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Biorxiv : the Preprint Server for Biology|February 26, 2024
Evaluation and optimization of sequence-based gene regulatory deep learning modelsAbdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, et al.
Nature Biotechnology|October 11, 2024
A community effort to optimize sequence-based deep learning models of gene regulationAbdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, et al.
Biorxiv : the Preprint Server for Biology|November 28, 2024
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factorsArttu Jolma, Kaitlin U Laverty, Ali Fathi, et al.
Plos One|May 6, 2024
Annotation of nuclear lncRNAs based on chromatin interactionsSaumya Agrawal, Andrey Buyan, Jessica Severin, et al.
Plos One|April 28, 2026
Correction: Annotation of nuclear lncRNAs based on chromatin interactionsSaumya Agrawal, Andrey Buyan, Jessica Severin, et al.
Nature|August 5, 2026
An expanded codebook of human transcription factor DNA-binding specificityArttu Jolma, Kaitlin U Laverty, Ali Fathi, et al.
Biorxiv : the Preprint Server for Biology|December 3, 2025
Inferring binding specificities of human transcription factors with the wisdom of crowdsNikita Gryzunov, Dmitry Penzar, Vasilii Kamenets, et al.
Communications Biology|November 7, 2025
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factorsIlya E Vorontsov, Ivan Kozin, Sergey Abramov, et al.
Biorxiv : the Preprint Server for Biology|November 28, 2024
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factorsIlya E Vorontsov, Ivan Kozin, Sergey Abramov, et al.
Genome Research|July 29, 2020
Functional annotation of human long noncoding RNAs via molecular phenotypingJordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, et al.
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