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Center for Artificial Intelligence and Modeling: Publications

Song, C. L., Main, E. J., Simmons, F., Liu, S., Phillabaum, B., Dahmen, K. A., Hudson, E. W., Hoffman, J. E., & Carlson, E. W. (2023). Critical nematic correlations throughout the superconducting doping range in Bi2−zPb zSr2−yLa yCuO6+x. Nature communications, 14(1), [2622]. https://doi.org/10.1038/s41467-023-38249-3

Jops, K., & O’Dwyer, J. P. (2023). Life history complementarity and the maintenance of biodiversity. Nature. https://doi.org/10.1038/s41586-023-06154-w

Cannavale, C. N., Edwards, C. G., Liu, R., Keye, S. A., Iwinski, S. J., Holscher, H. D., Renzi-Hammond, L., & Khan, N. A. (2023). Macular pigment is inversely related to circulating C-reactive protein concentrations in school-aged children. Nutrition Research, 114, 13-19. https://doi.org/10.1016/j.nutres.2023.03.003

Bailey, M. A., Thompson, S. V., Mysonhimer, A. R., Bennett, J. N., Vanhie, J. J., De Lisio, M., Burd, N. A., Khan, N. A., & Holscher, H. D. (2023). Dietary fiber intake and fecal short chain fatty acid concentrations are associated with lower plasma lipopolysaccharide-binding protein and inflammation. American Journal of Physiology - Gastrointestinal and Liver Physiology, 324(5), G369-G377. https://doi.org/10.1152/ajpgi.00176.2021

Pan, C., Chien, E., & Milenkovic, O. (2023). Unlearning Graph Classifiers with Limited Data Resources. In ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023 (pp. 716-726). (ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023). Association for Computing Machinery. https://doi.org/10.1145/3543507.3583547

Hughes, R. L., Pindus, D. M., Khan, N. A., Burd, N. A., & Holscher, H. D. (2023). Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity. Medicine and Science in Sports and Exercise, 55(4), 680-689. https://doi.org/10.1249/MSS.0000000000003096

O’Shaughnessy, M. R., Schiff, D. S., Varshney, L. R., Rozell, C. J., & Davenport, M. A. (2023). What governs attitudes toward artificial intelligence adoption and governance? Science and Public Policy, 50(2), 161-176. [scac056]. https://doi.org/10.1093/scipol/scac056

Kong, W., Qian, Y., Stewart, P. S., & Lu, T. (2023). De novo engineering of a bacterial lifestyle program. Nature chemical biology, 19(4), 488-497. https://doi.org/10.1038/s41589-022-01194-1

Pan, C., Chien, E., Tabaghi, P., Peng, J., & Milenkovic, O. (2023). Provably accurate and scalable linear classifiers in hyperbolic spaces. Knowledge and Information Systems, 65(4), 1817-1850. https://doi.org/10.1007/s10115-022-01820-3

Rashid, F., Dubinkina, V., Ahmad, S., Maslov, S., & Irudayaraj, J. M. K. (2023). Gut Microbiome-Host Metabolome Homeostasis upon Exposure to PFOS and GenX in Male Mice. Toxics, 11(3), [281]. https://doi.org/10.3390/toxics11030281

Fei, F., Mia, M. S., Elbanna, A. E., & Choo, J. (2023). A phase-field model for quasi-dynamic nucleation, growth, and propagation of rate-and-state faults. International Journal for Numerical and Analytical Methods in Geomechanics, 47(2), 187-211. https://doi.org/10.1002/nag.3465

Phuc Nguyen, T. V., Yao, T., & Golding, I. (2023). Co-infecting phages impede each other's entry into the cell. Biophysical journal, 122(3S1), 273a. https://doi.org/10.1016/j.bpj.2022.11.1559

Splichal, I., Donovan, S. M., Kindlova, Z., Stranak, Z., Neuzil Bunesova, V., Sinkora, M., Polakova, K., Valaskova, B., & Splichalova, A. (2023). Release of HMGB1 and Toll-like Receptors 2, 4, and 9 Signaling Are Modulated by Bifidobacterium animalis subsp. lactis BB-12 and Salmonella Typhimurium in a Gnotobiotic Piglet Model of Preterm Infants. International journal of molecular sciences, 24(3), [2329]. https://doi.org/10.3390/ijms24032329

