Publications

As IMCI grows and matures, we are seeing more and more research articles being published. Here’s our growing list of publications that cite CMCI P20GM104420.

If you are interested in announcing your upcoming journal publication to the general public, please contact University Communications and Marketing (UCM) Science and Content Writer Leigh Cooper. She may be able to help you with a press release, social media, etc. Reach out soon after your paper has been accepted and before you publish.

If you have a publication that belongs on this list, please see grant citation and publication expectations.

Creagh JW, Rolfsmeier M, Evans KJ, Bizarria R, Reetz DC, Badigian TJ, Fredericks LR, Hasenoehrl AM, Brown AP, Graves BM, Alexander CK, Rodrigues A, Stoffregen EP, Patel JS, Ytreberg FM, Rowley PA.0.The Saccharomyces killer toxin K62 is a protein of the aerolysin family. mBio0:e01425-25.https://doi.org/10.1128/mbio.01425-25

Xu C, Kim TT, Kirsch I, Plöderl M, Amsterdam JD, Pigott HE. (2025) Restoring STAR*D: A Reanalysis of Drug-Switch Therapy After Failed SSRI Treatment Using Patient-Level Data with Fidelity to the Original STAR*D Research Protocol. medRxiv : the preprint server for health sciences:2025.02.10.25321991. https://doi.org/10.1101/2025.02.10.25321991 PMID:39990569 PMCID:PMC11844611

Perez M, Actis M, Sanchez I, Hernandez-Vargas EA, González AH. (2025) Multi-objective control to schedule therapies for acute viral infections. Journal of mathematical biology 90(2):25. https://doi.org/10.1007/s00285-025-02188-y PMID:39904788 PMCID:PMC12119099

Meadows T, Coats ER, Narum S, Top EM, Ridenhour BJ, Stalder T. (2025) Epidemiological model can forecast COVID-19 outbreaks from wastewater-based surveillance in rural communities. Water research 268(Pt A):122671. https://doi.org/10.1016/j.watres.2024.122671 PMID:39488168 PMCID:PMC11614685

Kvamme J, Badsha MB, Martin EA, Wu J, Wang X, Fu AQ. (2025) Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues. Genetics 230(2):iyaf064. https://doi.org/10.1093/genetics/iyaf064 PMID:40179003 PMCID:PMC12135172

Spencer EK, Miller CR, Bull JJ. (2025) Standardized methods for rearing a moth larva, Manduca sexta, in a laboratory setting. PloS one 20(4):e0316776. https://doi.org/10.1371/journal.pone.0316776 PMID:40299873 PMCID:PMC12040098

Kim TT, Xu C, Amsterdam JD. (2025) Comparison of effectiveness and side effects of selegiline transdermal system versus oral monoamine oxidase inhibitors and tricyclic antidepressants for treatment-resistant depression. Journal of affective disorders 376:47-51. https://doi.org/10.1016/j.jad.2025.02.003 PMID:39904463 PMCID:PMC11867850

Phan TA, Fitzsimons DP. (2025) Modeling the effects of thin filament near-neighbor cooperative interactions in mammalian myocardium. The Journal of general physiology 157(2):e202413582. https://doi.org/10.1085/jgp.202413582 PMID:39869069 PMCID:PMC11771317

Alharbi F, Vakanski A, Zhang B, Elbashir MK, Mohammed M. (2025) Comparative Analysis of Multi-Omics Integration Using Graph Neural Networks for Cancer Classification. IEEE access : practical innovations, open solutions 13:37724-36. https://doi.org/10.1109/access.2025.3540769 PMID:40123934 PMCID:PMC11928009

Li S, Lund-Andersen P, Wang SH, Ytreberg FM, Naik MT, Patel JS, Rowley PA. (2025) The identification of a novel interaction site for the human immunodeficiency virus capsid on nucleoporin 153. The Journal of general virology 106(5):002104. https://doi.org/10.1099/jgv.0.002104 PMID:40366356 PMCID:PMC12078792

Condon DE, Schroeder BK, Rowley PA, Ytreberg FM. (2025) Discovery of novel targets for important human and plant fungal pathogens via an automated computational pipeline HitList. PloS one 20(6):e0323991. https://doi.org/10.1371/journal.pone.0323991 PMID:40460077 PMCID:PMC12132981

Alharbi F, Budhiraja N, Vakanski A, Zhang B, Elbashir MK, Guduru H, Mohammed M. (2025) Interpretable graph Kolmogorov-Arnold networks for multi-cancer classification and biomarker identification using multi-omics data. Scientific reports 15(1):27607. https://doi.org/10.1038/s41598-025-13337-0 PMID:40730661 PMCID:PMC12307575

Spencer EK, Eline Y, Saucedo L, Linzan K, Paull K, Miller CR, Peters TL, Van Leuven JT. (2025) Bacteriophage resistance evolution in a honey bee pathogen. bioRxiv : the preprint server for biology:2024.07.09.602782. https://doi.org/10.1101/2024.07.09.602782 PMID:39026776 PMCID:PMC11257554

Hassan M, Vakanski A, Zhang B, Xian M. (2025) Do Sharpness-Based Optimizers Improve Generalization in Medical Image Analysis. IEEE access : practical innovations, open solutions 13:82972-85. https://doi.org/10.1109/ACCESS.2025.3568641 PMID:40443707 PMCID:PMC12121992

Sarafoglou A, Hoogeveen S, van den Bergh D, Aczel B, Albers CJ, Althoff T, Botvinik-Nezer R, Busch NA, Cataldo AM, Devezer B, van Dongen NNN, Dreber A, Fried EI, Hoekstra R, Hoffman S, Holzmeister F, Huber J, Huntington-Klein N, Ioannidis J, Johannesson M, Kirchler M, Loken E, Mangin JF, Matzke D, Menkveld AJ, Nilsonne G, van Ravenzwaaij D, Schweinsberg M, Schulz-Kuempel H, Shanks DR, Simons DJ, Spellman BA, Stoevenbelt AH, Szaszi B, Trübutschek D, Tuerlinckx F, Uhlmann EL, Vanpaemel W, Wicherts J, Wagenmakers EJ. (2024) Subjective evidence evaluation survey for many-analysts studies. Royal Society open science 11(7):240125. https://doi.org/10.1098/rsos.240125 PMID:39050728 PMCID:PMC11265885

