Publications

Here’s our growing list of publicaitons that cite CMCI P20GM104420.

If you are interested in announcing your upcoming journal publication to the general public, please contact our Communications Research Assistant, Austin at aeldridge@uidaho.edu.

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

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Bizarria Jr R, Creagh JW, Corrêa Dos Santos RA, Givens LL, Coss SA, Badigian TJ, Chavez AV, Tekle RT, Fredstrom N, Ytreberg FM, Dunham MJ, Rodrigues A, Rowley PA. (2026) Novel killer yeasts and toxins from the gardens of fungus-growing ants. Applied and environmental microbiology 92(2):e0224625. https://doi.org/10.1128/aem.02246-25 PMID:41562610 PMCID:PMC12875307

Fogg LG, Isari S, Barnes JE, Patel JS, Marshall N, Salzburger W, de Busserolles F, Cortesi F. (2026) Deep-sea fish reveal an alternative developmental trajectory for vertebrate vision. Science advances 12(7):eadx2596. https://doi.org/10.1126/sciadv.adx2596 PMID:41671374 PMCID:PMC12893277

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 13:37724-37736. https://doi.org/10.1109/access.2025.3540769 PMID:40123934 PMCID:PMC11928009

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. Microbiology (Reading, England) 171(8):. https://doi.org/10.1099/mic.0.001595 PMID:40833425 PMCID:PMC12453123

Chakrabarti L, Zhang B, Tian H, Vakanski A, Xian M. (2025) Automated Skin Cancer Report Generation via a Knowledge-Distilled Vision-Language Model. IEEE access : practical innovations, open solutions 13:136320-136335. https://doi.org/10.1109/access.2025.3591750 PMID:40969250 PMCID:PMC12443370

Hassan M, Vakanski A, Zhang B, Xian M. (2025) GCSAM: Gradient Centralized Sharpness Aware Minimization. IEEE access : practical innovations, open solutions 13:182661-182674. https://doi.org/10.1109/access.2025.3624332 PMID:41221151 PMCID:PMC12599882

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 13:82972-82985. https://doi.org/10.1109/ACCESS.2025.3568641 PMID:40443707 PMCID:PMC12121992

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, 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

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

Creagh JW, Rolfsmeier M, Evans KJ, Bizarria Jr 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. (2025) The Saccharomyces killer toxin K62 is a protein of the aerolysin family. mBio 16(12):e0142525. https://doi.org/10.1128/mbio.01425-25 PMID:41217184 PMCID:PMC12691639

Blanco-Rodriguez R, Anderson A, Hernandez-Vargas E. (2025) Linking within-host immune dynamics to between-host transmission and reinfection risk. Journal of theoretical biology 613:112210. https://doi.org/10.1016/j.jtbi.2025.112210 PMID:40744268 PMCID:PMC12456430

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

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):. https://doi.org/10.1085/jgp.202413582 PMID:39869069 PMCID:PMC11771317

Li S, Lund-Andersen P, Wang S, 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):. https://doi.org/10.1099/jgv.0.002104 PMID:40366356 PMCID:PMC12078792

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

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

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):. https://doi.org/10.1093/genetics/iyaf064 PMID:40179003 PMCID:PMC12135172

Bull JJ, Koelle K, Antia R. (2025) Waning immunity drives respiratory virus evolution and reinfection. Evolution, medicine, and public health 13(1):101-110. https://doi.org/10.1093/emph/eoaf002 PMID:40443498 PMCID:PMC12121555

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

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

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

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

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

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 J, 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 E. (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

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

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

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

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

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

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

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

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

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

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

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

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):. https://doi.org/10.3390/nu16132040 PMID:38999788 PMCID:PMC11243250

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

Chiarelli TJ, Grieshaber NA, Appa C, Grieshaber SS. (2023) Computational Modeling of the Chlamydial Developmental Cycle Reveals a Potential Role for Asymmetric Division. mSystems 8(2):e0005323. https://doi.org/10.1128/msystems.00053-23 PMID:36927072 PMCID:PMC10134819

Devezer B, Buzbas EO. (2023) Rigorous exploration in a model-centric science via epistemic iteration. Journal of applied research in memory and cognition 12(2):189-194. https://doi.org/10.1037/mac0000121 PMID:38405689 PMCID:PMC10888142

Sapozhnikov Y, Patel JS, Ytreberg FM, Miller CR. (2023) Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability. BMC bioinformatics 24(1):426. https://doi.org/10.1186/s12859-023-05537-0 PMID:37953256 PMCID:PMC10642056

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 : practical innovations, open solutions 11:79480-79494. https://doi.org/10.1109/access.2023.3298569 PMID:37608804 PMCID:PMC10443928

Seamon E, Megheib M, Williams CJ, Murphy CF, Brown HF. (2023) Estimating County Level Health Indicators Using Spatial Microsimulation. Population, space and place 29(5):. https://doi.org/10.1002/psp.2647 PMID:37822803 PMCID:PMC10564386

Patel JR, Park KJV, Bradshaw AS, Phan T, Fitzsimons DP. (2023) Cooperative mechanisms underlie differences in myocardial contractile dynamics between large and small mammals. The Journal of general physiology 155(11):. https://doi.org/10.1085/jgp.202213315 PMID:37725091 PMCID:PMC10509357

Shareef B, Xian M, Vakanski A, Wang H. (2023) Breast Ultrasound Tumor Classification Using a Hybrid Multitask CNN-Transformer Network. Medical image computing and computer-assisted intervention : MICCAI … International Conference on Medical Image Computing and Computer-Assisted Intervention 14223:344-353. https://doi.org/10.1007/978-3-031-43901-8_33 PMID:38601088 PMCID:PMC11006090

Ellis JR, Bull JJ, Rowley PA. (2023) Fungal Glycoside Hydrolases Display Unique Specificities for Polysaccharides and Staphylococcus aureus Biofilms. Microorganisms 11(2):. https://doi.org/10.3390/microorganisms11020293 PMID:36838258 PMCID:PMC9964650

