Joe R & Teresa Lozano School of Medicine

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2019

Cellular refractive index comparison of various prostate cancer and noncancerous cell lines via photonic-crystal biosensor

Deluna, F., Cadena, M., Wang, B., Sun, L. Z. & Ye, J. Y., Jan 1 2019, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII. Leary, J. F., Tarnok, A. & Farkas, D. L. (eds.). SPIE, 108810K. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10881).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

GenApp, containers and ABACO

Brookes, E. H. & Stubbs, J., Jul 28 2019, Proceedings of the Practice and Experience in Advanced Research Computing: Rise of the Machines (Learning), PEARC 2019. Association for Computing Machinery, 3332191. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Integrating quantitative imaging and computational modeling to predict the spatiotemporal distribution of 186Re nanoliposomes for recurrent glioblastoma treatment

Woodall, R. T., Hormuth, D. A., Abdelmalik, M. R. A., Wu, C., Feng, X., Phillips, W. T., Bao, A., Hughes, T. J. R., Brenner, A. J. & Yankeelov, T. E., Jan 1 2019, Medical Imaging 2019: Physics of Medical Imaging. Bosmans, H., Chen, G-H. & Schmidt, T. G. (eds.). SPIE, 109483M. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10948).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Predicting diabetes in healthy population through machine learning

Abbas, H., Alic, L., Rios, M., Abdul-ghani, M. A. & Qaraqe, K., Jun 1 2019, Proceedings - 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems, CBMS 2019. Institute of Electrical and Electronics Engineers Inc., p. 567-570 4 p. 8787404. (Proceedings - IEEE Symposium on Computer-Based Medical Systems; vol. 2019-June).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2018

In-vivo fluorescence detection of breast cancer growth factor receptors by fiber-optic probe

Bustamante, G., Wang, B., Deluna, F., Sun, L. & Ye, J. Y., Jan 1 2018, Optical Biopsy XVI: Toward Real-Time Spectroscopic Imaging and Diagnosis. SPIE, Vol. 10489. 104890E

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Label-free in vitro prostate cancer cell detection via photonic-crystal biosensor

Deluna, F., Ding, X., Sagredo, I., Bustamante, G., Sun, L. & Ye, J. Y., Jan 1 2018, Biophysics, Biology and Biophotonics III: The Crossroads. SPIE, Vol. 10504. 105040D

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Quantitative image-based phosphorus-31 MR spectroscopy for evaluating age-based differences in skeletal muscle metabolites

Deng, S., Ripley, E. M., Vasquez, J. A., Tripathy, D., Defronzo, R. A. & Clarke, G. D., Jan 1 2018, Medical Imaging 2018: Physics of Medical Imaging. SPIE, Vol. 10573. 105732T

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2017

A primary morphological classifier for skin lesion images

Macatangay, J. M. A., Ruiz, C. R. & Usatine, R. P., Jan 1 2017, Full Papers Proceedings. Bourke, P. & Skala, V. (eds.). May ed. University of West Bohemia, Vol. 2701. p. 55-64 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Biologically relevant simulations for validating risk models under small-sample conditions

Bokov, A. F., Manuel, L. S., Tirado-Ramos, A., Gelfond, J. A. & Pletcher, S. D., Sep 1 2017, 2017 IEEE Symposium on Computers and Communications, ISCC 2017. Institute of Electrical and Electronics Engineers Inc., p. 290-295 6 p. 8024544

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Evaluation of a novel label-free photonic-crystal biosensor imaging system for the detection of prostate cancer cells

DeLuna, F., Ding, X. F., Sun, L. & Ye, J. Y., Jan 1 2017, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XV. SPIE, Vol. 10068. 100681H

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Genapp integrated with openstack supports elastic computing on jetstream technical paper

Brookes, E. H. & Savelyev, A., Jul 9 2017, PEARC 2017 - Practice and Experience in Advanced Research Computing 2017: Sustainability, Success and Impact. Association for Computing Machinery, Vol. Part F128771. a11

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Identification and localization of trauma-related biomarkers using matrix assisted laser desorption/ionization imaging mass spectrometry

Jones, K., Reilly, M. A. & Glickman, R. D., 2017, Visualizing and Quantifying Drug Distribution in Tissue. SPIE, Vol. 10046. 100460G

Research output: Chapter in Book/Report/Conference proceedingConference contribution