Bull JJ, Koelle K, Antia R. (2024) Waning immunity drives respiratory virus evolution and reinfection. bioRxiv : the preprint server for biology:2024.07.23.604867. https://doi.org/10.1101/2024.07.23.604867 PMID:39091870 PMCID:PMC11291175

Rockey DD, Wang X, Debrine A, Grieshaber N, Grieshaber SS. (2024) Metabolic dormancy in Chlamydia trachomatis treated with different antibiotics. Infection and immunity 92(2):e0033923. https://doi.org/10.1128/iai.00339-23 PMID:38214508 PMCID:PMC10863404

Ellis JR, Rowley PA. (2024) An apparent lack of synergy between degradative enzymes against Staphylococcus aureus biofilms. microPublication biology 2024. https://doi.org/10.17912/micropub.biology.001119 PMID:38596361 PMCID:PMC11002645

Blanco-Rodríguez R, Tetteh JNA, Hernández-Vargas E. (2024) Assessing the impacts of vaccination and viral evolution in contact networks. Scientific reports 14(1):15753. https://doi.org/10.1038/s41598-024-66070-5 PMID:38977773 PMCID:PMC11231155

Lyu Y, Kim BJ, Patel JS, Dallas DC, Chen Y. (2024) Human Milk Protein-Derived Bioactive Peptides from In Vitro-Digested Colostrum Exert Antimicrobial Activities against Common Neonatal Pathogens. Nutrients 16(13):2040. https://doi.org/10.3390/nu16132040 PMID:38999788 PMCID:PMC11243250

Barnes JE, América Chi L, Marty Ytreberg F, Patel JS. (2024) Leveraging neural networks to correct FoldX free energy estimates. bioRxiv : the preprint server for biology:2024.09.23.614615. https://doi.org/10.1101/2024.09.23.614615 PMID:39386633 PMCID:PMC11463479

Spencer EK, Miller CR, Bull J. (2024) Standardized methods for rearing a moth larva, Manduca sexta, in a laboratory setting. bioRxiv : the preprint server for biology:2024.12.18.629232. https://doi.org/10.1101/2024.12.18.629232 PMID:39763740 PMCID:PMC11702677

Bull JJ, Krone SM. (2024) Mathematical comparison of protocols for adapting a bacteriophage to a new host. Virus evolution 10(1):veae100. https://doi.org/10.1093/ve/veae100 PMID:39717707 PMCID:PMC11665826

Zhong V, Ketchum N, Mackenzie JK, Garcia X, Rowley PA. (2024) Inhibition of diastatic yeasts by Saccharomyces killer toxins to prevent hyperattenuation during brewing. Applied and environmental microbiology 90(10):e0107224. https://doi.org/10.1128/aem.01072-24 PMID:39264169 PMCID:PMC11497815

Fogg LG, Isari S, Barnes JE, Patel JS, Marshall NJ, Salzburger W, Cortesi F, de Busserolles F. (2024) Deep-sea fish reveal alternative pathway for vertebrate visual development. bioRxiv : the preprint server for biology:2024.10.10.617579. https://doi.org/10.1101/2024.10.10.617579 PMID:39416096 PMCID:PMC11483065

Almocera AES, González AH, Hernandez-Vargas EA. (2024) Confinement tonicity on epidemic spreading. Journal of mathematical biology 88(4):46. https://doi.org/10.1007/s00285-024-02064-1 PMID:38519724 PMCID:PMC11067545

Dixon M, Phan TA, Dallon JC, Tian JP. (2024) Mathematical model for IL-2-based cancer immunotherapy. Mathematical biosciences 372:109187. https://doi.org/10.1016/j.mbs.2024.109187 PMID:38575057 PMCID:PMC11193449

Bull JJ, Wichman HA, Krone SM, Molineux IJ. (2024) Controlling Recombination to Evolve Bacteriophages. Cells 13(7):585. https://doi.org/10.3390/cells13070585 PMID:38607024 PMCID:PMC11011186

Buzbas EO, Devezer B. (2024) Statistics in Service of Metascience: Measuring Replication Distance with Reproducibility Rate. Entropy (Basel, Switzerland) 26(10):842. https://doi.org/10.3390/e26100842 PMID:39451919 PMCID:PMC11507548

Seamon E, Ridenhour BJ, Miller CR, Johnson-Leung J. (2024) Spatial Modeling of Sociodemographic Risk for COVID-19 Mortality. medRxiv : the preprint server for health sciences:2023.07.21.23292785. https://doi.org/10.1101/2023.07.21.23292785 PMID:37546990 PMCID:PMC10402221

Taylor MB, Warwick AR, Skophammer R, Boyer JM, Geck RC, Gunkelman K, Walson M, Rowley PA, Dunham MJ. (2024) yEvo: A modular eukaryotic genetics and evolution research experience for high school students. Ecology and evolution 14(1):e10811. https://doi.org/10.1002/ece3.10811 PMID:38192907 PMCID:PMC10771926

Tovissodé CF, Baumgaertner B. (2024) Heterogeneous risk tolerance, in-groups, and epidemic waves. Frontiers in applied mathematics and statistics 10:1360001. https://doi.org/10.3389/fams.2024.1360001 PMID:38818516 PMCID:PMC11138946

Paull K, Spencer E, Miller CR, Van Leuven JT. (2024) Viral adaptations to alternative hosts in the honey bee pathogen Paenibacillus larvae. bioRxiv : the preprint server for biology:2024.09.01.610711. https://doi.org/10.1101/2024.09.01.610711 PMID:39257743 PMCID:PMC11384002

Chi LA, Pandey SK, Kolodziejczyk W, Lund-Andersen P, Barnes JE, Kapusta K, Patel JS. (2024) Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins. bioRxiv : the preprint server for biology:2024.09.24.614827. https://doi.org/10.1101/2024.09.24.614827 PMID:39386526 PMCID:PMC11463405

Hoang C, Phan TA, Turtle CJ, Tian JP. (2024) A stochastic framework for evaluating CAR T cell therapy efficacy and variability. Mathematical biosciences 368:109141. https://doi.org/10.1016/j.mbs.2024.109141 PMID:38190882 PMCID:PMC11097280

