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Yangming Ou, Ph.D.

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Overview

Mentoring
Machine Learning on MRI[login at prompt]
Available: 12/11/18, Expires: 12/31/21

Several ongoing research projects developing and/or using machine learning (artificial intelligence) algorithms and tools on magnetic resonance imaging (MRI) for disease detection, prognosis/outcome prediction, and sub-population clustering and classification. Applications include: characterization of brain disorders, quantification of nutrition's effects on neurodevelopment, understanding the mechanism of radiation-related neurocognitive outcomes in tumor survivors, early detection of psychosis, generic prediction of clinical variables (age, neurocognitive outcomes, ...), etc.


Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. St Baldrick Scholar Award (OU, YANGMING) Jul 1, 2019 - Jun 30, 2022
    St Baldrick's Foundation
    Find Targets to Improve Neurocognition in Pediatric Brain Tumors Survivors
    Role Description: This study aims to find subjects who are at risk to develop neurocognitive impairment after survival from pediatric brain tumors, and to find neuroanatomic mechanisms that mediate the radiotherapy-outcome relationship. Both are for preparing baseline evidence for future study of interventions and radiotherapy optimizations that aim to improve the neurocognitive outcomes for survivors from pediatric brain tumors.
    Role: Principal Investigator
  2. Corporate Sponsored Research Grant (GRANT, P. ELLEN / OU, YANGMING) Mar 1, 2019 - Aug 15, 2019
    Abbott Nutrition
    Maternal Diet, Milk and Infant Brain
    Role Description: We aim to study how mother diet affects infant brain development through mediating mother milk nutrient components, and to study the effect of feeding patterns (breast- versus formula-feeding) on infant brain development.
    Role: co-Principal Investigator
  3. Faculty Career Development Award (OU, YANGMING) Jul 3, 2017 - Jun 28, 2019
    Harvard Medical School / Boston Children's Hospital
    Developing Brain Atlases to Standardize MRI Interpretation of Neonatal Brain Injury
    Role: Principal Investigator
  4. Corporate Sponsored Research Grant (GRANT, ELLEN / OU, YANGMING) Jan 2, 2017 - Jun 30, 2017
    General Electric (GE) Healthcare
    Normative MRI Exemplars and Atlases to Quantify Early Life Brain Development
    Role: co-Principal Investigator
  5. CRM 0518525 (OU, YANGMING) Sep 1, 2016 - Aug 31, 2017
    Microsoft Azure Research Award
    Steamline Analysis of Multi-Site Clinical MRI on Azure Cloud
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Zöllei L, Iglesias JE, Ou Y, Grant PE, Fischl B. Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years. Neuroimage. 2020 May 19; 116946. PMID: 32442637.
    Citations:    
  2. Xue M, Sun FR, Ou YN, Shen XN, Li HQ, Huang YY, Dong Q, Tan L, Yu JT. Association of cerebrospinal fluid neurogranin levels with cognition and neurodegeneration in Alzheimer's disease. Aging (Albany NY). 2020 May 18; 12. PMID: 32421689.
    Citations:    
  3. Morton SU, Vyas R, Gagoski B, Vu C, Litt J, Larsen RJ, Kuchan MJ, Lasekan JB, Sutton BP, Grant PE, Ou Y. Maternal Dietary Intake of Omega-3 Fatty Acids Correlates Positively with Regional Brain Volumes in 1-Month-Old Term Infants. Cereb Cortex. 2020 Apr 14; 30(4):2057-2069. PMID: 31711132.
    Citations:    
  4. Yu X, Zuk J, Perdue MV, Ozernov-Palchik O, Raney T, Beach SD, Norton ES, Ou Y, Gabrieli JDE, Gaab N. Putative protective neural mechanisms in prereaders with a family history of dyslexia who subsequently develop typical reading skills. Hum Brain Mapp. 2020 Mar 13. PMID: 32166830.