ThIEF: Finding genome-wide trajectories of epigenetics marks

Polishko, A., Hasan, M. A., Pan, W., Bunnik, E. M., Le Roch, K. & Lonardi, S., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Vol. 88. 19

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Using Prevalence Patterns to Discover Un-mapped Flowsheet Data in an Electronic Health Record Data Warehouse

Bokov, A. F., Bos, A. B., Manuel, L. S., Tirado-Ramos, A., Kittrell, P., Jackson, C. E. & Olin, G. P., Nov 10 2017, Proceedings - 2017 IEEE 30th International Symposium on Computer-Based Medical Systems, CBMS 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-June. p. 324-327 4 p. 8104211

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2016

All optical experimental design for neuron excitation, inhibition, and action potential detection

Walsh, A. J., Tolstykh, G., Martens, S., Sedelnikova, A., Ibey, B. L. & Beier, H. T., 2016, Clinical and Translational Neurophotonics; Neural Imaging and Sensing; and Optogenetics and Optical Manipulation. SPIE, Vol. 9690. 96901P

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

All-optical optoacoustic microscopy system based on probe beam deflection technique

Maswadi, S. M., Tsyboulskic, D., Roth, C. C., Glickman, R. D., Beier, H. T., Oraevsky, A. A. & Ibey, B. L., 2016, Photons Plus Ultrasound: Imaging and Sensing 2016. SPIE, Vol. 9708. 970818

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Collapsed variational Bayesian inference of the author-topic model: Application to large-scale coordinate-based meta-analysis

Ngo, G. H., Eickhoff, S. B., Fox, P. T. & Yeo, B. T. T., Aug 24 2016, PRNI 2016 - 6th International Workshop on Pattern Recognition in Neuroimaging. Institute of Electrical and Electronics Engineers Inc., 7552332

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Conductivity affects nanosecond electrical pulse induced pressure transient formation

Roth, C. C., Barnes, R. A., Ibey, B. L., Beier, H. T. & Glickman, R. D., 2016, Optical Interactions with Tissue and Cells XXVII. SPIE, Vol. 9706. 97060V

Research output: Chapter in Book/Report/Conference proceedingConference contribution

MRI based biomarker for brain aging in rodents and non-human primates

Frankea, K., Dahnke, R., Clarke, G. D., Kuo, A., Li, C., Nathanielsz, P., Schwab, M. & Gaser, C., Aug 24 2016, PRNI 2016 - 6th International Workshop on Pattern Recognition in Neuroimaging. Institute of Electrical and Electronics Engineers Inc., 7552326

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Power spectrum-based genomic feature extraction from high-throughput ChIP-seq sequences

Tang, B., Zhou, Y. & Jin, V. X., Jan 1 2016, Intelligent Computing Theories and Application - 12th International Conference, ICIC 2016, Proceedings. Premaratne, P., Huang, D-S. & Bevilacqua, V. (eds.). Springer Verlag, p. 439-447 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9771).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Protein-protein binding before and after photo-modification of albumin

Rozinek, S. C., Glickman, R. D., Thomas, R. J. & Brancaleon, L., 2016, Optical Interactions with Tissue and Cells XXVII. SPIE, Vol. 9706. 97061J

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Seizure onset zone localization from many invasive EEG channels using directed functional connectivity

Van Mierlo, P., Coito, A., Vulliémoz, S. & Lie, O., Nov 28 2016, 2016 24th European Signal Processing Conference, EUSIPCO 2016. European Signal Processing Conference, EUSIPCO, Vol. 2016-November. p. 255-259 5 p. 7760249

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Short infrared (IR) laser pulses can induce nanoporation

Roth, C. C., Barnes, R. A., Ibey, B. L., Glickman, R. D. & Beier, H. T., 2016, Clinical and Translational Neurophotonics; Neural Imaging and Sensing; and Optogenetics and Optical Manipulation. SPIE, Vol. 9690. 96901L

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations
2015

Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme

Chiu, Y. C., Liang, K. W., Hsiao, T. H., Chen, Y. & Chuang, E. Y., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., p. 171-176 6 p. 7359676

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

A performance predictor for ultrascan supercomputer calculations

Kim, H., Brookes, E. H. & Demeler, B., Jul 26 2015, ACM International Conference Proceeding Series. Association for Computing Machinery, Vol. 2015-July. a42

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Cells exposed to nanosecond electrical pulses exhibit biomarkers of mechanical stress

Roth, C. C., Barnes, R. A., Ibey, B. L., Beier, H. T., Moen, E. K. & Glickman, R. D., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9326. 932612

