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BioCoder: a benchmark for bioinformatics code generation with large language models
Tang, Xiangru, Qian, Bill, Gao, Rick, Chen, Jiakang, Chen, Xinyun, Gerstein, Mark B
Published in Bioinformatics (Oxford, England) (28.06.2024)
Published in Bioinformatics (Oxford, England) (28.06.2024)
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Journal Article
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
Varabyou, Ales, Sommer, Markus J., Erdogdu, Beril, Shinder, Ida, Minkin, Ilia, Chao, Kuan-Hao, Park, Sukhwan, Heinz, Jakob, Pockrandt, Christopher, Shumate, Alaina, Rincon, Natalia, Puiu, Daniela, Steinegger, Martin, Salzberg, Steven L., Pertea, Mihaela
Published in Genome Biology (30.10.2023)
Published in Genome Biology (30.10.2023)
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Journal Article
Revisiting the Impact of Anti-patterns on Fault-Proneness: A Differentiated Replication
Ikama, Aurel, Du, Vincent, Belias, Philippe, Muse, Biruk Asmare, Khomh, Foutse, Hamdaqa, Mohammad
Published in Proceedings / IEEE International Working Conference on Source Code Analysis and Manipulation (01.10.2022)
Published in Proceedings / IEEE International Working Conference on Source Code Analysis and Manipulation (01.10.2022)
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Conference Proceeding
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
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
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
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
Sparse Codebook Model of Local Structures for Retrieval of Focal Liver Lesions Using Multiphase Medical Images
Chen, Yen-Wei, Hu, Hongjie, Lin, Lanfen, Xu, Yingying, Han, Xian-Hua, Wang, Jian, Jin, Chongwu
Published in International journal of biomedical imaging (01.01.2017)
Published in International journal of biomedical imaging (01.01.2017)
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Journal Article