Rana, P., & Varshney, L. R. (2023). Exploring limits to tree planting as a natural climate solution. Journal of Cleaner Production, 384, [135566]. https://doi.org/10.1016/j.jclepro.2022.135566

Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (2023). Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults. The Journal of nutrition, 152(12), 2956-2965. [nxac195]. https://doi.org/10.1093/jn/nxac195

Holthaus, T. A., Kashi, M., Cannavale, C. N., Edwards, C. G., Aguiñaga, S., Walk, A. D. M., Burd, N. A., Holscher, H. D., & Khan, N. A. (2023). MIND Dietary Pattern Adherence Is Selectively Associated with Cognitive Processing Speed in Middle-Aged Adults. The Journal of nutrition, 152(12), 2941-2949. [nxac203]. https://doi.org/10.1093/jn/nxac203

Kim, Y., Shin, J., Cassuto, Y., & Varshney, L. R. (2023). Distributed Boosting Classification Over Noisy Communication Channels. IEEE Journal on Selected Areas in Communications, 41(1), 141-154. https://doi.org/10.1109/JSAC.2022.3221972

Gabrys, R., Pattabiraman, S., & Milenkovic, O. (2023). Reconstruction of Sets of Strings From Prefix/Suffix Compositions. IEEE Transactions on Communications, 71(1), 3-12. https://doi.org/10.1109/TCOMM.2022.3222341

Rana, V., Chien, E., Peng, J., & Milenkovic, O. (2023). Small-Sample Estimation of the Mutational Support and Distribution of SARS-CoV-2. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(1), 668-682. https://doi.org/10.1109/TCBB.2022.3165395

Jeong, Y., Kong, W., Lu, T., & Irudayaraj, J. (2023). Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors. Biosensors and Bioelectronics, 219, [114809]. https://doi.org/10.1016/j.bios.2022.114809

Nambiar, A., Liu, S., Heflin, M., Forsyth, J. M., Maslov, S., Hopkins, M., & Ritz, A. (2023). Transformer Neural Networks for Protein Family and Interaction Prediction Tasks. Journal of Computational Biology, 30(1), 95-111. https://doi.org/10.1089/cmb.2022.0132

McMath, A. L., Iwinski, S., Shen, S., Bost, K. F., Donovan, S. M., & Khan, N. A. (2023). Adherence to screen time and physical activity guidelines is associated with executive function in US toddlers participating in the STRONG Kids 2 birth cohort study. The Journal of Pediatrics, 252, 22-30.e6. https://doi.org/10.1016/j.jpeds.2022.08.026

Pattabiraman, S., Gabrys, R., & Milenkovic, O. (Accepted/In press). Coding for Polymer-Based Data Storage. IEEE Transactions on Information Theory, 1. https://doi.org/10.1109/TIT.2023.3267620

Cannavale, C. N., Mysonhimer, A. R., Bailey, M. A., Cohen, N. J., Holscher, H. D., & Khan, N. A. (2023). Consumption of a fermented dairy beverage improves hippocampal-dependent relational memory in a randomized, controlled cross-over trial. Nutritional Neuroscience, 26(3), 265-274. https://doi.org/10.1080/1028415X.2022.2046963

Huang, C., Clark, G. G., Zaki, F. R., Won, J., Ning, R., Boppart, S. A., Elbanna, A. E., & Nguyen, T. H. (2023). Effects of phosphate and silicate on stiffness and viscoelasticity of mature biofilms developed with simulated drinking water. Biofouling, 39(1), 36-46. https://doi.org/10.1080/08927014.2023.2177538

Vinderola, G., Cotter, P. D., Freitas, M., Gueimonde, M., Holscher, H. D., Ruas-Madiedo, P., Salminen, S., Swanson, K. S., Sanders, M. E., & Cifelli, C. J. (2023). Fermented foods: a perspective on their role in delivering biotics. Frontiers in Microbiology, 14, [1196239]. https://doi.org/10.3389/fmicb.2023.1196239

