Author

Daniel Ramirez

Hospital for Special Surgery;

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

Click to filter author papers

Bioengineering· 1 Neuroscience· 1 Pharmacology & Toxicology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1

Frequent Co-Authors

Adam W. HantmaniD· 1 shared Ahmad ElsayediD· 1 shared Amina Zafar· 1 shared Ataur KatebiiD· 1 shared Benjamin J. ArthuriD· 1 shared Brandon MooreiD· 1 shared Bridget M. Cole· 1 shared Bruno Dos Santos· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

1 shared paperNeuroscience

Adam W. HantmanORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Patient-Derived Synovium-on-a-Chip Recapitulates Disease and Treatment Response and Permits Study of Resistance

Ruiqi Chen, Theresa Wampler Muskardin, Fanghao Shi, Yeji Lee, Christele Felix, Carolyn Harris, Lunan Liu, Eric Suh, Emily Wu, Scott Rodeo, David Mayman, Daniel Ramirez, Katsuo Kurabayashi, Timothy B. Niewold, Weiqiang Chen

This paper develops a patient-derived synovium-on-a-chip model to study RA disease and treatment response, finding that it correlates with clinical outcomes and identifies ECM signaling as a resistance mechanism.

bioRxiv · Nov 2, 2026 · PreprintBioengineering

Attentive graph neural network models for the prediction of blood-brain barrier permeability

Jesse W. Collins, Mahmoud Ebrahimkhani, Daniel Ramirez, Jonathan Deiloff, Mauro Gonzalez, Mostafa Abedi, Laurence Philippe-Venec, Bridget M. Cole, Brandon Moore, Jennifer O. Nwankwo

This study benchmarks machine learning models for predicting blood-brain barrier permeability, showing attentive graph neural networks outperform traditional methods.

bioRxiv · Oct 12, 2024 · PreprintPharmacology & Toxicology

Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML

Ataur Katebi, Xiaowen Chen, Daniel Ramirez, Sheng Li, Mingyang Lu

The paper develops a computational approach to model core gene regulatory networks in IDH mutant AML, identifying key regulators like DNMT1 and E2F1 supported by patient survival data.

npj Systems Biology and Applications · Apr 9, 2024Peer-reviewedSystems Biology

Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain

Johan Winnubst, Erhan Bas, Tiago Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Benjamin J. Arthur, Christopher M. Bruns, Konrad Rokicki, David Schauder, Donald J. Olbris, Sean D. Murphy, David Ackerman, Cameron Arshadi, Perry Baldwin, , Jayaram V. Chandrashekar

The paper reconstructs 1,000 projection neurons in the mouse brain, revealing new cell types and organizational principles of long-range connectivity.

Cell · Jan 1, 2019Peer-reviewedNeuroscience