J. Ferrie

发表

Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film

Jonathan W. Choi, P. Gopalan, Yongho Joo, 2015 .

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

R. Tjian, X. Darzacq, J. Ferrie, 2021, Genes & development.

Potential Artifacts in Sample Preparation Methods Used for Imaging Amyloid Oligomers and Protofibrils due to Surface-Mediated Fibril Formation.

Z. Fakhraai, Yi-Chih Lin, E. Petersson, 2017, The journal of physical chemistry. B.

Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening† †Electronic supplementary information (ESI) available: In silico compound screening, binding assays, chemical synthesis, photo-crosslinking and fibril analysis. See DOI: 10.1039/d0sc

R. Mach, V. Lee, Chia-Ju Hsieh, 2020, Chemical science.

Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA)

R. Tjian, X. Darzacq, G. Dailey, 2022, eLife.

"Structure"-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation.

R. Tjian, X. Darzacq, J. Karr, 2022, Molecular cell.

A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins

E. Petersson, J. Ferrie, James Petersson, 2020, bioRxiv.

Alpha Synuclein Fibrils Contain Multiple Binding Sites for Small Molecules.

R. Mach, Chia-Ju Hsieh, E. Petersson, 2018, ACS chemical neuroscience.

A comparative protease stability study of synthetic macrocyclic peptides that mimic two endocrine hormones.

D. Guarracino, J. Ferrie, J. J. Gruskos, 2013, Bioorganic & medicinal chemistry letters.

Thioamide Substitution Selectively Modulates Proteolysis and Receptor Activity of Therapeutic Peptide Hormones.

Taylor M. Barrett, M. R. Hayes, E. Petersson, 2017, Journal of the American Chemical Society.

Thioamide Labeling of Proteins through a Combination of Semisynthetic Methods

E. Petersson, J. Ferrie, Christopher R Walters, 2017 .

Proximity-assisted photoactivation (PAPA): Detecting molecular interactions in live-cell single-molecule imaging

R. Tjian, X. Darzacq, G. Dailey, 2021, bioRxiv.

Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine

E. Petersson, J. Ferrie, Sam Giannakoulias, 2021, Scientific Reports.

Improving the Fluorescent Probe Acridonylalanine Through a Combination of Theory and Experiment.

G. A. Petersson, Taylor M. Barrett, A. K. Muthusamy, 2018, Journal of physical organic chemistry.

Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin.

E. Petersson, J. Ferrie, Christopher R Walters, 2018, Chemical communications.

Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis.

V. Lee, E. Petersson, D. Covell, 2016 .

Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity

V. Uversky, K. Caldwell, G. Caldwell, 2019, Scientific Reports.

Synthesis and characterization of high affinity fluorogenic α-synuclein probes.

J. Trojanowski, R. Mach, V. Lee, 2020, Chemical communications.

Electronic interactions of i, i + 1 dithioamides: increased fluorescence quenching and evidence for n-to-π* interactions.

E. Petersson, J. Ferrie, D. Chenoweth, 2016, Chemical communications.

Fluorescent Probes for Studying Thioamide Positional Effects on Proteolysis Reveal Insight into Resistance to Cysteine Proteases

Taylor M. Barrett, E. Petersson, J. Ferrie, 2019, Chembiochem : a European journal of chemical biology.

Rosetta Machine Learning Models Accurately Classify Positional Effects of Thioamides on Proteolysis.

Taylor M. Barrett, E. Petersson, J. Ferrie, 2020, The journal of physical chemistry. B.

Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein.

Yi-Chih Lin, E James Petersson, John J Ferrie, 2018, Biophysical journal.

Identification of a Putative α-synuclein Radioligand Using an in silico Similarity Search

R. Mach, B. Lopresti, C. Mathis, 2023, Molecular Imaging and Biology.

p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs

R. Tjian, X. Darzacq, G. Dailey, 2023, bioRxiv.

Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability.

M. Bornstein, R. Kohli, E. Petersson, 2018, ACS chemical biology.

Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning.

Sam Giannakoulias, Sumant R Shringari, John J Ferrie, 2020, Chemical communications.

Rosetta Custom Score Functions Accurately Predict ΔΔG of Mutations at Protein-Protein Interfaces Using Machine Learning

Sumant Shringari, Sam Giannakoulias, John J. Ferrie, 2020, bioRxiv.

Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity

V. Uversky, K. Caldwell, G. Caldwell, 2019, Scientific Reports.

Improved Modeling of Thioamide FRET Quenching by Including Conformational Restriction and Coulomb Coupling.

E. Petersson, J. Ferrie, Jimin Yoon, 2020, The journal of physical chemistry. B.

FIRST MEASUREMENT OF THE LEFT-RIGHT ASYMMETRY IN Z-BOSON PRODUCTION

P. G. Verdini, J. S. Whitaker, G. Chadwick, 1993 .

First results from SLD with polarized electron beam at SLC

Sokoloff, P. G. Verdini, J. S. Whitaker, 1992 .

p300 is an obligate integrator of combinatorial transcription factor inputs.

X. Darzacq, G. Dailey, J. Ferrie, 2023, Molecular cell.

Multicolor protein FRET with tryptophan, selective coumarin-cysteine labeling, and genetic acridonylalanine encoding.

J. Ferrie, N. Ieda, Christopher R Walters, 2017, Chemical communications.

Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin.

E. Petersson, J. Ferrie, Christopher R Walters, 2018, Chemical communications.