George, I., Chen, X., & Varshney, L. R. (2023). Search for Extraterrestrial Intelligence as One-Shot Hypothesis Testing. In 2023 57th Annual Conference on Information Sciences and Systems, CISS 2023 (2023 57th Annual Conference on Information Sciences and Systems, CISS 2023). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CISS56502.2023.10089645

Wang, W., Lee, H., Jankelow, A. M., Hoang, T. H., Bacon, A., Sun, F., Chae, S., Kindratenko, V., Koprowski, K., Stavins, R. A., Ceriani, D., Engelder, Z., King, W. P., Do, M. N., Bashir, R., Valera, E., & Cunningham, B. T. (2023). Smartphone Clip-On Instrument and Microfluidic Processor for Rapid Sample-to-Answer Detection of Zika Virus in Whole Blood Using Spatial RT-LAMP. In G. L. Cote (Ed.), Optical Diagnostics and Sensing XXIII: Toward Point-of-Care Diagnostics [123870D] (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 12387). SPIE. https://doi.org/10.1117/12.2649267

Tzen, B., Raj, A., Raginsky, M., & Bach, F. (2023). Variational Principles for Mirror Descent and Mirror Langevin Dynamics. IEEE Control Systems Letters, 7, 1542-1547. https://doi.org/10.1109/LCSYS.2023.3274069

Fridman, Y., Wang, Z., Maslov, S., & Goyal, A. (2022). Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments. PLoS computational biology, 18(12), [e1010244]. https://doi.org/10.1371/journal.pcbi.1010244

Milenkovic, O., Hernandez, A. G., Zhao, H., & Tabatabaei, S. (2022). Nick-based Data Storage In Native Nucleic Acids. (U.S. Patent No. 11538554).

Mysonhimer, A. R., & Holscher, H. D. (2022). Gastrointestinal Effects and Tolerance of Nondigestible Carbohydrate Consumption. Advances in Nutrition, 13(6), 2237-2276. [nmac094]. https://doi.org/10.1093/advances/nmac094

Holscher, H. D., Chumpitazi, B. P., Dahl, W. J., Fahey, G. C., Liska, D. J., Slavin, J. L., & Verbeke, K. (2022). Perspective: Assessing Tolerance to Nondigestible Carbohydrate Consumption. Advances in Nutrition, 13(6), 2084-2097. [nmac091]. https://doi.org/10.1093/advances/nmac091

Shomorony, I. (2022). Data-driven precision medicine through the analysis of biological functional modules. Cell Reports Medicine, 3(12), [100876]. https://doi.org/10.1016/j.xcrm.2022.100876

Xu, A., & Raginsky, M. (2022). Minimum Excess Risk in Bayesian Learning. IEEE Transactions on Information Theory, 68(12), 7935-7955. https://doi.org/10.1109/TIT.2022.3176056

Chen, Y., Huerta, E. A., Duarte, J., Harris, P., Katz, D. S., Neubauer, M. S., Diaz, D., Mokhtar, F., Kansal, R., Park, S. E., Kindratenko, V. V., Zhao, Z., & Rusack, R. (2022). A FAIR and AI-ready Higgs boson decay dataset. Scientific Data, 9(1), [31]. https://doi.org/10.1038/s41597-021-01109-0

Bailey, R. L., Stang, J. S., Davis, T. A., Naimi, T. S., Schneeman, B. O., Dewey, K. G., Donovan, S. M., Novotny, R., Kleinman, R. E., Taveras, E. M., Bazzano, L., Snetselaar, L. G., de Jesus, J., Casavale, K. O., Stoody, E. E., Goldman, J. D., Moshfegh, A. J., Rhodes, D. G., Herrick, K. A., ... Pannucci, T. R. (2022). Dietary and Complementary Feeding Practices of US Infants, 6 to 12 Months: A Narrative Review of the Federal Nutrition Monitoring Data. Journal of the Academy of Nutrition and Dietetics, 122(12), 2337-2345.e1. https://doi.org/10.1016/j.jand.2021.10.017

