Image, Informatics and Intelligence (i3) Lab | Publications

 

Selected Publications

2021

Susan Sotardi, Randy L Gollub, Sara V Bates, Rebecca Weiss, Shawn N Murphy, Ellen P Grant, and Yangming Ou. 2021. “Voxelwise and Regional Brain Apparent Diffusion Coefficient Changes on MRI from Birth to 6 Years of Age.” Radiology, 298, 2, Pp. 415-424.

2020

Sheng He, Randy L Gollub, Shawn N Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L Robertson, Ellen P Grant, and Yangming Ou. 2020. BRAIN AGE ESTIMATION USING LSTM ON CHILDREN'S BRAIN MRI Proc IEEE Int Symp Biomed Imaging, 2020, Pp. 420-423.

Haiyan Wang, Guoqiang Han, Haojiang Li, Guihua Tao, Enhong Zhuo, Lizhi Liu, Hongmin Cai, and Yangming Ou. 2020. A Collaborative Dictionary Learning Model for Nasopharyngeal Carcinoma Segmentation on Multimodalities MR Sequences Comput Math Methods Med, 2020, Pp. 7562140.

Nianyin Zeng, Siyang Zuo, Guoyan Zheng, Yangming Ou, and Tong Tong. 2020. “Editorial: Artificial Intelligence for Medical Image Analysis of Neuroimaging Data.” Front Neurosci, 14, Pp. 480.

Yiming Xiao, Hassan Rivaz, Matthieu Chabanas, Maryse Fortin, Ines Machado, Yangming Ou, Mattias P Heinrich, Julia A Schnabel, Xia Zhong, Andreas Maier, Wolfgang Wein, Roozbeh Shams, Samuel Kadoury, David Drobny, Marc Modat, and Ingerid Reinertsen. 2020. “Evaluation of MRI to Ultrasound Registration Methods for Brain Shift Correction: The CuRIOUS2018 Challenge.” IEEE Trans Med Imaging, 39, 3, Pp. 777-786.

Jingwen Yang, Xinran Dong, Yu Hu, Qingsheng Peng, Guihua Tao, Yangming Ou, Hongmin Cai, and Xiaohong Yang. 2020. “Fully Automatic Arteriovenous Segmentation in Retinal Images via Topology-Aware Generative Adversarial Networks.” Interdiscip Sci, 12, 3, Pp. 323-334.

Lilla Zöllei, Juan Eugenio Iglesias, Yangming Ou, Ellen P Grant, and Bruce Fischl. 2020. “Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years.” arXiv preprint arXiv:2001.03091.

Lilla Zöllei, Juan Eugenio Iglesias, Yangming Ou, Ellen P Grant, and Bruce Fischl. 2020. “Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years.” Neuroimage, 218, Pp. 116946.

Shasha Li, Marziye Eshghi, Sheraz Khan, Qiyuan Tian, Juho Joutsa, Yangming Ou, Qing Mei Wang, Jian Kong, Bruce Robert Rosen, Jyrki Ahveninen, and Aapo Nummenmaa. 2020. “Localizing central swallowing functions by combining non-invasive brain stimulation with neuroimaging.” Brain Stimul, 13, 5, Pp. 1207-1210.

Sarah U Morton, Rutvi Vyas, Borjan Gagoski, Catherine Vu, Jonathan Litt, Ryan J Larsen, Matthew J Kuchan, John B Lasekan, Brad P Sutton, Ellen P Grant, and Yangming Ou. 2020. “Maternal Dietary Intake of Omega-3 Fatty Acids Correlates Positively with Regional Brain Volumes in 1-Month-Old Term Infants.” Cereb Cortex, 30, 4, Pp. 2057-2069.

Lin Qi, Haoran Zhang, Xuehao Cao, Xuyang Lyu, Lisheng Xu, Benqiang Yang, and Yangming Ou. 2020. “Multi-Scale Feature Fusion Convolutional Neural Network for Concurrent Segmentation of Left Ventricle and Myocardium in Cardiac MR Images.” Journal of Medical Imaging and Health Informatics, 10, 5, Pp. 1023–1032.