Bruger EL, Hying ZT, Singla D, Márquez Reyes NL, Pandey SK, Patel JS, Bazurto JV. (2024) Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1. Applied and environmental microbiology 90(7):e0031024. https://doi.org/10.1128/aem.00310-24 PMID:38934615 PMCID:PMC11323934

Fulton MD, Yama DJ, Dahl E, Johnson JL. (2024) Hsp90 and cochaperones have two genetically distinct roles in regulating eEF2 function. PLoS genetics 20(12):e1011508. https://doi.org/10.1371/journal.pgen.1011508 PMID:39652595 PMCID:PMC11651573

Bizarria R, Creagh JW, Badigian TJ, Corrêa Dos Santos RA, Coss SA, Tekle RT, Fredstrom N, Ytreberg FM, Dunham MJ, Rodrigues A, Rowley PA. (2024) The Prevalence of Killer Yeasts in the Gardens of Fungus-Growing Ants and the Discovery of Novel Killer Toxin named Ksino. bioRxiv : the preprint server for biology:2024.10.14.618321. https://doi.org/10.1101/2024.10.14.618321 PMID:39463942 PMCID:PMC11507743

Peters TL, Schow J, Spencer E, Van Leuven JT, Wichman H, Miller C. (2024) Directed evolution of bacteriophages: thwarted by prolific prophage. Applied and environmental microbiology 90(11):e0088424. https://doi.org/10.1128/aem.00884-24 PMID:39475284 PMCID:PMC11577772

Chi LA, Barnes JE, Patel JS, Ytreberg FM. (2024) Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data. Scientific reports 14(1):23122. https://doi.org/10.1038/s41598-024-72491-z PMID:39366988 PMCID:PMC11452645

Chi LA, Barnes JE, Suresh Patel J, Ytreberg FM. (2024) Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data. bioRxiv : the preprint server for biology:2024.05.22.595230. https://doi.org/10.1101/2024.05.22.595230 PMID:38826284 PMCID:PMC11142147

Moxley TA, Johnson-Leung J, Seamon E, Williams C, Ridenhour BJ. (2024) Application of elastic net regression for modeling COVID-19 sociodemographic risk factors. PloS one 19(1):e0297065. https://doi.org/10.1371/journal.pone.0297065 PMID:38277346 PMCID:PMC10817220

Peters TL, Schow J, Spencer E, Van Leuven JT, Wichman H, Miller C. (2024) Directed evolution of bacteriophages: impacts of prolific prophage. bioRxiv : the preprint server for biology:2024.06.28.601269. https://doi.org/10.1101/2024.06.28.601269 PMID:38979301 PMCID:PMC11230397

Afrin, Farjana; Mateen, Sameena; Oman, Jordan; Lai, James C.K.; Barrott, Jared; Pashikanti, Srinath. (2023). Natural Products and Small Molecules Targeting Cellular Ceramide Metabolism to Enhance Apoptosis in Cancer Cells. Cancers (Basel), 15(18):4645. doi:10.3390/cancers15184645

Buzbas, Erkan; Devezer, Berna; Baumgartner, Bert. (2023). The logical structure of experiments lays the foundation for a theory of reproducibility. Royal Society Open Science, 10(3):221042. doi: 10.1098/rsos.221042

Chiok, K; Hutchinson, K; Miller, L; Bose, S; Miura, T. (2023). Proinflammatory Responses in SARS-CoV-2 and Soluble Spike Glycoprotein in S1 Subunit Activated Human Macrophages. Viruses, 15(3):754. doi: 10.3390/v15030754

Curtsinger, H; Zeng, X; Mather, Z; Ballyk, M; Phan, T; Nui, B; Pu, J; Bartee, M; Tian, J; Bartee, E. (2023). High Levels of Extracellular Potassium Can Delay Myxoma Virus Replication by Preventing Release of Virions from the Endosomes. J Virol, 97(1);e0129422. doi: 10.1128/jvi.01294-22.

Ellis, J; Bull, J; Rowley, P. (2023). Fungal Glycoside Hydrolases Display Unique Specifities for Polysaccharides and Staphylococcus aureus Biofilms. Microorganisms, 11(2):293. doi:10.3390/microorganisms11020293

Ferguson, J; Gonzalez-Gonzalez, A; Kaiser, J; Winzer, S; Anast, J; Ridenhour, B; Miura, T; Parent, C. (2023). Hidden variable models reveal the effects of infection from changes in host survival. PLOS Computational Biology, 19(2):e1010910. doi: 10.1371/journal.pcbi.1010910

Zhang, B; Vakanski, A; Xian, M. (2023). BI-RADS-NET-V2: A Composite Multi-Task Neural Network for Computer-Aided Diagnosis of Breast Cancer in Ultrasound Images with Semantic and Quantitative Explanations. IEEE Access, 11:79480-79494. doi: 10.1109/access.2023.3298569

Barnes, Jonathan; Lund-Andersen, Peik; Patel, Jagdish; Ytreberg, F Marty. (2022). The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6. Nature Scientific Reports, 12(1):18819. doi: 10.1038/s41598-022-23482-5

Barnes, J. E., Miller, C. R., & Ytreberg, F. M. (2022). Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins, 10.1002/prot.26328. Advance online publication. https://doi.org/10.1002/prot.26328

Baumgaertner, Bert; Justwan, Florian. (2022). The preference for belief, issue polarization, and echo chambers. Synthese, 200(5):412, doi: 10.1007/s11229-022-03880-y

Beach, S; Hull, M; Ytreberg, FM; Patel, J; Miura, T. (2022). Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein. J Virol, 96(13):e0035322. doi:10.1128/jvi.00353-22

Bull, J; Wichman, H; Krone, S. (2022). Modeling the Directed Evolution of Broad Host Range Phages. Antibiotics (Basel), 11(12):1709, doi: 10.3390/antiobiotics11121709

Busby, T. J., Miller, C. R., Moran, N. A., & Van Leuven, J. T. (2022). Global Composition of the Bacteriophage Community in Honey Bees. mSystems, 7(2), e0119521. https://doi.org/10.1128/msystems.01195-21

Butte S., Wang H., Xian M., Vakanski A. (2022). Sharp-GAN: Sharpness Loss Regularized GAN for Histopathology Image Synthesis. IEEE International Symposium on Biomedical Imaging (ISBI).