Long, A. A., Wright, W. J., Gu, X., Thackray, A., Nakib, M., Uhl, J. T., & Dahmen, K. A. (2022). Experimental evidence that shear bands in metallic glasses nucleate like cracks. Scientific reports, 12(1), [18499]. https://doi.org/10.1038/s41598-022-22548-8

Brown, M. D., Shinn, L. M., Reeser, G., Browning, M., Schwingel, A., Khan, N. A., & Holscher, H. D. (2022). Fecal and soil microbiota composition of gardening and non-gardening families. Scientific reports, 12(1), [1595]. https://doi.org/10.1038/s41598-022-05387-5

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Fredrickson, R. L., Wang, T., Wong, G. N., Uelmen, J., Maslov, S., Weiner, Z. J., Tkachenko, A. V., Zhang, H., Liu, Z., Ibrahim, A., Patel, S. J., Paul, J. M., Vance, N. P., Gulick, J. G., ... Burke, M. D. (2022). Mitigation of SARS-CoV-2 transmission at a large public university. Nature communications, 13(1), [3207]. https://doi.org/10.1038/s41467-022-30833-3

Abdelmeguid, M., & Elbanna, A. (2022). Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme. Journal of Geophysical Research: Solid Earth, 127(12), [e2022JB024548]. https://doi.org/10.1029/2022JB024548

Sashittal, P., Zaccaria, S., & El-Kebir, M. (2022). Parsimonious Clone Tree Integration in cancer. Algorithms for Molecular Biology, 17(1), [3]. https://doi.org/10.1186/s13015-022-00209-9

Pan, C., Tabatabaei, S. K., Tabatabaei Yazdi, S. M. H., Hernandez, A. G., Schroeder, C. M., & Milenkovic, O. (2022). Rewritable two-dimensional DNA-based data storage with machine learning reconstruction. Nature communications, 13(1), [2984]. https://doi.org/10.1038/s41467-022-30140-x

Khandelwal, A., Athreya, N., Tu, M. Q., Janavicius, L. L., Yang, Z., Milenkovic, O., Leburton, J. P., Schroeder, C. M., & Li, X. (2022). Self-assembled microtubular electrodes for on-chip low-voltage electrophoretic manipulation of charged particles and macromolecules. Microsystems and Nanoengineering, 8(1), [27]. https://doi.org/10.1038/s41378-022-00354-6

Nagarajan, K., Ni, C., & Lu, T. (2022). Agent-Based Modeling of Microbial Communities. ACS synthetic biology, 11(11), 3564-3574. https://doi.org/10.1021/acssynbio.2c00411

Ni, C., & Lu, T. (2022). Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations. ACS synthetic biology, 11(11), 3714-3723. https://doi.org/10.1021/acssynbio.2c00322

Xiong, J., Yang, A., Raginsky, M., & Rosenbaum, E. (2022). Neural Ordinary Differential Equation Models of Circuits: Capabilities and Pitfalls. IEEE Transactions on Microwave Theory and Techniques, 70(11), 4869-4884. https://doi.org/10.1109/TMTT.2022.3208896

Sommer, K. M., Jespersen, J. C., Sutkus, L. T., Lee, Y., Donovan, S. M., & Dilger, R. N. (2022). Oral gamma-cyclodextrin-encapsulated tributyrin supplementation in young pigs with experimentally induced colitis. Journal of animal science, 100(11), [skac314]. https://doi.org/10.1093/jas/skac314

Smith, R., Varshney, L. R., Nagayama, S., Kazama, M., Kitagawa, T., Managi, S., & Ishikawa, Y. (2022). A computational neuroscience perspective on subjective wellbeing within the active inference framework. International Journal of Wellbeing, 12(4), 102-131. https://doi.org/10.5502/ijw.v12i4.2659

Berger, B., Tian, D., Li, W. V., El-Kebir, M., Tomescu, A. I., Singh, R., Beerenwinkel, N., Li, Y., Boucher, C., & Bar-Joseph, Z. (2022). What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems, 13(10), 781-785. https://doi.org/10.1016/j.cels.2022.09.005