    Citations:    
  5. Weiss RJ, Bates SV, Song Y, Zhang Y, Herzberg EM, Chen YC, Gong M, Chien I, Zhang L, Murphy SN, Gollub RL, Grant PE, Ou Y. Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy. J Transl Med. 2019 11 21; 17(1):385. PMID: 31752923.
    Citations:    
  6. Machado I, Toews M, George E, Unadkat P, Essayed W, Luo J, Teodoro P, Carvalho H, Martins J, Golland P, Pieper S, Frisken S, Golby A, Wells Iii W, Ou Y. Deformable MRI-Ultrasound registration using correlation-based attribute matching for brain shift correction: Accuracy and generality in multi-site data. Neuroimage. 2019 11 15; 202:116094. PMID: 31446127.
    Citations:    
  7. Xiao Y, Rivaz H, Chabanas M, Fortin M, Machado I, Ou Y, Heinrich MP, Schnabel JA, Zhong X, Maier A, Wein W, Shams R, Kadoury S, Drobny D, Modat M, Reinertsen I. Evaluation of MRI to Ultrasound Registration Methods for Brain Shift Correction: The CuRIOUS2018 Challenge. IEEE Trans Med Imaging. 2020 03; 39(3):777-786. PMID: 31425023.
    Citations:    
  8. Ly KI, Vakulenko-Lagun B, Emblem KE, Ou Y, Da X, Betensky RA, Kalpathy-Cramer J, Duda DG, Jain RK, Chi AS, Plotkin SR, Batchelor TT, Sorensen G, Rosen BR, Gerstner ER. Publisher Correction: Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI. Sci Rep. 2019 Jun 14; 9(1):8721. PMID: 31197238.
    Citations:    
  9. Cole AR, Perry DA, Raza A, Nedder AP, Pollack E, Regan WL, van den Bosch SJ, Polizzotti BD, Yang E, Davila D, Afacan O, Warfield SK, Ou Y, Sefton B, Everett AD, Neil JJ, Lidov HGW, Mayer JE, Kheir JN. Perioperatively Inhaled Hydrogen Gas Diminishes Neurologic Injury Following Experimental Circulatory Arrest in Swine. JACC Basic Transl Sci. 2019 Apr; 4(2):176-187. PMID: 31061920.
    Citations:    
  10. Ly KI, Vakulenko-Lagun B, Emblem KE, Ou Y, Da X, Betensky RA, Kalpathy-Cramer J, Duda DG, Jain RK, Chi AS, Plotkin SR, Batchelor TT, Sorensen G, Rosen BR, Gerstner ER. Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI. Sci Rep. 2018 11 20; 8(1):17062. PMID: 30459364.
    Citations:    Fields:    
  11. Ou Y, Zöllei L, Da X, Retzepi K, Murphy SN, Gerstner ER, Rosen BR, Grant PE, Kalpathy-Cramer J, Gollub RL. Field of View Normalization in Multi-Site Brain MRI. Neuroinformatics. 2018 10; 16(3-4):431-444. PMID: 29353341.
    Citations:    Fields:    
  12. Pinto ALR*, Ou Y*, Sahin M, Grant PE. Quantitative Apparent Diffusion Coefficient Mapping May Predict Seizure Onset in Children With Sturge-Weber Syndrome. Pediatric Neurology. 2018. View Publication.
  13. Pinto ALR, Ou Y, Sahin M, Grant PE. Quantitative Apparent Diffusion Coefficient Mapping May Predict Seizure Onset in Children With Sturge-Weber Syndrome. Pediatr Neurol. 2018 07; 84:32-38. PMID: 29753575.
    Citations:    Fields:    
  14. Davatzikos C, Rathore S, Bakas S, Pati S, Bergman M, Kalarot R, Sridharan P, Gastounioti A, Jahani N, Cohen E, Akbari H, Tunc B, Doshi J, Parker D, Hsieh M, Sotiras A, Li H, Ou Y, Doot RK, Bilello M, Fan Y, Shinohara RT, Yushkevich P, Verma R, Kontos D. Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome. J Med Imaging (Bellingham). 2018 Jan; 5(1):011018. PMID: 29340286.
    Citations: 2     
  15. Lauer A, Da X, Hansen MB, Boulouis G, Ou Y, Cai X, Liberato Celso Pedrotti A, Kalpathy-Cramer J, Caruso P, Hayden DL, Rost N, Mouridsen K, Eichler FS, Rosen B, Musolino PL. ABCD1 dysfunction alters white matter microvascular perfusion. Brain. 2017 Dec 01; 140(12):3139-3152. PMID: 29136088.
    Citations:    Fields:    Translation:Humans
  16. Zhou M, Scott J, Chaudhury B, Hall L, Goldgof D, Yeom KW, Iv M, Ou Y, Kalpathy-Cramer J, Napel S, Gillies R, Gevaert O, Gatenby R. Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches. AJNR Am J Neuroradiol. 2018 02; 39(2):208-216. PMID: 28982791.
    Citations: 3     Fields:    
  17. Tu X, Xie M, Gao J, Ma Z, Chen D, Wang Q, Finlayson SG, Ou Y, Cheng JZ. Automatic Categorization and Scoring of Solid, Part-Solid and Non-Solid Pulmonary Nodules in CT Images with Convolutional Neural Network. Sci Rep. 2017 09 01; 7(1):8533. PMID: 28864824.
    Citations: 3     Fields:    
  18. Bernardis E, Zhang Y, Konukoglu E, Ou Y, Javitz HS, Axel L, Metaxas D, Desjardins B, Pohl KM. eCurves: A Temporal Shape Encoding. IEEE Trans Biomed Eng. 2018 04; 65(4):733-744. PMID: 28641243.
    Citations:    Fields:    
  19. Ou Y, Zöllei L, Retzepi K, Castro V, Bates SV, Pieper S, Andriole KP, Murphy SN, Gollub RL, Grant PE. Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old. Hum Brain Mapp. 2017 06; 38(6):3052-3068. PMID: 28371107.
    Citations:    Fields:    Translation:Humans
  20. Dinh CV, Steenbergen P, Ghobadi G, van der Poel H, Heijmink SW, de Jong J, Isebaert S, Haustermans K, Lerut E, Oyen R, Ou Y, Christos D, van der Heide UA. Multicenter validation of prostate tumor localization using multiparametric MRI and prior knowledge. Med Phys. 2017 Mar; 44(3):949-961. PMID: 28039927.
    Citations:    Fields:    Translation:Humans
  21. Kalpathy-Cramer J, Chandra V, Da X, Ou Y, Emblem KE, Muzikansky A, Cai X, Douw L, Evans JG, Dietrich J, Chi AS, Wen PY, Stufflebeam S, Rosen B, Duda DG, Jain RK, Batchelor TT, Gerstner ER. Phase II study of tivozanib, an oral VEGFR inhibitor, in patients with recurrent glioblastoma. J Neurooncol. 2017 02; 131(3):603-610. PMID: 27853960.
    Citations: 5     Fields:    Translation:HumansCTClinical Trials
  22. Doshi J, Erus G, Ou Y, Resnick SM, Gur RC, Gur RE, Satterthwaite TD, Furth S, Davatzikos C. MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection. Neuroimage. 2016 Feb 15; 127:186-195. PMID: 26679328.
    Citations: 16     Fields:    Translation:Humans
  23. Ou Y, Gollub RL, Retzepi K, Reynolds N, Pienaar R, Pieper S, Murphy SN, Grant PE, Zöllei L. Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images. Neuroimage. 2015 Nov 15; 122:246-61. PMID: 26260429.
    Citations: 2     Fields:    Translation:HumansCells
  24. Rojas KD, Montero ML, Yao J, Messing E, Fazili A, Joseph J, Ou Y, Rubens DJ, Parker KJ, Davatzikos C, Castaneda B. Methodology to study the three-dimensional spatial distribution of prostate cancer and their dependence on clinical parameters. J Med Imaging (Bellingham). 2015 Jul; 2(3):037502. PMID: 26236756.
