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Recent Publications*


Epigenetic Programming during thymic development sets the stage for optimal function in effector T cells via DNA demethylation
Athmane Teghanemt, Priyanjali Pulipati, Kenneth Day, Matt Yorek, Ren Yi, Kara Misel-Wuchter, Henry L Keen, Christy Au, Thorsten Maretzky, Prajwal Gurung, Dan R. Littman, Priya D. Issuree
bioRxiv 2021.05.03.442517; doi: https://doi.org/10.1101/2021.05.03.442517

Teghanemt, A., Pulipati, P., Misel-Wuchter, K., Keen, HL., et al. CD4 expression in effector T cells depends on DNA demethylation over a developmentally established stimulus-responsive element. Nature  Communication 13, 1477 (2022). https://doi.org/10.1038/s41467-022-28914-4

(Abstract) RNA Sequencing Reveals Transcriptional Changes in Muscle Tissue in Response to Muscle Pain in Exercised and Sedentary Mice.  J Lesnak, K Hayashi, A Plumb, MS Chimenti, KA Sluka - The Journal of Pain, 2022

Seligman, K. L., Shearer, A. E., Frees, K., Nishimura, C., Kolbe, D., Dunn, C., Hansen, M. R., Gantz, B. J., & Smith, R. J. H. (2022). Genetic Causes of Hearing Loss in a Large Cohort of Cochlear Implant Recipients. Otolaryngology–Head and Neck Surgery, 166(4), 734–737. https://doi.org/10.1177/01945998211021308

Hirsch, Y., Tangshewinsirikul, C., Booth, K.T. et al. A synonymous variant in MYO15A enriched in the Ashkenazi Jewish population causes autosomal recessive hearing loss due to abnormal splicing. Eur J Hum Genet 29, 988–997 (2021). https://doi.org/10.1038/s41431-020-00790-w

Todd, B.P., Chimenti, M.S., Luo, Z. et al. Traumatic brain injury results in unique microglial and astrocyte transcriptomes enriched for type I interferon response. J Neuroinflammation 18, 151 (2021). https://doi.org/10.1186/s12974-021-02197-w

Derek Simonsen, Nicole Cady, Chunyun Zhang, Rachel L Shrode, Michael L McCormick, Douglas R Spitz, Michael S Chimenti, Kai Wang, Ashutosh Mangalam, Hans-Joachim Lehmler, The Effects of Benoxacor on the Liver and Gut Microbiome of C57BL/6 Mice, Toxicological Sciences, Volume 186, Issue 1, March 2022, Pages 102–117, https://doi.org/10.1093/toxsci/kfab142


Ratcliff J, Thurman A (2020). aggregateBioVar: Differential Gene Expression Analysis for Multi-subject scRNA-seq. R package version 1.0.0,  https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab337/6273181

Wang, Zhaoming; Chimenti, Michael S; Strouse, Christopher; Weiner, George J."T cells, particularly activated CD4+ cells, maintain anti-CD20-mediated NK cell viability and antibody dependent cellular cytotoxicity."  Cancer Immunology, Immunotherapy.  1-13, 2021. Springer Berlin Heidelberg.

Sabree, Shakoora A; Voigt, Andrew P; Blackwell, Sue E; Vishwakarma, Ajaykumar; Chimenti, Michael S; Salem, Aliasger K; Weiner, George J. "Direct and indirect immune effects of CMP-001, a virus-like particle containing a TLR9 agonist."  Journal for Immunotherapy of Cancer.  9:6. 2021. BMJ Publishing Group.

Thurman, Andrew L; Ratcliff, Jason A; Chimenti, Michael S; Pezzulo, Alejandro A. "Differential gene expression analysis for multi-subject single cell RNA sequencing studies with aggregateBioVar" BMC Bioinformatics. 2021. 

