The BioFrontiers Institute was built on a vision of creating a flexible and supportive environment for scientists and engineers to work across disciplines on projects that might be outside the realm of traditional research in their area. Our researchers have a passion for their science and openness to new ideas, allowing them to work across disciplines to embrace even the most complex problems. Currently, BioFrontiers faculty, partners, and facilities are organized around four interdisciplinary research areas. 

Computational Biology

Using computational, statistical and mathematical approaches to extract knowledge from large sets of biological data and to model biological systems.

Bioimaging: From Molecules to Organisms

Applying physical principles to visualize, measure and understand key biological processes.

New Therapeutic Paradigms

Using chemical principles to develop innovative medicine, including new approaches, new drugs and new vaccines.

Regenerative Biology

Engineering medical solutions through biological processes.

Faculty Publications

  • Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2. PNAS

  • Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nature Methods 

  • Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties. Psychopharmacology 

  • An In Vitro and In Vivo Comparison of Cartilage Growth in Chondrocyte-Laden Matrix Metalloproteinase-Sensitive Poly(Ethylene Glycol) Hydrogels with Localized Transforming Growth Factor β3. Acta Biomaterialia

  • Mesenchymal Stem Cells Delivered in a Novel Cartilage Mimetic Hydrogel for the Treatment of Focal Chondral Lesions in an Equine Animal Model. Orthopaedic Journal of Sports Medicine 

  • Understanding and Improving Mechanical Properties in 3D printed Parts Using a Dual-Cure Acrylate-Based Resin for Stereolithography. Advanced Engineering Materials

  • Assessment and prevention of cartilage degeneration surrounding a focal chondral defect in the porcine model. Biochemical Biophysical Research Communications

  • A comparison of human mesenchymal stem cell osteogenesis in poly(ethylene glycol) hydrogels as a function of MMP-sensitive crosslinker and crosslink density in chemically defined medium. Biotechnology and Bioengineering

  • The effects of dynamic compressive loading on human mesenchymal stem cell osteogenesis in the stiff layer of a bilayer hydrogel. Journal of Tissue Engineering and Regenerative Medicine

  • Photopolymerizable Injectable Cartilage Mimetic Hydrogel for the Treatment of Focal Chondral Lesions: A Proof of Concept Study in a Rabbit Animal Model. American Journal of Sports Medicine

  • C9orf72 and Triplet Repeat Disorder RNAs: G-quadruplex formation, binding to PRC2 and implications for disease mechanisms. RNA 

  • Doesn't matter if it's fair…as long as you win. Science

  • Environmental Changes and the Dynamics of Musical Identity. arXiv 

  • Productivity, prominence, and the effects of academic environment. PNAS 

  • Scale-free Networks are rare. Nature Communications 

  • On the frequency and severity of interstate wars. arXiv

  • Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. bioRxiv

  • ATAC-seq signal processing and recurrent neural networks can identify RNA polymerase activity. bioRxiv 

  • Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One 

  • Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties. Psychopharmacology 

  • Phosphorylation of HPV-16 L2 Contributes To Efficient Virus Infectious Entry. Virus-Cell Interactions 

  • Viral replication centers and the DNA damage response in JC virus-infected cells. Virology 

  • Productivity, prominence, and the effects of academic environment. PNAS 

  • Bayes-optimal estimation of overlap between populations of fixed size. PLoS Computational Biology 

  • svtools: population-scale analysis of structural variation. ISCB 

  • High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Research 

  • Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harb Perspect Biology 

  • A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nature Communications 

  • High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity. Genome Reserach 

  • Characterization of Predicted Small Proteins. Biophysical Journal 

  • The Tug1 Locus is Essential for Male Fertility. BioRxiv 

  • TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation. Cell Reports

  • Selective use of primate CD4 receptors by HIV-1. PLoS Biology 

  • TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation. Cell Reports 

  • A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species. PNAS 

  • A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV). PNAS 

  • How host genetics dictates successful viral zoonosis. PLoS Biology 

  • FGF-2 inhibits contractile properties of valvular interstitial cell myofibroblasts encapsulated in 3D MMP-degradable hydrogels. APL Bioengineering
  • Immunofunctional Photodegradable Poly(ethylene glycol) Hydrogel Surfaces for the Capture and Release of Rare Cells. Colloids and Surfaces B: Biointerfaces

