Papers

2017


Ellen M. Black, Michael S. Chimenti, Craig L. Just.  Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment.  Accepted for publication at Peer J.

Michael S. Chimenti, Kate M. O’Brien, Morgan Farnell, Tom Tabler, Thomas Bair, Joey L. Bray, Matthew W. Nonnenmann.  Metagenomic survey of fungal communities in poultry production environments.  In preparation.

Nathan Schularick, Michael S. Chimenti, Benjamin Darbro, Marlan Hansen.   Somatic driver mutations in vestibular schwannoma (VS).   In preparation.

2016


Julie Wertz, Thomas Bair, Michael S. Chimenti.  PyVar: An Extensible Framework for Variant Annotator Comparison.  biorxiv.  doi: http://dx.doi.org/10.1101/078386.

O’Brien K, Chimenti MS, Farnell M, Tabler T, Bair T, Bray J, and Nonnenmann MW.  High Throughput Genomic Sequencing of Bioaerosols in Broiler Chicken Production Facilities.  Microbial Biotechnology.  2016 Nov; 9(6): 782-791.

Alverez C, Bulfer SL, Chakrasali R, Chimenti MS, Deshaies RJ, Green N, Kelly M, LaPorte MG, Lewis TS, Liang M, Moore WJ, Neitz RJ, Peshkov VA, Walters MA, Zhang F, Arkin MR, Wipf P, Huryn DM. Allosteric Indole Amide Inhibitors of p97: Identification of a Novel Probe of the Ubiquitin Pathway. ACS Med Chem Lett. 2016 Feb 11; 7(2):182-7. PMID: 26985295.

2015


Chimenti MS, Bulfer S, Kelly M, Jacobson M, Neitz J, James T, Arkin M. A fragment-based ligand screen against part of a large protein machine: the ND1 domains of the AAA+ ATPase p97/VCP.  Journal of Biomolecular Screening.  doi:10.1177/1087057115570550

2013


Choi, C, Webb BA, Chimenti MS, Jacobson MP, and Barber DL (2013). pH Sensing by FAK-His58 Regulates Focal Adhesion Remodeling. Journal of Cell Biology. 202 (6): 849-859.

Pfaff SJ, Chimenti MS, Kelly MJS, and Arkin MR (2013). Biophysical methods for identifying fragment-based inhibitors of protein-protein interactions. Methods in Molecular Biology. [Book Chapter].

2012


Chimenti MS, Kumar P, Pemble H, Thompson O, Jacobson MP, and Wittmann T (2012). Multisite phosphorylation modulates CLASP-EB1 interactions by disrupting arginine-glutamate salt bridge networks. Journal of Biological Chemistry. 287: 17050-17064.

Chimenti MS, Khangulov VS, Robinson AC, Heroux A, Majumdar A, Schlessman JL and Garcia-Moreno B (2012). Structural reorganization coupled to the ionization of internal residues in proteins; survey of 25 lysine residues. Structure. 20 (6): 1071-1085.

2011


Chimenti MS, Castaneda CA, Majumdar A, Garcia-Moreno B (2011). Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein. Journal of Molecular Biology. 405 (2): 361-377.

Webb BA, Chimenti MS, Jacobson MP, and Barber DL (2011). Dysregulated pH: A Perfect Storm for Cancer Progression. Nature Reviews Cancer 11: 671-677.

Kitahara R, Hata K, Maeno A, Akasaka K, Chimenti MS, Garcia-Moreno B, Schroer MA, Jeworrek C, Toland M, Winter R, Roche J, Roumestand C, Montet de Guillen K, and Royer AC (2011). Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH. Proteins 79 (4): 1293-1305.

2010


Schroer MS, Paulus M, Jeworrek C, Krywka C, Schmacke S, Zhai Y, Chimenti MS, Royer, CA, Garcia-Moreno B, Toland M, and Winter R (2010). High Pressure SAXS study of folded and unfolded ensembles of a protein. Biophysical Journal 99 (10): 3430-3437.

2008


Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, and Garcia-Moreno B (2008). Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease. Journal of Molecular Biology 379: 1045-1062.

Harms MJ, Schlessman JL, Chimenti MS, Sue GR, Damjanovic A, and Garcia-Moreno B (2008). A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein water interface as a determinant of pKa values. Protein Science 17: 833-845.

Takayama Y, Castaneda CA, Chimenti MS, Garcia-Moreno B, and Iwahara J (2008). Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein. Journal of the American Chemical Society 130: 6714-6715.

Leave a Reply

Your email address will not be published.

A blog about bioinformatics, genomic research, and data analysis. Follow me on Twitter @ChimentiMichael