Jun Zhao, Gen Lin, Minglei Zhuo, Zaiwen Fan, Liyun Miao, Likun Chen, Aiping Zeng, Rong Yin, Yangming Ou, Zhihui Shi, Jie Yin, Wen Gao, Jianhua Chen, Xiangdong Zhou, Yong Zeng, Xiang Liu, Huamin Xu, Rongrong Chen, Xuefeng Xia, and David P Carbone. 2020. “Next-generation sequencing based mutation profiling reveals heterogeneity of clinical response and resistance to osimertinib.” Lung Cancer, 141, Pp. 114-118.

Sheng He, Randy L Gollub, Shawn N Murphy, Juan David Perez, Sanjay Prabhu, Rudolph Pienaar, Richard L Robertson, Ellen P Grant, and Yangming Ou. 2020. “Brain Age Estimation Using LSTM on Children's Brain MRI.” IEEE International Symposium on Biomedical Imaging (ISBI).

Xi Yu, Jennifer Zuk, Meaghan V Perdue, Ola Ozernov-Palchik, Talia Raney, Sara D Beach, Elizabeth S Norton, Yangming Ou, John DE Gabrieli, and Nadine Gaab. 2020. “Deformable MRI-Ultrasound registration using correlation-based attribute matching for brain shift correction: Accuracy and generality in multi-site data.” Neuroimage, 202, Pp. 116094.

Maryse Fortin, Ines Machado, Yangming Ou, Mattias P Heinrich, Julia A Schnabel, Xia Zhong, Andreas Maier, Wolfgang Wein, Roozbeh Shams, Samuel Kadoury, and others. 2019. “Evaluation of MRI to ultrasound registration methods for brain shift correction: The CuRIOUS2018 Challenge."

Rebecca J Weiss, Sara V Bates, Ya'nan Song, Yue Zhang, Emily M Herzberg, Yih-Chieh Chen, Maryann Gong, Isabel Chien, Lily Zhang, Shawn N Murphy, Randy L Gollub, Ellen P Grant, and Yangming Ou. 2019. “Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy.” J Transl Med, 17, 1, Pp. 385.

Rebecca J Weiss, Sara V Bates, Ya’nan Song, Yue Zhang, Emily M Herzberg, Yih-Chieh Chen, Maryann Gong, Isabel Chien, Lily Zhang, Shawn N Murphy, and others. 2019. “Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy.” Journal of translational medicine, 17, 1, Pp. 1–16.

Alexis R Cole, Dorothy A Perry, Ali Raza, Arthur P Nedder, Elizabeth Pollack, William L Regan, Sarah J van den Bosch, Brian D Polizzotti, Edward Yang, Daniel Davila, Onur Afacan, Simon K Warfield, Yangming Ou, Brenda Sefton, Allen D Everett, Jeffrey J Neil, Hart GW Lidov, John E Mayer, and John N Kheir. 2019. “Perioperatively Inhaled Hydrogen Gas Diminishes Neurologic Injury Following Experimental Circulatory Arrest in Swine.” JACC Basic Transl Sci, 4, 2, Pp. 176-187.

Ina K Ly, Bella Vakulenko-Lagun, Kyrre E Emblem, Yangming Ou, Xiao Da, Rebecca A Betensky, Jayashree Kalpathy-Cramer, Dan G Duda, Rakesh K Jain, Andrew S Chi, and others. 2019. “Publisher Correction: Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI.” Scientific reports, 9, 1, Pp. 1–1.

Ina K Ly, Bella Vakulenko-Lagun, Kyrre E Emblem, Yangming Ou, Xiao Da, Rebecca A Betensky, Jayashree Kalpathy-Cramer, Dan G Duda, Rakesh K Jain, Andrew S Chi, Scott R Plotkin, Tracy T Batchelor, Gregory Sorensen, Bruce R Rosen, and Elizabeth R Gerstner. 2019. “Publisher Correction: Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI.” Sci Rep, 9, 1, Pp. 8721.

Xi Yu, Jennifer Zuk, Meaghan V Perdue, Ola Ozernov-Palchik, Talia Raney, Sara D Beach, Elizabeth S Norton, Yangming Ou, John DE Gabrieli, and Nadine Gaab. 2019. “Putative protective neural mechanisms in pre-readers with a family history of dyslexia who subsequently develop typical reading skills.” bioRxiv, Pp. 707786.