Hydrazone covalent adaptable networks modulate extracellular matrix deposition for cartilage tissue engineering. Acta Biomaterialia

Secondary photocrosslinking of click hydrogels to probe myoblast mechanotransduction in three dimensions. Journal of the American Chemical Society

Rescuing mesenchymal stem cell regenerative properties on hydrogel substrates post serial expansion. Bioengineering and Translational Medicine

Polymers at the Interface with Biology. American Chemical Society

Adaptable Fast Relaxing Boronate-Based Hydrogels for Probing Cell–Matrix Interactions. Advanced Science

A Reversible and Repeatable Thiol−Ene Bioconjugation for Dynamic Patterning of Signaling Proteins in Hydrogels. American Chemical Society

Recapitulating Physical Changes in the Extracellular Matrix with Dynamic Hydrogels. Biomaterials

A Reversible and Repeatable Thiol–Ene Bioconjugation for Dynamic Patterning of Signaling Proteins in Hydrogels. American Chemical Society

Photopolymerized dynamic hydrogels with tunable viscoelastic properties through thioester exchange. Biomaterials

Partial flocculation for spray drying of spherical mixed metal oxide particles. Journal of the American Ceramic Society

Synthesis of Microgel Sensors for Spatial and Temporal Monitoring of Protease Activity. ACS Biomaterials

Reversible Control of Network Properties in Azobenzene-Containing Hyaluronic Acid-Based Hydrogels. American Chemical Society

Thermal stabilization of biologics with photoresponsive hydrogels. American Chemical Society Biomacromolecules

Engineering precision biomaterials for personalized medicine. Science Translational Medicine

Understanding and Improving Mechanical Properties in 3D printed Parts Using a Dual-Cure Acrylate-Based Resin for Stereolithography. Advanced Engineering Materials

Photopolymerizable Injectable Cartilage Mimetic Hydrogel for the Treatment of Focal Chondral Lesions: A Proof of Concept Study in a Rabbit Animal Model. The American Journal of Sports Medicine

The role of chondroitin sulfate in regulating hypertrophy during MSC chondrogenesis in a cartilage mimetic hydrogel under dynamic loading. Biomaterials

Understanding and Improving Mechanical Properties in 3D printed Parts Using a Dual‐Cure Acrylate‐Based Resin for Stereolithography. Advanced Engineering Materials

Biomimetic soft fibrous hydrogels for contractile and pharmacologically responsive smooth muscle. Acta Biomaterielia

In vitro and in vivo models for assessing the host response to biomaterials. Drug Discovery Today: Disease Models

Biomimetic soft fibrous hydrogels for contractile and pharmacologically responsive smooth muscle. Acta Biomaterielia

The effects of hydroxyapatite nanoparticles embedded in a MMP-sensitive photoclickable PEG hydrogel on encapsulated MC3T3-E1 pre-osteoblasts. Biomedical Materials

Cytocompatibility and Cellular Internalization of PEGylated "Clickable" Nucleic Acid Oligomers. American Chemical Society

Zwitterionic PEG-PC hydrogels modulate the foreign body response in a modulus-dependent manner. American Chemical Society

Regenerative Medicine Approaches for the Treatment of Pediatric Physeal Injuries. Tissue Engineering Part B Reviews

The in vitro effects of macrophages on the osteogenic capabilities of MC3T3-E1 cells encapsulated in a biomimetic poly(ethylene glycol) hydrogel. Acta Biomaterielia

Effects of cell adhesion motif, fiber stiffness, and cyclic strain on tenocyte gene expression in a tendon mimetic fiber composite hydrogel. Biochemical and Biophysical Research Communication

A MMP7-sensitive photoclickable biomimetic hydrogel for MSC encapsulation towards engineering human cartilage. Journal of Biomedical Materials Research

The Host Response in Tissue Engineering: Crosstalk Between Immune cells and Cell-laden Scaffolds. Biomedical Engineering

Current and novel injectable hydrogels to treat focal chondral lesions: Properties and applicability. Journal of Orthopaedic Research

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate. Genome Bio

The placenta goes viral: Retroviruses control gene expression in pregnancy PLoS Biology

A Lifelong Passion for All Things Ribonucleic. Cell

Fission yeast telosomes: non-canonical histone-containing chromatin structures dependent on shelterin and RNA. Oxford Academic

