Bibliography

Bibliography

UvA-DARE (Digital Academic Repository) Multi-view learning and deep learning for heterogeneous biological data to maintain oral health Imangaliyev, S.K. Publication date 2016 Document Version Final published version Link to publication Citation for published version (APA): Imangaliyev, S. K. (2016). Multi-view learning and deep learning for heterogeneous biological data to maintain oral health. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:01 Oct 2021 Bibliography [1] L. Abusleme, A. K. Dupuy, N. Dutzan, N. Silva, J. A. Burleson, L. D. Strausbaugh, J. Gamonal, and P. I. Diaz. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J, 7(5):1016– 1025, May 2013. [2] Alan Aderem. Systems biology: its practice and challenges. Cell, 121(4):511–513, 2005. [3] Salem Alelyani, Jiliang Tang, and Huan Liu. Feature selection for clustering: A review. Data Clustering: Algorithms and Applications, 29, 2013. [4] Jose´ Leopoldo Ferreira Antunes, Marco Aurelio´ Peres, Antonio Carlos Frias, Edgard Michel Crosato, and Maria Gabriela Haye Biazevic. Gingival health of ado- lescents and the utilization of dental services, state of Sao˜ Paulo, Brazil. Revista de Saude´ Publica´ , 42(2):191–199, 2008. [5] Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Ya- mada, Daniel R Mende, Gabriel R Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, et al. Enterotypes of the human gut microbiome. Nature, 473(7346):174–180, 2011. [6] World Medical Association et al. World medical association declaration of Helsinki: ethical principles for medical research involving human subjects. JAMA, 310(20):2191, 2013. [7] Wanping Aw and Shinji Fukuda. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach. In Seminars in immunopathology, volume 37, pages 5–16. Springer, 2015. [8] Albert-Laszl´ o´ Barabasi,´ Natali Gulbahce, and Joseph Loscalzo. Network medicine: a network-based approach to human disease. Nature Reviews Genetics, 12(1):56–68, 2011. [9] Jirina Bartkova, Jiri Lukas, Per Guldberg, Jan Alsner, Alexei F Kirkin, Jesper Zeuthen, and Jiri Bartek. The p16-cyclin D/CDK4-prb pathway as a functional unit frequently altered in melanoma pathogenesis. Cancer Research, 56(23):5475–5483, 1996. [10] Alessandro Beghini, Carla B Ripamonti, Paolo Peterlongo, Gaia Roversi, Roberto Cairoli, Enrica Morra, and Lidia Larizza. RNA hyperediting and alternative splicing 123 of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia. Human molecular genetics, 9(15):2297–2304, 2000. [11] Richard E Bellman. Adaptive control processes: a guided tour. Princeton university press, 2015. [12] Yoshua Bengio, Pascal Lamblin, Dan Popovici, Hugo Larochelle, et al. Greedy layer- wise training of deep networks. Advances in neural information processing systems, 19:153, 2007. [13] James Bergstra, Fred´ eric´ Bastien, Olivier Breuleux, Pascal Lamblin, Razvan Pascanu, Olivier Delalleau, Guillaume Desjardins, David Warde-Farley, Ian Goodfellow, Ar- naud Bergeron, et al. Theano: Deep learning on GPUs with Python. In NIPS 2011, BigLearning Workshop, Granada, Spain, 2011. [14] James Bergstra and Yoshua Bengio. Random search for hyper-parameter optimization. The Journal of Machine Learning Research, 13(1):281–305, 2012. [15] Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani, and Luciano Milanesi. Methods for the integration of multi-omics data: mathematical aspects. BMC Bioinformatics, 17(2):167, 2016. [16] Giske Biesbroek, Elisabeth AM Sanders, Guus Roeselers, Xinhui Wang, Martien PM Caspers, Krzysztof Trzcinski,´ Debby Bogaert, and Bart JF Keijser. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PloS one, 7(3):e32942, 2012. [17] Giske Biesbroek, Evgeni Tsivtsivadze, Elisabeth AM Sanders, Roy Montijn, Reinier H Veenhoven, Bart JF Keijser, and Debby Bogaert. Early respiratory micro- biota composition determines bacterial succession patterns and respiratory health in children. American journal of respiratory and critical care medicine, 190(11):1283– 1292, 2014. [18] Sergio Bizzarro, Bruno G Loos, Marja L Laine, Wim Crielaard, and Egija Zaura. Subgingival microbiome in smokers and non-smokers in periodontitis: an exploratory study using traditional targeted techniques and a next-generation sequencing. Journal of clinical periodontology, 40(5):483–492, 2013. [19] Avrim Blum and Tom Mitchell. Combining labeled and unlabeled data with co- training. In Proceedings of the eleventh annual conference on Computational learning theory, pages 92–100, New York, NY, USA, 1998. ACM. [20] Elhanan Borenstein. Computational systems biology and in silico modeling of the human microbiome. Briefings in bioinformatics, 13(6):769–780, 2012. [21] Hanneke Borgdorff et al. The vaginal microbiome: Associations with sexually trans- mitted infections and the mucosal immune response. PhD thesis, University of Ams- terdam, 2016. 