Publications

Last name changed from Garcia to Karner in 2013. † denotes co-first authorship.

This page highlights the papers most central to my current research program first, followed by manuscripts in preparation, earlier publications, and dissertation work.

Featured Publications

Karner H†, Mittmann TC†, Chen VW, Borah AA, Langen A, Yousefi H, Fish L, Zaro BW, Navickas A, Goodarzi H. (2026). Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer. Science Advances 12, eaea9061.

Co-First Author

We systematically measured mRNA stability across diverse breast cancer models and built GreyHound, an interpretable deep-learning framework to identify regulators of RNA decay. This work revealed that RBMS3 stabilizes a metastasis-suppressive transcript program centered on TXNIP, linking post-transcriptional regulation directly to breast cancer progression.

DOI link

Keshavarzi Arshadi A†, Salem M†, Karner H†, Garcia K, Arab A, Yuan JS, Goodarzi H. (2024). Functional microRNA-targeting drug discovery by graph-based deep learning. Patterns 5, 100909.

Co-First Author

We developed RiboStrike, a deep-learning framework that identified small molecules with anti-miR-21 activity. I contributed to the experimental validation, helping test candidate compounds through reporter assays and RNA-seq and showing that the top hit reduced lung metastases in a breast cancer mouse model.

DOI link

Karner HM, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. (2020). Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence. Journal of Molecular Biology 432:283-300.

First Author · Featured Article · Cover Art

I showed that the human lncRNA JPX remains functionally conserved despite major sequence and structural divergence from mouse Jpx: it still binds CTCF and can rescue Xist-related defects in mouse embryonic stem cells.

DOI link

In Preparation

Karimzadeh M†, Karner H†, Fish L†, Emadi A, Leonetti M, Kelley D, Najafabadi HS, Linder J, Goodarzi H. (In Prep) A high-resolution protein-RNA binding atlas for structure-aware interaction prediction and post-transcriptional regulatory modeling. (Co-First Author)

Additional Publications / Earlier Work

Earlier work spans lncRNA biology, noncoding RNA regulation, and collaborative projects that shaped my experimental and mechanistic approach to RNA biology.

Dissertation

Functional Characterization of Human LncRNA JPX

Doctor of Philosophy in Biological Sciences, University of California, Irvine, 2019. Advisor: Sha Sun.

My dissertation focused on the human lncRNA JPX and asked how RNA function can be conserved despite rapid sequence divergence. I showed that human JPX is structurally divergent from mouse Jpx yet remains functionally conserved, including robust CTCF binding and rescue of Jpx-deficient mouse embryonic stem cells. I also extended this work into ovarian cancer, where reduced JPX and XIST expression in higher-grade tumors suggested a broader link between X chromosome inactivation-linked lncRNAs and tumor progression.

Dissertation PDF Google Scholar