Kuehn, D., Zeisel, S. H., Orenstein, D. F., German, J. B., Field, C. J., Teerdhala, S., Knezevic, A., Patil, S., Donovan, S. M., & Lönnerdal, B. (2022). Effects of a Novel High-Quality Protein Infant Formula on Energetic Efficiency and Tolerance: A Randomized Trial. Journal of Pediatric Gastroenterology and Nutrition, 75(4), 521-528. https://doi.org/10.1097/MPG.0000000000003490

Lalani, Z., Chu, G., Hsu, S., Kagawa, S., Xiang, M., Zaccaria, S., & El-Kebir, M. (2022). CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLoS computational biology, 18(10), [e1010614]. https://doi.org/10.1371/journal.pcbi.1010614

Liu, X., & Milenkovic, O. (2022). Finding the second-best candidate under the Mallows model. Theoretical Computer Science, 929, 39-68. https://doi.org/10.1016/j.tcs.2022.06.029

Nijholt, E., & Deville, L. (2022). Dynamical systems defined on simplicial complexes: Symmetries, conjugacies, and invariant subspaces. Chaos, 32(9), [093131]. https://doi.org/10.1063/5.0093842

Greenberg, G., & Shomorony, I. (2022). Improving bacterial genome assembly using a test of strand orientation. Bioinformatics, 38, II34-II41. https://doi.org/10.1093/bioinformatics/btac516

Abdelmeguid, M., & Elbanna, A. (2022). Sequences of seismic and aseismic slip on bimaterial faults show dominant rupture asymmetry and potential for elevated seismic hazard. Earth and Planetary Science Letters, 593, [117648]. https://doi.org/10.1016/j.epsl.2022.117648

Amlani, F., Bhat, H. S., Simons, W. J. F., Schubnel, A., Vigny, C., Rosakis, A. J., Efendi, J., Elbanna, A. E., Dubernet, P., & Abidin, H. Z. (2022). Supershear shock front contribution to the tsunami from the 2018 Mw7.5 Palu, Indonesia earthquake. Geophysical Journal International, 230(3), 2089-2097. https://doi.org/10.1093/gji/ggac162

Punyasena, S. W., Haselhorst, D. S., Kong, S., Fowlkes, C. C., & Moreno, J. E. (2022). Automated identification of diverse Neotropical pollen samples using convolutional neural networks. Methods in Ecology and Evolution, 13(9), 2049-2064. https://doi.org/10.1111/2041-210X.13917

Salners, T., Curry, J. F., Hinkle, A. R., Babuska, T. F., Argibay, N., DelRio, F. W., Chandross, M., & Dahmen, K. (2022). Linking Friction Scales from Nano to Macro via Avalanches. Tribology Letters, 70(3), [82]. https://doi.org/10.1007/s11249-022-01619-x

Gibbs, T., Zhang, Y., Miller, Z. R., & ODwyer, J. P. (2022). Stability criteria for the consumption and exchange of essential resources. PLoS computational biology, 18(9), [e1010521]. https://doi.org/10.1371/journal.pcbi.1010521

Chien, E., Tabaghi, P., & Milenkovic, O. (2022). HyperAid: Denoising in Hyperbolic Spaces for Tree-fitting and Hierarchical Clustering. In KDD 2022 - Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 201-211). (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining). Association for Computing Machinery. https://doi.org/10.1145/3534678.3539378

Deter, H. S., & Lu, T. (2022). Engineering microbial consortia with rationally designed cellular interactions. Current Opinion in Biotechnology, 76, 102730. https://doi.org/10.1016/j.copbio.2022.102730

Aguilar-Lopez, M., Wetzel, C., MacDonald, A., Ho, T. T. B., & Donovan, S. M. (2022). Metagenomic profile of the fecal microbiome of preterm infants consuming mother’s own milk with bovine milk–based fortifier or infant formula: a cross-sectional study. American Journal of Clinical Nutrition, 116(2), 435-445. https://doi.org/10.1093/ajcn/nqac081

