The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning. - Janine Arloth; Gökcen Eraslan; Till F. M. Andlauer; Jade Martins; Stella Iurato; Brigitte Kühnel; Melanie Waldenberger; Josef Frank; Ralf Gold; Bernhard Hemmer; Felix Luessi; Sandra Nischwitz; et al. (PLoS Comput. Biol., 2020)

ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data. - Maria Osmala; Gökcen Eraslan; Harri Lähdesmäki (Bioinform., 2022)

GFlowNet Assisted Biological Sequence Editing. - Pouya M. Ghari; Alex M. Tseng; Gökcen Eraslan; Romain Lopez; Tommaso Biancalani; Gabriele Scalia; Ehsan Hajiramezanali (NeurIPS, 2024)

Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models. - Masatoshi Uehara; Yulai Zhao 002; Ehsan Hajiramezanali; Gabriele Scalia; Gökcen Eraslan; Avantika Lal; Sergey Levine; Tommaso Biancalani (NeurIPS, 2024)

regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. - Avantika Lal; David Garfield; Tommaso Biancalani; Gökcen Eraslan (RECOMB, 2024)

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding. - Xiner Li; Yulai Zhao 002; Chenyu Wang 003; Gabriele Scalia; Gökcen Eraslan; Surag Nair; Tommaso Biancalani; Aviv Regev; Sergey Levine; Masatoshi Uehara (CoRR, 2024)

A mechanistically interpretable neural network for regulatory genomics. - Alex M. Tseng; Gökcen Eraslan; Tommaso Biancalani; Gabriele Scalia (CoRR, 2024)