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SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul
Published in Nature methods (01.03.2020)
Published in Nature methods (01.03.2020)
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Journal Article
ISMRM Raw data format: A proposed standard for MRI raw datasets
Inati, Souheil J., Naegele, Joseph D., Zwart, Nicholas R., Roopchansingh, Vinai, Lizak, Martin J., Hansen, David C., Liu, Chia‐Ying, Atkinson, David, Kellman, Peter, Kozerke, Sebastian, Xue, Hui, Campbell‐Washburn, Adrienne E., Sørensen, Thomas S., Hansen, Michael S.
Published in Magnetic resonance in medicine (01.01.2017)
Published in Magnetic resonance in medicine (01.01.2017)
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Journal Article
Probabilistic programming in Python using PyMC3
Salvatier, John, Wiecki, Thomas V., Fonnesbeck, Christopher
Published in PeerJ. Computer science (06.04.2016)
Published in PeerJ. Computer science (06.04.2016)
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Journal Article
Hidden Markov modeling for maximum probability neuron reconstruction
Athey, Thomas L., Tward, Daniel J., Mueller, Ulrich, Vogelstein, Joshua T., Miller, Michael I.
Published in Communications biology (25.04.2022)
Published in Communications biology (25.04.2022)
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Journal Article
PyRates—A code-generation tool for modeling dynamical systems in biology and beyond
Gast, Richard, Knösche, Thomas R., Kennedy, Ann
Published in PLoS computational biology (27.12.2023)
Published in PLoS computational biology (27.12.2023)
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Journal Article
Structural homology guided alignment of cysteine rich proteins
Shafee, Thomas M. A., Robinson, Andrew J., van der Weerden, Nicole, Anderson, Marilyn A.
Published in SpringerPlus (12.01.2016)
Published in SpringerPlus (12.01.2016)
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Journal Article
PyGeNN: A Python Library for GPU-Enhanced Neural Networks
Knight, James C., Komissarov, Anton, Nowotny, Thomas
Published in Frontiers in neuroinformatics (22.04.2021)
Published in Frontiers in neuroinformatics (22.04.2021)
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Journal Article
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
The atomic simulation environment-a Python library for working with atoms
Hjorth Larsen, Ask, Jørgen Mortensen, Jens, Blomqvist, Jakob, Castelli, Ivano E, Christensen, Rune, Du ak, Marcin, Friis, Jesper, Groves, Michael N, Hammer, Bjørk, Hargus, Cory, Hermes, Eric D, Jennings, Paul C, Bjerre Jensen, Peter, Kermode, James, Kitchin, John R, Leonhard Kolsbjerg, Esben, Kubal, Joseph, Kaasbjerg, Kristen, Lysgaard, Steen, Bergmann Maronsson, Jón, Maxson, Tristan, Olsen, Thomas, Pastewka, Lars, Peterson, Andrew, Rostgaard, Carsten, Schiøtz, Jakob, Schütt, Ole, Strange, Mikkel, Thygesen, Kristian S, Vegge, Tejs, Vilhelmsen, Lasse, Walter, Michael, Zeng, Zhenhua, Jacobsen, Karsten W
Published in Journal of physics. Condensed matter (12.07.2017)
Published in Journal of physics. Condensed matter (12.07.2017)
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Journal Article
Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies
Levine, Adam P, Connor, Thomas M F, Oygar, D Deren, Neild, Guy H, Segal, Anthony W, Maxwell, Patrick H, Gale, Daniel P
Published in BMC genomics (10.03.2015)
Published in BMC genomics (10.03.2015)
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Journal Article
A conversion tool for translating Python-based machine learning models to structured text codes
Campos, Yasmin Adriane de Paula, Pereira, Paulo Haron da Silva, Duarte, Robson Aparecido, Perez, José Manuel Gonzalez Túbio, Pessin, Gustavo, Pinto, Thomas Vargas Barsante
Published in SoftwareX (01.02.2025)
Published in SoftwareX (01.02.2025)
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Journal Article
Recent advances in the SISSO method and their implementation in the SISSO++ code
Purcell, Thomas A. R., Scheffler, Matthias, Ghiringhelli, Luca M.
Published in The Journal of chemical physics (21.09.2023)
Published in The Journal of chemical physics (21.09.2023)
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Journal Article
CUPyDO - An integrated Python environment for coupled fluid-structure simulations
Thomas, D., Cerquaglia, M.L., Boman, R., Economon, T.D., Alonso, J.J., Dimitriadis, G., Terrapon, V.E.
Published in Advances in engineering software (1992) (01.02.2019)
Published in Advances in engineering software (1992) (01.02.2019)
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Journal Article