Hoang, T. H., Zehni, M., Xu, H., Heintz, G., Zallek, C., & Do, M. N. (2022). Towards a Comprehensive Solution for a Vision-Based Digitized Neurological Examination. IEEE Journal of Biomedical and Health Informatics, 26(8), 4020-4031. https://doi.org/10.1109/JBHI.2022.3167927

Liechty, J. M., Keck, A. S., Sloane, S., Donovan, S. M., & Fiese, B. H. (2022). Assessing Transdisciplinary Scholarly Development: A Longitudinal Mixed Method Graduate Program Evaluation. Innovative Higher Education, 47(4), 661-681. https://doi.org/10.1007/s10755-022-09593-x

Huang, X., Xin, Y., & Lu, T. (2022). A systematic, complexity-reduction approach to dissect the kombucha tea microbiome. eLife, 11, [e76401]. https://doi.org/10.7554/eLife.76401

Zhang, S., Leistico, J. R., Cho, R. J., Cheng, J. B., & Song, J. S. (2022). Spectral clustering of single-cell multi-omics data on multilayer graphs. Bioinformatics, 38(14), 3600-3608. https://doi.org/10.1093/bioinformatics/btac378

Wang, X., Shih, H. Y., & Goldenfeld, N. (2022). Stochastic Model for Quasi-One-Dimensional Transitional Turbulence with Streamwise Shear Interactions. Physical review letters, 129(3), [034501]. https://doi.org/10.1103/PhysRevLett.129.034501

Zhang, C., Sashittal, P., Xiang, M., Zhang, Y., Kazi, A., & El-Kebir, M. (2022). Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Molecular biology and evolution, 39(7), [msac133]. https://doi.org/10.1093/molbev/msac133

Das, P., & Varshney, L. R. (2022). Explaining Artificial Intelligence Generation and Creativity: Human interpretability for novel ideas and artifacts. IEEE Signal Processing Magazine, 39(4), 85-95. https://doi.org/10.1109/MSP.2022.3141365

Naik, A., Varshney, L. R., Hassaneen, W., & Arnold, P. M. (2022). Letter: Development of Machine Learning-Based Models to Predict Treatment Response to Spinal Cord Stimulation. Neurosurgery, 91(1), e30. https://doi.org/10.1227/neu.0000000000002017

Ishaq, S. L., Wissel, E. F., Wolf, P. G., Grieneisen, L., Eggleston, E. M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J., Weatherford Darling, K., Pearson, A. L., Wertheim, F. S., Johnson, A. J., Hodges, L., Young, S. K., Nielsen, C. C., Kozyrskyj, A. L., MacRae, J. D., Myers, E. M., ... Hosler, S. (2022). Designing the Microbes and Social Equity Symposium: A Novel Interdisciplinary Virtual Research Conference Based on Achieving Group-Directed Outputs. Challenges, 13(2). https://doi.org/10.3390/challe13020030

Xu, Y., Yang, J., Li, W., Song, S., Shi, Y., Wu, L., Sun, J., Hou, M., Wang, J., Jia, X., Zhang, H., Huang, M., Lu, T., Gan, J., & Feng, Y. (2022). Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target. PLoS pathogens, 18(7 July), [e1010615]. https://doi.org/10.1371/journal.ppat.1010615

Ge, X., Goodwin, R. T., Yu, H., Romero, P., Abdelrahman, O., Sudhalkar, A., Kusuma, J., Cialdella, R., Garg, N., & Varshney, L. R. (2022). Accelerated Design and Deployment of Low-Carbon Concrete for Data Centers. In Proceedings of the 4th ACM SIGCAS/SIGCHI Conference on Computing and Sustainable Societies, COMPASS 2022 (pp. 340-352). (ACM International Conference Proceeding Series; Vol. Par F180472). Association for Computing Machinery. https://doi.org/10.1145/3530190.3534817