Cox, G., Gonzalez, A. J., Ijezie, E. C., Rodriguez, A., Miller, C. R., Van Leuven, J. T., & Miura, T. A. (2022). Priming With Rhinovirus Protects Mice Against a Lethal Pulmonary Coronavirus Infection. Frontiers in immunology, 13, 886611. https://doi.org/10.3389/fimmu.2022.886611

Eilertsen, M; Davie, W; Patel, D; Barnes, J; Karlsen, R; Mountford, J; Stenkamp, D; Patel, J; Helvik, J. (2022). An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity. Front Neuroanat, 11;16:945344. doi: 10.3389fnana.2022.945344

Gao, Fuchang; Ma, Yiqing; Zhang, Boyu, Xian, Min. (2022) SepNet: A neural network for directionally correlated data. Neural Netw, 153:215-223. doi: 10.1016/j.neunet.2022.06.005.

Haag, S; Martinez-Alvarez, J; Schiele, N; Bernards, M. (2022). Delivery of Bioactive Albumin from Multi-Functional Polyampholyte Hyrdogels. J Appl Polym Sci. 139(5):e52846. doi: 10.1002/app.52846

Hernandez-Mejia, G; Sanchez, E; Chan, V; Hernandez-Vargas, E. (2022) Impulsive Neural Control to Schedule Antivirals and Immunomodulators for COVID-19. Proc IEEE Conf Decis Control, 2022:5633-5638. doi: 10.1109/cdc51059.2022.9992454.

Li, S; Patel, JS; Crabtree, AM; Rebenstein, BM; Lund-Anderson, PK; Ytreberg, FM; Rowley, PA. (2022). Defining the HIV Capsid Binding Site of Nucleoporin 153. mSphere, 7(5)e0031022. doi: 10.1128/msphere.00310-22

Jhutty, Suneet; Boehme, Julia; Jeron, Andreas; Volckmar, Julia; Schultz, Kristin; Schreiber, Jens; Schugart, Klaus; Zhou, Kaj; Steinheimer, Jan; Stocker, Horst; Stegemann-Koniszewski, Bruder, Dunja; Hernandez-Vargas, Esteban. (2022). Predicting Influenza A Virus Infection in the Lung from Hematological Data with Machine Learning. mSystems, 7(6):e0045922. doi: 10.1128/msystems.00459-22.

Joseph, N., & Kolok, A. S. (2022). Assessment of Pediatric Cancer and Its Relationship to Environmental Contaminants: An Ecological Study in Idaho. GeoHealth, 6(3), e2021GH000548. https://doi.org/10.1029/2021GH000548

Kuan, M; Caruso, L; Zavala, A; Rana, P; O’Dowd, J; Tempera, I; Fortunato, E. (2022). Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1. J Jirol, 96(20):e0133622. doi: 10.1128/jvi.01336-22

Lee, M; Creagh, J; Fredericks, L; Crabtree, A; Patel, J; Rowley, P. (2022). The Characterization of a Novel Virus Discovered in the Yeast Pichia membranifaciens. Viruses, 14(3):594. doi:10.3390/v14030594

Mehta, H; Ibarra, D; Marx, C; Miller, C; Shamoo, Y. (2022). Mutational Switch-Backs Can Accelerate Evolution of Francisella to a Combination of Ciprofloxacin and Doxycycline. Front Microbiol, 9;13: 904822. doi: 10.3389/fmicb.2022.904822

Nguyen, L; Haltmeier, M; Kowar, R; Do, N. (2022). Analysis for Full-Field Photoacoustic Tomography with Variable Sound Speed. SIAM Journal on Imaging Sciences, 15(3): 1213-1228. doi: 10.1137/21m1463409

Noddings, C; Wang, R; Johnson, J; Agard, D. (2022). Structure of Hsp90-p23-GR reveals the Hsp90 client-remodelling mechanism. Nature, 601(7893):465-469. doi: 10.1038/s41586-021-04236-1

Patel, D., Haag, S. L., Patel, J. S., Ytreberg, F. M., & Bernards, M. T. (2022). Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. Journal of chemical information and modeling, 62(5), 1282–1293. https://doi.org/10.1021/acs.jcim.1c01104

Phan, T; Tian, J. (2022). Hopf bifurcation without parameters in deterministic and stochastic modeling of cancer virotherapy, part II. J Math Anal Appl, 515(2), NIHMS1883942. doi: 10.1016/j.jmaa.2022.126444

Ridenhour, B. J., Sarathchandra, D., Seamon, E., Brown, H., Leung, F. Y., Johnson-Leon, M., Megheib, M., Miller, C. R., & Johnson-Leung, J. (2022). Effects of trust, risk perception, and health behavior on COVID-19 disease burden: Evidence from a multi-state US survey. PloS one, 17(5), e0268302. https://doi.org/10.1371/journal.pone.0268302

Shareef, B; Vakanski, A; Freer, P; Xian, M. (2022). ESTAN: Enhanced Small Tumor-Aware Network for Breast Ultrasound Image Segmentation. Healthcare (Basel), 10(11):2262. doi: 10.3390/healthcare10112262

Shi J., Vakanski A., Xian M., Ding J., Ning C. (2022). EMT-Net: Efficient multitask network for computer-aided diagnosis of breast cancer. IEEE International Symposium on Biomedical Imaging (ISBI).

Wang, H., Xian, M., Vakanski, A. (2022). TA-Net: Topology-Aware Network for Gland Segmentation. IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2022, 3241-3249.