    Citations: 1     
  25. Sotiras A*, Ou Y*, Paragios N, Davatzikos C. Handbook of Biomedical Imaging; Methodologies and Clinical Research. Graph-based Deformable Image Registration. 2015. View Publication.
  26. Wu J, Ou Y, Weinstein SP, Conant EF, Yu N, Hoshmand V, Keller B, Ashraf AB, Rosen M, DeMichele A, Davatzikos C, Kontos D. SPIE Medical Imaging. Quantification of Tumor Changes during Neoadjuvant Chemotherapy with Longitudinal Breast DCE-MRI Registration. 2015; 9414.
  27. Petitjean C, Zuluaga MA, Bai W, Dacher JN, Grosgeorge D, Caudron J, Ruan S, Ayed IB, Cardoso MJ, Chen HC, Jimenez-Carretero D, Ledesma-Carbayo MJ, Davatzikos C, Doshi J, Erus G, Maier OM, Nambakhsh CM, Ou Y, Ourselin S, Peng CW, Peters NS, Peters TM, Rajchl M, Rueckert D, Santos A, Shi W, Wang CW, Wang H, Yuan J. Right ventricle segmentation from cardiac MRI: a collation study. Med Image Anal. 2015 Jan; 19(1):187-202. PMID: 25461337.
    Citations: 11     Fields:    Translation:Humans
  28. Ou Y, Weinstein SP, Conant EF, Englander S, Da X, Gaonkar B, Hsieh MK, Rosen M, DeMichele A, Davatzikos C, Kontos D. Deformable registration for quantifying longitudinal tumor changes during neoadjuvant chemotherapy. Magn Reson Med. 2015 Jun; 73(6):2343-56. PMID: 25046843.
    Citations: 5     Fields:    Translation:Humans
  29. Ou Y, Akbari H, Bilello M, Da X, Davatzikos C. Comparative evaluation of registration algorithms in different brain databases with varying difficulty: results and insights. IEEE Trans Med Imaging. 2014 Oct; 33(10):2039-65. PMID: 24951685.
    Citations: 15     Fields:    Translation:Humans
  30. Serpa MH, Ou Y, Schaufelberger MS, Doshi J, Ferreira LK, Machado-Vieira R, Menezes PR, Scazufca M, Davatzikos C, Busatto GF, Zanetti MV. Neuroanatomical classification in a population-based sample of psychotic major depression and bipolar I disorder with 1 year of diagnostic stability. Biomed Res Int. 2014; 2014:706157. PMID: 24575411.
    Citations: 7     Fields:    Translation:Humans
  31. Litjens G, Toth R, van de Ven W, Hoeks C, Kerkstra S, van Ginneken B, Vincent G, Guillard G, Birbeck N, Zhang J, Strand R, Malmberg F, Ou Y, Davatzikos C, Kirschner M, Jung F, Yuan J, Qiu W, Gao Q, Edwards PE, Maan B, van der Heijden F, Ghose S, Mitra J, Dowling J, Barratt D, Huisman H, Madabhushi A. Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge. Med Image Anal. 2014 Feb; 18(2):359-73. PMID: 24418598.
    Citations: 14     Fields:    Translation:Humans
  32. Doshi J, Erus G, Ou Y, Gaonkar B, Davatzikos C. Multi-atlas skull-stripping. Acad Radiol. 2013 Dec; 20(12):1566-76. PMID: 24200484.
    Citations: 28     Fields:    Translation:Humans
  33. Da X, Toledo JB, Zee J, Wolk DA, Xie SX, Ou Y, Shacklett A, Parmpi P, Shaw L, Trojanowski JQ, Davatzikos C. Integration and relative value of biomarkers for prediction of MCI to AD progression: spatial patterns of brain atrophy, cognitive scores, APOE genotype and CSF biomarkers. Neuroimage Clin. 2014; 4:164-73. PMID: 24371799.
    Citations: 33     Fields:    Translation:Humans
  34. Zanetti MV, Schaufelberger MS, Doshi J, Ou Y, Ferreira LK, Menezes PR, Scazufca M, Davatzikos C, Busatto GF. Neuroanatomical pattern classification in a population-based sample of first-episode schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry. 2013 Jun 03; 43:116-25. PMID: 23261522.