Jankelow, A. M., Lee, H., Wang, W., Hoang, T. H., Bacon, A., Sun, F., Chae, S., Kindratenko, V., Koprowski, K., Stavins, R. A., Ceriani, D. D., Engelder, Z. W., King, W. P., Do, M. N., Bashir, R., Valera, E., & Cunningham, B. T. (2022). Smartphone clip-on instrument and microfluidic processor for rapid sample-to-answer detection of Zika virus in whole blood using spatial RT-LAMP. Analyst, 147(17), 3838-3853. https://doi.org/10.1039/d2an00438k

Abolfathi, M., Shomorony, I., Vahid, A., & Jafarian, J. H. (2022). A Game-Theoretically Optimal Defense Paradigm against Traffic Analysis Attacks using Multipath Routing and Deception. In SACMAT 2022 - Proceedings of the 27th ACM Symposium on Access Control Models and Technologies (pp. 67-78). (Proceedings of ACM Symposium on Access Control Models and Technologies, SACMAT). Association for Computing Machinery. https://doi.org/10.1145/3532105.3535015

Bandak, D., Goldenfeld, N., Mailybaev, A. A., & Eyink, G. (2022). Dissipation-range fluid turbulence and thermal noise. Physical Review E, 105(6), [065113]. https://doi.org/10.1103/PhysRevE.105.065113

Davis, E. C., Wang, M., & Donovan, S. M. (2022). Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum. Microorganisms, 10(6). https://doi.org/10.3390/microorganisms10061155

Bode, L., & Donovan, S. M. (2022). Fructooligosaccharides are not the same as Fucosylated Human Milk Oligosaccharides. Advances in Nutrition, 13(3), 972-973. https://doi.org/10.1093/advances/nmac033

Goyal, M., Serrano, G., Argemi, J., Shomorony, I., Hernaez, M., & Ochoa-Alvarez, I. (2022). JIND: Joint integration and discrimination for automated single-cell annotation. Bioinformatics, 38(9), 2488-2495. https://doi.org/10.1093/bioinformatics/btac140

Bhimaraju, A., Chatterjee, A., & Varshney, L. R. (2022). Expected Extinction Times of Epidemics With State-Dependent Infectiousness. IEEE Transactions on Network Science and Engineering, 9(3), 1104-1116. https://doi.org/10.1109/TNSE.2021.3131954

Colussi, J., Morgan, E. L., Schnitkey, G. D., & Padula, A. D. (2022). How Communication Affects the Adoption of Digital Technologies in Soybean Production: A Survey in Brazil. Agriculture (Switzerland), 12(5), [611]. https://doi.org/10.3390/agriculture12050611

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Sutkus, L. T., Joung, S., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Donovan, S. M., & Dilger, R. N. (2022). Influence of 2′-Fucosyllactose and Bifidobacterium longum Subspecies infantis Supplementation on Cognitive and Structural Brain Development in Young Pigs. Frontiers in Neuroscience, 16, [860368]. https://doi.org/10.3389/fnins.2022.860368

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Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M., & Milenkovic, O. (2022). Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing. Nano letters, 22(5), 1905-1914. https://doi.org/10.1021/acs.nanolett.1c04203

Ellis, J. L., Wang, M., Fu, X., Fields, C. J., Donovan, S. M., & Booth, S. L. (2022). Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis. Current Developments in Nutrition, 6(3), [nzac019]. https://doi.org/10.1093/cdn/nzac019

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Lee, N. M., Varshney, L. R., Michelson, H. C., Goldsmith, P., & Davis, A. (2022). Digital trust substitution technologies to support smallholder livelihoods in Sub-Saharan Africa. Global Food Security, 32, [100604]. https://doi.org/10.1016/j.gfs.2021.100604

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Shomorony, I., & Heckel, R. (2022). Information-Theoretic Foundations of DNA Data Storage. Foundations and Trends in Communications and Information Theory, 19(1), 1-106. https://doi.org/10.1561/0100000117

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Kern, J., Dupraz, E., Aïssa-El-Bey, A., Varshney, L. R., & Leduc-Primeau, F. (2022). Optimizing the Energy Efficiency of Unreliable Memories for Quantized Kalman Filtering. Sensors, 22(3), [853]. https://doi.org/10.3390/s22030853

