hlapp commited on
Commit
3d26a52
·
verified ·
1 Parent(s): 0eca5eb

Adds bioRxiv preprint reference and citation

Browse files
Files changed (1) hide show
  1. README.md +16 -38
README.md CHANGED
@@ -46,7 +46,7 @@ Trained BlueSTARR models take as input DNA sequences of length 300, 600, and 1k
46
  <!-- Provide the basic links for the model. -->
47
 
48
  - **Code:** [BlueSTARR](https://github.com/Duke-IGVF/BlueSTARR)
49
- - **Paper:** [More Information Needed]
50
  <!--- **Demo:** [More Information Needed--encouraged] -->
51
 
52
  ### Out-of-Scope Use
@@ -110,47 +110,25 @@ Code to train BlueSTARR models and to perform inference with them can be found i
110
 
111
  ## Citation
112
 
113
- <!-- If there is a paper introducing the model, the Bibtex information for that should go in this section.
114
-
115
- See notes at top of file about selecting a license.
116
- If you choose CC0: This model is dedicated to the public domain for the benefit of scientific pursuits. We ask that you cite the model and journal paper using the below citations if you make use of it in your research.
117
-
118
- -->
119
 
120
  **BibTeX:**
121
 
122
- [More Information Needed]
123
- <!--
124
- Replace "<>"s with your info:
125
-
126
- If you use our model in your work, please cite the model and associated paper.
127
-
128
- **Model**
129
- ```​
130
- @software{<ref_code>,
131
- author = {<author1 and author2>},
132
- doi = {<doi once generated>},
133
- title = {<title>},
134
- version = {<version#>},
135
- year = {<year>},
136
- url = {https://huggingface.co/imageomics/<model_name>}
137
  }
138
- ```
139
-
140
- -for an associated paper:
141
- **Paper**
142
- ```​
143
- @article{<ref_code>,
144
- title = {<title>},
145
- author = {<author1 and author2>},
146
- journal = {<journal_name>},
147
- year = <year>,
148
- url = {<DOI_URL>},
149
- doi = {<DOI>}
150
- }
151
- ```​
152
- -->
153
-
154
 
155
  ## Acknowledgements
156
 
 
46
  <!-- Provide the basic links for the model. -->
47
 
48
  - **Code:** [BlueSTARR](https://github.com/Duke-IGVF/BlueSTARR)
49
+ - **Paper:** Revathy Venukuttan, Richard Doty, Alexander Thomson, Yutian Chen, Boyao Li, Yuncheng Duan, Alejandro Barrera, Katherine Dura, Kuei-Yueh Ko, Hilmar Lapp, Timothy E Reddy, Andrew S Allen, William H Majoros (2026). Modeling gene regulatory perturbations via deep learning from high-throughput reporter assays. bioRxiv 2026.03.27.714770; doi: https://doi.org/10.64898/2026.03.27.714770
50
  <!--- **Demo:** [More Information Needed--encouraged] -->
51
 
52
  ### Out-of-Scope Use
 
110
 
111
  ## Citation
112
 
113
+ <!-- If there is a paper introducing the model, the Bibtex information for that should go in this section. -->
 
 
 
 
 
114
 
115
  **BibTeX:**
116
 
117
+ If you use our model in your work, please cite the associated paper:
118
+
119
+ ```
120
+ @article {Venukuttan2026.03,
121
+ author = {Venukuttan, Revathy and Doty, Richard and Thomson, Alexander and Chen, Yutian and Li, Boyao and Duan, Yuncheng and Barrera, Alejandro and Dura, Katherine and Ko, Kuei-Yueh and Lapp, Hilmar and Reddy, Timothy E and Allen, Andrew S and Majoros, William H},
122
+ title = {Modeling gene regulatory perturbations via deep learning from high-throughput reporter assays},
123
+ elocation-id = {2026.03.27.714770},
124
+ year = {2026},
125
+ doi = {10.64898/2026.03.27.714770},
126
+ publisher = {Cold Spring Harbor Laboratory},
127
+ URL = {https://www.biorxiv.org/content/early/2026/03/31/2026.03.27.714770},
128
+ eprint = {https://www.biorxiv.org/content/early/2026/03/31/2026.03.27.714770.full.pdf},
129
+ journal = {bioRxiv}
 
 
130
  }
131
+ ```
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
132
 
133
  ## Acknowledgements
134