscience. Sci Data 8, 56 (2021). https://doi.org/10.1038/s41597-021-00823-z https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878753/pdf/41597_2021_Article_823.pdf
Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards
Published in Indiana University ProQuest Dissertations Publishing, 2021
Although the [white matter] architecture has been studied for hundreds of years, much is still unknown. This has hindered efforts to associate characteristics of the white matter with human behavior, development, and disorders. Here, we seek to ameliorate this.
Recommended citation: Bullock, D. (2021). Computational Segmentation of White Matter Anatomy: Methods, Insights, and Standards. https://www.proquest.com/docview/2566003752/fulltextPDF/93E6DF93FFA241EFPQ/1
A model of the development of major white matter pathways within and between ventral and dorsal visual streams
Published in Journal of Vision, 2021
We propose a model that posits that the development of PVP white matter is related to the flow of neural activity from the ventral visual stream and to the dorsal visual stream.
Recommended citation: Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2021). A model of the development of major white matter pathways within and between ventral and dorsal visual streams. Journal of Vision, 21(9), 2698-2698. https://doi.org/10.1167/jov.21.9.2698
Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?
Published in NeuroImage, 2021
42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. 
Recommended citation: Schilling, K. G., Rheault, F., Petit, L., Hansen, C. B., Nath, V., Yeh, F. C., ... & Descoteaux, M. (2021). Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?. NeuroImage, 243, 118502. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855321/pdf/nihms-1777494.pdf
Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints
Published in Cerebral Cortex, 2022
Here, we analyzed intracerebral EEG from 11 epileptic patients viewing a stimulus sequence beginning with a neutral face with direct gaze. An overlap analysis of posterior white matter tractography endpoints (from 1066 healthy brains) relative to active intracerebral electrodes in the 11 patients showed likely involvement of both dorsal and ventral posterior white matter pathways. 
Recommended citation: Babo-Rebelo, M., Puce, A., Bullock, D., Hugueville, L., Pestilli, F., Adam, C., ... & George, N. (2022). Visual information routes in the posterior dorsal and ventral face network studied with intracranial neurophysiology and white matter tract endpoints. Cerebral Cortex, 32(2), 342-366. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8754371/pdf/bhab212.pdf
A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century
Published in Cerebral Cortex, 2022
Here, we characterized the connections, morphology, traversal, and functions of the major white matter tracts in the brain. There are major discrepancies across different accounts of white matter tract anatomy, hindering our attempts to accurately map the connectivity of the human brain.
Recommended citation: Daniel N Bullock, Elena A Hayday, Mark D Grier, Wei Tang, Franco Pestilli, Sarah R Heilbronner, A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century, Cerebral Cortex, Volume 32, Issue 20, 15 October 2022, Pages 4524–4548, https://doi.org/10.1093/cercor/bhab500 https://psyarxiv.com/fvk5r/download?format=pdf
Development of white matter tracts between and within the dorsal and ventral streams
Published in Brain Structure and Function, 2022
We used reproducible, cloud-computing methods and diffusion imaging from adults and children (ages 5-8 years) to compare PVP development to that of tracts within the ventral and dorsal pathways. Overall, results suggest a potential role for the PVP in the development of the dorsal visual stream that may be related to its ability to facilitate interactions between ventral and dorsal streams during learning. 
Recommended citation: Vinci-Booher, S., Caron, B., Bullock, D., James, K., & Pestilli, F. (2022). Development of white matter tracts between and within the dorsal and ventral streams. Brain Structure and Function, 227(4), 1457-1477. https://www.biorxiv.org/content/10.1101/2021.01.27.428423.full.pdf
The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI
Published in Current Research in Neurobiology, 2022
Despite their respective receptor specificities, both clozapine (CLZ) and deschloroclozapine (DCZ) have partial affinity for a variety of endogenous receptors and can induce dose-specific changes even in naïve animals. This complicates their use as actuator ligands for Designer Receptors Exclusively Activated by Designer Drugs (DREADDs). In this study we aimed to examine the effects of these compounds on resting-state functional connectivity (rs-FC) and intrinsic neural timescales (INTs) in drug-naïve, non-human primates. 
Recommended citation: Adriana K. Cushnie, Daniel N. Bullock, Ana M. G. Manea, Wei Tang, Jan Zimmermann, Sarah R.Heilbronner, The use of chemogenetic actuator ligands in nonhuman primate DREADDs-fMRI, Current Research in Neurobiology, in press, https://doi.org/10.1016/j.crneur.2022.100072 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9860110/pdf/main.pdf
brainlife.io: A decentralized and open source cloud platform to support neuroscience research
Published in arXiv, 2023
…Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. this http URL automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here this http URLs technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility…
Recommended citation: Hayashi, S., Caron, B. A., Heinsfeld, A. S., Vinci-Booher, S., McPherson, B., Bullock, D. N., ... & Pestilli, F. (2023). brainlife. io: A decentralized and open source cloud platform to support neuroscience research. ArXiv.Current Research in Neurobiology, revision under review, https://doi.org/10.48550/arXiv.2306.02183 https://arxiv.org/ftp/arxiv/papers/2306/2306.02183.pdf
A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule
Published in Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2024
The anterior limb of the internal capsule (ALIC) is a white matter structure that connects the prefrontal cortex (PFC) to the brainstem, thalamus, and subthalamic nucleus… we developed a novel diffusion tractography pipeline that generates reliable and biologically validated ALIC white matter reconstructions.
Recommended citation: Sretavan, K., Braun, H., Liu, Z., Bullock, D., Palnitkar, T., Patriat, R., Chandrasekaran, J., Brenny, S., Johnson, M. D., Widge, A. S., Harel, N., & Heilbronner, S. R. (2024). A Reproducible Pipeline for Parcellation of the Anterior Limb of the Internal Capsule. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 9(12), 1249-1261. https://doi.org/10.1016/j.bpsc.2024.07.008 https://www.sciencedirect.com/science/article/pii/S2451902224001964/pdfft
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
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