Wang, R. Y., Noddings, C. M., Kirschke, E., Myasnikov, A. G., Johnson, J. L., & Agard, D. A. (2022). Structure of Hsp90-Hsp70-Hop-GR reveals the Hsp90 client-loading mechanism. Nature, 601(7893), 460–464. https://doi.org/10.1038/s41586-021-04252-1

Zhang, B; Wang, S; Gao, F. (2022). Contrastive Metric Learning for Lithium Super-ionic Conductor Screening. SN Computer Science, 3(6):465. doi: 10.1007/s42979-022-01370-z

Zhang, Y., Xian, M., Cheng, H. D., Shareef, B., Ding, J., Xu, F., Huang, K., Zhang, B., Ning, C., & Wang, Y. (2022). BUSIS: A Benchmark for Breast Ultrasound Image Segmentation. Healthcare (Basel, Switzerland), 10(4), 729. https://doi.org/10.3390/healthcare10040729

Badsha, M. B., Martin, E. A., & Fu, A. Q. (2021). MRPC: An R Package for Inference of Causal Graphs. Frontiers in genetics, 12, 651812. https://doi.org/10.3389/fgene.2021.651812

Bazurto, J. V., Bruger, E. L., Lee, J. A., Lambert, L. B., & Marx, C. J. (2021). Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens. Journal of bacteriology, 203(9), e00589-20. Advance online publication. https://doi.org/10.1128/JB.00589-20

Bazurto, J. V., Nayak, D. D., Ticak, T., Davlieva, M., Lee, J. A., Hellenbrand, C. N., Lambert, L. B., Benski, O. J., Quates, C. J., Johnson, J. L., Patel, J. S., Ytreberg, F. M., Shamoo, Y., & Marx, C. J. (2021). EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde. PLoS biology, 19(5), e3001208. https://doi.org/10.1371/journal.pbio.3001208

Bazurto, J. V., Riazi, S., D’Alton, S., Deatherage, D. E., Bruger, E. L., Barrick, J. E., & Marx, C. J. (2021). Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition. Microorganisms, 9(2), 347. https://doi.org/10.3390/microorganisms9020347

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Biggs, K., Bailes, C. L., Scott, L., Wichman, H. A., & Schwartz, E. J. (2021). Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage. Viruses, 13(7), 1389. https://doi.org/10.3390/v13071389

Devezer, B., Navarro, D. J., Vandekerckhove, J., & Ozge Buzbas, E. (2021). The case for formal methodology in scientific reform. Royal Society open science, 8(3), 200805. https://doi.org/10.1098/rsos.200805

Epstein, L., Dubois, Z., Smith, J., Lee, Y., & Harrington, K. (2021). Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum. Bio Systems, 208, 104483. https://doi.org/10.1016/j.biosystems.2021.104483

Fredericks, L. R., Lee, M. D., Crabtree, A. M., Boyer, J. M., Kizer, E. A., Taggart, N. T., Roslund, C. R., Hunter, S. S., Kennedy, C. B., Willmore, C. G., Tebbe, N. M., Harris, J. S., Brocke, S. N., & Rowley, P. A. (2021). The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina. PLoS genetics, 17(2), e1009341. https://doi.org/10.1371/journal.pgen.1009341

Fredericks, L. R., Lee, M. D., Eckert, H. R., Li, S., Shipley, M. A., Roslund, C. R., Boikov, D. A., Kizer, E. A., Sobel, J. D., & Rowley, P. A. (2021). Vaginal Isolates of Candida glabrata Are Uniquely Susceptible to Ionophoric Killer Toxins Produced by Saccharomyces cerevisiae. Antimicrobial agents and chemotherapy, 65(7), e0245020. https://doi.org/10.1128/AAC.02450-20

Grieshaber, N. A., Runac, J., Turner, S., Dean, M., Appa, C., Omsland, A., & Grieshaber, S. S. (2021). The sRNA Regulated Protein DdbA Is Involved in Development and Maintenance of the Chlamydia trachomatis EB Cell Form. Frontiers in cellular and infection microbiology, 11, 692224. https://doi.org/10.3389/fcimb.2021.692224

Haag SL, Schiele NR, Bernards MT. Enhancement and mechanisms of MC3T3-E1 osteoblast-like cell adhesion to albumin through calcium exposure. Biotechnol Appl Biochem. 2021 Feb 15:10.1002/bab.2126. doi: 10.1002/bab.2126. Epub ahead of print. PMID: 33586804; PMCID: PMC8364568.

Haag SL, Schiele NR, Bernards MT. Enhancement and mechanisms of MC3T3-E1 osteoblast-like cell adhesion to albumin through calcium exposure. Biotechnol Appl Biochem. 2021 Feb 15:10.1002/bab.2126. doi: 10.1002/bab.2126. Epub ahead of print. PMID: 33586804; PMCID: PMC8364568.

Hohrman, K., Gonçalves, D., Morano, K. A., & Johnson, J. L. (2021). Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects. Genetics, 217(3), iyab009. https://doi.org/10.1093/genetics/iyab009

Kuan, M. I., Jaeger, H. K., Balemba, O. B., O’Dowd, J. M., Duricka, D., Hannemann, H., Marx, E., Teissier, N., Gabrielli, L., Bonasoni, M. P., Keithley, E. M., & Fortunato, E. A. (2021). Human Cytomegalovirus Interactions with the Basement Membrane Protein Nidogen 1. Journal of virology, 95(3), e01506-20. https://doi.org/10.1128/JVI.01506-20

Patel, D., Patel, J. S., & Ytreberg, F. M. (2021). Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy. Journal of chemical theory and computation, 17(4), 2457–2464. https://doi.org/10.1021/acs.jctc.0c01045

Remien, C. H., Eckwright, M. J., & Ridenhour, B. J. (2021). Structural identifiability of the generalized Lotka-Volterra model for microbiome studies. Royal Society open science, 8(7), 201378. https://doi.org/10.1098/rsos.201378

Rowley, P. A., Ellahi, A., Han, K., Patel, J. S., Van Leuven, J. T., & Sawyer, S. L. (2021). Nuku, a family of primate retrocopies derived from KU70. G3 (Bethesda, Md.), 11(8), jkab163. https://doi.org/10.1093/g3journal/jkab163

Vakanski, A., Xian, M. (2021). Evaluation of Complexity Measures for Deep Learning Generalization in Medical Image Analysis. IEEE 31st International Workshop on Machine Learning for Signal Processing (MLSP), 2021, 1-6.