124 [22] Lieuwe DJ Bos et al. Diagnosis of pulmonary injury and infection by exhaled breath analysis. PhD thesis, University of Amsterdam, 2014. [23]L eon´ Bottou. Stochastic gradient descent tricks. In Neural Networks: Tricks of the Trade - Second Edition, pages 421–436. 2012. [24] Leon Bottou, Antoine Bordes, and Seyda Ertekin. LASVM, 2009. http://mloss. org/software/view/23/. [25] DJ Bradshaw, AS McKee, and PD Marsh. Effects of carbohydrate pulses and pH on population shifts within oral microbial communities in vitro. Journal of Dental Research, 68(9):1298–1302, 1989. [26] Ulf Brefeld, Thomas Gartner,¨ Tobias Scheffer, and Stefan Wrobel. Efficient co- regularised least squares regression. In Proceedings of the International Conference on Machine learning, pages 137–144, New York, NY, USA, 2006. ACM. [27] Ulf Brefeld and Tobias Scheffer. Co-EM support vector learning. In Proceedings of the 21st International Conference on Machine learning, page 16, New York, NY, USA, 2004. ACM. [28] Howard Brody, Michael Russell Rip, Peter Vinten-Johansen, Nigel Paneth, and Stephen Rachman. Map-making and myth-making in Broad Street: the London cholera epidemic, 1854. The Lancet, 356(9223):64–68, 2000. [29] Deng Cai, Chiyuan Zhang, and Xiaofei He. Unsupervised feature selection for multi- cluster data. In Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 333–342. ACM, 2010. [30] Lien Callewaert and Chris W Michiels. Lysozymes in the animal kingdom. Journal of biosciences, 35(1):127–160, 2010. [31] Girish Chandrashekar and Ferat Sahin. A survey on feature selection methods. Com- puters & Electrical Engineering, 40(1):16–28, 2014. [32] Olivier Chapelle, Bernhard Scholkopf,¨ Alexander Zien, et al. Semi-supervised learn- ing. MIT press Cambridge, 2006. [33] Kamalika Chaudhuri, Sham M Kakade, Karen Livescu, and Karthik Sridharan. Multi- view clustering via canonical correlation analysis. In Proceedings of the 26th annual international conference on machine learning, pages 129–136. ACM, 2009. [34] Damien Chaussabel and Bali Pulendran. A vision and a prescription for big data- enabled medicine. Nature immunology, 16(5):435–439, 2015. [35] Lujia Chen, Chunhui Cai, Vicky Chen, and Xinghua Lu. Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. BMC Bioinformatics, 17(1):97, 2016. 125 [36] Tiejun Cheng, Yanli Wang, and Stephen H Bryant. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. Bioinformatics, 26(22):2881–2888, 2010. [37] Dongyun Yi Chenping Hou, Feiping Nie and Yi Wu. Feature selection via joint em- bedding learning and sparse regression. In Proceedings of the Twenty-Second Inter- national Joint Conference on Artificial Intelligence - Volume Volume Two, IJCAI’11, pages 1324–1329. AAAI Press, 2011. [38] Janet Chow, Haiqing Tang, and Sarkis K Mazmanian. Pathobionts of the gastrointesti- nal microbiota and inflammatory disease. Current opinion in immunology, 23(4):473– 480, 2011. [39] Dan C. Ciresan, Alessandro Giusti, Luca Maria Gambardella, and Jurgen¨ Schmidhu- ber. Mitosis detection in breast cancer histology images with deep neural networks. In Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - 16th International Conference, Nagoya, Japan, September 22-26, 2013, Proceedings, Part II, pages 411–418, 2013. [40] Mete Civelek and Aldons J Lusis. Systems genetics approaches to understand com- plex traits. Nature Reviews Genetics, 15(1):34–48, 2014. [41] Ton J Cleophas and Aeilko

View Full Text

Details

  • File Type
    pdf
  • Upload Time
    -
  • Content Languages
    English
  • Upload User
    Anonymous/Not logged-in
  • File Pages
    21 Page
  • File Size
    -

Download

Channel Download Status
Express Download Enable

Copyright

We respect the copyrights and intellectual property rights of all users. All uploaded documents are either original works of the uploader or authorized works of the rightful owners.

  • Not to be reproduced or distributed without explicit permission.
  • Not used for commercial purposes outside of approved use cases.
  • Not used to infringe on the rights of the original creators.
  • If you believe any content infringes your copyright, please contact us immediately.

Support

For help with questions, suggestions, or problems, please contact us