Deep learning based Nucleus Classification in pancreas histological images

Authors: Chang, Young Hwan, Thibault, Guillaume, Madin, Owen, Azimi, Vahid, Meyers, Cole, Johnson, Brett, Link, Jason, Margolin, Adam, Gray, Joe W.

Source: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) Engineering in Medicine and Biology Society (EMBC), 2017 39th Annual International Conference of the IEEE. :672-675 Jul, 2017

Relation: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Multiplexed immunohistochemistry image analysis using sparse coding

Authors: Chang, Young Hwan, Tsujikawa, Takahiro, Margolin, Adam, Coussens, Lisa M., Gray, Joe W.

Source: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) Engineering in Medicine and Biology Society (EMBC), 2017 39th Annual International Conference of the IEEE. :4046-4049 Jul, 2017

Relation: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Breast cancer histopathology image analysis pipeline for tumor purity estimation

Authors: Azimi, Vahid, Chang, Young Hwan, Thibault, Guillaume, Smith, Jaclyn, Tsujikawa, Takahiro, Kukull, Benjamin, Jensen, Bradden, Corless, Christopher, Margolin, Adam, Gray, Joe W.

Source: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017) Biomedical Imaging (ISBI 2017), 2017 IEEE 14th International Symposium on. :1137-1140 Apr, 2017

Relation: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017)

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics

Authors: Chang, Young Hwan, Thibault, Guillaume, Azimi, Vahid, Johnson, Brett, Jorgens, Danielle, Link, Jason, Margolin, Adam, Gray, Joe W.

Source: 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference of the. :1175-1178 Aug, 2016

Relation: 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

Multivariate dependence and genetic networks inference

Authors: Margolin, Adam A., Wang, Kai, Califano, Andrea, Nemenman, Ilya

Source: IET Syst Biol 4, 428, 2010

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1001.1681

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism

Authors: Davis, Ryan J., Gönen, Mehmet, Margineantu, Daciana H., Handeli, Shlomo, Swanger, Jherek, Hoellerbauer, Pia, Paddison, Patrick J., Gu, Haiwei, Raftery, Daniel, Grim, Jonathan E., Hockenbery, David M., Margolin, Adam A., Clurman, Bruce E.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2018 May . 115(21), 5462-5467.

Access URL: https://www.jstor.org/stable/26509844

Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Authors: Wang, Kai, Nemenman, Ilya, Banerjee, Nilanjana, Margolin, Adam, Califano, Andrea

Source: RECOMB'06 Proceedings, LNCS 3909, Springer, 2006

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/q-bio/0510030

Conditional Network Analysis Identifies Candidate Regulator Genes in Human B Cells

Authors: Wang, Kai, Banerjee, Nilanjana, Margolin, Adam, Nemenman, Ilya, Basso, Katia, Favera, Riccardo, Califano, Andrea

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/q-bio/0411003

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

Authors: Margolin, Adam A., Nemenman, Ilya, Basso, Katia, Klein, Ulf, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo Dalla, Califano, Andrea

Source: BMC Bioinformatics 2006, 7(Suppl 1):S7

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/q-bio/0410037

On The Reconstruction of Interaction Networks with Applications to Transcriptional Regulation

Authors: Margolin, Adam A., Nemenman, Ilya, Wiggins, Chris, Stolovitzky, Gustavo, Califano, Andrea

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/q-bio/0410036

Svpluscnv: analysis and visualization of complex structural variation data

Authors: Lopez, Gonzalo, Egolf, Laura E, Giorgi, Federico M, Diskin, Sharon J, Margolin, Adam A

Source: Bioinformatics. 37(13):1912-1914

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125388474.0x000001&indx=1&recIds=ETOCvdc_100125388474.0x000001

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Authors: Afsari, Bahman, Airola, Antti, Aittokallio, Tero, Bivol, Adrian, Boehm, Jesse S., Bunte, Kerstin, Carlin, Daniel, Chang, Yu-Chuan, Chen, Tenghui, Chong, Zechen, Chopra, Sahil, Cowley, Glenn S., Deran, Alden, Ellrott, Kyle, Elmarakeby, Haitham, Fertig, Elana J., Gonçalves, Emanuel, Gönen, Mehmet, Gong, Pinghua, Gopalacharyulu, Peddinti, Graim, Kiley, Guan, Yuanfang, Hafemeister, Christoph, Hahn, William C., Heath, Lenwood, Hoff, Bruce, Howell, Sara, Jaiswal, Alok, Karasuyama, Masayuki, Kaski, Samuel, Kędziorski, Łukasz, Khan, Suleiman A., Khemka, Niraj, King, Erh-kan, Lauria, Mario, Liu, Mark, Machado, Daniel, Mamitsuka, Hiroshi, Marbach, Daniel, Margolin, Adam A., Mazurkiewicz, Mateusz, Menden, Michael P., Migacz, Szymon, Newton, Yulia, Ng, Sam, Nie, Zhi, Norman, Thea C., Pahikkala, Tapio, Paull, Evan, Praveen, Paurush, Priami, Corrado, Rizzetto, Simone, Rocha, Miguel, Root, David E., Rudd, Cameron, Rudnicki, Witold R., Saez-Rodriguez, Julio, Sokolov, Artem, Song, Lei, Stolovitzky, Gustavo, Stuart, Joshua M., Sun, Duanchen, Szalai, Bence, Tang, Hao, Tang, Jing, Tsherniak, Aviad, Uzunangelov, Vladislav, Vazquez, Francisca, Wang, Tao, Wang, Difei, Weir, Barbara A., Wennerberg, Krister, Wu, Ling-yun, Xiao, Guanghua, Xie, Yang, Ye, Jieping, Ye, Yuting, Zhan, Xiaowei, Zhou, Wanding, Zhu, Fan

