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references.bib
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@article{Chawla2013,
author = {Chawla, Konika and Tripathi, Sushil and Thommesen, Liv and L{\ae}greid, Astrid and Kuiper, Martin},
doi = {10.1093/bioinformatics/btt432},
issn = {14602059},
journal = {Bioinformatics},
mendeley-groups = {Databases},
month = {oct},
number = {19},
pages = {2519--2520},
pmid = {23933972},
publisher = {Oxford University Press},
title = {{TFcheckpoint: A curated compendium of specific DNA-binding RNA polymerase II transcription factors}},
url = {www.tfcheckpoint.org},
volume = {29},
year = {2013}
}
@article{Carbon2019,
author = {Carbon, S. and Douglass, E. and Dunn, N. and Good, B. and Harris, N. L. and Lewis, S. E. and Mungall, C. J. and Basu, S. and Chisholm, R. L. and Dodson, R. J. and Hartline, E. and Fey, P. and Thomas, P. D. and Albou, L. P. and Ebert, D. and Kesling, M. J. and Mi, H. and Muruganujan, A. and Huang, X. and Poudel, S. and Mushayahama, T. and Hu, J. C. and LaBonte, S. A. and Siegele, D. A. and Antonazzo, G. and Attrill, H. and Brown, N. H. and Fexova, S. and Garapati, P. and Jones, T. E.M. and Marygold, S. J. and Millburn, G. H. and Rey, A. J. and Trovisco, V. and {Dos Santos}, G. and Emmert, D. B. and Falls, K. and Zhou, P. and Goodman, J. L. and Strelets, V. B. and Thurmond, J. and Courtot, M. and Osumi, D. S. and Parkinson, H. and Roncaglia, P. and Acencio, M. L. and Kuiper, M. and Lreid, A. and Logie, C. and Lovering, R. C. and Huntley, R. P. and Denny, P. and Campbell, N. H. and Kramarz, B. and Acquaah, V. and Ahmad, S. H. and Chen, H. and Rawson, J. H. and Chibucos, M. C. and Giglio, M. and Nadendla, S. and Tauber, R. and Duesbury, M. J. and Del, N. T. and Meldal, B. H.M. and Perfetto, L. and Porras, P. and Orchard, S. and Shrivastava, A. and Xie, Z. and Chang, H. Y. and Finn, R. D. and Mitchell, A. L. and Rawlings, N. D. and Richardson, L. and Sangrador-Vegas, A. and Blake, J. A. and Christie, K. R. and Dolan, M. E. and Drabkin, H. J. and Hill, D. P. and Ni, L. and Sitnikov, D. and Harris, M. A. and Oliver, S. G. and Rutherford, K. and Wood, V. and Hayles, J. and Bahler, J. and Lock, A. and Bolton, E. R. and {De Pons}, J. and Dwinell, M. and Hayman, G. T. and Laulederkind, S. J.F. and Shimoyama, M. and Tutaj, M. and Wang, S. J. and D'Eustachio, P. and Matthews, L. and Balhoff, J. P. and Aleksander, S. A. and Binkley, G. and Dunn, B. L. and Cherry, J. M. and Engel, S. R. and Gondwe, F. and Karra, K. and MacPherson, K. A. and Miyasato, S. R. and Nash, R. S. and Ng, P. C. and Sheppard, T. K. and {Shrivatsav Vp}, A. and Simison, M. and Skrzypek, M. S. and Weng, S. and Wong, E. D. and Feuermann, M. and Gaudet, P. and Bakker, E. and Berardini, T. Z. and Reiser, L. and Subramaniam, S. and Huala, E. and Arighi, C. and Auchincloss, A. and Axelsen, K. and Argoud, G. P. and Bateman, A. and Bely, B. and Blatter, M. C. and Boutet, E. and Breuza, L. and Bridge, A. and Britto, R. and Bye-A-Jee, H. and Casals-Casas, C. and Coudert, E. and Estreicher, A. and Famiglietti, L. and Garmiri, P. and Georghiou, G. and Gos, A. and Gruaz-Gumowski, N. and Hatton-Ellis, E. and Hinz, U. and Hulo, C. and Ignatchenko, A. and Jungo, F. and Keller, G. and Laiho, K. and Lemercier, P. and Lieberherr, D. and Lussi, Y. and Mac-Dougall, A. and