Chiok K, Hutchison K, Miller LG, Bose S, Miura TA. (2023) Proinflammatory Responses in SARS-CoV-2 and Soluble Spike Glycoprotein S1 Subunit Activated Human Macrophages. Viruses 15(3):. https://doi.org/10.3390/v15030754 PMID:36992463 PMCID:PMC10052676

Curtsinger HD, Zeng X, Mather Z, Ballyk M, Phan TA, Niu B, Pu J, Bartee MY, Tian JP, Bartee E. (2023) High Levels of Extracellular Potassium Can Delay Myxoma Virus Replication by Preventing Release of Virions from the Endosomes. Journal of virology 97(1):e0129422. https://doi.org/10.1128/jvi.01294-22 PMID:36602363 PMCID:PMC9888205

Pinky L, DeAguero JR, Remien CH, Smith AM. (2023) How Interactions during Viral-Viral Coinfection Can Shape Infection Kinetics. Viruses 15(6):. https://doi.org/10.3390/v15061303 PMID:37376603 PMCID:PMC10301061

Blanco-Rodríguez R, Ordoñez-Jiménez F, Almocera AES, Chinney-Herrera G, Hernandez-Vargas E. (2023) Topological data analysis of antibody dynamics of severe and non-severe patients with COVID-19. Mathematical biosciences 361:109011. https://doi.org/10.1016/j.mbs.2023.109011 PMID:37149125 PMCID:PMC10159681

Buzbas EO, Devezer B, Baumgaertner B. (2023) The logical structure of experiments lays the foundation for a theory of reproducibility. Royal Society open science 10(3):221042. https://doi.org/10.1098/rsos.221042 PMID:36938532 PMCID:PMC10014247

Ijezie EC, O’Dowd JM, Kuan MI, Faeth AR, Fortunato EA. (2023) HCMV Infection Reduces Nidogen-1 Expression, Contributing to Impaired Neural Rosette Development in Brain Organoids. Journal of virology 97(5):e0171822. https://doi.org/10.1128/jvi.01718-22 PMID:37125912 PMCID:PMC10231252

Huang L, Yuan Y, Lewis C, Kud J, Kuhl JC, Caplan A, Dandurand L, Zasada I, Xiao F. (2023) NILR1 perceives a nematode ascaroside triggering immune signaling and resistance. Current biology : CB 33(18):3992-3997.e3. https://doi.org/10.1016/j.cub.2023.08.017 PMID:37643618

Phan TA, Sarower F, Duan J, Tian JP. (2023) Stochastic dynamics of human papillomavirus delineates cervical cancer progression. Journal of mathematical biology 87(6):85. https://doi.org/10.1007/s00285-023-02018-z PMID:37951849 PMCID:PMC11085997

Ferguson JM, González-González A, Kaiser JA, Winzer SM, Anast JM, Ridenhour B, Miura TA, Parent CE. (2023) Hidden variable models reveal the effects of infection from changes in host survival. PLoS computational biology 19(2):e1010910. https://doi.org/10.1371/journal.pcbi.1010910 PMID:36812266 PMCID:PMC9987815

Taggart NT, Crabtree AM, Creagh JW, Bizarria Jr R, Li S, de la Higuera I, Barnes JE, Shipley MA, Boyer JM, Stedman KM, Ytreberg FM, Rowley PA. (2023) Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae. PLoS pathogens 19(6):e1011418. https://doi.org/10.1371/journal.ppat.1011418 PMID:37285383 PMCID:PMC10281585

Mercier R, Yama D, LaPointe P, Johnson JL. (2023) Hsp90 mutants with distinct defects provide novel insights into cochaperone regulation of the folding cycle. PLoS genetics 19(5):e1010772. https://doi.org/10.1371/journal.pgen.1010772 PMID:37228112 PMCID:PMC10246838

Noddings CM, Johnson JL, Agard DA. (2023) Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor. Nature structural & molecular biology 30(12):1867-1877. https://doi.org/10.1038/s41594-023-01128-y PMID:37945740 PMCID:PMC10716051

Afrin F, Mateen S, Oman J, Lai JCK, Barrott JJ, Pashikanti S. (2023) Natural Products and Small Molecules Targeting Cellular Ceramide Metabolism to Enhance Apoptosis in Cancer Cells. Cancers 15(18):. https://doi.org/10.3390/cancers15184645 PMID:37760612 PMCID:PMC10527029

Karimzadeh M, Vakanski A, Xian M, Zhang B. (2023) POST-HOC EXPLAINABILITY OF BI-RADS DESCRIPTORS IN A MULTI-TASK FRAMEWORK FOR BREAST CANCER DETECTION AND SEGMENTATION. IEEE International Workshop on Machine Learning for Signal Processing : [proceedings]. IEEE International Workshop on Machine Learning for Signal Processing 2023. https://doi.org/10.1109/mlsp55844.2023.10286006 PMID:38572141 PMCID:PMC10989244

Wang H, Xian M, Vakanski A, Shareef B. (2023) SIAN: STYLE-GUIDED INSTANCE-ADAPTIVE NORMALIZATION FOR MULTI-ORGAN HISTOPATHOLOGY IMAGE SYNTHESIS. Proceedings. IEEE International Symposium on Biomedical Imaging 2023. https://doi.org/10.1109/isbi53787.2023.10230507 PMID:38572450 PMCID:PMC10989245

Butte S, Wang H, Vakanski A, Xian M. (2023) ENHANCED SHARP-GAN FOR HISTOPATHOLOGY IMAGE SYNTHESIS. Proceedings. IEEE International Symposium on Biomedical Imaging 2023. https://doi.org/10.1109/isbi53787.2023.10230516 PMID:38572451 PMCID:PMC10989243

