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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS
Johnson, Jeanette A. I., Tsang, Ashley P., Mitchell, Jacob T., Zhou, David L., Bowden, Julia, Davis-Marcisak, Emily, Sherman, Thomas, Liefeld, Ted, Loth, Melanie, Goff, Loyal A., Zimmerman, Jacquelyn W., Kinny-Köster, Ben, Jaffee, Elizabeth M., Tamayo, Pablo, Mesirov, Jill P., Reich, Michael, Fertig, Elana J., Stein-O’Brien, Genevieve L.
Published in Nature protocols (01.12.2023)
Published in Nature protocols (01.12.2023)
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Journal Article
Toward a unified framework for interpreting machine-learning models in neuroimaging
Kohoutová, Lada, Heo, Juyeon, Cha, Sungmin, Lee, Sungwoo, Moon, Taesup, Wager, Tor D., Woo, Choong-Wan
Published in Nature protocols (01.04.2020)
Published in Nature protocols (01.04.2020)
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Journal Article
Simulated annealing aided genetic algorithm for gene selection from microarray data
Marjit, Shyam, Bhattacharyya, Trinav, Chatterjee, Bitanu, Sarkar, Ram
Published in Computers in biology and medicine (01.05.2023)
Published in Computers in biology and medicine (01.05.2023)
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Journal Article
PyImageJ: A library for integrating ImageJ and Python
Rueden, Curtis T., Hiner, Mark C., Evans, Edward L., Pinkert, Michael A., Lucas, Alice M., Carpenter, Anne E., Cimini, Beth A., Eliceiri, Kevin W.
Published in Nature methods (01.11.2022)
Published in Nature methods (01.11.2022)
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Journal Article
Combining high throughput array synthesis and growth algorithm to discover TNF-α binders with new structures and properties
Lin, Weilin, Gandhi, Shanil, Bhattarai, Prabesh, Kasa, Keida, Kizil, Caghan, Zhang, Yixin
Published in European journal of medicinal chemistry (15.02.2023)
Published in European journal of medicinal chemistry (15.02.2023)
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Journal Article
Python tools for structural tasks in chemistry
Ryzhkov, Fedor V., Ryzhkova, Yuliya E., Elinson, Michail N.
Published in Molecular diversity (01.08.2025)
Published in Molecular diversity (01.08.2025)
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Journal Article
Towards understanding bugs in Python interpreters
Liu, Di, Feng, Yang, Yan, Yanyan, Xu, Baowen
Published in Empirical software engineering : an international journal (01.01.2023)
Published in Empirical software engineering : an international journal (01.01.2023)
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Journal Article
Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors
Peng, Yun, Gao, Shuzheng, Gao, Cuiyun, Huo, Yintong, Lyu, Michael R.
Published in Proceedings / International Conference on Software Engineering (14.04.2024)
Published in Proceedings / International Conference on Software Engineering (14.04.2024)
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Conference Proceeding
SAB: An open-access Python-based integrated platform for fully automated emergent sustainability assessment of biorefineries
Zarafshani, Hanie, Watjanatepin, Ponnapat, Navare, Kranti, Sauve, Giovanna, Van Acker, Karel
Published in The international journal of life cycle assessment (01.04.2024)
Published in The international journal of life cycle assessment (01.04.2024)
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Journal Article
LASSIM—A network inference toolbox for genome-wide mechanistic modeling
Magnusson, Rasmus, Mariotti, Guido Pio, Köpsén, Mattias, Lövfors, William, Gawel, Danuta R., Jörnsten, Rebecka, Linde, Jörg, Nordling, Torbjörn E. M., Nyman, Elin, Schulze, Sylvie, Nestor, Colm E., Zhang, Huan, Cedersund, Gunnar, Benson, Mikael, Tjärnberg, Andreas, Gustafsson, Mika
Published in PLoS computational biology (01.06.2017)
Published in PLoS computational biology (01.06.2017)
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Journal Article