About

Ellen Youngsoo Rim is an Assistant Professor of Chemical Engineering at Stanford University. Her research focuses on sustainably enhancing plant productivity and resilience through protein engineering, addressing environmental stressors such as pathogen infection, drought, and heat that threaten global food security and plant carbon sequestration. She engineers proteins involved in plant immune and hormone signaling pathways using directed evolution in high-throughput single cell systems, a synthetic biology approach that enables rapid development of proteins with novel or improved functions. Her work combines directed evolution with machine learning to analyze large datasets generated during the process, and engineered proteins are introduced into plants to improve crop yields and climate resilience. Ellen Rim completed her Ph.D. at Stanford University in 2020, followed by postdoctoral training at the University of California, Davis, in 2025. She holds a B.A. from Harvard University, earned in 2012. Her research aims to contribute to sustainable agriculture and environmental resilience through innovative protein engineering techniques.

Research topics

• Biology
• Environmental resource management
• Natural resource economics
• Genetics
• Ecology
• Environmental science
• Cell biology

Selected publications

• Vascularization of neonatal liver lobules presages adult liver size

  Nature Communications · 2025-11-13

  articleOpen access

  Organs vary in size between and within species to match organismal needs. Theoretical work has proposed that scaling of organs and body parts relies on energy-transport systems, the vascular system in mammals. Here, we use quantitative clonal mapping and volumetric imaging combined with novel molecular and genetic tools to identify temporal and spatial constraints that establish mouse liver size. We find that adult liver size is foreshadowed during a neonatal period when functional units, termed lobules, initiate growth. Nascent lobules are vascularized by prominent sprouting angiogenesis of the hepatic vein, restricted to the periphery of the organ. When Wnt signals are ablated in the single cell-layered mesothelium at the periphery, neonatal growth is disturbed, and the liver adopts a compromised size set point. Similarly, when venous angiogenesis is inhibited, nascent lobules remain small and the liver fails to reach proper size. In unperturbed animals, vein sprouting rapidly declines within a week after birth and well before hepatocyte division stops. These findings suggest that vascularization in the neonate assists in the determination of adult liver size. Together, these results lead us to propose a vasculature-centric experimental framework for studying organ size control and scaling in mammals.

  PublisherDOI

• Combining Directed Evolution with Machine Learning Enables Accurate Genotype-to-Phenotype Predictions

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-29 · 3 citations

  preprintOpen access

  Abstract Linking sequence variation to phenotypic effects is critical for efficient exploitation of large genomic datasets. Here we present a novel approach combining directed evolution with protein language modeling to characterize naturally-evolved variants of a rice immune receptor. Using high-throughput directed evolution, we engineered the rice immune receptor Pik-1 to bind and recognize the fungal proteins Avr-PikC and Avr-PikF, which evade detection by currently characterized Pik-1 alleles. A protein language model was fine-tuned on this data to correlate sequence variation with ligand binding behavior. This modeling was then used to characterize Pik-1 variants found in the 3,000 Rice Genomes Project dataset. Two variants scored highly for binding against Avr-PikC, and in vitro analyses confirmed their improved ligand binding over the wild-type Pik-1 receptor. Overall, this machine learning approach identified promising sources of disease resistance in rice and shows potential utility for exploring the phenotypic variation of other proteins of interest.

  PublisherOA PDFDOI

• Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance

  Theoretical and Applied Genetics · 2025-08-08 · 4 citations

  reviewOpen access

  Integrating innovative technologies into plant breeding is critical to bolster food and nutritional security under biotic and abiotic stresses in changing climates. While breeding efforts have focused primarily on yield and stress tolerance, emerging evidence highlights the need to also prioritize nutritional quality. Advanced molecular breeding approaches have enhanced our ability to develop improved crop varieties and could be substantially informed by the routine integration of crop modeling and remote sensing technologies. This review article discusses the potential of combining crop modeling and sensing with molecular breeding to address the dual challenge of nutritional quality and stress tolerance. We provide overviews of stress response strategies, challenges in breeding for quality traits, and the use of environmental data in genomic prediction. We also describe the status of crop modeling and sensing technologies in grain legumes, rice, and leafy greens, alongside the status of -omics tools in these crops and the use of AI with directed evolution to identify novel resistance genes. We describe the pairwise and three-way integration of AI-enabled sensing and biophysically and empirically constrained crop modeling into breeding to enable prediction of phenotypic and breeding values and dissection of genotype-by-environment-by-management interactions with increasing fidelity, efficiency, and temporal/spatial resolution to inform selection decisions. This article highlights current initiatives and future trends that focus on leveraging these advancements to develop more climate-resilient and nutritionally dense crops, ultimately enhancing the effectiveness of molecular breeding.