Crabtree AM, Taggart NT, Lee MD, Boyer JM, Rowley PA. (2023) The prevalence of killer yeasts and double-stranded RNAs in the budding yeast Saccharomyces cerevisiae. FEMS yeast research 23. https://doi.org/10.1093/femsyr/foad046 PMID:37935474 PMCID:PMC10664976

Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT. (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 PMID:35194993 PMCID:PMC9007495

Joseph N, Kolok AS. (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 PMID:35310467 PMCID:PMC8917512

Lee MD, Creagh JW, Fredericks LR, Crabtree AM, Patel JS, Rowley PA. (2022) The Characterization of a Novel Virus Discovered in the Yeast Pichia membranifaciens. Viruses 14(3):. https://doi.org/10.3390/v14030594 PMID:35337001 PMCID:PMC8951182

Barnes JE, Miller CR, Ytreberg FM. (2022) Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins 90(7):1474-1485. https://doi.org/10.1002/prot.26328 PMID:35218569 PMCID:PMC9177791

Eilertsen M, Davies WIL, Patel D, Barnes JE, Karlsen R, Mountford JK, Stenkamp DL, Patel JS, Helvik JV. (2022) An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity. Frontiers in neuroanatomy 16:945344. https://doi.org/10.3389/fnana.2022.945344 PMID:35899127 PMCID:PMC9309310

Li S, Patel JS, Yang J, Crabtree AM, Rubenstein BM, Lund-Andersen PK, Ytreberg FM, Rowley PA. (2022) Defining the HIV Capsid Binding Site of Nucleoporin 153. mSphere 7(5):e0031022. https://doi.org/10.1128/msphere.00310-22 PMID:36040047 PMCID:PMC9599535

Barnes JE, Lund-Andersen PK, Patel JS, Ytreberg FM. (2022) The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6. Scientific reports 12(1):18819. https://doi.org/10.1038/s41598-022-23482-5 PMID:36335244 PMCID:PMC9637166

Mehta HH, Ibarra D, Marx CJ, Miller CR, Shamoo Y. (2022) Mutational Switch-Backs Can Accelerate Evolution of Francisella to a Combination of Ciprofloxacin and Doxycycline. Frontiers in microbiology 13:904822. https://doi.org/10.3389/fmicb.2022.904822 PMID:35615518 PMCID:PMC9125183

Haag SL, Martinez-Alvarez J, Schiele NR, Bernards MT. (2022) Delivery of Bioactive Albumin from Multi-Functional Polyampholyte Hydrogels. Journal of applied polymer science 139(35):. https://doi.org/10.1002/app.52846 PMID:36404914 PMCID:PMC9673991

Phan TA, Tian JP. (2022) Hopf bifurcation without parameters in deterministic and stochastic modeling of cancer virotherapy, part II. Journal of mathematical analysis and applications 515(2):. https://doi.org/10.1016/j.jmaa.2022.126444 PMID:37008889 PMCID:PMC10062412

Haag SL, Schiele NR, Bernards MT. (2022) Enhancement and mechanisms of MC3T3-E1 osteoblast-like cell adhesion to albumin through calcium exposure. Biotechnology and applied biochemistry 69(2):492-502. https://doi.org/10.1002/bab.2126 PMID:33586804 PMCID:PMC8364568

Wang RY, Noddings CM, Kirschke E, Myasnikov AG, Johnson JL, Agard DA. (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 PMID:34937942 PMCID:PMC9179170

Shareef B, Vakanski A, Freer PE, Xian M. (2022) ESTAN: Enhanced Small Tumor-Aware Network for Breast Ultrasound Image Segmentation. Healthcare (Basel, Switzerland) 10(11):. https://doi.org/10.3390/healthcare10112262 PMID:36421586 PMCID:PMC9690845

Zhang B, Wang S, Gao F. (2022) Contrastive Metric Learning for Lithium Super-ionic Conductor Screening. SN computer science 3(6):. https://doi.org/10.1007/s42979-022-01370-z PMID:37608869 PMCID:PMC10443933

Baumgaertner B, Justwan F. (2022) The preference for belief, issue polarization, and echo chambers. Synthese 200(5):. https://doi.org/10.1007/s11229-022-03880-y PMID:36274926 PMCID:PMC9583733

Bull JJ, Wichman HA, Krone SM. (2022) Modeling the Directed Evolution of Broad Host Range Phages. Antibiotics (Basel, Switzerland) 11(12):. https://doi.org/10.3390/antibiotics11121709 PMID:36551366 PMCID:PMC9774779

Butte S, Wang H, Xian M, Vakanski A. (2022) SHARP-GAN: SHARPNESS LOSS REGULARIZED GAN FOR HISTOPATHOLOGY IMAGE SYNTHESIS. Proceedings. IEEE International Symposium on Biomedical Imaging 2022. https://doi.org/10.1109/isbi52829.2022.9761534 PMID:35530970 PMCID:PMC9074846

Ridenhour BJ, Sarathchandra D, Seamon E, Brown H, Leung F, Johnson-Leon M, Megheib M, Miller CR, 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 PMID:35594254 PMCID:PMC9122183

Cox G, Gonzalez AJ, Ijezie EC, Rodriguez A, Miller CR, Van Leuven JT, Miura TA. (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 PMID:35711419 PMCID:PMC9196734

Mokhtari EB, Ridenhour BJ. (2022) Filtering ASVs/OTUs via mutual information-based microbiome network analysis. BMC bioinformatics 23(1):380. https://doi.org/10.1186/s12859-022-04919-0 PMID:36114453 PMCID:PMC9482178

Noddings CM, Wang RY, Johnson JL, Agard DA. (2022) Structure of Hsp90-p23-GR reveals the Hsp90 client-remodelling mechanism. Nature 601(7893):465-469. https://doi.org/10.1038/s41586-021-04236-1 PMID:34937936 PMCID:PMC8994517