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

GenApp module execution and airavata integration

Brookes, E. H., Anjum, N., Curtis, J. E., Marru, S., Singh, R. & Pierce, M., Jan 23 2015, Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis. Institute of Electrical and Electronics Engineers Inc., p. 9-12 4 p. 7021841

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Haptics-enabled surgical training system with guidance using deep learning

Biglari, E., Feng, M., Quarles, J., Sako, E. Y., Calhoon, J. H., Rodriguez, R. & Feng, Y., 2015, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 9177. p. 267-278 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9177).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hybrid feature selection methods for online biomedical publication classification

Ma, L., Zhang, Y., Sunderraman, R., Fox, P. T., Laird, A. R., Turner, J. A. & Turner, M. D., Oct 16 2015, 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2015. Institute of Electrical and Electronics Engineers Inc., 7300320

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Model-based and context-specific background correction and differential methylation testing for MBDCap-seq

Liu, Y., Wilson, D., Leach, R. J. & Chen, Y., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., p. 214-219 6 p. 7359683

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Online biomedical publication classification using Multi-Instance Multi-Label algorithms with feature reduction

Ren, D., Ma, L., Zhang, Y., Sunderraman, R., Fox, P. T., Laird, A. R., Turner, J. A. & Turner, M. D., Sep 11 2015, Proceedings of 2015 IEEE 14th International Conference on Cognitive Informatics and Cognitive Computing, ICCI*CC 2015. Institute of Electrical and Electronics Engineers Inc., p. 234-241 8 p. 7259391

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Opto-acoustic image fusion technology for diagnostic breast imaging in a feasibility study

Zalev, J., Clingman, B., Herzog, D., Miller, T., Ulissey, M., Stavros, A. T., Oraevsky, A., Lavin, P., Kist, K. A., Dornbluth, N. C. & Otto, P. M., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9419. 941909

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations

Patho-finder-A fast and accurate program for pathogen identification through RNA-seq

Wu, C. T., Hsiao, T. H., Chiu, Y. C., Hsu, Y. C., Chuang, E. Y. & Chen, Y., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., p. 1148-1151 4 p. 7359843

Research output: Chapter in Book/Report/Conference proceedingConference contribution

The apache airavata application programming interface: Overview and evaluation with the Ultrascan Science Gateway

Pierce, M., Marru, S., Demeler, B., Singh, R. & Gorbet, G., Jan 23 2015, Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis. Institute of Electrical and Electronics Engineers Inc., p. 25-29 5 p. 7021845

Research output: Chapter in Book/Report/Conference proceedingConference contribution

21 Scopus citations
2014

Abdominal adipose tissue quantification on water-suppressed and non-water-suppressed MRI at 3T using semi-automated FCM clustering algorithm

Valaparla, S. K., Peng, Q., Gao, F. & Clarke, G. D., Jan 1 2014, Medical Imaging 2014: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE, 903802. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9038).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

An open extensible multitarget application generation tool for simple rapid deployment of multiscale scientific codes

Brookes, E. H., Jan 1 2014, Proceedings of the XSEDE 2014 Conference: Engaging Communities. Association for Computing Machinery, 53. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Characterization of acoustic shockwaves generated by exposure to nanosecond electrical pulses

Roth, C. C., Maswadi, S., Ibey, B. L., Beier, H. T. & Glickman, R. D., Jan 1 2014, Optical Interactions with Tissue and Cells XXV; and Terahertz for Biomedical Applications. SPIE, 89411O. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8941).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Combining Meta- and mega-analytic approaches for multi-site diffusion imaging based genetic studies: From the enigma-DTI working group

Jahanshad, N., Kochunov, P., Nichols, T. E., Sprooten, E., Mandl, R. C., Almasy, L., Brouwer, R. M., Curran, J. E., De Zubicaray, G. I., Dimitrova, R., Fox, P. T., Hong, L. E., Landman, B. A., Lemaitre, H., Lopez, L., Martin, N. G., McMahon, K. L., Mitchell, B. D., Olvera, R. L., Peterson, C. P. & 17 others, Sussmann, J. E., Toga, A. W., Wardlaw, J. M., Wright, M. J., Wright, S. N., Bastin, M. E., McIntosh, A. M., Boomsma, D. I., Kahn, R. S., Den Braber, A., Deary, I. J., Pol, H. E. H., Williamson, D., Blangero, J., Van't Ent, D., Glahn, D. C. & Thompson, P. M., Jul 29 2014, 2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014. Institute of Electrical and Electronics Engineers Inc., p. 1234-1238 5 p. 6868099. (2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test