    Citations: 10     Fields:    Translation:Humans
  35. Ou Y. Development and Validations of a Deformable Registration Algorithm of Medical Images: Applications to Brain, Breast and Prostate Studies. 2012.
  36. Ou Y, Ye DH, Pohl KM, Davatzikos C. Validation of DRAMMS among 12 Popular Methods in Cross-Subject Cardiac MRI Registration. Biomed Image Regist Proc. 2012 Jul; 7359:209-219. PMID: 28603787.
    Citations: 1     
  37. Bernardis E, Konukoglu E, Ou Y, Metaxas DN, Desjardins B, Pohl KM. Temporal shape analysis via the spectral signature. Med Image Comput Comput Assist Interv. 2012; 15(Pt 2):49-56. PMID: 23286031.
    Citations: 5     Fields:    Translation:Humans
  38. Ou Y, Sotiras A, Paragios N, Davatzikos C. DRAMMS: Deformable registration via attribute matching and mutual-saliency weighting. Med Image Anal. 2011 Aug; 15(4):622-39. PMID: 20688559.
    Citations: 81     Fields:    Translation:Humans
  39. Ou Y, Besbes A, Bilello M, Mansour M, Davatzikos C, Paragios N. Detecting mutually-salient landmark pairs with MRF regularization. IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI). 2010; 400-403.
  40. Sotiras A, Ou Y, Glocker B, Davatzikos C, Paragios N. Simultaneous geometric--iconic registration. Med Image Comput Comput Assist Interv. 2010; 13(Pt 2):676-83. PMID: 20879374.
    Citations: 5     Fields:    Translation:Humans
  41. Ou Y, Shen D, Zeng J, Sun L, Moul J, Davatzikos C. Sampling the spatial patterns of cancer: optimized biopsy procedures for estimating prostate cancer volume and Gleason Score. Med Image Anal. 2009 Aug; 13(4):609-20. PMID: 19524478.
    Citations: 5     Fields:    Translation:Humans
  42. Ou Y, Shen D, Feldman M, Tomaszewski J, Davatzikos C. Non-rigid registration between histological and MR images of the prostate: a joint segmentation and registration framework. Mathematical Method in Biomedical Image Analysis (MMBIA). 2009; 125-132.
  43. Ou Y, Davatzikos C. DRAMMS: deformable registration via attribute matching and mutual-saliency weighting. Inf Process Med Imaging. 2009; 21:50-62. PMID: 19694252.
    Citations: 8     Fields:    Translation:Animals
  44. Verma R, Zacharaki EI, Ou Y, Cai H, Chawla S, Lee SK, Melhem ER, Wolf R, Davatzikos C. Multiparametric tissue characterization of brain neoplasms and their recurrence using pattern classification of MR images. Acad Radiol. 2008 Aug; 15(8):966-77. PMID: 18620117.
    Citations: 35     Fields:    Translation:Humans
  45. Zhan Y, Ou Y, Feldman M, Tomaszeweski J, Davatzikos C, Shen D. Registering histologic and MR images of prostate for image-based cancer detection. Acad Radiol. 2007 Nov; 14(11):1367-81. PMID: 17964460.
    Citations: 23     Fields:    Translation:Humans
  46. Cai H, Verma R, Ou Y, Lee SK, Melhem ER, Davatzikos C. Probabilistic segmentation of brain tumors based on multi-modality magnetic resonance images. IEEE International Symposium on Biomedical Imaging: From Nano to Macro, (ISBI). 2007; 600-603.
  47. Xing Y, Ou Y, Englander S, Schnall M, Shen D. Simultaneous estimation and segmentation of T1 map for breast parenchyma measurement. IEEE International Symposium on Biomedical Imaging: From Nano to Macro, (ISBI). 2007; 332-335.
  48. Periaswamy S, Ou Y, Jerebko A. System and Method for Automatic Extraction of Spinal Cord from 3D Volumetric Images. 2007.
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.