Journal article Open Access
The evolution, evolvability and engineering of gene regulatory DNA
Eeshit Dhaval Vaishnav;
Carl de Boer;
Aviv Regev
All the data and trained models associated with the manuscript : 'The evolution, evolvability and engineering of gene regulatory DNA' can be found here.
The manuscript can be found at : https://doi.org/10.1038/s41586-022-04506-6
Note that the terms "Malleable" and "Plastic" in reference to the archetypes are used interchangeably. Every variable and column in the code and data that mentions "Plastic" is referring to the "Malleable" archetype. This term was updated from "Malleable" to "Plastic" in the final version of the manuscript at the request of a Reviewer.
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(6.5 GB)
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1011_genomes_ortho_seq_EL.tsv.gz
md5:2ac25f3c6a1c50857dd09b48e6b54db7 |
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1_inspect_test_data_and_reproduce_prediction_scatterplots.ipynb
md5:3f62d967569a432761ea1c8c4a1e5240 |
2.6 MB | Download |
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complex_media_expression.h5
md5:0f642b543000d4a1adee35bdaadcf1e8 |
250.8 MB | Download |
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complex_media_fitness_function.h5
md5:c863b809684cd575c4f873d0a07f50b9 |
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complex_media_fitness_function_summary.svg
md5:3726cddbb8cd92d232d33fb8520f13fd |
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complex_media_model_params.csv
md5:b153740e98441f484813b49719d27511 |
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complex_media_model_params.pkl
md5:bd6b0286147d324c314c95151984caf5 |
455 Bytes | Download |
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complex_media_scaler.save
md5:ed1f4fb9899c4b5640d76a363fa6a4d3 |
616 Bytes | Download |
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complex_media_training_data_Glu.txt
md5:4983ec724b503f06e5f466a6c3aaea45 |
3.6 GB | Download |
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defined_media_expression.h5
md5:9534956b7e63ff69ae96db37010b7c07 |
168.3 MB | Download |
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defined_media_fitness_function.h5
md5:a12239ecc3a3e3ac4904de7277d1b83c |
5.3 MB | Download |
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defined_media_model_params.csv
md5:5c5ab298b44f5d6452f0fcc0afe5e5f1 |
356 Bytes | Download |
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defined_media_model_params.pkl
md5:25595931bc4a8ca95c2d3c33811bafbf |
455 Bytes | Download |
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defined_media_scaler.save
md5:1ea655fc216ba1f2bb4cd9d9be47ffda |
616 Bytes | Download |
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defined_media_training_data_SC_Ura.txt
md5:bd94100c15d7575e265c002cf6e84712 |
2.5 GB | Download |
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Drift_complex.csv
md5:c22b1a8f65f335ebe718ad8dc5c178e0 |
445.7 kB | Download |
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Drift_defined.csv
md5:8721fe25c635c6c919e292a791070de6 |
446.1 kB | Download |
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Drift_delta_complex.csv
md5:8fc1ea3ee8d6289c999919ed222ba5bb |
450.6 kB | Download |
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Drift_delta_defined.csv
md5:47014f1ca60190486e920b71f66e9f4b |
451.0 kB | Download |
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Native_complex.csv
md5:9cae7d2d03b77ae8334575014bd1eccb |
592.2 kB | Download |
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Native_defined.csv
md5:e6971520fc1dd825f44d5a7e84179f2e |
594.3 kB | Download |
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Random_testdata_complex_media.txt
md5:fafd8196d8e939ee288bdfee0450199c |
427.2 kB | Download |
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Random_testdata_defined_media.csv
md5:18e6435a0f6844de957f9eaf558c3f7c |
2.3 MB | Download |
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README.md
md5:7ad19b1c17ff596a09fbf8a97769bcbc |
1.1 kB | Download |
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S288C_reference_promoter_expression_in_both_media.tsv
md5:af115c1f858e5e0b4add6e645828141c |
8.1 MB | Download |
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SSWM_complex.csv
md5:b504b6932af84617aef7e172fc2e0da3 |
1.5 MB | Download |
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SSWM_defined.csv
md5:2fd9af9ab5774237ec750a0f78579a38 |
942.1 kB | Download |
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SSWM_delta_complex.csv
md5:dde6c15d9dc60041e2762e4e8ef46acc |
411.6 kB | Download |
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SSWM_delta_defined.csv
md5:06652a8427f241474414c260217ff4c3 |
245.7 kB | Download |
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Supplementary_Table_1.xlsx
md5:031eb99f736aa23cfe4a081c25c58841 |
1.1 MB | Download |
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Indexed in
- Publication date:
- March 9, 2022
- DOI:
-
- License (for files):
- Creative Commons Attribution 4.0 International