Author

Cesar Miguel Valdez Cordova

Johannes Kepler University of LinzORCID 0000-0002-8074-5525Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Approach:benchmark study· 1 Assay:ChIP-seq· 1 Approach:deep learning· 1 Approach:diffusion model· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:perturbation response prediction· 1

Frequent Co-Authors

Aaron WenteleriD· 2 shared Alex Hawkins‐HookeriD· 1 shared Amaya Gallagher-SyediD· 1 shared Aniketh Janardhan ReddyiD· 1 shared Cameron Smith· 1 shared Emily S. W. WongiD· 1 shared Lithin Karmel Louis· 1 shared Luca PinelloiD· 1 shared

Activity by Year

2024-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Aaron WentelerORCID

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2 papers

Recent·Most cited

PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction

Aaron Wenteler, Martina Occhetta, Nikhil Branson, Victor Curean, Magdalena Huebner, William Dee, William Connell, Siu Pui Chung, Alex Hawkins‐Hooker, Yasha Ektefaie, Cesar Miguel Valdez Cordova, Amaya Gallagher-Syed

This study benchmarks zero-shot single-cell foundation model embeddings for perturbation effect prediction and finds they do not consistently improve over baseline models under distribution shift.

bioRxiv · Oct 2, 2024 · PreprintBioinformatics

DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements

Lucas F. daSilva, Simon Senan, Zain Munir Patel, Aniketh Janardhan Reddy, Sameer Gabbita, Zach Nussbaum, Cesar Miguel Valdez Cordova, Aaron Wenteler, Noah Weber, Tin M. Tunjic, Talha Ahmad Khan, Zelun Li, Cameron Smith, Matei Bejan, Lithin Karmel Louis, , Luca Pinello

DNA-Diffusion uses diffusion models to generate cell type-specific regulatory DNA sequences that modulate chromatin accessibility and gene expression.

bioRxiv · Feb 1, 2024 · PreprintSynthetic Biology