Division of Basic Sciences

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  • SlicerSALT: Shape AnaLysis Toolbox

    Vicory, J., Pascal, L., Hernandez, P., Fishbaugh, J., Prieto, J., Mostapha, M., Huang, C., Shah, H., Hong, J., Liu, Z., Michoud, L., Fillion-Robin, J. C., Gerig, G., Zhu, H., Pizer, S. M., Styner, M. & Paniagua, B., 2018, Shape in Medical Imaging - International Workshop, ShapeMI 2018, Held in Conjunction with MICCAI 2018, Proceedings. Lombaert, H., Paniagua, B., Egger, B., Lüthi, M., Reuter, M. & Wachinger, C. (eds.). Springer Verlag, p. 65-72 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11167 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    21 Scopus citations

  • Soft-split sparse regression based random forest for predicting future clinical scores of Alzheimer’s disease

    Huang, L., Gao, Y., Jin, Y., Thung, K. H. & Shen, D., 2015, Machine Learning in Medical Imaging - 6th International Workshop, MLMI 2015 Held in Conjunction with MICCAI 2015, Proceedings. Zhou, L., Shi, Y., Wang, L. & Wang, Q. (eds.). Springer Verlag, p. 246-254 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9352).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    9 Scopus citations

  • Sparse Bayesian graphical models for RPPA time course data

    Mitra, R., Mueller, P., Ji, Y., Mills, G. & Lu, Y., 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012. p. 113-117 5 p. 6507742. (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations

  • Sparse decomposition of gene expression data to infer transcriptional modules guided by motif information

    Gong, T., Xuan, J., Chen, L., Riggins, R. B., Wang, Y., Hoffman, E. P. & Clarke, R., 2008, Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. p. 244-255 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4983 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access

  • Spectral feature selection and its application in high dimensional gene expression studies

    Wang, Z., Qiu, P., Xu, W. & Liu, Y., Sep 20 2014, ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, p. 314-320 7 p. (ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    2 Scopus citations

  • Statistical disease mapping for heterogeneous neuroimaging studies

    Liu, R., Huang, C., Li, T., Yang, L. & Zhu, H., May 23 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018. IEEE Computer Society, p. 1415-1418 4 p. (Proceedings - International Symposium on Biomedical Imaging; vol. 2018-April).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations

  • Stratified Test Alleviates Batch Effects in Single-Cell Data

    Liang, S., Liang, Q., Chen, R. & Chen, K., 2020, Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings. Martín-Vide, C., Vega-Rodríguez, M. A. & Wheeler, T. (eds.). Springer, p. 167-177 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12099 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    1 Scopus citations

  • Structured sparse kernel learning for imaging genetics based alzheimer’s disease diagnosis

    Peng, J., An, L., Zhu, X., Jin, Y. & Shen, D., 2016, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2016 - 19th International Conference, Proceedings. Unal, G., Ourselin, S., Joskowicz, L., Sabuncu, M. R. & Wells, W. (eds.). Springer Verlag, p. 70-78 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9901 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    34 Scopus citations

  • Tailor the longitudinal anaysis for NIH longitudinal normal brain developmental study

    Chen, Y., An, H., Shen, D., Zhu, H. & Lin, W., Jul 29 2014, 2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014. Institute of Electrical and Electronics Engineers Inc., p. 1206-1209 4 p. 6868092. (2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    1 Scopus citations

  • Temporal assessment of radiomic features on clinical mammography in a high-risk population

    Mendel, K. R., Li, H., Lan, L., Chan, C. W., King, L. M., Tayob, N., Whitman, G., El-Zein, R., Bedrosian, I. & Giger, M. L., 2018, Medical Imaging 2018: Computer-Aided Diagnosis. Mori, K. & Petrick, N. (eds.). SPIE, 105753Q. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10575).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Temporal mammographic registration for evaluation of architecture changes in cancer risk assessment

    Mendel, K., Li, H., Tayob, N., El-Zein, R., Bedrosian, I. & Giger, M., 2019, Medical Imaging 2019: Computer-Aided Diagnosis. Mori, K. & Hahn, H. K. (eds.). SPIE, 1095041. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10950).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations

  • The effective diagnosis of schizophrenia by using multi-layer RBMs deep networks

    Qiao, C., Lin, D. D., Cao, S. L. & Wang, Y. P., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 603-606 4 p. 7359751. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    5 Scopus citations

