Referenced Papers (7)
Multimodal masked autoencoders learn transferable representations
Xinyang Geng, Hao Liu, Lisa Lee, Dale Schuurmans, Sergey Levine, Pieter Abbeel
arXiv [cs.CV], 2022
"This paper is used as an example of a text-vision multi-modal masked model to introduce the concept of masking across modalities, which is the core inspiration for the Nona framework."
Chromatin position effects assayed by thousands of reporters integrated in parallel
Waseem Akhtar, Johann de Jong, Alexey V Pindyurin, Ludo Pagie, Wouter Meuleman, Jeroen de Ridder
Cell, 2013
"This paper is cited to introduce the TRIP-seq assay, which is used for a downstream evaluation of the context-aware Nona model's ability to predict gene expression upon integration of a reporter gene."
Promoter-intrinsic and local chromatin features determine gene repression in LADs
Christ Leemans, Marloes C H van der Zwalm, Laura Brueckner, Federico Comoglio, Tom van Schaik, Ludo Pagie
Cell, 2019
"This citation refers to the dataset used for evaluating the model's performance on TRIP-seq predictions, demonstrating that the context-aware model improves accuracy."
Effect of genomic and cellular environments on gene expression noise
Clarice K Y Hong, Avinash Ramu, Siqi Zhao, Barak A Cohen
bioRxiv, 2022
"This citation refers to a more recent dataset used to further validate that adding genomic context information improves the model's TRIP-seq prediction capabilities."
Caduceus: Bi-directional equivariant long-range DNA sequence modeling
Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, Volodymyr Kuleshov
ICML, 2024
"The speaker uses Caduceus as an example of a standard, unconditioned masked DNA language model to contrast its learned features with those of their functionally-informed Nona model."
Direct observation of the neural computations underlying a single decision
Natalie A Steinemann, Gabriel M Stine, Eric M Trautmann, Ariel Zylberberg, Daniel M Wolpert, Michael N Shadlen
bioRxiv, 2022
"This paper is cited as evidence for the sequence preference of the Tn5 enzyme used in ATAC-seq, a key concept for the speaker's analysis of genotype prediction from ATAC-seq data."
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Anusri Pampari, A Shcherbina, Evgeny Z Kvon, Michael Kosicki, Surag Nair, Soumya Kundu
bioRxiv, 2025
"This paper is cited as further evidence for the sequence bias of the Tn5 enzyme, which is foundational to the speaker's work on linking ATAC-seq fragment files back to individual genotypes."