Jia-bin Huang, Enhong Zhuo, Haojiang Li, Lizhi Liu, Hongmin Cai, and Yangming Ou. 2019. “Achieving Accurate Segmentation of Nasopharyngeal Carcinoma in MR Images Through Recurrent Attention.” International Conference on Medical Image Computing and Computer-Assisted Intervention 11768, Pp. 494–502. Springer, Cham.

Inês Machado, Matthew Toews, Elizabeth George, Prashin Unadkat, Walid Essayed, Jie Luo, Pedro Teodoro, Herculano Carvalho, Jorge Martins, Polina Golland, Steve Pieper, Sarah Frisken, Alexandra Golby, William 3rd M Wells, and Yangming Ou. 2019. “Deformable MRI-Ultrasound registration using correlation-based attribute matching for brain shift correction: Accuracy and generality in multi-site data.” NeuroImage, 202, Pp. 116094 (19 pages).

Yiming Xiao, Hassan Rivaz, Matthieu Chabanas, Maryse Fortin, Ines Machado, Yangming Ou, Mattias P Heinrich, Julia A Schnabel, Xia Zhong, Andreas Maier, and others. 2019. “Evaluation of MRI to ultrasound registration methods for brain shift correction: The CuRIOUS2018 Challenge.” IEEE Transactions on Medical Imaging, 39, 3, Pp. 777-786.

Sarah U. Morton, Rutvi Vyas, Borjan Gagoski, Catherine Vu, Jonathan Litt, Ryan Larsen, Matthew J Kuchan, John B Lasekan, Brad P Sutton, Ellen P Grant, and Yangming Ou. 2019. “Maternal dietary intake of omega-3 fatty acids correlates positively with regional brain volumes in 1-month-old term infants.” Cerebral Cortex, Pp. bhz222.

Ya’nan Song, Sara V Bates, Randy L Gollub, Rebecca J Weiss, Sheng He, CJ Cobos, S Sotardi, Yue Zhang, Tonghua Liu, Ellen P Grant, and others. 2019. “Probabilistic atlases of neonatal hypoxic ischemic injury.” In Proceedings at pediatric academic society (PAS), Pp. 24–30.

2018

Christos Davatzikos, Saima Rathore, Spyridon Bakas, Sarthak Pati, Mark Bergman, Ratheesh Kalarot, Patmaa Sridharan, Aimilia Gastounioti, Nariman Jahani, Eric Cohen, and others. 2018. “Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.” Journal of medical imaging, 5, 1, Pp. 011018.

Christos Davatzikos, Saima Rathore, Spyridon Bakas, Sarthak Pati, Mark Bergman, Ratheesh Kalarot, Patmaa Sridharan, Aimilia Gastounioti, Nariman Jahani, Eric Cohen, Hamed Akbari, Birkan Tunc, Jimit Doshi, Drew Parker, Michael Hsieh, Aristeidis Sotiras, Hongming Li, Yangming Ou, Robert K Doot, Michel Bilello, Yong Fan, Russell T Shinohara, Paul Yushkevich, Ragini Verma, and Despina Kontos. 2018. “Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.” J Med Imaging (Bellingham), 5, 1, Pp. 011018.

Elena Bernardis, Yong Zhang, Ender Konukoglu, Yangming Ou, Harold S Javitz, Leon Axel, Dimitris Metaxas, Benoit Desjardins, and Kilian M Pohl. 2018. “eCurves: A Temporal Shape Encoding.” IEEE Trans Biomed Eng, 65, 4, Pp. 733-744.

Yangming Ou, Lilla Zöllei, Xiao Da, Kallirroi Retzepi, Shawn N Murphy, Elizabeth R Gerstner, Bruce R Rosen, Ellen P Grant, Jayashree Kalpathy-Cramer, and Randy L Gollub. 2018. “Field of View Normalization in Multi-Site Brain MRI.” Neuroinformatics, 16, 3-4, Pp. 431-444.

Yangming Ou, Lilla Zöllei, Xiao Da, Kallirroi Retzepi, Shawn N Murphy, Elizabeth R Gerstner, Bruce R Rosen, Ellen P Grant, Jayashree Kalpathy-Cramer, and Randy L Gollub. 2018. “Field of view normalization in multi-site brain MRI.” Neuroinformatics, 16, 3-4, Pp. 431–444.