Kuan MI, Caruso LB, Zavala AG, Rana PSJB, O’Dowd JM, Tempera I, Fortunato EA. (2022) Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1. Journal of virology 96(20):e0133622. https://doi.org/10.1128/jvi.01336-22 PMID:36218358 PMCID:PMC9599421

Jhutty SS, Boehme JD, Jeron A, Volckmar J, Schultz K, Schreiber J, Schughart K, Zhou K, Steinheimer J, Stöcker H, Stegemann-Koniszewski S, Bruder D, Hernandez-Vargas EA. (2022) Predicting Influenza A Virus Infection in the Lung from Hematological Data with Machine Learning. mSystems 7(6):e0045922. https://doi.org/10.1128/msystems.00459-22 PMID:36346236 PMCID:PMC9765554

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. https://doi.org/10.1137/21m1463409 PMID:37153495 PMCID:PMC10162777

Hernandez-Mejia G, Sánchez EN, Chan VM, Hernandez-Vargas EA. (2022) Impulsive Neural Control to Schedule Antivirals and Immunomodulators for COVID-19. Proceedings of the … IEEE Conference on Decision & Control. IEEE Conference on Decision & Control 2022:5633-5638. https://doi.org/10.1109/cdc51059.2022.9992454 PMID:37051484 PMCID:PMC10084739

Gao F, Ma Y, Zhang B, Xian M. (2022) SepNet: A neural network for directionally correlated data. Neural networks : the official journal of the International Neural Network Society 153:215-223. https://doi.org/10.1016/j.neunet.2022.06.005 PMID:35751957 PMCID:PMC10112384

Beach SS, Hull MA, Ytreberg FM, Patel JS, Miura TA. (2022) Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein. Journal of virology 96(13):e0035322. https://doi.org/10.1128/jvi.00353-22 PMID:35678603 PMCID:PMC9278155

Wang H, Xian M, Vakanski A. (2022) TA-Net: Topology-Aware Network for Gland Segmentation. IEEE Winter Conference on Applications of Computer Vision. IEEE Winter Conference on Applications of Computer Vision 2022:3241-3249. https://doi.org/10.1109/wacv51458.2022.00330 PMID:35509894 PMCID:PMC9063467

Busby TJ, Miller CR, Moran NA, Van Leuven JT. (2022) Global Composition of the Bacteriophage Community in Honey Bees. mSystems 7(2):e0119521. https://doi.org/10.1128/msystems.01195-21 PMID:35343797 PMCID:PMC9040601

Shi J, Vakanski A, Xian M, Ding J, Ning C. (2022) EMT-NET: EFFICIENT MULTITASK NETWORK FOR COMPUTER-AIDED DIAGNOSIS OF BREAST CANCER. Proceedings. IEEE International Symposium on Biomedical Imaging 2022. https://doi.org/10.1109/isbi52829.2022.9761438 PMID:35530971 PMCID:PMC9074851

Biggs KRH, Bailes CL, Scott L, Wichman HA, Schwartz EJ. (2021) Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage. Viruses 13(7):. https://doi.org/10.3390/v13071389 PMID:34372595 PMCID:PMC8310164

Remien CH, Eckwright MJ, Ridenhour BJ. (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 PMID:34295510 PMCID:PMC8292772

Fredericks LR, Lee MD, Eckert HR, Li S, Shipley MA, Roslund CR, Boikov DA, Kizer EA, Sobel JD, Rowley PA. (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 PMID:33972245 PMCID:PMC8218651

Benoit YD, Mitchell RR, Wang W, Orlando L, Boyd AL, Tanasijevic B, Aslostovar L, Shapovalova Z, Doyle M, Bergin CJ, Vojnits K, Casado FL, Di Lu J, Porras DP, García-Rodriguez JL, Russell J, Zouggar A, Masibag AN, Caba C, Koteva K, Kinthada LK, Patel JS, Andres SN, Magolan J, Collins TJ, Wright GD, Bhatia M. (2021) Targeting SUMOylation dependency in human cancer stem cells through a unique SAE2 motif revealed by chemical genomics. Cell chemical biology 28(10):1394-1406.e10. https://doi.org/10.1016/j.chembiol.2021.04.014 PMID:33979648 PMCID:PMC8542640

Rowley PA, Ellahi A, Han K, Patel JS, Van Leuven JT, Sawyer SL. (2021) Nuku, a family of primate retrocopies derived from KU70. G3 (Bethesda, Md.) 11(8):. https://doi.org/10.1093/g3journal/jkab163 PMID:34849803 PMCID:PMC8496227

Wang B, Tsakiridis EE, Zhang S, Llanos A, Desjardins EM, Yabut JM, Green AE, Day EA, Smith BK, Lally JSV, Wu J, Raphenya AR, Srinivasan KA, McArthur AG, Kajimura S, Patel JS, Wade MG, Morrison KM, Holloway AC, Steinberg GR. (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 PMID:34453052 PMCID:PMC8397754

Van Leuven JT, Ederer MM, Burleigh K, Scott L, Hughes RA, Codrea V, Ellington AD, Wichman HA, Miller CR. (2021) ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome biology and evolution 13(2):. https://doi.org/10.1093/gbe/evaa214 PMID:33045052 PMCID:PMC7881332

Kuan MI, Jaeger HK, Balemba OB, O’Dowd JM, Duricka D, Hannemann H, Marx E, Teissier N, Gabrielli L, Bonasoni MP, Keithley EM, Fortunato EA. (2021) Human Cytomegalovirus Interactions with the Basement Membrane Protein Nidogen 1. Journal of virology 95(3):. https://doi.org/10.1128/JVI.01506-20 PMID:33177203 PMCID:PMC7925088

Fredericks LR, Lee MD, Crabtree AM, Boyer JM, Kizer EA, Taggart NT, Roslund CR, Hunter SS, Kennedy CB, Willmore CG, Tebbe NM, Harris JS, Brocke SN, Rowley PA. (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 PMID:33539346 PMCID:PMC7888664