Magrane, M. and Martin, M. J. and Masson, P. and Natale, D. A. and Hyka, N. N. and Pedruzzi, I. and Pichler, K. and Poux, S. and Rivoire, C. and Rodriguez-Lopez, M. and Sawford, T. and Speretta, E. and Shypitsyna, A. and Stutz, A. and Sundaram, S. and Tognolli, M. and Tyagi, N. and Warner, K. and Zaru, R. and Wu, C. and Chan, J. and Cho, J. and Gao, S. and Grove, C. and Harrison, M. C. and Howe, K. and Lee, R. and Mendel, J. and Muller, H. M. and Raciti, D. and {Van Auken}, K. and Berriman, M. and Stein, L. and Sternberg, P. W. and Howe, D. and Toro, S. and Westerfield, M.},
doi = {10.1093/nar/gky1055},
issn = {13624962},
journal = {Nucleic Acids Research},
keywords = {genes},
mendeley-groups = {Databases},
month = {jan},
number = {D1},
pages = {D330--D338},
pmid = {30395331},
publisher = {Oxford University Press},
title = {{The Gene Ontology Resource: 20 years and still GOing strong}},
url = {http://geneontology.org/go-cam.},
volume = {47},
year = {2019}
}
@article{McInnes2018a,
archivePrefix = {arXiv},
arxivId = {1802.03426},
author = {McInnes, Leland and Healy, John and Melville, James},
eprint = {1802.03426},
file = {:home/john/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/McInnes, Healy, Melville - 2018 - UMAP Uniform Manifold Approximation and Projection for Dimension Reduction.pdf:pdf},
mendeley-groups = {Machine Learning},
month = {feb},
title = {{UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction}},
url = {http://arxiv.org/abs/1802.03426 https://github.com/jlmelville/uwot},
year = {2018}
}
@article{Schmeier2017,
author = {Schmeier, Sebastian and Alam, Tanvir and Essack, Magbubah and Bajic, Vladimir B.},
doi = {10.1093/nar/gkw1007},
issn = {13624962},
journal = {Nucleic Acids Research},
keywords = {mandibulofacial dysostosis,mice,transcription factor},
month = {jan},
number = {D1},
pages = {D145--D150},
pmid = {27789689},
publisher = {Oxford University Press},
title = {{TcoF-DB v2: Update of the database of human and mouse transcription co-factors and transcription factor interactions}},
url = {https://academic.oup.com/nar/article/45/D1/D145/2333914},
volume = {45},
year = {2017}
}
@article{Lovering2021,
annote = {The list of human DbTFs from GREEKC (2021):
https://www.ebi.ac.uk/QuickGO/targetset/dbTF},
author = {Lovering, Ruth C. and Gaudet, Pascale and Acencio, Marcio L. and Ignatchenko, Alex and Jolma, Arttu and Fornes, Oriol and Kuiper, Martin and Kulakovskiy, Ivan V. and L{\ae}greid, Astrid and Martin, Maria J. and Logie, Colin},
doi = {10.1016/J.BBAGRM.2021.194765},
issn = {1874-9399},
journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms},
mendeley-groups = {Datasets},
month = {oct},
pages = {194765},
publisher = {Elsevier},
title = {{A GO catalogue of human DNA-binding transcription factors}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1874939921000833},
year = {2021}
}
@article{Kim2021,
author = {Kim, Gi Bae and Gao, Ye and Palsson, Bernhard O. and Lee, Sang Yup},
doi = {10.1073/pnas.2021171118},
issn = {10916490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = {jan},
number = {2},
pmid = {33372147},
publisher = {National Academy of Sciences},
title = {{DeepTFactor: A deep learning-based tool for the prediction of transcription factors}},
url = {https://www.pnas.org/content/118/2/e2021171118},
volume = {118},
year = {2021}
}