Hannele Ruohola‐Baker

This study shows that computationally designed proteins can template and confine hydroxyapatite mineralization, providing a framework for programmable protein-guided mineralization.

This paper designs a de novo Tie2 binder that activates the Angiopoietin-Tie2 pathway without integrin engagement, showing improved therapeutic potential in a mouse model of ARDS.

This paper demonstrates that AI-designed receptor modulators can drive efficient human fibroblast-to-muscle transdifferentiation by rewiring extracellular signaling.

Conditioning RFdiffusion on edge beta-strand pairing yields specific binders to polar targets, with in silico success above 9.2% versus 0.98% for hotspot-only conditioning.

This study shows that rapamycin affects germline stem cell quiescence differently across genetic backgrounds in Drosophila, with mitophagy playing a key role in quiescence persistence.

The paper designs novel cytokines by fusing computationally generated receptor-binding domains, identifying several that activate signaling pathways and have specific biological effects.

This paper designs a synthetic ligand, H2F, that induces HER2-FGFR proximity to reprogram fibroblasts into myogenic cells and promote myogenic regeneration.

This study develops human iPSC-derived salivary gland organoids that model diabetic dysfunction, showing impaired oxidative phosphorylation and FOXO1 nuclear localization in response to Metformin.

This study identifies functional non-coding variants associated with orofacial cleft by combining GWAS, reporter assays, and stem cell modeling.

The paper designs de novo proteins called NeoNectins that specifically bind integrin α5β1, enhancing cell attachment and tissue integration in biomaterials.

The paper designs TrkA agonists that activate neuronal differentiation and neurite outgrowth without triggering pain-related gene expression.

The paper demonstrates that a designed soluble Notch agonist can drive iAM maturation without odontoblast contact, revealing DLX3's role in ameloblast-specific Enamelin and MMP20 expression.

The paper identifies a regulatory variant in IRF6 associated with increased cleft palate risk in Finland and shows it disrupts IRF6 enhancer function.

This paper introduces a top-down reinforcement learning approach to design protein nanomaterials, resulting in more compact and robust icosahedral assemblies than previously observed.

The paper establishes a single-cell atlas of human tooth development and uses it to guide the in vitro differentiation of ameloblasts from iPSCs, developing a mineralizing enamel organoid system.

The paper designs and characterizes trivalent miniprotein binders that neutralize SARS-CoV-2 variants with low pM IC50 values and provide prophylactic and therapeutic protection in mice.

This paper designs small, stable proteins that bind to diverse target proteins using only structural information, achieving nanomolar to picomolar affinities.

The paper designs binary 2D protein co-assemblies that form ordered, biologically active materials with potential therapeutic applications.

The paper uses a computationally designed PRC2 inhibitor, EBdCas9, to identify functional TATA boxes in distal promoter regions and demonstrate their role in gene activation.

The paper maps cardiac differentiation at single-cell resolution, identifies HOPX dysregulation, and shows hypertrophic signaling is required for HOPX transcription in hPSC-derived cardiomyocytes.

The paper compares epigenomic and 3D genome architecture between naive and primed human embryonic stem cells, showing differences in enhancer marking and chromatin domain organization.

Isolator improves isoform-level RNA-Seq analysis by reducing variance and increasing agreement between samples through a Bayesian hierarchical model and bias correction.