Lehman, S. Y., Christman, L. E., Jacobs, D. T., Johnson, N. S. D. E. F., Palchoudhuri, P., Tieman, C. E., Vajpeyi, A., Wainwright, E. R., Walker, J. E., Wilson, I. S., LeBlanc, M., McFaul, L. W., Uhl, J. T., & Dahmen, K. A. (2022). Universal aspects of cohesion. Granular Matter, 24(1), [35]. https://doi.org/10.1007/s10035-021-01188-1

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El-Kebir, M., Morris, Q., Oesper, L., & Sahinalp, S. C. (2022). Emerging Topics in Cancer Evolution. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27, 397-401.

Daniels, V. C., Monaco, M. H., Wang, M., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Dilger, R. N., & Donovan, S. M. (2022). Evaluation of 2’-fucosyllactose and bifidobacterium longum subspecies infantis on growth, organ weights, and intestinal development of piglets. Nutrients, 14(1), [199]. https://doi.org/10.3390/nu14010199

Liu, J. M., Solem, C., Lu, T., & Jensen, P. R. (2022). Harnessing lactic acid bacteria in synthetic microbial consortia. Trends in Biotechnology, 40(1), 8-11. https://doi.org/10.1016/j.tibtech.2021.09.002

Levick, K., Heckel, R., & Shomorony, I. (2022). Achieving the Capacity of a DNA Storage Channel with Linear Coding Schemes. In 2022 56th Annual Conference on Information Sciences and Systems, CISS 2022 (pp. 218-223). (2022 56th Annual Conference on Information Sciences and Systems, CISS 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CISS53076.2022.9751151

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Ravi, A. N., Vahid, A., & Shomorony, I. (2022). Capacity of the Shotgun Sequencing Channel. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 210-215). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT50566.2022.9834409

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Hanson, J., & Raginsky, M. (2022). Fitting an immersed submanifold to data via Sussmann's orbit theorem. In 2022 IEEE 61st Conference on Decision and Control, CDC 2022 (pp. 5323-5328). (Proceedings of the IEEE Conference on Decision and Control; Vol. 2022-December). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CDC51059.2022.9993382

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Raman, R. K., & Varshney, L. R. (2022). Information-Theoretic Approaches to Blockchain Scalability. In Springer Optimization and Its Applications (pp. 257-296). (Springer Optimization and Its Applications; Vol. 194). Springer. https://doi.org/10.1007/978-3-031-07535-3_8

Hawthorne, K. M., Castle, J., & Donovan, S. M. (2022). Meat Helps Make Every Bite Count An Ideal First Food for Infants. Nutrition Today, 57(1), 8-13. https://doi.org/10.1097/NT.0000000000000523

Markowitz, S., Snyder, C., Eldar, Y. C., & Do, M. N. (2022). Multimodal Unrolled Robust PCA for Background Foreground Separation. IEEE Transactions on Image Processing, 31, 3553-3564. https://doi.org/10.1109/TIP.2022.3172851

Saldi, N., Başar, T., & Raginsky, M. (Accepted/In press). Partially Observed Discrete-Time Risk-Sensitive Mean Field Games. Dynamic Games and Applications. https://doi.org/10.1007/s13235-022-00453-z

Bhimaraju, A., & Varshney, L. R. (2022). Scheduling Group Tests over Time. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 886-891). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT50566.2022.9834434

Marla, L., Varshney, L. R., Shah, D., Prakash, N. A., & Gale, M. E. (2022). Short and Wide Network Paths. IEEE Transactions on Network Science and Engineering, 9(2), 524-537. https://doi.org/10.1109/TNSE.2021.3123311

Wu, X., Hanganu, A., Hoshino, A., & Varshney, L. R. (2022). Source Identification for Exosomal Communication via Protein Language Models. In 2022 IEEE 32nd International Workshop on Machine Learning for Signal Processing, MLSP 2022 (IEEE International Workshop on Machine Learning for Signal Processing, MLSP; Vol. 2022-August). IEEE Computer Society. https://doi.org/10.1109/MLSP55214.2022.9943418

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