Grieshaber NA, Runac J, Turner S, Dean M, Appa C, Omsland A, Grieshaber SS. (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 PMID:34368013 PMCID:PMC8343073

Van Leuven JT, Gonzalez AJ, Ijezie EC, Wixom AQ, Clary JL, Naranjo MN, Ridenhour BJ, Miller CR, Miura TA. (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 PMID:34160242 PMCID:PMC8265665

Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, Marx CJ. (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 PMID:34038406 PMCID:PMC8153426

Bazurto JV, Riazi S, D’Alton S, Deatherage DE, Bruger EL, Barrick JE, Marx CJ. (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):. https://doi.org/10.3390/microorganisms9020347 PMID:33578755 PMCID:PMC7916467

Yuksel MK, Remien CH, Karki B, Bull JJ, Krone SM. (2021) 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 PMID:33664955 PMCID:PMC7910803

Devezer B, Navarro DJ, 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 PMID:34035933 PMCID:PMC8101540

Zhang B, Vakanski A, Xian M. (2021) BI-RADS-NET: AN EXPLAINABLE MULTITASK LEARNING APPROACH FOR CANCER DIAGNOSIS IN BREAST ULTRASOUND IMAGES. IEEE International Workshop on Machine Learning for Signal Processing : [proceedings]. IEEE International Workshop on Machine Learning for Signal Processing 2021. https://doi.org/10.1109/mlsp52302.2021.9596314 PMID:35509454 PMCID:PMC9063460

Vakanski A, Xian M. (2021) EVALUATION OF COMPLEXITY MEASURES FOR DEEP LEARNING GENERALIZATION IN MEDICAL IMAGE ANALYSIS. IEEE International Workshop on Machine Learning for Signal Processing : [proceedings]. IEEE International Workshop on Machine Learning for Signal Processing 2021. https://doi.org/10.1109/mlsp52302.2021.9596501 PMID:35527797 PMCID:PMC9071170

Bazurto JV, Bruger EL, Lee JA, Lambert LB, Marx CJ. (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):. https://doi.org/10.1128/JB.00589-20 PMID:33619153 PMCID:PMC8092166

Patel D, Patel JS, Ytreberg FM. (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 PMID:33709712 PMCID:PMC8044032

Badsha MB, Martin EA, Fu AQ. (2021) MRPC: An R Package for Inference of Causal Graphs. Frontiers in genetics 12:651812. https://doi.org/10.3389/fgene.2021.651812 PMID:33995486 PMCID:PMC8120292

Hohrman K, Gonçalves D, Morano KA, Johnson JL. (2021) Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects. Genetics 217(3):. https://doi.org/10.1093/genetics/iyab009 PMID:33789348 PMCID:PMC8045699

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 PMID:34271083 PMCID:PMC8416962

Vakanski A, Xian M, Freer PE. (2020) Attention-Enriched Deep Learning Model for Breast Tumor Segmentation in Ultrasound Images. Ultrasound in medicine & biology 46(10):2819-2833. https://doi.org/10.1016/j.ultrasmedbio.2020.06.015 PMID:32709519 PMCID:PMC7483681

Yang J, Naik N, Patel JS, Wylie CS, Gu W, Huang J, Ytreberg FM, Naik MT, Weinreich DM, Rubenstein BM. (2020) Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness. PloS one 15(5):e0233509. https://doi.org/10.1371/journal.pone.0233509 PMID:32470971 PMCID:PMC7259980

Patel D, Kuyucak S, Doupnik CA. (2020) Structural Determinants Mediating Tertiapin Block of Neuronal Kir3.2 Channels. Biochemistry 59(7):836-850. https://doi.org/10.1021/acs.biochem.9b01098 PMID:31990535 PMCID:PMC7524040

Gao FC, Lai MJ. (2020) A New H 2 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 PMID:33603567 PMCID:PMC7888265

Chiarelli TJ, Grieshaber NA, Omsland A, Remien CH, Grieshaber SS. (2020) Single-Inclusion Kinetics of Chlamydia trachomatis Development. mSystems 5(5):. https://doi.org/10.1128/mSystems.00689-20 PMID:33051378 PMCID:PMC7567582

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 PMID:33312394 PMCID:PMC7733529

Tyson RC, Hamilton SD, Lo AS, Baumgaertner BO, Krone SM. (2020) The Timing and Nature of Behavioural Responses Affect the Course of an Epidemic. Bulletin of mathematical biology 82(1):14. https://doi.org/10.1007/s11538-019-00684-z PMID:31932981 PMCID:PMC7223272

Belsare AV, Gompper ME, Keller B, Sumners J, Hansen L, Millspaugh JJ. (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. https://doi.org/10.1016/j.ecolmodel.2019.108919 PMID:32189826 PMCID:PMC7079769

Liao Y, Vakanski A, Xian M, Paul D, Baker R. (2020) A review of computational approaches for evaluation of rehabilitation exercises. Computers in biology and medicine 119:103687. https://doi.org/10.1016/j.compbiomed.2020.103687 PMID:32339122 PMCID:PMC7189627

Martin KP, MacKenzie SM, Barnes JW, Ytreberg FM. (2020) Protein Stability in Titan’s Subsurface Water Ocean. Astrobiology 20(2):190-198. https://doi.org/10.1089/ast.2018.1972 PMID:31730377 PMCID:PMC7041334

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 PMID:33312395 PMCID:PMC7733528

Torrevillas BK, Garrison SM, McKeeken AJ, Patel D, Van Leuven JT, Dizon NI, Rivas KI, Hathaway NJ, Bailey JA, Waitumbi JN, Kifude CM, Oyieko J, Stewart VA, 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 PMID:33324580 PMCID:PMC7725689

Gonzalez TR, Martin KP, Barnes JE, Patel JS, Ytreberg FM. (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 PMID:33347442 PMCID:PMC7751979

Patel D, Barnes JE, Davies WIL, Stenkamp DL, Patel JS. (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 PMID:33085657 PMCID:PMC7605715

