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.
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2023
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
2022
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
2021
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
Benoit, Y. D., Mitchell, R. R., Wang, W., Orlando, L., Boyd, A. L., Tanasijevic, B., Aslostovar, L., Shapovalova, Z., Doyle, M., Bergin, C. J., Vojnits, K., Casado, F. L., Di Lu, J., Porras, D. P., García-Rodriguez, J. L., Russell, J., Zouggar, A., Masibag, A. N., Caba, C., Koteva, K., … 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
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.
2020
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
2019
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
2018
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
Patel, J. S., & Ytreberg, F. M. (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. doi:10.1021/acs.jctc.7b00660
Rowley, P. A., Patterson, K., Sandmeyer, S. B., & Sawyer, S. L. (2018). Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS genetics, 14(4), e1007325. doi:10.1371/journal.pgen.1007325
Suchar, V. A., Aziz, N., Bowe, A., Burke, A., & Wiest, M. M. (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. doi:10.1016/j.apgeog.2017.10.003
Vakanski, A., Jun, H. P., Paul, D., & Baker, R. (2018). A Data Set of Human Body Movements for Physical Rehabilitation Exercises. Data, 3(1), 2. doi:10.3390/data3010002
2017
Damase, T. R., Ellington, A. D., & Allen, P.B. (2017). Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis. BioTechniques, 62(6), 275-282. doi: 10.2144/000114557
Ferguson, J. M., Reichert, B. E., Fletcher, R. J., Jr, & Jager, H. I. (2017). Detecting population-environmental interactions with mismatched time series data. Ecology, 98(11), 2813–2822. doi:10.1002/ecy.1966
Gomulkiewicz, R., Krone, S. M., & Remien, C. H. (2017). Evolution and the duration of a doomed population. Evolutionary applications, 10(5), 471–484. doi:10.1111/eva.12467
González-González, A., Hug, S. M., Rodríguez-Verdugo, A., Patel, J. S., & Gaut, B. S. (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. doi:10.1093/molbev/msx216
Hopkins, J. B., 3rd, Ferguson, J. M., Tyers, D. B., & Kurle, C. M. (2017). Selecting the best stable isotope mixing model to estimate grizzly bear diets in the Greater Yellowstone Ecosystem. PloS one, 12(5), e0174903. doi:10.1371/journal.pone.0174903
Ridenhour, B. J., Brooker, S. L., Williams, J. E., Van Leuven, J. T., Miller, A. W., Dearing, M. D., & Remien, C. H. (2017). Modeling time-series data from microbial communities. The ISME journal, 11(11), 2526–2537. doi:10.1038/ismej.2017.107
Vakanski, A., Ferguson, J. M., & Lee, S. (2017). Metrics for Performance Evaluation of Patient Exercises during Physical Therapy. International journal of physical medicine & rehabilitation, 5(3), 403. doi:10.4172/2329-9096.1000403
Van Leuven, J. T., Ridenhour, B. J., Gonzalez, A. J., Miller, C. R., & Miura, T. A. (2017). Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PloS one, 12(6), e0178408. doi:10.1371/journal.pone.0178408
Vasdekis, A. E., Silverman, A. M., & Stephanopoulos, G. (2017). Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica. PloS one, 12(1), e0168889. doi:10.1371/journal.pone.0168889
2016
Baumgaertner, B. O., Tyson, R. T., & Krone, S. M. (2016). Opinion strength influences the spatial dynamics of opinion formation. The Journal of mathematical sociology, 40(4), 207–218. doi:10.1080/0022250X.2016.1205049
Brown, C. J., Quates, C. J., Mirabzadeh, C. A., Miller, C. R., Wichman, H. A., Miura, T. A., & Ytreberg, F. M. (2016). New Perspectives on Ebola Virus Evolution. PloS one, 11(8), e0160410. doi:10.1371/journal.pone.0160410
Miller, C. R., Johnson, E. L., Burke, A. Z., Martin, K. P., Miura, T. A., Wichman, H. A., Brown, C. J., Ytreberg, F. M. (2016). Initiating a watch list for Ebola virus antibody escape mutations. PeerJ, 4, e1674. doi:10.7717/peerj.1674
Nardin, L. G., Miller, C. R., Ridenhour, B. J., Krone, S. M., Joyce, P., & Baumgaertner, B. O. (2016). Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ, 4, e2678. doi:10.7717/peerj.2678
Vakanski, A., Ferguson, J. M., & 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), 118.
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.