Van Leuven, J. T., Ederer, M. M., Burleigh, K., Scott, L., Hughes, R. A., Codrea, V., Ellington, A. D., Wichman, H. A., & Miller, C. R. (2021). ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome biology and evolution, 13(2), evaa214. https://doi.org/10.1093/gbe/evaa214

Van Leuven, J. T., Gonzalez, A. J., Ijezie, E. C., Wixom, A. Q., Clary, J. L., Naranjo, M. N., Ridenhour, B. J., Miller, C. R., & Miura, T. A. (2021). Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms. mSphere, 6(3), e0047921. https://doi.org/10.1128/mSphere.00479-21

Wang, B., Tsakiridis, E. E., Zhang, S., Llanos, A., Desjardins, E. M., Yabut, J. M., Green, A. E., Day, E. A., Smith, B. K., Lally, J., Wu, J., Raphenya, A. R., Srinivasan, K. A., McArthur, A. G., Kajimura, S., Patel, J. S., Wade, M. G., Morrison, K. M., Holloway, A. C., & Steinberg, G. R. (2021). The pesticide chlorpyrifos promotes obesity by inhibiting diet-induced thermogenesis in brown adipose tissue. Nature communications, 12(1), 5163. https://doi.org/10.1038/s41467-021-25384-y

Zhang, B., Vakanski, A., Xian, M. (2021). Bi-Rads-Net: An Explainable Multitask Learning Approach for Cancer Diagnosis in Breast Ultrasound Images. IEEE 31st International Workshop on Machine Learning for Signal Processing (MLSP), 2021, 1–6.

Badsha, M.B., Li, R., Liu, B. et al. (2020). Imputation of single-cell gene expression with an autoencoder neural network. Quant Biol., 8(1):78-94. doi:10.1007/s40484-019-0192-7

Baumgaertner, B., Ridenhour, B. J., Justwan, F., Carlisle, J. E., & Miller, C. R. (2020). Risk of disease and willingness to vaccinate in the United States: A population-based survey. PLoS medicine, 17(10), e1003354. https://doi.org/10.1371/journal.pmed.1003354

Belsare A, Gompper M, Keller B, Sumners J, Hansen L, Millspaugh J. Size matters: Sample size assessments for chronic wasting disease surveillance using an agent-based modeling framework. MethodsX. 2020;7:100953. Published 2020 Jun 11. doi:10.1016/j.mex.2020.100953

Belsare, Aniruddha V., Gompper, Matthew E., Keller, Barbara, Sumners, Jason, Hansen, Lonnie, Millspaugh, Joshua J. (2020). An agent-based framework for improving wildlife disease surveillance: A case study of chronic wasting disease in Missouri white-tailed deer. Ecological Modelling, 417, 108919. doi:10.1016/j.ecolmodel.2019.108919

Belsare, A., & Vanak, A. T. (2020). Modelling the challenges of managing free-ranging dog populations. Scientific reports, 10(1), 18874. https://doi.org/10.1038/s41598-020-75828-6

Chiarelli, T. J., Grieshaber, N. A., Omsland, A., Remien, C. H., & Grieshaber, S. S. (2020). Single-Inclusion Kinetics of Chlamydia trachomatis Development. mSystems, 5(5), e00689-20. https://doi.org/10.1128/mSystems.00689-20

Faber MS, Van Leuven JT, Ederer MM, Sapozhnikov Y, Wilson ZL, Wichman HA, Whitehead TA, Miller CR. (2020). Saturation Mutagenesis Genome Engineering of Infective ΦX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly. ACS Synth Biol., 9(1):125-131. doi:10.1021/acssynbio.9b00411

Fan, H, Su, B, Ma, C., Rowley, P. A., & Jayaram, M. A Bipartite Thermodynamic-kinetic Contribution By an Activating Mutation to RDF-independent Excision By a Phage Serine Integrase. Nucleic Acids Research, vol. 48, no. 12, 2020, pp. 6413-6430. doi:10.1093/nar/gkaa401

Fredericks LR, Lee MD, Roslund CR, Crabtree AM, Allen PB, Rowley PA. The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella. PLoS One. 2020;15(7):e0230767. Published 2020 Jul 30. doi:10.1371/journal.pone.0230767

Gao, F. C., & Lai, M. J. (2020). A New H2 Regularity Condition of the Solution to Dirichlet Problem of the Poisson Equation and Its Applications. Acta mathematica Sinica, English series, 36(1), 21–39. https://doi.org/10.1007/s10114-019-8015-3

Gonzalez, T. R., Martin, K. P., Barnes, J. E., Patel, J. S., & Ytreberg, F. M. (2020). Assessment of software methods for estimating protein-protein relative binding affinities. PloS one, 15(12), e0240573. https://doi.org/10.1371/journal.pone.0240573

Issaka Salia, O., & Mitchell, D. M. (2020). Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. BMC genomics, 21(1), 870. https://doi.org/10.1186/s12864-020-07273-8

Krey, K. L., Nabity, P. D., Blubaugh, C. K., Fu, Z., Van Leuven, J. T., Reganold, J. P., Berim, A., Gang, D. R., Jensen, A. S., & Snyder, W. E. (2020). Organic Farming Sharpens Plant Defenses in the Field. Frontiers in sustainable food systems, 4, 97. https://doi.org/10.3389/fsufs.2020.00097

Liao, Y., Vakanski, A., & Xian, M. (2020). A Deep Learning Framework for Assessing Physical Rehabilitation Exercises. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 28(2):468-477. doi:10.1109/TNSRE.2020.2966249

Liao, Y., Vakanski, A., Xian, M., & Freer, P.E. (2020). A Review of Computational Approaches for Evaluation of Rehabilitation Exercises. Computers in Biology and Medicine, Volume 119, 103687. doi.org/10.1016/j.compbiomed.2020.103687

Martin, Kyle P., MacKenzie, Shannon M., Barnes, Jason W., & Ytreberg, F. Marty. (2020). Protein stability in Titan’s subsurface water ocean. Astrobiology, 20(2), 190-198. doi:10.1089/ast.2018.1972.

Mirabzadeh, C. A., & Ytreberg, F. M. (2020). Implementation of adaptive integration method for free energy calculations in molecular systems. PeerJ. Computer science, 6, e264. https://doi.org/10.7717/peerj-cs.264

Patel, D., Kuyucak, S., Doupnik, C.A. (2020). Structural determinants mediating tertiaphin block of neuronal Kir3.2 channels. Biochemistry, 59(7):836-850. doi:10.1021/acs.biochem.9b01098.

