Thurman, Andrew L, Ratcliff, Jason A, Chimenti, Michael S, Pezzulo, Alejandro A, and Mathelier, Anthony. “Differential Gene Expression Analysis for Multi-subject Single-cell RNA-sequencing Studies with AggregateBioVar.” Bioinformatics., 2021,

Sabree SA, Voigt AP, Blackwell SE, et al. Direct and indirect immune effects of CMP-001, a virus-like particle containing a TLR9 agonist. Journal for ImmunoTherapy of Cancer 2021; 9: e002484.  doi: 10.1136/jitc-2021-002484

Wang, Z., Chimenti, M.S., Strouse, C. et al. “T cells, particularly activated CD4+ cells, maintain anti-CD20-mediated NK cell viability and antibody dependent cellular cytotoxicity. Cancer Immunol Immunother (2021).

Merritt, Nicole, Garcia, Keith, Rajendran, Dushyandi, Lin, Zhen-Yuan, Zhang, Xiaomeng, Mitchell, Katrina A, Borcherding, Nicholas, Fullenkamp, Colleen, Chimenti, Michael S, Gingras, Anne-Claude, Harvey, Kieran F, and Tanas, Munir R. “TAZ-CAMTA1 and YAP-TFE3 Alter the TAZ/YAP Transcriptome by Recruiting the ATAC Histone Acetyltransferase Complex.” ELife. 10 (2021): E62857.

Allred, Merri-Grace, Chimenti, Michael S, Ciecko, Ashley E, Chen, Yi-Guang, and Lieberman, Scott M. “Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice. International Journal of Molecular Sciences. 22, no. 7 (2021): 3767.

Borcherding, N., Vishwakarma, A., Voigt, A.P. et al. “Mapping the immune environment in clear cell renal carcinoma by single-cell genomics.”  Nature Commun Biol 4, 122 (2021). [N.B. I was removed from the author list for this publication without my knowledge or consent, despite clearly being included on the 2019 pre-print (below)]


Oliver W. Gramlich, Alexander J. Brown, Cheyanne R. Godwin, Michael S. Chimenti, Lauren K. Boland, James A. Ankrum, Randy H. Kardon. “Systemic Mesenchymal Stem Cell Treatment Mitigates Structural and Functional Retinal Ganglion Cell Degeneration in a Mouse Model of Multiple Sclerosis.Trans. Vis. Sci. Tech. 2020;9(8):16. doi:

Debreceni IL, Chimenti MS, Serreze DV, Geurts AM, Chen Y-G, Lieberman SM. “Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice.”  International Journal of Molecular Sciences. 2020; 21(24):9478.

Sophia C. Gaynor, Eric T. Monson, Marie E. Gaine, Michael S. Chimenti, Rachel D. Reichman, Meredith Parsons, Lalita Oonthonpan, Peter P. Zandi, James B. Potash, Virginia L. Willour.  “Male-specific association of the 2p25 region with suicide attempt in bipolar disorder. ” Journal of Psychiatric Research. Volume 121, 2020.  

Kumuthini J, Chimenti M, Nahnsen S, Peltzer A, Meraba R, McFadyen R, et al. (2020) “Ten simple rules for providing effective bioinformatics research support.PLoS Comput Biol 16(3): e1007531.

T Wahls, MS Chimenti, J Kamholz, H Urnovitz. “RNA Differential Expression In Serial Blood Samples Of Relapsing Remitting Multiple Sclerosis Patients Correlates With Clinically Reported Flares.” Multiple Sclerosis. 26, no. 1_ SUPPL (2020): 81.


Ajaykumar Vishwakarma, Nick Bocherding, Michael S. Chimenti, Purshottam Vishwakarma, Kenneth Nepple, Aliasger Salem, Russell W. Jenkins, Weizhou Zhang, Yousef Zakharia.  Mapping the Immune Landscape In Clear Cell Renal Carcinoma By Single-Cell RNA-seq. biorxiv.  doi:

Sara B. Mitchell, Michael S. Chimenti, Hiroyuki Kawano, Tsun Ming, Tom Yeun, Ashley E. Sjurson, Sadahiro Iwabuchi, Kevin L Knudtson, Thomas B Bair, Diana Kolbe, N. Charles Harata.  Transcriptome profiles in brains of mice heterozygous for a DYT1 dystonia-associated mutation in the endogenous Tor1a gene.  biorxiv 825505 [Preprint].  October 31, 2019.  Available from:


Black EM, Chimenti MS, Just CL. (2018). Metagenomic analysis of nitrogen cycling genes in upper Mississippi river sediment with mussel assemblages.  Microbiology Open.  Volume 8: 5.  Available online, May 2019. .  


Black EM, Chimenti MS, Just CL. (2017) Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment. PeerJ 5:e3536


Julie Wertz, Thomas Bair, Michael S. Chimenti.  PyVar: An Extensible Framework for Variant Annotator Comparison.  biorxiv.  doi:

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.


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 Screeningdoi:10.1177/1087057115570550

Pfaff S.J., Chimenti M.S., Kelly M.J.S., Arkin M.R. (2015) Biophysical Methods for Identifying Fragment-Based Inhibitors of Protein-Protein Interactions. In: Meyerkord C., Fu H. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 1278. Humana Press, New York, NY


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.


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.


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.


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.


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.

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