Author

Daniel H. Kim

University of California, Santa Cruz

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

Biology Disciplines

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Genomics· 4 Cell Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Research Focus:differential expression· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

David Carrillo· 3 shared Roman E. ReggiardoiD· 3 shared Sreelakshmi Velandi Maroli· 3 shared Mehmet Ozgün OzeniD· 2 shared Utkan DemirciiD· 2 shared Vikas PedduiD· 2 shared Alan Y. Hsu· 1 shared Alexander HilliD· 1 shared

Activity by Year

2020-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersGenomics

David Carrillo

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

RNA liquid biopsy via nanopore sequencing for novel biomarker discovery and cancer early detection

Vikas Peddu, Alexander Hill, Sreelakshmi Velandi Maroli, Connor Mattingly, Joshua M.V. Gardner, Karen H. Miga, Rebecca Claire Fitzgerald, Daniel H. Kim

This study uses long-read nanopore sequencing of cell-free RNA to detect early-stage cancer and discover novel biomarkers, identifying 270,679 intergenic RNAs and potential therapeutic targets.

bioRxiv · Jul 2, 2025 · PreprintGenomics

RABEP1 amplifies front signaling in neutrophil migration

Daniel H. Kim, Ramizah Syahirah, Conwy Zheng, Chang Ding, Alan Y. Hsu, Sheng Liu, Jun Wan, Qing Deng

This study identifies RABEP1 as a key regulator of neutrophil migration by promoting endosomal recycling, Rac activation, and actin polymerization in zebrafish and human cells.

bioRxiv · May 8, 2025 · PreprintCell Biology

Transposable element RNA dysregulation in mutant KRAS(G12C) 3D lung cancer spheroids

David Carrillo, Roman E. Reggiardo, John Lim, Gary L. Mantalas, Vikas Peddu, Daniel H. Kim

This study investigates how KRAS(G12C) mutations affect transposable element RNA expression in 3D lung cancer spheroids, finding mutation-specific TE RNA dysregulation and activation of Alu-derived RNAs with innate immunity genes.

bioRxiv · Feb 27, 2023 · PreprintGenomics

Extracellular RNA signatures of mutant KRAS(G12C) lung adenocarcinoma cells

Reem Khojah, Roman E. Reggiardo, Mehmet Ozgün Ozen, Sreelakshmi Velandi Maroli, David Carrillo, Utkan Demirci, Daniel H. Kim

This study identifies specific extracellular RNA signatures secreted by mutant KRAS(G12C) lung adenocarcinoma cells that correlate with patient survival.

bioRxiv · Feb 23, 2022 · PreprintGenomics

Epigenomic reprogramming of repetitive noncoding RNAs and IFN-stimulated genes by mutant KRAS

Roman E. Reggiardo, Sreelakshmi Velandi Maroli, Haley Halasz, Mehmet Ozgün Ozen, David Carrillo, Erin LaMontagne, Lila Whitehead, Eejung Kim, Shivani Malik, Jason D. Fernandes, Georgi K. Marinov, Eric Andrew Collisson, Utkan Demirci, Daniel H. Kim

This study identifies how mutant KRAS reprograms the noncoding transcriptome, upregulating repetitive noncoding RNAs and inducing IFN-stimulated genes through epigenetic and RNA-based mechanisms.

bioRxiv · Nov 4, 2020 · PreprintGenomics