  • The role of dead-end in germ-cell tumor development

    Zhu, R., Bhattacharya, C. & Matin, A., Dec 2007, Testicular Chromosome Structure and Gene Expression. Blackwell Publishing Inc., p. 181-186 6 p. (Annals of the New York Academy of Sciences; vol. 1120).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    13 Scopus citations

  • Three-dimensional imaging of the developing mouse female reproductive organs with optical coherence tomography

    Burton, J. C., Wang, S., Behringer, R. R. & Larina, I. V., 2016, Optical Methods in Developmental Biology IV. Choma, M. A., Fraser, S. E. & Rollins, A. M. (eds.). SPIE, 97160E. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9716).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations

  • TIMER: Tensor image morphing for elastic registration

    Yap, P. T., Wu, G., Zhu, H., Lin, W. & Shen, D., 2009, 2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, CVPR Workshops 2009. IEEE Computer Society, p. 1-8 8 p. 5204350. (2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, CVPR Workshops 2009).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Toward exhaustive gating of flow cytometry data

    Qiu, P., 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012. p. 183-186 4 p. 6507759. (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    1 Scopus citations

  • Towards practical temporal relation extraction from clinical notes: An analysis of direct temporal relations

    Lee, H. J., Zhang, Y., Xu, J., Tao, C., Xu, H. & Jiang, M., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1272-1275 4 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    5 Scopus citations

  • TPCNN: Two-phase patch-based convolutional neural network for automatic brain tumor segmentation and survival prediction

    Zhou, F., Li, T., Li, H. & Zhu, H., 2018, Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 3rd International Workshop, BrainLes 2017, Held in Conjunction with MICCAI 2017, Revised Selected Papers. Menze, B., Crimi, A., Kuijf, H., Reyes, M. & Bakas, S. (eds.). Springer Verlag, p. 274-286 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10670 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    9 Scopus citations

  • Tracking the herd: Resynchronization analysis of cell-cycle gene expression data in saccharomyces cerevisiae

    Qiu, P., Wang, Z. J. & Liu, K. J. R., 2005, Proceedings of the 2005 27th Annual International Conference of the Engineering in Medicine and Biology Society, IEEE-EMBS 2005. p. 4826-4829 4 p. 1615552. (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; vol. 7 VOLS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations

  • Tractography-embedded white matter stream clustering

    Jin, Y. & Cetingul, H. E., Jul 21 2015, 2015 IEEE 12th International Symposium on Biomedical Imaging, ISBI 2015. IEEE Computer Society, p. 432-435 4 p. 7163904. (Proceedings - International Symposium on Biomedical Imaging; vol. 2015-July).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    4 Scopus citations

  • Tumor cell-substrate stabilization mediated by integrins

    Patton, J. T., McIntire, L. V., Menter, D. G. & Nicolson, G. L., 1994, Materials Research Society Symposium Proceedings. Publ by Materials Research Society, p. 147-152 6 p. (Materials Research Society Symposium Proceedings; vol. 331).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    5 Scopus citations

  • Two-stage multiscale adaptive regression methods for twin neuroimaging data

    Li, Y., Gilmore, J. H., Wang, J., Styner, M., Lin, W. & Zhu, H., 2011, Multimodal Brain Image Analysis - First International Workshop, MBIA 2011, Held in Conjunction with MICCAI 2011, Proceedings. p. 102-109 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7012 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • UNC-Utah NA-MIC DTI framework: Atlas based fiber tract analysis with application to a study of nicotine smoking addiction

    Verde, A. R., Berger, J. B., Gupta, A., Farzinfar, M., Kaiser, A., Chanon, V. W., Boettiger, C., Johnson, H., Matsui, J., Sharma, A., Goodlett, C., Shi, Y., Zhu, H., Gerig, G., Gouttard, S., Vachet, C. & Styner, M., 2013, Medical Imaging 2013: Image Processing. 86692D. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8669).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    3 Scopus citations

  • Understanding scanner upgrade effects on brain integrity & connectivity measures

    Zhan, L., Jahanshad, N., Jin, Y., Nir, T. M., Leonardo, C. D., Bernstein, M. A., Borowski, B., Jack, C. R. & Thompson, P. M., Jul 29 2014, 2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014. Institute of Electrical and Electronics Engineers Inc., p. 234-237 4 p. 6867852. (2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Scopus citations

  • Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations

    Cao, S., Qin, H., Gossmann, A., Deng, H. W. & Wang, Y. P., Sep 9 2015, BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 241-249 9 p. (BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Unsupervised grow-cut: Cellular automata-based medical image segmentation

    Ghosh, P., Antani, S. K., Long, L. R. & Thoma, G. R., 2011, Proceedings - 2011 1st IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2011. p. 40-47 8 p. 6061452. (Proceedings - 2011 1st IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2011).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    36 Scopus citations

  • Unsupervised inference of arbor morphology progression for microglia from confocal microscope images

    Xu, Y., Savelonas, M., Qiu, P., Trett, K., Shain, W. & Roysam, B., 2013, ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging: From Nano to Macro. p. 1356-1359 4 p. 6556784. (Proceedings - International Symposium on Biomedical Imaging).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    5 Scopus citations

  • Unsupervised segmentation of lungs from chest radiographs

    Ghosh, P., Antani, S. K., Long, L. R. & Thoma, G. R., 2012, Medical Imaging 2012: Computer-Aided Diagnosis. Vol. 8315. 831532

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    2 Scopus citations

  • Using directed information for influence discovery in interconnected dynamical systems

    Rao, A., Hero, A. O., States, D. J. & Engel, J. D., 2008, Advanced Signal Processing Algorithms, Architectures, and Implementations XVIII. 70740P. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 7074).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    2 Scopus citations

  • UTH-CCB: The Participation of the SemEval 2015 Challenge - Task 14

    Xu, J., Zhang, Y., Wang, J., Wu, Y., Jiang, M., Soysal, E. & Xu, H., 2015, SemEval 2015 - 9th International Workshop on Semantic Evaluation, co-located with the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL-HLT 2015 - Proceedings. Nakov, P., Zesch, T., Cer, D. & Jurgens, D. (eds.). Association for Computational Linguistics (ACL), p. 311-314 4 p. (SemEval 2015 - 9th International Workshop on Semantic Evaluation, co-located with the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL-HLT 2015 - Proceedings).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    11 Scopus citations

  • UTHealth at SemEval-2016 task 12: An end-to-end system for temporal information extraction from clinical notes

    Lee, H. J., Zhang, Y., Xu, J., Moon, S., Wang, J., Wu, Y. & Xu, H., 2016, SemEval 2016 - 10th International Workshop on Semantic Evaluation, Proceedings. Association for Computational Linguistics (ACL), p. 1292-1297 6 p. (SemEval 2016 - 10th International Workshop on Semantic Evaluation, Proceedings).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    36 Scopus citations

  • Utilizing multiple particle tracking microrheology and traction force microscopy to monitor mechanical progression of differentiating mesenchymal stem cells

    McAndrews, K., McGrail, D. J., Quach, N. & Dawson, M. R., 2013, Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future. AIChE, p. 853-854 2 p. (Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Voxel-wise group analysis of dti

    Liu, Z., Zhu, H., Marks, B. L., Katz, L. M., Goodlett, C. B., Gerig, G. & Styner, M., 2009, Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. IEEE Computer Society, p. 807-810 4 p. 5193172. (Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    18 Scopus citations

  • Voxelwise spectral diffusional connectivity and its applications to Alzheimer's disease and intelligence prediction

    Li, J., Jin, Y., Shi, Y., Dinov, I. D., Wang, D. J., Toga, A. W. & Thompson, P. M., 2013, Medical Image Computing and Computer-Assisted Intervention, MICCAI 2013 - 16th International Conference, Proceedings. PART 1 ed. Springer Verlag, p. 655-662 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8149 LNCS, no. PART 1).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    11 Scopus citations

  • White matter integrity in traumatic brain injury: Effects of permissible fiber turning angle

    Dennis, E. L., Jin, Y., Kernan, C., Babikian, T., Mink, R., Babbitt, C., Johnson, J., Giza, C. C., Asarnow, R. F. & Thompson, P. M., Jul 21 2015, 2015 IEEE 12th International Symposium on Biomedical Imaging, ISBI 2015. IEEE Computer Society, p. 930-933 4 p. 7164023. (Proceedings - International Symposium on Biomedical Imaging; vol. 2015-July).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    8 Scopus citations