  PublisherOA PDFDOI

• Directed Evolution of a Plant Immune Receptor for Broad Spectrum Effector Recognition

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-01 · 8 citations

  preprintOpen access1st authorCorresponding

  Abstract Rapid development of immune receptors that protect crops from emerging pathogens is a critical challenge 1,2 . While novel immune receptors that recognize previously undetected pathogen effectors could provide protection against a wider range of pathogens, engineering such receptors has been constrained by the low throughput and speed of in planta testing. We established yeast surface display as a high throughput platform to recapitulate plant immune receptor-ligand interactions and evolve new binding capabilities. Using this directed evolution platform, we engineered the ligand binding domain of the rice immune receptor Pik-1 to recognize diverse effectors from the fast-evolving fungal pathogen Magnaporthe oryzae. Our approach yielded Pik-1 ligand binding domains with affinity for variants of the M. oryzae effector Avr-Pik that previously escaped detection by known rice alleles of Pik-1, with in planta assays confirming functional recognition of these effectors. Additional rounds of mutagenesis and selection led to a Pik-1 domain that binds all tested Avr-Pik variants as well as the evolutionarily divergent effector AvrPiz-t. These results demonstrate the potential of directed evolution to engineer immune receptors with new-to-nature recognition of a wide range of pathogen-derived ligands and accelerate development of broad spectrum resistance in crops.

  PublisherDOI

• 12237 Monosynaptic Gabaergic Signaling From Suprachiasmatic Nucleus Neuromedin S Neurons To Preoptic Area Kisspeptin Neurons In Mice

  Journal of the Endocrine Society · 2024-10-01 · 1 citations

  articleOpen access

  Abstract Disclosure: W.I. Abdulmajeed: None. B.B. Jamieson: None. S.X. Thomas: None. Y. Rim: None. A.G. Novak: None. R.E. Campbell: None. R. Piet: None. In female rodents, projections from suprachiasmatic nucleus (SCN) neurons relay timing cues to the gonadotropin-releasing hormone (GnRH) neuronal network for the preovulatory surge. Kisspeptin (KISS1) neurons of the rostral periventricular area of the third ventricle (RP3V) are thought to integrate these cues with estradiol positive feedback to drive GnRH neuron activity, the gonadotropin surge and ovulation. We recently reported that SCN neuron projections release arginine vasopressin (AVP), thereby stimulating female RP3VKiss[1] neuron action potential firing in an estrous cycle stage-dependent manner. In the SCN, AVP is expressed in a subset of neuromedin S (NMS) neurons, a neuronal population essential for circadian rhythms. Moreover, a previous report indicates that exogenous NMS stimulates LH secretion in female rodents. SCNNMS neurons might, therefore, play a role in timing the preovulatory surge. However, whether SCNNMS neurons project to and regulate the activity of RP3VKISS[1] neurons is currently unknown. To address this question, we combined anterograde viral tract-tracing and channelrhodopsin-2 (ChR2)- assisted circuit mapping. Female mice expressing Cre recombinase in NMS cells (NMS-Cre) received stereotaxic injections in the SCN of adeno-associated viral vectors (AAVs) carrying the Cre-dependent sequence for mCherry. Fluorescence immunohistochemistry revealed that mCherry-expressing fibers come in close apposition with the great majority (>80%) of KISS1-immunoreactive neurons in the RP3V, suggesting a SCNNMS-to-RP3VKISS[1] neuron circuit. To interrogate this circuit, we next injected AAVs carrying Cre-dependent channelrhodopsin (ChR2) in the SCN of female NMS-Cre mice that also express the green fluorescent protein in KISS1 cells. Blue LED light (460-487 nm) activation of ChR2-expressing SCNNMS neuronal fibers in the RP3V evoked postsynaptic currents (PSCs) in most KISS1 neurons recorded in whole-cell voltage clamp (-60 mV) in brain slices. Evoked PSCs had short latencies and were blocked by bath application of 0.5 µM tetrodotoxin (TTX), indicating that they were generated by action potential-dependent release. Addition of 100 µM 4-Aminopyridine (4-AP, a potassium channel blocker) to TTX rescued these responses, indicating the existence of a monosynaptic SCNNMS-to-RP3VKISS[1] connection. In addition, evoked PSCs were suppressed by 5 µM gabazine, a GABAA receptor antagonist, but not by 20 µM NBQX and 50 µM D-AP5, AMPA- and NMDA-type glutamate receptor antagonists, respectively, revealing that SCNNMS projections release GABA onto RP3VKISS[1] neurons. Together, our findings are consistent with SCNNMS neurons extending monosynaptic GABAergic projections to RP3VKISS[1] neurons. Further studies are needed to determine the impact of these projections on RP3VKISS[1] neuron activity and the role they might play in the preovulatory surge. Presentation: 6/1/2024