Allred, Merri-Grace; Chimenti, Michael S; Ciecko, Ashley E; Chen, Yi-Guang; Lieberman, Scott M. "Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice" International Journal of Molecular Sciences. 22:7. 3767. 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. "TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex" Elife, 10:e62857. 2021. eLife Sciences Publications Limited


Nicole Merritt, Keith Garcia, Dushyandi Rajendran, Zhen-Yuan Lin, Xiaomeng Zhang, Katrina M. Mitchell,  Nicholas Borcherding,  Colleen Fullenkamp, Michael Chimenti, Anne-Claude Gingras, Kieran F. Harvey, Munir R. Tanas.  TAZ-CAMTA1 and YAP-TFE3 modulate the basal TAZ/YAP transcriptional program by recruiting the ATAC histone acetyltransferase complex. bioRxiv 2020.09.07.286633; doi: https://doi.org/10.1101/2020.09.07.286633

Kumuthini J, Chimenti M, Nahnsen S, Peltzer A, Meraba R, et al. (2020) Ten simple rules for providing effective bioinformatics research support. PLOS Computational Biology 16(3): e1007531. https://doi.org/10.1371/journal.pcbi.1007531

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 SclerosisTrans. Vis. Sci. Tech. 2020;9(8):16. doi: https://doi.org/10.1167/tvst.9.8.16.

Heather A Stiff, Christina M Sloan-Heggen, Ashley Ko, Wanda L Pfeifer, Diana L Kolbe, Carla J Nishimura, Kathy L Frees, Kevin T Booth, Donghong Wang, Amy E Weaver, Hela Azaiez, John Kamholz, Richard J H Smith, Arlene V Drack. Is it Usher syndrome? Collaborative diagnosis and molecular genetics of patients with visual impairment and hearing loss. Ophthalmic Genet 2020 Apr;41(2):151-158. doi: 10.1080/13816810.2020.1747088. Epub 2020 Apr 13.

W Daniel Walls, Hideaki Moteki, Taylor R Thomas, Shin-Ya Nishio, Hidekane Yoshimura, Yoichiro Iwasa, Kathy L Frees, Carla J Nishimura, Hela Azaiez, Kevin T Booth, Robert J Marini, Diana L Kolbe, A Monique Weaver, Amanda M Schaefer, Kai Wang, Terry A Braun, Shin-Ichi Usami, Peter G Barr-Gillespie, Guy P Richardson, Richard J Smith, Thomas L Casavant. A comparative analysis of genetic hearing loss phenotypes in European/American and Japanese populations.  Hum Genet 2020 Oct;139(10):1315-1323. doi: 10.1007/s00439-020-02174-y. Epub 2020 May 7.

Ajaykumar Vishwakarma, Nicholas Bocherding, Michael S. Chimenti,  Purshottam Vishwakarma,  Kenneth Nepple,  Aliasger Salem,  Russell W. Jenkins,  Weizhou Zhang,  Yousef Zakharia.  Mapping the Immune Landscape of Clear Cell Renal Cell Carcinoma by Single-Cell RNA-seq. bioRxiv 824482; https://doi.org/10.1101/824482. 

Sara B. Mitchell, Michael S. Chimenti, Hiroyuki Kawano, Tsun Ming Tom Yuen, 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; doi: https://doi.org/10.1101/825505. 

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, Pages 151-158.  https://doi.org/10.1016/j.jpsychires.2019.11.009.



Agbor LN, Nair AR, Wu J, Lu KT, Davis DR, Keen HL, Quelle FW, McCormick JA, Singer JD, Sigmund CD.  Conditional deletion of smooth muscle Cullin-3 causes severe progressive hypertension.  JCI Insight. 2019 Jun 11;5. pii: 129793.  https://doi.org/10.1172/jci.insight.129793

Black, EM, Chimenti, MS, Just, CL.  Metagenomic analysis of nitrogen‐cycling genes in upper Mississippi river sediment with mussel assemblages. MicrobiologyOpen 2019; 8:e739. https://doi.org/10.1002/mbo3.739

Mukohda M, Fang S, Wu J, Agbor LN, Nair AR, Ibeawuchi SC, Hu C, Liu X, Lu KT, Guo DF, Davis DR, Keen HL, Quelle FW, Sigmund CD. RhoBTB1 protects against hypertension and arterial stiffness by restraining phosphodiesterase 5 activity.  J Clin Invest. 2019 Mar 21;129(6):2318-2332. doi: https://doi.org/10.1172/JCI123462. 