Ina K Ly, Bella Vakulenko-Lagun, Kyrre E Emblem, Yangming Ou, Xiao Da, Rebecca A Betensky, Jayashree Kalpathy-Cramer, Dan G Duda, Rakesh K Jain, Andrew S Chi, Scott R Plotkin, Tracy T Batchelor, Gregory Sorensen, Bruce R Rosen, and Elizabeth R Gerstner. 2018. “Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI.” Sci Rep, 8, 1, Pp. 17062.

Ina K Ly, Bella Vakulenko-Lagun, Kyrre E Emblem, Yangming Ou, Xiao Da, Rebecca A Betensky, Jayashree Kalpathy-Cramer, Dan G Duda, Rakesh K Jain, Andrew S Chi, and others. 2018. “Probing tumor microenvironment in patients with newly diagnosed glioblastoma during chemoradiation and adjuvant temozolomide with functional MRI.” Scientific reports, 8, 1, Pp. 1–13.

Anna LR Pinto, Yangming Ou, Mustafa Sahin, and Ellen P Grant. 2018. “Quantitative Apparent Diffusion Coefficient Mapping May Predict Seizure Onset in Children With Sturge-Weber Syndrome.” Pediatr Neurol, 84, Pp. 32-38.

Anna LR Pinto, Yangming Ou, Mustafa Sahin, and Ellen P Grant. 2018. “Quantitative apparent diffusion coefficient mapping may predict seizure onset in children with Sturge-Weber syndrome.” Pediatric neurology, 84, Pp. 32–38.

Mu Zhou, Jacob Scott, Baishali Chaudhury, Lawrence Hall, Dmitry Goldgof, Kristen W Yeom, Michael Iv, Yangming Ou, Jayashree Kalpathy-Cramer, Sandy Napel, and others. 2018. “Radiomics in brain tumor: image assessment, quantitative feature descriptors, and machine-learning approaches.” American Journal of Neuroradiology, 39, 2, Pp. 208–216.

Inês Machado, Matthew Toews, Jie Luo, Prashin Unadkat, Walid Essayed, Elizabeth George, Pedro Teodoro, Herculano Carvalho, Jorge Martins, Polina Golland, and others. 2018. “Deformable MRI-ultrasound registration via attribute matching and mutual-saliency weighting for image-guided neurosurgery.” Simulation, Image Processing, and Ultrasound Systems for Assisted Diagnosis and Navigation. Springer, Cham.

2017

Arne Lauer, Xiao Da, Mikkel Bo Hansen, Gregoire Boulouis, Yangming Ou, Xuezhu Cai, Afonso Liberato Celso Pedrotti, Jayashree Kalpathy-Cramer, Paul Caruso, Douglas L Hayden, Natalia Rost, Kim Mouridsen, Florian S Eichler, Bruce Rosen, and Patricia L Musolino. 2017. “ABCD1 dysfunction alters white matter microvascular perfusion.” Brain, 140, 12, Pp. 3139-3152.

Arne Lauer, Xiao Da, Mikkel Bo Hansen, Gregoire Boulouis, Yangming Ou, Xuezhu Cai, Afonso Liberato Celso Pedrotti, Jayashree Kalpathy-Cramer, Paul Caruso, Douglas L Hayden, and others. 2017. “ABCD1 dysfunction alters white matter microvascular perfusion.” Brain, 140, 12, Pp. 3139–3152.

Xiaoguang Tu, Mei Xie, Jingjing Gao, Zheng Ma, Daiqiang Chen, Qingfeng Wang, Samuel G Finlayson, Yangming Ou, and Jie-Zhi Cheng. 2017. “Automatic categorization and scoring of solid, part-solid and non-solid pulmonary nodules in CT images with convolutional neural network.” Scientific reports, 7, 1, Pp. 1–10.

Xiaoguang Tu, Mei Xie, Jingjing Gao, Zheng Ma, Daiqiang Chen, Qingfeng Wang, Samuel G Finlayson, Yangming Ou, and Jie-Zhi Cheng. 2017. “Automatic Categorization and Scoring of Solid, Part-Solid and Non-Solid Pulmonary Nodules in CT Images with Convolutional Neural Network.” Sci Rep, 7, 1, Pp. 8533.

Elena Bernardis, Yong Zhang, Ender Konukoglu, Yangming Ou, Harold S Javitz, Leon Axel, Dimitris Metaxas, Benoit Desjardins, and Kilian M Pohl. 2017. “eCurves: A Temporal Shape Encoding.” IEEE Transactions on Biomedical Engineering, 65, 4, Pp. 733–744.