  PublisherOA PDFDOI

• Liver size is predetermined in the neonate by adding lobules at the periphery

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-10-14 · 1 citations

  preprintOpen access

  Abstract Organs vary in size between and within species to match organismal needs 1,2 . Decades-old theoretical work has proposed that scaling of organs and body parts relative to the body relies on the features of energy-transport systems, the vascular system in mammals 3 . Yet, experimental studies on whether or how vascularization helps determine organ size have lagged behind. The mammalian liver is a remarkable example, as liver size scales proportionally with high precision between individuals 4 . Here, we use quantitative clonal mapping, volumetric imaging, and genetic perturbations combined with novel molecular and genetic tools to identify the temporal and spatial constraints that establish mouse liver size. We find that adult liver size is predetermined during a neonatal period when new functional units, termed lobules, are added to the organ. New lobules are vascularized by prominent sprouting angiogenesis of the hepatic vein, restricted to the periphery of the organ. When Wnt signals are ablated in the single cell-layered mesothelium at the periphery, lobule growth fails, and the organ adopts a compromised size set point. Remarkably, within a week after birth and well before hepatocyte division stops, vein sprouting rapidly declines and lobule addition concludes, setting a limit on the final liver size. These findings posit that vascularization in the neonate constrains and helps determine adult liver size. Together, these results propose a novel, vasculature-centric experimental framework for studying organ size control and scaling in mammals.

  PublisherOA PDFDOI

• APEX2-Mediated Proximity Labeling of Wnt Receptor Interactors Upon Pathway Activation

  PubMed · 2023-03-21 · 1 citations

  articleOpen access1st authorCorresponding

  The Wnt signaling pathway regulates metazoan development, tissue homeostasis, and regeneration. Many outstanding questions in Wnt signal transduction revolve around the molecular events immediately following Wnt-receptor interactions. To identify binding partners of the Wnt receptor Frizzled 7 (Fzd7) upon pathway activation, we tagged Fzd7 with APEX2, an enzyme that allows biotinylation of proximal interactors with high temporal and spatial resolution. Upon confirming proper localization and signaling activity of APEX2-tagged Fzd7, we labeled proximal interactors of Fzd7 with or without Wnt3a stimulation. Mass spectrometry analysis of biotinylated interactors identified several known Wnt pathway proteins. Top interactors enriched upon Wnt treatment were involved in actin cytoskeleton regulation, vesicle trafficking, or phospholipid modification. Proteins enriched in the Wnt-activated Fzd7 interactome that are without established roles in Wnt signaling warrant further examination.

  PublisherOA PDFDOI

• The Wnt Pathway: From Signaling Mechanisms to Synthetic Modulators

  Annual Review of Biochemistry · 2022 · 469 citations

  1st authorCorresponding
  • Biology
  • Cell biology
  • Genetics

  The Wnt pathway is central to a host of developmental and disease-related processes. The remarkable conservation of this intercellular signaling cascade throughout metazoan lineages indicates that it coevolved with multicellularity to regulate the generation and spatial arrangement of distinct cell types. By regulating cell fate specification, mitotic activity, and cell polarity, Wnt signaling orchestrates development and tissue homeostasis, and its dysregulation is implicated in developmental defects, cancer, and degenerative disorders. We review advances in our understanding of this key pathway, from Wnt protein production and secretion to relay of the signal in the cytoplasm of the receiving cell. We discuss the evolutionary history of this pathway as well as endogenous and synthetic modulators of its activity. Finally, we highlight remaining gaps in our knowledge of Wnt signal transduction and avenues for future research.

  PublisherOA PDFDOI

• Plant immunity: Rice XA21-mediated resistance to bacterial infection

  Proceedings of the National Academy of Sciences · 2022-02-07 · 54 citations

  articleOpen access

  Significance The mechanisms plants employ to resist infection were unknown until just a few decades ago. We now understand that plants utilize diverse classes of immune receptors to recognize and respond to pathogenic microbes and pests. This paper describes the development of the plant immunity field, from early studies on the genetics of disease resistance to our increasing knowledge of how plant receptors interact with their microbial ligands, with an emphasis on the rice immune receptor XA21 and its bacterial ligand.

  PublisherOA PDFDOI

• Climate change challenges, plant science solutions

  The Plant Cell · 2022 · 189 citations

  • Biology
  • Environmental resource management
  • Natural resource economics

  Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

  PublisherDOI

Frequent coauthors

• Carolyn M. Phillips

  University of Southern California

  20 shared

• Taiowa A. Montgomery

  Colorado State University

  18 shared

• Sylvia E. J. Fischer

  Harvard University

  16 shared

• Chi Zhang

  16 shared

• Robert H. Dowen

  University of North Carolina at Chapel Hill

  16 shared

• Roel Nusse

  Stanford University

  12 shared

• Gary Ruvkun

  Brandeis University

  12 shared

• Roeland Nusse

  Stanford University

  8 shared

Education

• Ph.D., Chemical Engineering

  Stanford University

  2015

• M.S., Chemical Engineering

  University of California, Berkeley

  2010

• B.S., Chemical Engineering

  University of California, Berkeley

  2009