Belsare A, Vanak AT. (2020) Modelling the challenges of managing free-ranging dog populations. Scientific reports 10(1):18874. https://doi.org/10.1038/s41598-020-75828-6 PMID:33139803 PMCID:PMC7608676

Baumgaertner B, Ridenhour BJ, Justwan F, Carlisle JE, Miller CR. (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 PMID:33057373 PMCID:PMC7561115

Badsha MB, Li R, Liu B, Li YI, Xian M, Banovich NE, Fu AQ. (2020) Imputation of single-cell gene expression with an autoencoder neural network. Quantitative biology (Beijing, China) 8(1):78-94. https://doi.org/10.1007/s40484-019-0192-7 PMID:32274259 PMCID:PMC7144625

Fredericks LR, Lee MD, Roslund CR, Crabtree AM, Allen PB, Rowley PA. (2020) The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella. PloS one 15(7):e0230767. https://doi.org/10.1371/journal.pone.0230767 PMID:32730254 PMCID:PMC7392296

Fan H, Su B, Ma C, Rowley PA, Jayaram M. (2020) A bipartite thermodynamic-kinetic contribution by an activating mutation to RDF-independent excision by a phage serine integrase. Nucleic acids research 48(12):6413-6430. https://doi.org/10.1093/nar/gkaa401 PMID:32479633 PMCID:PMC7337939

Belsare A, Gompper M, Keller B, Sumners J, Hansen L, Millspaugh J. (2020) Size matters: Sample size assessments for chronic wasting disease surveillance using an agent-based modeling framework. MethodsX 7:100953. https://doi.org/10.1016/j.mex.2020.100953 PMID:32612939 PMCID:PMC7317228

Issaka Salia O, Mitchell DM. (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 PMID:33287696 PMCID:PMC7720500

Krey KL, Nabity PD, Blubaugh CK, Fu Z, Van Leuven JT, Reganold JP, Berim A, Gang DR, Jensen AS, Snyder WE. (2020) Organic Farming Sharpens Plant Defenses in the Field. Frontiers in sustainable food systems 4. https://doi.org/10.3389/fsufs.2020.00097 PMID:33073178 PMCID:PMC7566882

Liao Y, Vakanski A, Xian M. (2020) A Deep Learning Framework for Assessing Physical Rehabilitation Exercises. IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society 28(2):468-477. https://doi.org/10.1109/TNSRE.2020.2966249 PMID:31940544 PMCID:PMC7032994

Mirabzadeh CA, Ytreberg FM. (2020) Implementation of adaptive integration method for free energy calculations in molecular systems. PeerJ. Computer science 6. https://doi.org/10.7717/peerj-cs.264 PMID:33457645 PMCID:PMC7808261

Chiarelli TJ, Grieshaber NA, Grieshaber SS. (2020) Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis. Journal of visualized experiments : JoVE. https://doi.org/10.3791/61365 PMID:32597859 PMCID:PMC8265183

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 synthetic biology 9(1):125-131. https://doi.org/10.1021/acssynbio.9b00411 PMID:31825605 PMCID:PMC7055157

Justwan F, Baumgaertner B, Carlisle JE, Carson E, Kizer J. (2019) The effect of trust and proximity on vaccine propensity. PloS one 14(8):e0220658. https://doi.org/10.1371/journal.pone.0220658 PMID:31461443 PMCID:PMC6713324

Bull JJ, Levin BR, Molineux IJ. (2019) Promises and Pitfalls of In Vivo Evolution to Improve Phage Therapy. Viruses 11(12):. https://doi.org/10.3390/v11121083 PMID:31766537 PMCID:PMC6950294

Vasdekis AE, Alanazi H, Silverman AM, Williams CJ, Canul AJ, Cliff JB, Dohnalkova AC, Stephanopoulos G. (2019) Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging. Nature communications 10(1):848. https://doi.org/10.1038/s41467-019-08717-w PMID:30783105 PMCID:PMC6381102

Ferguson JM, Miura TA, Miller CR. (2019) A two-stage experimental design for dilution assays. Biometrics 75(3):1009-1016. https://doi.org/10.1111/biom.13032 PMID:30690720 PMCID:PMC7199778

Brown CJ, Mtui D, Oswald BP, Van Leuven JT, Vallender EJ, Schultz-Darken N, Ross CN, Tardif SD, Austad SN, Forney LJ. (2019) Comparative genomics of Bifidobacterium species isolated from marmosets and humans. American journal of primatology 81(10-11):e983. https://doi.org/10.1002/ajp.22983 PMID:31062394 PMCID:PMC6900142

Wichman HA, Scott L, Howell EK, Martinez AR, Yang L, Baker RJ. (2019) Flying Around in the Genome: Characterization of LINE-1 in Chiroptera. Special publications (Texas Tech University. Museum) 71:379-392. PMID:32095030 PMCID:PMC7039574

Miller CR. (2019) The treacheries of adaptation. Science (New York, N.Y.) 366(6464):418-419. https://doi.org/10.1126/science.aaz5189 PMID:31649180

Bull JJ, Remien CH, Gomulkiewicz R, Krone SM. (2019) Spatial structure undermines parasite suppression by gene drive cargo. PeerJ 7:e7921. https://doi.org/10.7717/peerj.7921 PMID:31681512 PMCID:PMC6824332

Yang L, Scott L, Wichman HA. (2019) Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mobile DNA 10:22. https://doi.org/10.1186/s13100-019-0164-5 PMID:31139266 PMCID:PMC6530004

Patel JS, Quates CJ, Johnson EL, Ytreberg FM. (2019) Expanding the watch list for potential Ebola virus antibody escape mutations. PloS one 14(3):e0211093. https://doi.org/10.1371/journal.pone.0211093 PMID:30897171 PMCID:PMC6428255

Damase TR, Allen PB. (2019) Idiosyncrasies of thermofluorimetric aptamer binding assays. BioTechniques 66(3):121-127. https://doi.org/10.2144/btn-2018-0128 PMID:30764639 PMCID:PMC6466456

