Browse by CSHL Author

Paper

Tang, Ziqi, Somia, Nirali, Yu, Yiyang, Koo, Peter K (July 2025) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. Genome Biology, 26 (1). ISSN 1474-760X (Public Dataset)

Zhou, Jessica, Rizzo, Kaeli, Tang, Ziqi, Koo, Peter K (November 2024) Uncertainty-aware genomic deep learning with knowledge distillation. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Sarkar, Anirban, Tang, Ziqi, Zhao, Chris, Koo, Peter (May 2024) Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion. bioRxiv. (Submitted)

Tang, Ziqi, Koo, Peter K (March 2024) Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv. (Public Dataset) (Submitted)

Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (December 2023) Current approaches to genomic deep learning struggle to fully capture human genetic variation. Nature Genetics, 55 (12). pp. 2021-2022. ISSN 1061-4036

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

Karakida Kawaguchi, Risa, Tang, Ziqi, Fischer, Stephan, Rajesh, Chandana, Tripathy, Rohit, Koo, Peter K, Gillis, Jesse (December 2022) Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Briefings in Bioinformatics. bbac541. ISSN 1467-5463

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (December 2022) Evaluating deep learning for predicting epigenomic profiles. Nature Machine Intelligence, 4 (12). pp. 1088-1100. ISSN 2522-5839

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (May 2022) Evaluating deep learning for predicting epigenomic profiles. bioRxiv. (Unpublished)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter (2022) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. bioRxiv. (Submitted)

Kawaguchi, Risa Karakida, Tang, Ziqi, Fischer, Stephan, Tripathy, Rohit, Koo, Peter, Gillis, Jesse (April 2021) Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility. bioRxiv. (Unpublished)

Thesis

Tang, Ziqi (April 2024) Exploring the Representational Power of Genomic Deep Learning Models. PhD thesis, Cold Spring Harbor Laboratory.