L Zollei, Yangming Ou, Juan Iglesias, Ellen P Grant, and Bruce Fischl. 2017. “FreeSurfer image processing pipeline for infant clinical MRI images.” In Proceedings of the Organization for Human Brain Mapping Conference. Vol. 1703.

Yangming Ou, RL Gollub, Jing Wang, Qianqian Fan, Sara Bates, Joseph Chou, Rebecca Weiss, Kallirroi Retzepis, Steve Pieper, Camilo Jaimes, and others. 2017. “MRI Detection of Neonatal Hypoxic Ischemic Encephalopathy: Machine vs Radiologists.” Organization for Human Brain Mapping (OHBM).

Cuong Viet Dinh, Peter Steenbergen, Ghazaleh Ghobadi, Henk van der Poel, Stijn WTPJ Heijmink, Jeroen de Jong, Sofie Isebaert, Karin Haustermans, Evelyne Lerut, Raymond Oyen, and others. 2017. “Multicenter validation of prostate tumor localization using multiparametric MRI and prior knowledge.” Medical physics, 44, 3, Pp. 949–961.

Cuong Viet Dinh, Peter Steenbergen, Ghazaleh Ghobadi, Henk van der Poel, Stijn WTPJ Heijmink, Jeroen de Jong, Sofie Isebaert, Karin Haustermans, Evelyne Lerut, Raymond Oyen, Yangming Ou, Davatzikos Christos, and Uulke A van der Heide. 2017. “Multicenter validation of prostate tumor localization using multiparametric MRI and prior knowledge.” Med Phys, 44, 3, Pp. 949-961.

Jayashree Kalpathy-Cramer, Vyshak Chandra, Xiao Da, Yangming Ou, Kyrre E Emblem, Alona Muzikansky, Xuezhu Cai, Linda Douw, John G Evans, Jorg Dietrich, Andrew S Chi, Patrick Y Wen, Stephen Stufflebeam, Bruce Rosen, Dan G Duda, Rakesh K Jain, Tracy T Batchelor, and Elizabeth R Gerstner. 2017. “Phase II study of tivozanib, an oral VEGFR inhibitor, in patients with recurrent glioblastoma.” J Neurooncol, 131, 3, Pp. 603-610.

Jayashree Kalpathy-Cramer, Vyshak Chandra, Xiao Da, Yangming Ou, Kyrre E Emblem, Alona Muzikansky, Xuezhu Cai, Linda Douw, John G Evans, Jorg Dietrich, and others. 2017. “Phase II study of tivozanib, an oral VEGFR inhibitor, in patients with recurrent glioblastoma.” Journal of neuro-oncology, 131, 3, Pp. 603–610.

Chengzhi Zhou, Tao Chen, Zhanhong Xie, Yinyin Qin, Yangming Ou, Jiexia Zhang, Shiyue Li, Rongchang Chen, and Nanshan Zhong. 2017. “RACK1 forms a complex with FGFR1 and PKM2, and stimulates the growth and migration of squamous lung cancer cells.” Mol Carcinog, 56, 11, Pp. 2391-2399.

Yangming Ou, Lilla Zöllei, Kallirroi Retzepi, Victor Castro, Sara V Bates, Steve Pieper, Katherine P Andriole, Shawn N Murphy, Randy L Gollub, and Patricia Ellen Grant. 2017. “Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old.” Hum Brain Mapp, 38, 6, Pp. 3052-3068.

Yangming Ou, Lilla Zöllei, Kallirroi Retzepi, Victor Castro, Sara V Bates, Steve Pieper, Katherine P Andriole, Shawn N Murphy, Randy L Gollub, and Patricia Ellen Grant. 2017. “Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old.” Human brain mapping, 38, 6, Pp. 3052–3068.

Yi-Fen Yen, Jayashree Kalpathy-Cramer, Ciprian Catana, Xiao Da, Yangming Ou, Andrew L Beers, Jacob Hooker, Bruce Rosen, Tracy Batchelor, and Elizabeth R Gerstner. 2017. “Multimodal Imaging of Vascularity and Drug Delivery in GBM Patients Treated with Anti-angiogenesis Inhibitor.” In .