Patel, D., Barnes, J. E., Davies, W., Stenkamp, D. L., & Patel, J. S. (2020). Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance. PLoS computational biology, 16(10), e1008212. https://doi.org/10.1371/journal.pcbi.1008212

Shareef, B., Xian, M., & Vakanski, A. (2020). STAN: SMALL TUMOR-AWARE NETWORK FOR BREAST ULTRASOUND IMAGE SEGMENTATION. Proceedings. IEEE International Symposium on Biomedical Imaging, 2020, 1469–1473. https://doi.org/10.1109/isbi45749.2020.9098691

Torrevillas, B. K., Garrison, S. M., McKeeken, A. J., Patel, D., Van Leuven, J. T., Dizon, N. I., Rivas, K. I., Hathaway, N. J., Bailey, J. A., Waitumbi, J. N., Kifude, C. M., Oyieko, J., Stewart, V. A., & Luckhart, S. (2020). Plasmodium falciparum DHFR and DHPS Mutations Are Associated With HIV-1 Co-Infection and a Novel DHPS Mutation I504T Is Identified in Western Kenya. Frontiers in cellular and infection microbiology, 10, 600112. https://doi.org/10.3389/fcimb.2020.600112

Tyson, R., Baumgaertner, B., Hamilton, S., Lo, A., Krone, S. (2020). The timing and nature of behavioural responses affect the course of an epidemic. Bulletin of Mathematical Biology, Jan 14;82(1):14. doi:10.1007/s11538-019-00684-z.

Vakanski, A., Xian, M., & Freer, P.E. (2020). Attention-Enriched Deep Learning Model for Breast Tumor Segmentation in Ultrasound Images. Ultrasound in Medicine & Biology, 46(10): 2819-2833 doi.org/10.1016/j.ultrasmedbio.2020.06.015.

Wang, H., Xian, M., & Vakanski, A. (2020). BENDING LOSS REGULARIZED NETWORK FOR NUCLEI SEGMENTATION IN HISTOPATHOLOGY IMAGES. Proceedings. IEEE International Symposium on Biomedical Imaging, 2020, 258–262. https://doi.org/10.1109/isbi45749.2020.9098611

Yang, J., Naik, N., Patel, J. S., Wylie, C. S., Gu, W., Huang, J., Ytreberg, F. M., Naik, M. T., Weinreich, D. M., & Rubenstein, B. M. Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness. PLoS One. 2020;15(5):e0233509. Published 2020 May 29. doi:10.1371/journal.pone.0233509

Yuksel, M. K., Remien, C. H., Karki, B., Bull, J. J., & Krone, S. M. (2020). Vector dynamics influence spatially imperfect genetic interventions against disease. Evolution, medicine, and public health, 9(1), 1–10. https://doi.org/10.1093/emph/eoaa035

Badsha, M. B., & Fu, A. Q. (2019). Learning Causal Biological Networks With the Principle of Mendelian Randomization. Frontiers in genetics, 10, 460. doi:10.3389/fgene.2019.00460

Brown CJ, Mtui D, Oswald BP, Van Leuven JT, Vallender EJ, Schultz-Darken N, Ross CN, Tardif, SD, Austad, SN & Forney, LJ. Comparative genomics of Bifidobacterium species isolated from marmosets and humans. Am J Primatol. 2019;81(10-11):e983. doi:10.1002/ajp.22983

Bull, J. J., Remien, C. H., & Krone, S. M. (2019). Gene-drive-mediated extinction is thwarted by population structure and evolution of sib mating. Evolution, medicine, and public health, 2019(1), 66–81. doi:10.1093/emph/eoz014

Bull, J. J., Levin, B. R., & Molineux, I. J. (2019). Promises and Pitfalls of In Vivo Evolution to Improve Phage Therapy. Viruses, 11(12), 1083. https://doi.org/10.3390/v11121083

Bull, J. J., Nuismer SL, Antia R. (2019). Recombinant vector vaccine evolution. PLoS Comput Biol. 2019;15(7):e1006857. Published 2019 Jul 19. doi:10.1371/journal.pcbi.1006857

Bull J. J., Remien, C. H., Gomulkiewicz, R., & Krone, S. M. (2019). Spatial structure undermines parasite suppression by gene drive cargo. PeerJ. 2019;7:e7921. Published 2019 Oct 29. doi:10.7717/peerj.7921

Crabtree, A. M., Kizer, E. A., Hunter, S. S., Van Leuven, J. T., New, D. D., Fagnan, M. W., & Rowley, P. A. (2019). A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from Saccharomyces cerevisiae. Viruses, 11(1), 70. doi:10.3390/v11010070

Damase, T. R., & Allen, P. B. (2019). Idiosyncrasies of thermofluorimetric aptamer binding assays. BioTechniques, 66(3), 121–127. Advance online publication. doi:10.2144/btn-2018-0128

Damase, T.R., & Allen, P.B. (2019). Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity. Bioconjugate Chem, 30(1):2-12. doi:10.1021/acs.bioconjchem.8b00810

Devezer, B., Nardin, L. G., Baumgaertner, B., & Buzbas, E. O. (2019). Scientific discovery in a model-centric framework: Reproducibility, innovation, and epistemic diversity. PloS one, 14(5), e0216125. doi:10.1371/journal.pone.0216125

Ferguson, J., Miura, T., & Miller, C. R. (2019). A two-stage experimental design for dilution assays. Biometrics. In press. 2019;75(3):1009-1016. doi:10.1111/biom.13032

Gao F. (2019). A Probabilistic Characterization of Negative Definite Functions. High dimensional probability, 74, 41–53. https://doi.org/10.1007/978-3-030-26391-1_5

Justwan, F., Baumgaertner, B, Carlisle, J., Carson, E., & Kizer, J. (2019). The effect of trust and proximity on vaccine propensity. PloS one. 2019;14(8):e0220658. Published 2019 Aug 28. doi:10.1371/journal.pone.0220658

Krey, Karol L., Blubaugh Carmen K., Van Leuven, James T., Snyder, William E. (2019). Organic Soils Control Beetle Survival While Competitors Limit Aphid Population Growth. Environmental Entomology, 48(6), 1323–1330. doi:10.1093/ee/nvz100

Lee, J. A., Riazi, S., Nemati, S., Bazurto, J. V., Vasdekis, A. E., Ridenhour, B. J., … Marx, C. J. (2019). Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations. PLoS genetics, 15(11), e1008458. doi:10.1371/journal.pgen.1008458

Majmudar, J., Krone, S., Baumgaertner, B., & Tyson, R. (2019). Voter Models and External Influence. The Journal of Mathematical Sociology. In press.

