Research

Lesie Leinwand - The ATPase cycle of human muscle myosin II Isoforms: adaptation of a single mechanochemical cycle for different physiological roles. Journal of Biological Chemistry 

Stephanie Bryant - 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 

Aaron Clauset - Doesn't matter if it's fair…as long as you win. Science

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

Sara Sawyer - TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation. Cell Reports

Stephanie Bryant - 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

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

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

Ryan Layer - svtools: population-scale analysis of structural variation. ISCB 

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

Sara Sawyer - TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation. Cell Reports 

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

Lesie Leinwand - PEG‐Anthracene Hydrogels as an on‐Demand Stiffening Matrix to Study Mechanobiology. Angewandte Chemie International Edition 

Lesie Leinwand - Three-dimensional encapsulation of adult mouse cardiomyocytes in hydrogels with tunable stiffness. Progress in Biophysics and Molecular Biology 

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

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

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

Aaron Clauset - Environmental Changes and the Dynamics of Musical Identity. arXiv 

Aaron Clauset - Productivity, prominence, and the effects of academic environment. PNAS 

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

Dan Larremore - Productivity, prominence, and the effects of academic environment. PNAS 

John Rinn - Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harb Perspect Biology 

Sara Sawyer - How host genetics dictates successful viral zoonosis. PLoS Biology 

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

Amy Palmer - Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range. Journal of Physical Chemistry 

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

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

Aaron Clauset - Scale-free Networks are rare. Nature Communications 

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

Lesie Leinwand - The ancient sarcomeric myosins found in specialized muscles. BioMed Central 

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

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

John Rinn - Characterization of Predicted Small Proteins. Biophysical Journal 

John Rinn - The Tug1 Locus is Essential for Male Fertility. BioRxiv 

Lesie Leinwand - Novel Morphological and Functional Insights in Python Cardiac Biology. Biophysical Journal 

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

Stephanie Bryant - 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

Stephanie Bryant - 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

Aaron Clauset - On the frequency and severity of interstate wars. arXiv

Amy Palmer - Discovery of a ZIP7 inhibitor from a Notch pathway screen. Nature Chemical Biology 

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

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

Stephanie Bryant - 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

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

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

Kristi Anseth - FGF-2 inhibits contractile properties of valvular interstitial cell myofibroblasts encapsulated in 3D MMP-degradable hydrogels. APL Bioengineering

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

Stephanie Bryant - 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

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

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

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

Kristi Anseth - Immunofunctional Photodegradable Poly(ethylene glycol) Hydrogel Surfaces for the Capture and Release of Rare Cells. Colloids and Surfaces B: Biointerfaces

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

Dan Larremore - Robust entropy requires strong and balanced excitatory and inhibitory synapses. Chaos

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

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

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

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

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

Dan Larremore - Cited in Predicting scientific success. Nature

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

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

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

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

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

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

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

Kristi Anseth - Polymers at the Interface with Biology. American Chemical Society

Sabrina Spencer - Control of the Restriction Point by Rb and p21. PNAS

Aaron Clauset - Forest Improve Dietary Diversity. Science

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

Tom Cech - A Lifelong Passion for All Things Ribonucleic. Cell

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

Aaron Clauset - The misleading narrative of the canonical faculty productivity trajectory. PNAS

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

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

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

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

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

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

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

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

Dan Larremore - A physical model for efficient ranking in networks. Science Advances

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

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

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

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

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

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

Aaron Clauset - Thermodynamics of the Minimum Description Length on Community Detection. arXiv

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

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

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

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

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

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

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

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

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

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

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

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

Aaron Clauset - Automatically assembling a full census of an academic field. arXiv

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

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

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

Sara Sawyer - Control of yeast retrotransposons mediated through nucleoporin evolution. PLOS Genetics

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Stephanie Bryant - 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

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

John Rinn - Dynamic changes during the treatment of pancreatic cancer. Oncotarget

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

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

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

Robin Dowell - Enhancer RNA profiling predicts transcription factor activity. Genome Research

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

Aaron Clauset - Global reciprocity drives cooperation. Science

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

Kristi Anseth - Engineering precision biomaterials for personalized medicine. Science Translational Medicine

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

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

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

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