Source: In Cell Systems 22 November 2017 5(5):485-497

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

Authors: Palpant, Nathan J., Wang, Yuliang, Hadland, Brandon, Zaunbrecher, Rebecca J., Redd, Meredith, Jones, Daniel, Pabon, Lil, Jain, Rajan, Epstein, Jonathan, Ruzzo, Walter L., Zheng, Ying, Bernstein, Irwin, Margolin, Adam, Murry, Charles E.

Source: In Cell Reports 15 August 2017 20(7):1597-1608

Valection: design optimization for validation and verification studies

Authors: Cooper, Christopher, Yao, Delia, Sendorek, Dorota, Yamaguchi, Takafumi, P'ng, Christine, Houlahan, Kathleen, Caloian, Cristian, Fraser, Michael, Ellrott, Kyle, Margolin, Adam, Bristow, Robert, Stuart, Joshua, Boutros, Paul

Source: BMC bioinformatics. 19(1):1-11

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183813462.0x000001&indx=1&recIds=ETOCvdc_100183813462.0x000001

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Authors: Sendorek, Dorota, Caloian, Cristian, Ellrott, Kyle, Bare, J., Yamaguchi, Takafumi, Ewing, Adam, Houlahan, Kathleen, Norman, Thea, Margolin, Adam, Stuart, Joshua, Boutros, Paul

Source: BMC bioinformatics. 19(1):1-9

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161321661.0x000001&indx=1&recIds=ETOCvdc_100161321661.0x000001

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Authors: Lee, Anna, Ewing, Adam, Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen, Bare, J., Espiritu, Shadrielle, Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi, Kellen, Michael, Chen, Ken, Norman, Thea, Friend, Stephen, Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam, Stuart, Joshua, Boutros, Paul

Source: Genome biology. 19(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185396729.0x000001&indx=1&recIds=ETOCvdc_100185396729.0x000001

Population-level distribution and putative immunogenicity of cancer neoepitopes

Authors: Wood, Mary, Paralkar, Mayur, Paralkar, Mihir, Nguyen, Austin, Struck, Adam, Ellrott, Kyle, Margolin, Adam, Nellore, Abhinav, Thompson, Reid

Source: BMC cancer. 18(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161854494.0x000001&indx=1&recIds=ETOCvdc_100161854494.0x000001

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

Authors: Salomonis, Nathan, Dexheimer, Phillip J., Omberg, Larsson, Schroll, Robin, Bush, Stacy, Huo, Jeffrey, Schriml, Lynn, Ho Sui, Shannan, Keddache, Mehdi, Mayhew, Christopher, Shanmukhappa, Shiva Kumar, Wells, James, Daily, Kenneth, Hubler, Shane, Wang, Yuliang, Zambidis, Elias, Margolin, Adam, Hide, Winston, Hatzopoulos, Antonis K., Malik, Punam, Cancelas, Jose A., Aronow, Bruce J., Lutzko, Carolyn

Source: In Stem Cell Reports 12 July 2016 7(1):110-125

Kernelized Bayesian Transfer Learning
Proceedings of twenty-eighth AAAI Conference on Artificial Intelligence and the twenty-sixth Innovative Applications of Artificial Intelligence Conference [and the Fifth Symposium on Educational Advances in Artificial Intelligence]

Authors: Gönen, Mehmet, Margolin, Adam A.

Source: Proceedings of the National Conference on Artificial Intelligence. 28(3):1831-1839

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN600632514&indx=1&recIds=ETOCCN600632514

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

Authors: Tsujikawa, Takahiro, Kumar, Sushil, Borkar, Rohan N., Azimi, Vahid, Thibault, Guillaume, Chang, Young Hwan, Balter, Ariel, Kawashima, Rie, Choe, Gina, Sauer, David, El Rassi, Edward, Clayburgh, Daniel R., Kulesz-Martin, Molly F., Lutz, Eric R., Zheng, Lei, Jaffee, Elizabeth M., Leyshock, Patrick, Margolin, Adam A., Mori, Motomi, Gray, Joe W., Flint, Paul W., Coussens, Lisa M.

Source: Cell reports. 19(1):203-217

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100063241393.0x000001&indx=1&recIds=ETOCvdc_100063241393.0x000001