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 PMID:33145586 PMCID:PMC7604715

Damase TR, Allen PB. (2019) Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity. Bioconjugate chemistry 30(1):2-12. https://doi.org/10.1021/acs.bioconjchem.8b00810 PMID:30561987 PMCID:PMC6938684

Crabtree AM, Kizer EA, Hunter SS, Van Leuven JT, New DD, Fagnan MW, Rowley PA. (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):. https://doi.org/10.3390/v11010070 PMID:30654470 PMCID:PMC6356530

Krey KL, Blubaugh CK, Van Leuven JT, Snyder WE. (2019) Organic Soils Control Beetle Survival While Competitors Limit Aphid Population Growth. Environmental entomology 48(6):1323-1330. https://doi.org/10.1093/ee/nvz100 PMID:31553792 PMCID:PMC6885743

Van Leuven JT, Mao M, Xing DD, Bennett GM, McCutcheon JP. (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):. https://doi.org/10.1128/mBio.01950-18 PMID:31213566 PMCID:PMC6581868

Badsha MB, Fu AQ. (2019) Learning Causal Biological Networks With the Principle of Mendelian Randomization. Frontiers in genetics 10:460. https://doi.org/10.3389/fgene.2019.00460 PMID:31164902 PMCID:PMC6536645

Bull JJ, Remien CH, Krone SM. (2019) Gene-drive-mediated extinction is thwarted by population structure and evolution of sib mating. Evolution, medicine, and public health 2019(1):66-81. https://doi.org/10.1093/emph/eoz014 PMID:31191905 PMCID:PMC6556056

Williams C, Vakanski A, Lee S, Paul D. (2019) Assessment of physical rehabilitation movements through dimensionality reduction and statistical modeling. Medical engineering & physics 74:13-22. https://doi.org/10.1016/j.medengphy.2019.10.003 PMID:31668858 PMCID:PMC6875616

Bull JJ, Nuismer SL, Antia R. (2019) Recombinant vector vaccine evolution. PLoS computational biology 15(7):e1006857. https://doi.org/10.1371/journal.pcbi.1006857 PMID:31323032 PMCID:PMC6668849

Miura TA. (2019) Respiratory epithelial cells as master communicators during viral infections. Current clinical microbiology reports 6(1):10-17. https://doi.org/10.1007/s40588-019-0111-8 PMID:31592409 PMCID:PMC6779166

Lee JA, Riazi S, Nemati S, Bazurto JV, Vasdekis AE, Ridenhour BJ, Remien CH, Marx CJ. (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. https://doi.org/10.1371/journal.pgen.1008458 PMID:31710603 PMCID:PMC6858071

Musilova Z, Cortesi F, Matschiner M, Davies WIL, Patel JS, Stieb SM, de Busserolles F, Malmstrøm M, Tørresen OK, Brown CJ, Mountford JK, Hanel R, Stenkamp DL, Jakobsen KS, Carleton KL, Jentoft S, Marshall J, Salzburger W. (2019) Vision using multiple distinct rod opsins in deep-sea fishes. Science (New York, N.Y.) 364(6440):588-592. https://doi.org/10.1126/science.aav4632 PMID:31073066 PMCID:PMC6628886

Devezer B, Nardin LG, Baumgaertner B, Buzbas EO. (2019) Scientific discovery in a model-centric framework: Reproducibility, innovation, and epistemic diversity. PloS one 14(5):e0216125. https://doi.org/10.1371/journal.pone.0216125 PMID:31091251 PMCID:PMC6519896

Patel JS, Ytreberg FM. (2018) Fast Calculation of Protein-Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model. Journal of chemical theory and computation 14(2):991-997. https://doi.org/10.1021/acs.jctc.7b00660 PMID:29286646 PMCID:PMC5813277

Rowley PA, Patterson K, Sandmeyer SB, Sawyer SL. (2018) Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS genetics 14(4):e1007325. https://doi.org/10.1371/journal.pgen.1007325 PMID:29694349 PMCID:PMC5918913

Vakanski A, Jun H, Paul D, Baker R. (2018) A Data Set of Human Body Movements for Physical Rehabilitation Exercises. Data 3(1):. https://doi.org/10.3390/data3010002 PMID:29354641 PMCID:PMC5773117

Patel JS, Brown CJ, Ytreberg FM, Stenkamp DL. (2018) Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. PLoS computational biology 14(1):e1005974. https://doi.org/10.1371/journal.pcbi.1005974 PMID:29364888 PMCID:PMC5798944

Dutta R, Xing T, Swanson C, Heltborg J, Murdoch GK. (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. https://doi.org/10.1088/1361-6579/aaaaa2 PMID:29369819 PMCID:PMC5870834

Gonzalez AJ, Ijezie EC, Balemba OB, Miura TA. (2018) Attenuation of Influenza A Virus Disease Severity by Viral Coinfection in a Mouse Model. Journal of virology 92(23):. https://doi.org/10.1128/JVI.00881-18 PMID:30232180 PMCID:PMC6232468

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. PMID:30344962 PMCID:PMC6195368

Ferguson JM, Buzbas EO. (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. https://doi.org/10.1016/j.tpb.2018.03.004 PMID:29574050 PMCID:PMC6054576

Miller CR, Van Leuven JT, Wichman HA, Joyce P. (2018) Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical population biology 122:97-109. https://doi.org/10.1016/j.tpb.2017.10.006 PMID:29198859 PMCID:PMC5984659

Buzbas EO, Verdu P. (2018) Inference on admixture fractions in a mechanistic model of recurrent admixture. Theoretical population biology 122:149-157. https://doi.org/10.1016/j.tpb.2018.03.006 PMID:29604302 PMCID:PMC6054545