Miller, C. R., (2019). The treacheries of adaptation. Science, 366(6464), 418-419. doi:10.1126/science.aaz5189.

Miura, Tanya. (2019). Respiratory Epithelial Cells as Master Communicators during Viral Infections. Current Clinical Microbiology Reports. 2019;6(1):10-17. doi:10.1007/s40588-019-0111-8

Musilova, Z., Cortesi, F., Matschiner, M., Davies, W. I. L., Patel, J.S., Stieb, S.M., de Busserolles, F., Malmstrøm, M., Tørresen, O. K., Brown, C. J., Mountford, J. K., Hanel, R., Stenkamp, D. L., Jakobsen, K.S., Carleton, K.L., Jentoft, S, Marshall, J., & Salzburger, W. (2019). Vision using multiple distinct rod opsins in deep-sea fishes. Science, 364(6440), 588-592. doi:10.1126/science.aav4632.

Patel, J. S., Quates, C. J., Johnson, E. L., & Ytreberg, F. M. (2019). Expanding the watch list for potential Ebola virus antibody escape mutations. PloS one, 14(3), e0211093. doi:10.1371/journal.pone.0211093

Van Leuven, J. T., Mao, M., Xing, D. D., Bennett, G. M., & McCutcheon, J. P. (2019). Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery. mBio, 10(3), e01950-18. doi:10.1128/mBio.01950-18

Vasdekis, A. E., Alanazi, H., Silverman, A. M., Williams, C. J., Canul, A. J., Cliff, J. B., Dohnalkova, A. C., Stephanopoulos, G. (2019). Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging. Nature communications, 10(1), 848. doi:10.1038/s41467-019-08717-w

Wichman, H. A., Scott, L. A., Howell, E. K., Martinez, A. R., Yang, L., & Baker, R. (2019) Flying around in the genome: characterization of LINE-1 in Chiroptera. Spec Publ Tex Tech Univ Mus. 2019;71:379-392.

Williams, C., Vakanski, A., Lee, S., Paul., D. (2019). Assessment of physical rehabilitation movements through dimensionality reduction and statistical modeling. Medical Engineering & Physics, Dec,74:13-22. doi:10.1016/j.medengphy.2019.10.003.

Yang, L., Scott, L., & Wichman, H. A. (2019). Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mobile DNA, 10, 22. doi:10.1186/s13100-019-0164-5

Baumgaertner, B., Carlisle, J. E., & Justwan, F. (2018). The influence of political ideology and trust on willingness to vaccinate. PloS one, 13(1), e0191728. doi:10.1371/journal.pone.0191728

Baumgaertner, B. O., Fetros, P. A., Krone, S. M., & Tyson, R. C. (2018). Spatial opinion dynamics and the effects of two types of mixing. Physical review. E, 98(2-1), 022310. doi:10.1103/PhysRevE.98.022310

Bull, J. J., Christensen, K. A., Scott, C., Jack, B. R., Crandall, C. J., & Krone, S. M. (2018). Phage-Bacterial Dynamics with Spatial Structure: Self Organization around Phage Sinks Can Promote Increased Cell Densities. Antibiotics (Basel, Switzerland), 7(1), 8. doi:10.3390/antibiotics7010008

Buzbas, E. O., & Verdu, P. (2018). Inference on admixture fractions in a mechanistic model of recurrent admixture. Theoretical population biology, 122, 149–157. doi:10.1016/j.tpb.2018.03.006

Damase, T. R., Miura, T. A., Parent, C. E., & Allen, P. B. (2018). Application of the Open qPCR Instrument for the in Vitro Selection of DNA Aptamers against Epidermal Growth Factor Receptor and Drosophila C Virus. ACS combinatorial science, 20(2), 45–54. doi:10.1021/acscombsci.7b00138

Dutta, R., Xing, T., Swanson, C., Heltborg, J., & Murdoch, G. K. (2018). Comparison of flow and gas washout characteristics between pressure control and high-frequency percussive ventilation using a test lung. Physiological measurement, 39(3), 035001. doi:10.1088/1361-6579/aaaaa2

Ferguson, J. M., & Buzbas, E. O. (2018). Inference from the stationary distribution of allele frequencies in a family of Wright-Fisher models with two levels of genetic variability. Theoretical population biology, 122, 78–87. doi:10.1016/j.tpb.2018.03.004

Garry, D. J., Ellington, A. D., Molineux, I. J., & Bull, J. J. (2018). Viral attenuation by engineered protein fragmentation. Virus evolution, 4(1), vey017. doi:10.1093/ve/vey017

Gonzalez, A. J., Ijezie, E. C., Balemba, O. B., & Miura, T. A. (2018). Attenuation of Influenza A Virus Disease Severity by Viral Coinfection in a Mouse Model. Journal of virology, 92(23), e00881-18. doi:10.1128/JVI.00881-18

Hezarjaribi N, Dutta R, Xing T, Murdoch GK, Mazrouee S, Mortazavi BJ, Ghasemzadeh H. (2018). Monitoring Lung Mechanics during Mechanical Ventilation using Machine Learning Algorithms. Conference Proceeding IEEE, Engineering in Medicine and Biology Society, 2018, 1160-1163. doi: 10.1109/EMBC.2018.8512483

Justwan, F., Baumgaertner, B., Carlisle, J. E., Clark, A. K., & Clark, M. (2018). Social media echo chambers and satisfaction with democracy among Democrats and Republicans in the aftermath of the 2016 US elections. Journal of elections, public opinion and parties, 28(4), 424–442. doi:10.1080/17457289.2018.1434784

Li, L., & Vakanski, A. (2018). Generative Adversarial Networks for Generation and Classification of Physical Rehabilitation Movement Episodes. International journal of machine learning and computing, 8(5), 428–436.

Miller, C. R., Van Leuven, J. T., Wichman, H. A., & Joyce, P. (2018). Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical population biology, 122, 97–109. doi:10.1016/j.tpb.2017.10.006

Patel, J. S., Brown, C. J., Ytreberg, F. M., & Stenkamp, D. L. (2018). Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. PLoS computational biology, 14(1), e1005974. doi:10.1371/journal.pcbi.1005974

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Publications listed here were supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number P20GM104420. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.