Live-cell imaging reveals the dynamics of PRC2 and recruitment to chromatin by SUZ12-associated subunits. Genes and Development

In Crystallo Selection to Establish New RNA Crystal Contacts. Science Direct

Dynamics of human telomerase recruitment depend on template- telomere base pairing. Molecular Biology of the Cell

Prestige drives epistemic inequality in the diffusion of scientific ideas. EPJ Data Science

Predicting the outcomes of policy diffusion from U.S. states to federal law. arXiv

Automatically assembling a full census of an academic field. PLOS One

Forest Improve Dietary Diversity. Science

The misleading narrative of the canonical faculty productivity trajectory. PNAS

Thermodynamics of the Minimum Description Length on Community Detection. arXiv

Prestige drives epistemic inequality in the diffusion of scientific ideas. SpringerOpen

Automatically assembling a full census of an academic field. arXiv

Evaluating Overfit and Underfit in Models of Network Community Structure. arXiv

Trends and fluctuations in the severity of interstate wars. Science Advances

Global reciprocity drives cooperation. Science

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nature Immunology

PI(3,5)P2 Controls Vacuole Potassium Transport to Support Cellular Osmoregulation. Molecular Biology of the Cell

Detecting Differential Transcription Factor Activity from ATAC-Seq Data.Molecules Open Access Journals

miR-MaGiC improves quantification accuracy for small RNA-seq. Biomedical Central

Enhancer RNA profiling predicts transcription factor activity. Genome Research

In-Cell NMR within Budding Yeast Reveals Cytoplasmic Masking of Hydrophobic Residues of FG Repeats. BioPhysical Journal

The Expanding Zoo of In-Cell Protein NMR. BioPhysical Journal

In-cell NMR within budding yeast reveals cytoplasmic masking of hydrophobic residues of FG repeats. BioPhysical Journal

All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports

Robust entropy requires strong and balanced excitatory and inhibitory synapses. Chaos

Cited in Predicting scientific success. Nature

A physical model for efficient ranking in networks. Science Advances

Configuring Random Graph Models with Fixed Degree Sequences. Society for Industrial and Applied Mathematics

Pregnancy late in rodent life has detrimental effects on the heart. American Journal of Physiology

Dilated cardiomyopathy myosin mutants have reduced force-generating capacity. Biological Chemistry

Entrepreneurialism in the Translational Biologic Sciences: Why, How, and However. JACC: Basic to Translational Science

Fropofol prevents disease progression in hypertrophic cardiomyopathy. Journal of the American College of Cardiology

Allele-specific differences in transcriptome, miRNome, and mitochondrial function in two hypertrophic cardiomyopathy mouse models. JCI Insight

Superiority of SpiroZin2 Versus FluoZin-3 for monitoring vesicular Zn2+ allows tracking of lysosomal Zn2+ pools. Nature

Directed Evolution of Excited State Lifetime and Brightness in FusionRed using a Microfluidic Sorter. Integrative Biology

A Multicolor Split-Fluorescent Protein Approach to Visualize Listeria Protein Secretion in Infection. Biophysics Journal

Zinc transporters belonging to the Cation Diffusion Facilitator (CDF) family have complementary roles in transporting zinc out of the cytosol. PLoS Genetics

Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Bio

Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell reports

Interchromosomal interactions: A genomic love story of kissing chromosomes. JCB

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Systems

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. eLIFE

Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome. The EMBO Journal

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nature Communications

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell

Dynamic changes during the treatment of pancreatic cancer. Oncotarget

Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nature Structural and Molecular Biology

High-throughput identification of RNA nuclear enrichment sequences. The EMBO Journal

Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nature Genetics

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Molecular Cell

Species-Specific Deamidation of cGAS by Herpes Simplex Virus UL37 Protein Facilitates Viral Replication. Cell Host Microbe

Control of yeast retrotransposons mediated through nucleoporin evolution. PLOS Genetics

Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes. PLoS Pathogens

Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. Microbiology and Infectious Disease

Control of the Restriction Point by Rb and p21. PNAS

Single-cell imaging reveals MAPK pathway reactivation in drug-tolerant melanoma cells. Cancer Research

Ki67 is a Graded Rather than a Binary Marker of Proliferation versus Quiescence. Cell Reports