The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication JP Karr, JJ Ferrie, R Tjian, X Darzacq Genes & Development 36 (1-2), 7-16, 2022 | 80 | 2022 |
Thioamide substitution selectively modulates proteolysis and receptor activity of therapeutic peptide hormones X Chen, EG Mietlicki-Baase, TM Barrett, LE McGrath, K Koch-Laskowski, ... Journal of the American Chemical Society 139 (46), 16688-16695, 2017 | 80 | 2017 |
Alpha synuclein fibrils contain multiple binding sites for small molecules CJ Hsieh, JJ Ferrie, K Xu, I Lee, TJA Graham, Z Tu, J Yu, D Dhavale, ... ACS chemical neuroscience 9 (11), 2521-2527, 2018 | 52 | 2018 |
“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation JJ Ferrie, JP Karr, R Tjian, X Darzacq Molecular Cell 82 (21), 3970-3984, 2022 | 42 | 2022 |
Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity MJ Daniels, JB Nourse Jr, H Kim, V Sainati, M Schiavina, MG Murrali, ... Scientific reports 9 (1), 2937, 2019 | 39 | 2019 |
Electronic interactions of i, i+ 1 dithioamides: increased fluorescence quenching and evidence for n-to-π* interactions Y Huang, JJ Ferrie, X Chen, Y Zhang, DM Szantai-Kis, DM Chenoweth, ... Chemical communications 52 (50), 7798-7801, 2016 | 38 | 2016 |
Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis CM Haney, RF Wissner, JB Warner, YJ Wang, JJ Ferrie, DJ Covell, ... Organic & biomolecular chemistry 14 (5), 1584-1592, 2016 | 37 | 2016 |
Synthesis and characterization of high affinity fluorogenic α-synuclein probes Z Lengyel-Zhand, JJ Ferrie, B Janssen, CJ Hsieh, T Graham, K Xu, ... Chemical communications 56 (24), 3567-3570, 2020 | 34 | 2020 |
A comparative protease stability study of synthetic macrocyclic peptides that mimic two endocrine hormones JJ Ferrie, JJ Gruskos, AL Goldwaser, ME Decker, DA Guarracino Bioorganic & medicinal chemistry letters 23 (4), 989-995, 2013 | 34 | 2013 |
Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening JJ Ferrie, Z Lengyel-Zhand, B Janssen, MG Lougee, S Giannakoulias, ... Chemical Science 11 (47), 12746-12754, 2020 | 32 | 2020 |
Systematic evaluation of soluble protein expression using a fluorescent unnatural amino acid reveals no reliable predictors of tolerability ZM Hostetler, JJ Ferrie, MR Bornstein, I Sungwienwong, EJ Petersson, ... ACS chemical biology 13 (10), 2855-2861, 2018 | 28 | 2018 |
Using a FRET library with multiple probe pairs to drive Monte Carlo simulations of α-synuclein JJ Ferrie, CM Haney, J Yoon, B Pan, YC Lin, Z Fakhraai, E Rhoades, ... Biophysical Journal 114 (1), 53-64, 2018 | 26 | 2018 |
Multicolor protein FRET with tryptophan, selective coumarin-cysteine labeling, and genetic acridonylalanine encoding JJ Ferrie, N Ieda, CM Haney, CR Walters, I Sungwienwong, J Yoon, ... Chemical Communications 53 (80), 11072-11075, 2017 | 24 | 2017 |
Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin CR Walters, JJ Ferrie, EJ Petersson Chemical communications 54 (14), 1766-1769, 2018 | 23 | 2018 |
Potential artifacts in sample preparation methods used for imaging amyloid oligomers and protofibrils due to surface-mediated fibril formation YC Lin, MH Repollet-Pedrosa, JJ Ferrie, EJ Petersson, Z Fakhraai The Journal of Physical Chemistry B 121 (12), 2534-2542, 2017 | 21 | 2017 |
Improving the fluorescent probe acridonylalanine through a combination of theory and experiment I Sungwienwong, JJ Ferrie, JV Jun, C Liu, TM Barrett, ZM Hostetler, ... Journal of physical organic chemistry 31 (8), e3813, 2018 | 19 | 2018 |
A unified de novo approach for predicting the structures of ordered and disordered proteins JJ Ferrie, EJ Petersson The Journal of Physical Chemistry B 124 (27), 5538-5548, 2020 | 17 | 2020 |
Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA) TGW Graham, JJ Ferrie, GM Dailey, R Tjian, X Darzacq Elife 11, e76870, 2022 | 15 | 2022 |
Fluorescent probes for studying thioamide positional effects on proteolysis reveal insight into resistance to cysteine proteases C Liu, TM Barrett, X Chen, JJ Ferrie, EJ Petersson ChemBioChem 20 (16), 2059-2062, 2019 | 14 | 2019 |
Rosetta custom score functions accurately predict ΔΔ G of mutations at protein–protein interfaces using machine learning SR Shringari, S Giannakoulias, JJ Ferrie, EJ Petersson Chemical communications 56 (50), 6774-6777, 2020 | 12 | 2020 |