Suchar VA, Aziz N, Bowe A, Burke A, Wiest MM. (2018) An Exploration of the Spatiotemporal and Demographic Patterns of Ebola Virus Disease Epidemic in West Africa Using Open Access Data Sources. Applied geography (Sevenoaks, England) 90:272-281. https://doi.org/10.1016/j.apgeog.2017.10.003 PMID:30224832 PMCID:PMC6138046

Baumgaertner B, Carlisle JE, Justwan F. (2018) The influence of political ideology and trust on willingness to vaccinate. PloS one 13(1):e0191728. https://doi.org/10.1371/journal.pone.0191728 PMID:29370265 PMCID:PMC5784985

Faulkner M, Hannan S, Aristovich K, Avery J, Holder D. (2018) Characterising the frequency response of impedance changes during evoked physiological activity in the rat brain. Physiological measurement 39(3):034007. https://doi.org/10.1088/1361-6579/aab01f PMID:29451499

Baumgaertner BO, Fetros PA, Krone SM, Tyson RC. (2018) Spatial opinion dynamics and the effects of two types of mixing. Physical review. E 98(2-1):022310. https://doi.org/10.1103/PhysRevE.98.022310 PMID:30253497 PMCID:PMC6286154

Garry DJ, Ellington AD, Molineux IJ, Bull JJ. (2018) Viral attenuation by engineered protein fragmentation. Virus evolution 4(1):vey017. https://doi.org/10.1093/ve/vey017 PMID:29942657 PMCID:PMC6009699

Damase TR, Miura TA, Parent CE, Allen PB. (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. https://doi.org/10.1021/acscombsci.7b00138 PMID:29293309 PMCID:PMC6251946

Bull JJ, Christensen KA, Scott C, Jack BR, Crandall CJ, Krone SM. (2018) Phage-Bacterial Dynamics with Spatial Structure: Self Organization around Phage Sinks Can Promote Increased Cell Densities. Antibiotics (Basel, Switzerland) 7(1):. https://doi.org/10.3390/antibiotics7010008 PMID:29382134 PMCID:PMC5872119

Justwan F, Baumgaertner B, Carlisle JE, Clark AK, 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. https://doi.org/10.1080/17457289.2018.1434784 PMID:31231432 PMCID:PMC6587580

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. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 2018:1160-1163. https://doi.org/10.1109/EMBC.2018.8512483 PMID:30440597

VanLeuven JT, Ridenhour BJ, Gonzalez AJ, Miller CR, Miura TA. (2017) Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PloS one 12(6):e0178408. https://doi.org/10.1371/journal.pone.0178408 PMID:28575086 PMCID:PMC5456070

Damase TR, Ellington AD, Allen PB. (2017) Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis. BioTechniques 62(6):275-282. https://doi.org/10.2144/000114557 PMID:28625157 PMCID:PMC6800053

Vasdekis AE, Silverman AM, Stephanopoulos G. (2017) Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica. PloS one 12(1):e0168889. https://doi.org/10.1371/journal.pone.0168889 PMID:28052085 PMCID:PMC5215641

Vakanski A, Ferguson JM, Lee S. (2017) Metrics for Performance Evaluation of Patient Exercises during Physical Therapy. International journal of physical medicine & rehabilitation 5(3):. https://doi.org/10.4172/2329-9096.1000403 PMID:28752104 PMCID:PMC5526359

Ferguson JM, Reichert BE, Fletcher Jr RJ, Jager HI. (2017) Detecting population-environmental interactions with mismatched time series data. Ecology 98(11):2813-2822. https://doi.org/10.1002/ecy.1966 PMID:28759123 PMCID:PMC5704982

Ridenhour BJ, Brooker SL, Williams JE, Van Leuven JT, Miller AW, Dearing MD, Remien CH. (2017) Modeling time-series data from microbial communities. The ISME journal 11(11):2526-2537. https://doi.org/10.1038/ismej.2017.107 PMID:28786973 PMCID:PMC5649163

Hopkins 3rd JB, Ferguson JM, Tyers DB, Kurle CM. (2017) Selecting the best stable isotope mixing model to estimate grizzly bear diets in the Greater Yellowstone Ecosystem. PloS one 12(5):e0174903. https://doi.org/10.1371/journal.pone.0174903 PMID:28493929 PMCID:PMC5426898

Gomulkiewicz R, Krone SM, Remien CH. (2017) Evolution and the duration of a doomed population. Evolutionary applications 10(5):471-484. https://doi.org/10.1111/eva.12467 PMID:28515780 PMCID:PMC5427677

González-González A, Hug SM, Rodríguez-Verdugo A, Patel JS, Gaut BS. (2017) Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression. Molecular biology and evolution 34(11):2839-2855. https://doi.org/10.1093/molbev/msx216 PMID:28961910 PMCID:PMC5815632

Baumgaertner BO, Tyson RT, Krone SM. (2016) Opinion strength influences the spatial dynamics of opinion formation. The Journal of mathematical sociology 40(4):207-218. https://doi.org/10.1080/0022250X.2016.1205049 PMID:28529381 PMCID:PMC5435385

Vakanski A, Ferguson JM, Lee S. (2016) Mathematical Modeling and Evaluation of Human Motions in Physical Therapy Using Mixture Density Neural Networks. Journal of physiotherapy & physical rehabilitation 1(4):. PMID:28111643 PMCID:PMC5242735

Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM. (2016) Initiating a watch list for Ebola virus antibody escape mutations. PeerJ 4:e1674. https://doi.org/10.7717/peerj.1674 PMID:26925318 PMCID:PMC4768679

Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM. (2016) New Perspectives on Ebola Virus Evolution. PloS one 11(8):e0160410. https://doi.org/10.1371/journal.pone.0160410 PMID:27479005 PMCID:PMC4968807

Nardin LG, Miller CR, Ridenhour BJ, Krone SM, Joyce P, Baumgaertner BO. (2016) Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ 4:e2678. https://doi.org/10.7717/peerj.2678 PMID:27843714 PMCID:PMC5103819

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.