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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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.

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. mSystems7(2), e0119521.

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 immunology13, 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. GeoHealth6(3), e2021GH000548.

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 modeling62(5), 1282–1293.

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 one17(5), e0268302.

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. Nature601(7893), 460–464.

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.


Badsha, M. B., Martin, E. A., & Fu, A. Q. (2021). MRPC: An R Package for Inference of Causal Graphs. Frontiers in genetics12, 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 bacteriology203(9), e00589-20. Advance online publication.

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 formaldehydePLoS biology19(5), e3001208.

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 InhibitionMicroorganisms9(2), 347.

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 biology28(10), 1394–1406.e10.

Biggs, K., Bailes, C. L., Scott, L., Wichman, H. A., & Schwartz, E. J. (2021). Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage. Viruses13(7), 1389.

Devezer, B., Navarro, D. J., Vandekerckhove, J., & Ozge Buzbas, E. (2021). The case for formal methodology in scientific reform. Royal Society open science8(3), 200805.

Epstein, L., Dubois, Z., Smith, J., Lee, Y., & Harrington, K. (2021). Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum. Bio Systems208, 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 SaccharomycotinaPLoS genetics17(2), e1009341.

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 chemotherapy65(7), e0245020.

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 microbiology11, 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. Genetics217(3), 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 1Journal of virology95(3), e01506-20.

Patel, D., Patel, J. S., & Ytreberg, F. M. (2021). Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free EnergyJournal of chemical theory and computation17(4), 2457–2464.

Remien, C. H., Eckwright, M. J., & Ridenhour, B. J. (2021). Structural identifiability of the generalized Lotka-Volterra model for microbiome studies. Royal Society open science8(7), 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.

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 DeoptimizationGenome biology and evolution13(2), 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. mSphere6(3), e0047921.

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 communications12(1), 5163.

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 networkQuant 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 surveyPLoS medicine17(10), e1003354.

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 frameworkMethodsX. 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 reports10(1), 18874.

Chiarelli, T. J., Grieshaber, N. A., Omsland, A., Remien, C. H., & Grieshaber, S. S. (2020). Single-Inclusion Kinetics of Chlamydia trachomatis DevelopmentmSystems5(5), e00689-20.

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 AssemblyACS 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 IntegraseNucleic 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 mellonellaPLoS 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 ApplicationsActa mathematica Sinica, English series36(1), 21–39.

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 one15(12), e0240573.

Issaka Salia, O., & Mitchell, D. M. (2020). Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microgliaBMC genomics21(1), 870.

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 FieldFrontiers in sustainable food systems4, 97.

Liao, Y., Vakanski, A., & Xian, M. (2020). A Deep Learning Framework for Assessing Physical Rehabilitation ExercisesIEEE 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.

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 systemsPeerJ. Computer science6, e264.

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 absorbancePLoS computational biology16(10), e1008212.

Shareef, B., Xian, M., & Vakanski, A. (2020). STAN: SMALL TUMOR-AWARE NETWORK FOR BREAST ULTRASOUND IMAGE SEGMENTATIONProceedings. IEEE International Symposium on Biomedical Imaging2020, 1469–1473.

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 KenyaFrontiers in cellular and infection microbiology10, 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

Wang, H., Xian, M., & Vakanski, A. (2020). BENDING LOSS REGULARIZED NETWORK FOR NUCLEI SEGMENTATION IN HISTOPATHOLOGY IMAGESProceedings. IEEE International Symposium on Biomedical Imaging2020, 258–262.

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 fitnessPLoS 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 diseaseEvolution, medicine, and public health9(1), 1–10.


Badsha, M. B., & Fu, A. Q. (2019). Learning Causal Biological Networks With the Principle of Mendelian Randomization. Frontiers in genetics10, 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 humansAm 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 health2019(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 TherapyViruses11(12), 1083.

Bull, J. J., Nuismer SL, Antia R. (2019). Recombinant vector vaccine evolutionPLoS 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 cargoPeerJ. 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 cerevisiaeViruses11(1), 70. doi:10.3390/v11010070

Damase, T. R., & Allen, P. B. (2019). Idiosyncrasies of thermofluorimetric aptamer binding assays. BioTechniques66(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 one14(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 FunctionsHigh dimensional probability74, 41–53.

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 GrowthEnvironmental Entomology, 48(6), 1323–1330. doi:10.1093/ee/nvz100

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

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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 one14(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. mBio10(3), e01950-18. doi:10.1128/mBio.01950-18

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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 parties28(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 computing8(5), 428–436.

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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 evolution34(11), 2839–2855. doi:10.1093/molbev/msx216

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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 communitiesThe ISME journal11(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 TherapyInternational journal of physical medicine & rehabilitation5(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 virusesPloS one12(6), e0178408. doi:10.1371/journal.pone.0178408

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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 EvolutionPloS one11(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 mutationsPeerJ4, e1674. doi:10.7717/peerj.1674

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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.