Zhang, L., Meng, J., Liu, H., Cui, X., Zhang, S. W., Chen, Y. & Huang, Y., Feb 5 2014, 2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014. Institute of Electrical and Electronics Engineers Inc., p. 1368-1371 4 p. 7032349

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Fiber optic fluorescence microscopy for functional brain imaging in awake, mobile mice

Cha, J., Paukert, M., Bergles, D. E. & Kang, J. U., Jan 1 2014, Optical Techniques in Neurosurgery, Neurophotonics, and Optogenetics. SPIE, 89282N. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8928).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Intramyocellular lipid dependence on skeletal muscle fiber type and orientation characterized by diffusion tensor imaging and 1H-MRS

Valaparla, S. K., Gao, F., Abdul-Ghani, M. & Clarke, G. D., Jan 1 2014, Medical Imaging 2014: Image Processing. SPIE, 90340S. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9034).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multisensory interface for 5D stem cell image volumes

Koerner, M., Wait, E., Winter, M., Bjornsson, C., Cearley, E. K., Wang, Y., Goderie, S. K., Temple, S. & Cohen, A. R., Nov 2 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014. Institute of Electrical and Electronics Engineers Inc., p. 1178-1181 4 p. 6943806

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Opto-acoustic breast imaging with co-registered ultrasound

Zalev, J., Clingman, B., Herzog, D., Miller, T., Stavros, A. T., Oraevsky, A., Kist, K., Dornbluth, N. C. & Otto, P., Jan 1 2014, Medical Imaging 2014: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE, 90381J. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 9038).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Optoacoustic microscopy using laser beam deflection technique

Khachatryan, E., Maswadi, S., Tsyboulski, D. A., Barnes, E., Sardar, D., Oraevsky, A. A., Nash, K. & Glickman, R., Jan 1 2014, Photons Plus Ultrasound: Imaging and Sensing 2014. SPIE, 89432T. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8943).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Transcriptomic analysis by RNA-Seq and gene enrichment analysis

Nixon, S. E., González-Peña, D., Lawson, M. A., McCusker, R. H., O'Connor, J. C., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 27-31 5 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2013

Antagonistic activation patterns underlie multi-functionality of the right temporo-parietal junction

Bzdok, D., Langner, R., Eickhoff, S., Laird, A. R. & Fox, P. T., Oct 15 2013, Proceedings - 2013 3rd International Workshop on Pattern Recognition in Neuroimaging, PRNI 2013. p. 62-65 4 p. 6603557. (Proceedings - 2013 3rd International Workshop on Pattern Recognition in Neuroimaging, PRNI 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A simulation analysis of a patient-centered surgical home to improve outpatient surgical processes of care and outcomes

Morrice, D., Wang, D. E., Bard, J., Leykum, L., Noorily, S. & Veerapaneni, P., Dec 1 2013, Proceedings of the 2013 Winter Simulation Conference - Simulation: Making Decisions in a Complex World, WSC 2013. p. 2274-2286 13 p. 6721603. (Proceedings of the 2013 Winter Simulation Conference - Simulation: Making Decisions in a Complex World, WSC 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

BIMMER: A Bi-layer hidden Markov model for differential methylation analysis

Mao, Z., Huang, T. H. M., Chen, Y. & Huang, Y., Dec 1 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 99-102 4 p. 6732470. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Clinical feasibility study of combined opto-acoustic and ultrasonic imaging modality providing coregistered functional and anatomical maps of breast tumors

Zalev, J., Clingman, B., Smith, R. J., Herzog, D., Miller, T., Stavros, A. T., Ermilov, S., Conjusteau, A., Tsyboulski, D., Oraevsky, A. A., Kist, K., Dornbluth, N. C. & Otto, P., May 28 2013, Photons Plus Ultrasound: Imaging and Sensing 2013. 858103. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8581).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Scopus citations

Detection of oxidative stress biomarker-induced assembly of gold nanoparticles in retinal pigment epithelial cells

Yasmin, Z., Lee, Y., Maswadi, S., Glickman, R. & Nash, K. L., Apr 12 2013, Optical Interactions with Tissue and Cells XXIV. 85790E. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 8579).

Research output: Chapter in Book/Report/Conference proceedingConference contribution