Ranum PT, Goodwin AT, Yoshimura H, Kolbe DL, Walls WD, Koh JY, He DZZ, & Smith RJH.  Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing. Cell Rep. 2019 Mar 12;26(11):3160-3171.e3. doi: https://doi.org/10.1016/j.celrep.2019.02.053


Shearer AE, Frees K, Kolbe DL, Smith RJH. Comprehensive Genetic Testing for Deafness from Fresh and Archived Dried Blood Spots. Otolaryngol Head Neck Surg. 2018 Aug 28:194599818797291. doi: https://doi.org/10.1177/0194599818797291

Azaiez H, Booth KT, Ephraim SS, Crone B, Black-Ziegelbein EA, Marini RJ, Shearer AE, Sloan-Heggen CM, Kolbe D, Casavant T, Schnieders MJ, Nishimura C, Braun T, Smith RJH.  Genomic Landscape and Mutational Signatures of Deafness-Associated GenesAm J Hum Genet. 2018 Oct 4;103(4):484-497. doi: https://doi.org/10.1016/j.ajhg.2018.08.006. Epub 2018 Sep 20.

Sandgren JA, Deng G, Linggonegoro DW, Scroggins SM, Perschbacher KJ, Nair AR, Nishimura TE, Zhang SY, Agbor LN, Wu J, Keen HL, Naber MC, Pearson NA, Zimmerman KA, Weiss RM, Bowdler NC, Usachev YM, Santillan DA, Potthoff MJ, Pierce GL, Gibson-Corley KN, Sigmund CD, Santillan MK, Grobe JL.  Arginine vasopressin infusion is sufficient to model clinical features of preeclampsia in mice.​  JCI Insight. 2018 Oct 4;3(19). pii: 99403. doi: https://doi.org/10.1172/jci.insight.99403. 



O'Brien, Kate M, Chimenti, Michael S, Farnell, Morgan, Tabler, Tom, Bair, Thomas, Bray, Joey L., Nonnenmann, Matthew W. High throughput genomic sequencing of bioaerosols in broiler chicken production facilitiesMicrobial Biotechnology ( 2016) 9( 6), 782– 791 https://doi.org/10.1111/1751-7915.12380

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 sedimentPeerJ 5:e3536 https://doi.org/10.7717/peerj.3536

Sarah von Spiczak, Katherine L. Helbig, Deepali N. Shinde, Robert Huether, ..., Diana L. Kolbe, Georgie Hollingsworth, Bernd A. Neubauer, Hiltrud Muhle, Ulrich Stephani, Ingrid E. Scheffer, Sérgio D.J. Pena, Sanjay M. Sisodiya, Ingo Helbig.  DNM1 encephalopathy.  For the Epi4K Consortium, For the EuroEPINOMICS-RES NLES Working Group.  Neurology Jul 2017, 89 (4) 385-394; DOI: https://doi.org/10.1212/WNL.0000000000004152

Moteki, H., Azaiez, H., Sloan-Heggen, C. M., Booth, K., Nishio, S., Wakui, K., Kolbe, D, … Usami, S. (2016). Detection and Confirmation of Deafness-Causing Copy Number Variations in the STRC Gene by Massively Parallel Sequencing and Comparative Genomic HybridizationAnnals of Otology, Rhinology & Laryngology, 125(11), 918–923. https://doi.org/10.1177/0003489416661345

Julie Wertz, Qianli Liao, Thomas B Bair & Michael S Chimenti.  PyVar: An Extensible Framework for Variant Annotator Comparison. bioRxiv 078386; doi: https://doi.org/10.1101/078386


Policy on authorship and acknowledgement

The University of Iowa policy on authorship is listed here.  The policy is clear that intellectual contributions are the driver for inclusion on the co-author list.  A good litmus test for "intellectual contribution" is when one or more figures of the final manuscript result from our analysis work.  Both co-authorship and acknowledgement are an important part of how our division is evaluated. 

The ABRF recommendation published in Angeletti et al. in 1999 (FASEB Journal, 13:595), reads: 

“Intellectual interactions between resource and research scientists are essential to the success of each project. When this success results in publication, a citation in the acknowledgments section of a manuscript may be appropriate for routine analysis.  However, contributions from resource scientists that involve novel resource laboratory work and insight, experimental design, or advanced data analysis that make a publication possible or significantly enhance its value require co-authorship.”

Where our contribution is simply routine technical support or use of the division’s computational resources it may be appropriate to cite the Bioinformatics division as a part of the acknowledgements.  Here is how to acknowledge the Division: 

"Data presented herein were obtained at the Bioinformatics Division of the Iowa Institute of Human Genetics which is supported, in part, by the University of Iowa Carver College of Medicine."