Add detailed citation info

README.md

@@ -25,7 +25,7 @@ configs:
   - config_name: YM_1068
     data_files: "data/YM_1068/data.parquet"
 ---
-# A-Alpha Datasets
+# Open Protein–Protein Interaction Affinity Datasets with AlphaSeq
 
 Protein-protein interactions (PPIs) are fundamental to countless biological processes. One of the most informative biophysical properties of a PPI is the binding affinity: the strength of how two proteins interact. Yet, despite its importance, publicly available affinity data remains limited, constraining the development and benchmarking of protein modeling methods.
 
@@ -98,6 +98,24 @@ print(ds)
 | YM_0989 | Trastuzumab-scFv CDR3 Optimization Variants Iter0 x HER-2 | [details](./data/YM_0989/README.md) |
 | YM_0990 | Trastuzumab-scFv CDR+FW Optimization Variants Iter0 x HER-2 | [details](./data/YM_0990/README.md) |
 
+## References
+
+This dataset collection builds on the AlphaSeq high-throughput yeast mating assay technology and includes data from multiple publications:
+
+### Core Technology
+
+- Younger, D., Berger, S., Baker, D., & Klavins, E. (2017). High-throughput characterization of protein-protein interactions by reprogramming yeast mating. Proceedings of the National Academy of Sciences of the United States of America, 114(46), 12166–12171. [https://doi.org/10.1073/pnas.1705867114](https://doi.org/10.1073/pnas.1705867114)
+
+### Dataset Sources
+
+**YM_0005:**
+
+- Engelhart, E., Lopez, R., Emerson, R., Lin, C., Shikany, C., Guion, D., Kelley, M., & Younger, D. (2022). Massively multiplexed affinity characterization of therapeutic antibodies against SARS-CoV-2 variants. Antibody therapeutics, 5(2), 130–137. [https://doi.org/10.1093/abt/tbac011](https://doi.org/10.1093/abt/tbac011)
+
+**YM_0549, YM_0693, YM_0852, YM_0985, YM_0988, YM_0989, YM_0990, YM_1068:**
+
+- Agarwal, A. A., Harrang, J., Noble, D., McGowan, K. L., Lange, A. W., Engelhart, E., Lahman, M. C., Adamo, J., Yu, X., Serang, O., Minch, K. J., Wellman, K. Y., Younger, D. A., Lopez, R. M., & Emerson, R. O. (2025). AlphaBind, a domain-specific model to predict and optimize antibody-antigen binding affinity. mAbs, 17(1), 2534626. [https://doi.org/10.1080/19420862.2025.2534626](https://doi.org/10.1080/19420862.2025.2534626)
+
 ## Dataset schema
 
 | Column | Description |
@@ -143,8 +161,29 @@ Iter0 and Iter1 (abbreviated for Iteration) are our nomenclature for describing
 
 ### How should I cite this dataset?
 
-Please cite:
-A-Alpha Bio (2025). Open Protein–Protein Interaction Affinity Datasets. <https://huggingface.co/datasets/aalphabio/open-alphaseq>
+To properly acknowledge this work, please cite:
+
+1. **This dataset repository:**
+
+   ```text
+   A-Alpha Bio (2025). Open Protein–Protein Interaction Affinity Datasets with AlphaSeq.
+   https://huggingface.co/datasets/aalphabio/open-alphaseq
+   ```
+
+2. **The AlphaSeq technology paper:**
+
+   ```text
+   Younger, D., Berger, S., Baker, D., & Klavins, E. (2017).
+   High-throughput characterization of protein–protein interactions by reprogramming yeast mating.
+   Proceedings of the National Academy of Sciences, 114(46), 12166-12171.
+   https://doi.org/10.1073/pnas.1705867114
+   ```
+
+3. **The specific experiment paper(s) for the dataset(s) you use:**
+   - **If using YM_0005:** Cite the CoV epitope mapping paper (Engelhart et al., 2022) - see [References](#references) section
+   - **If using any other experiments (YM_0549, YM_0693, YM_0852, YM_0985, YM_0988, YM_0989, YM_0990, YM_1068):** Cite the AlphaBind paper (2025) - see [References](#references) section
+
+For complete citation details and DOI links, see the [References](#references) section above.
 
 ### Can I use this dataset for model training or benchmarking?
 

data/YM_0549/README.md

@@ -8,6 +8,8 @@ YM_0549 consists of VHH72 designs against SARS CoV-2 RBD. We wanted to perturb t
 
 This dataset includes 29765 unique VHHs and 8 unique RBD sequences. The alpha-library is the same as YM_1068.
 
+A more extensive methods section can be found in our publication [here](https://pmc.ncbi.nlm.nih.gov/articles/PMC12296056/).
+
 ## Misc dataset details
 
 We define the following binders: