Publications

Practical Guidelines for 13C-Based NMR Metabolomics.
Edison AS, Le Guennec A, Delaglio F, Kupče Ē, Edison AS, Le Guennec A, Delaglio F, Kupče Ē. 2019. Practical Guidelines for 13C-Based NMR Metabolomics. Methods in molecular biology (Clifton, N.J.) 2037: 69-95. DOI: 10.1007/978-1-4939-9690-2_5
Target highlights in CASP13: Experimental target structures through the eyes of their authors.
Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, et al. 2019. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 87(12): 1037-1057. DOI: 10.1002/prot.25805
An asymmetry that leads to activity.
Varney KM, Cook ME, Weber DJ, Varney KM, Cook ME, Weber DJ. 2019. An asymmetry that leads to activity. Proceedings of the National Academy of Sciences of the United States of America 116(36): 17614-17615. DOI: 10.1073/pnas.1912729116
Pro- and Anti-oxidant Properties of Redox-Active Catechol-Chitosan Films.
Kim E, Kang M, Liu H, Cao C, Liu C, Bentley WE, Qu X, Payne GF, Kim E, Kang M, Liu H, Cao C, Liu C, Bentley WE, Qu X, Payne GF. 2019. Pro- and Anti-oxidant Properties of Redox-Active Catechol-Chitosan Films. Frontiers in chemistry 7: 541. DOI: 10.3389/fchem.2019.00541
Validation of oxidative stress assay for schizophrenia.
Kim E, Keskey Z, Kang M, Kitchen C, Bentley WE, Chen S, Kelly DL, Payne GF, Kim E, Keskey Z, Kang M, Kitchen C, Bentley WE, Chen S, Kelly DL, Payne GF. 2019. Validation of oxidative stress assay for schizophrenia. Schizophrenia research 212: 126-133. DOI: 10.1016/j.schres.2019.07.057
Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder.
Donohue E, Khorsand S, Mercado G, Varney KM, Wilder PT, Yu W, MacKerell AD, Alexander P, Van QN, Moree B, et al. 2019. Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder. Proceedings of the National Academy of Sciences of the United States of America 116(35): 17290-17297. DOI: 10.1073/pnas.1905516116
Translatome Profiling of Plum Pox Virus-Infected Leaves in European Plum Reveals Temporal and Spatial Coordination of Defense Responses in Phloem Tissues.
Collum TD, Stone AL, Sherman DJ, Rogers EE, Dardick C, Culver JN, Collum TD, Stone AL, Sherman DJ, Rogers EE, Dardick C, Culver JN. 2020. Translatome Profiling of Plum Pox Virus-Infected Leaves in European Plum Reveals Temporal and Spatial Coordination of Defense Responses in Phloem Tissues. Molecular plant-microbe interactions : MPMI 33(1): 66-77. DOI: 10.1094/MPMI-06-19-0152-FI
Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.
Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, et al. 2019. Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human mutation 40(9): 1519-1529. DOI: 10.1002/humu.23875
Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation.
Andreoletti G, Pal LR, Moult J, Brenner SE, Andreoletti G, Pal LR, Moult J, Brenner SE. 2019. Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation. Human mutation 40(9): 1197-1201. DOI: 10.1002/humu.23876
Newcastle disease virus vectors expressing consensus sequence of the H7 HA protein protect broiler chickens and turkeys against highly pathogenic H7N8 virus.
Roy Chowdhury I, Yeddula SGR, Pierce BG, Samal SK, Kim SH, Roy Chowdhury I, Yeddula SGR, Pierce BG, Samal SK, Kim SH. 2019. Newcastle disease virus vectors expressing consensus sequence of the H7 HA protein protect broiler chickens and turkeys against highly pathogenic H7N8 virus. Vaccine 37(35): 4956-4962. DOI: 10.1016/j.vaccine.2019.07.028
CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases.
Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, et al. 2019. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Human mutation 40(9): 1373-1391. DOI: 10.1002/humu.23874
Engineering Escherichia coli for enhanced sensitivity to the autoinducer-2 quorum sensing signal.
Stephens K, Zargar A, Emamian M, Abutaleb N, Choi E, Quan DN, Payne G, Bentley WE, Stephens K, Zargar A, Emamian M, Abutaleb N, Choi E, Quan DN, Payne G, Bentley WE. 2019. Engineering Escherichia coli for enhanced sensitivity to the autoinducer-2 quorum sensing signal. Biotechnology progress 35(6): e2881. DOI: 10.1002/btpr.2881
Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.
Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, et al. 2019. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Human mutation 40(9): 1530-1545. DOI: 10.1002/humu.23868
Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data.
Bergonzo C, Grishaev A, Bergonzo C, Grishaev A. 2019. Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data. Journal of structural biology 207(3): 250-259. DOI: 10.1016/j.jsb.2019.07.001
Mass spectrometry enumeration of filamentous M13 bacteriophage.
Wang T, Nguyen A, Zhang L, Turko IV, Wang T, Nguyen A, Zhang L, Turko IV. 2019. Mass spectrometry enumeration of filamentous M13 bacteriophage. Analytical biochemistry 582: 113354. DOI: 10.1016/j.ab.2019.113354
Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5.
Monzon AM, Carraro M, Chiricosta L, Reggiani F, Han J, Ozturk K, Wang Y, Miller M, Bromberg Y, Capriotti E, et al. 2019. Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5. Human mutation 40(9): 1474-1485. DOI: 10.1002/humu.23856
TCR3d: The T cell receptor structural repertoire database.
Gowthaman R, Pierce BG, Gowthaman R, Pierce BG. 2019. TCR3d: The T cell receptor structural repertoire database. Bioinformatics (Oxford, England) 35(24): 5323-5325. DOI: 10.1093/bioinformatics/btz517
Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography.
Lei D, Liu J, Liu H, Cleveland TE, Marino JP, Lei M, Ren G, Lei D, Liu J, Liu H, Cleveland TE, Marino JP, Lei M, Ren G. 2019. Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography. Scientific reports 9(1): 8864. DOI: 10.1038/s41598-019-44978-7
A temperature-dependent conformational shift in p38α MAPK substrate-binding region associated with changes in substrate phosphorylation profile.
Deredge D, Wintrode PL, Tulapurkar ME, Nagarsekar A, Zhang Y, Weber DJ, Shapiro P, Hasday JD, Deredge D, Wintrode PL, Tulapurkar ME, Nagarsekar A, Zhang Y, Weber DJ, Shapiro P, Hasday JD. 2019. A temperature-dependent conformational shift in p38α MAPK substrate-binding region associated with changes in substrate phosphorylation profile. The Journal of biological chemistry 294(34): 12624-12637. DOI: 10.1074/jbc.RA119.007525
Assessment of methods for predicting the effects of PTEN and TPMT protein variants.
Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, et al. 2019. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Human mutation 40(9): 1495-1506. DOI: 10.1002/humu.23838