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Illinois IGB

Research Areas

Computing Genomes for Reproductive Health: Publications

Straub, A. P., Asa, E., Zhang, W., Nguyen, T. H., & Herzberg, M. (2020). In-situ graft-polymerization modification of commercial ultrafiltration membranes for long-term fouling resistance in a pilot-scale membrane bioreactor. Chemical Engineering Journal, 382, [122865].

Racioppi, L., Nelson, E. R., Huang, W., Mukherjee, D., Lawrence, S. A., Lento, W., ... McDonnell, D. P. (2019). CaMKK2 in myeloid cells is a key regulator of the immune-suppressive microenvironment in breast cancer. Nature communications, 10(1), [2450].

Fischer-Hwang, I., Ochoa, I., Weissman, T., & Hernaez, M. (2019). Denoising of Aligned Genomic Data. Scientific reports, 9(1), [15067].

Salem, W., Li, K., Krapp, C., Ingles, S. A., Bartolomei, M. S., Chung, K., ... McGinnis, L. K. (2019). Imatinib treatments have long-term impact on placentation and embryo survival. Scientific reports, 9(1), [2535].

For the Alzheimer’s Disease Neuroimaging Initiative, & Iyer, R. K. (2019). Predicting Short-term MCI-to-AD Progression Using Imaging, CSF, Genetic Factors, Cognitive Resilience, and Demographics. Scientific reports, 9(1), [2235].

Taneja, I., Reddy, B., Damhorst, G., Zhao, S. D., Hassan, U., Price, Z., ... Zhu, R. (2019). Publisher Correction: Combining Biomarkers with EMR Data to Identify Patients in Different Phases of Sepsis (Scientific Reports, (2017), 7, 1, (10800), 10.1038/s41598-017-09766-1). Scientific reports, 9(1), [17419].

Saboo, K. V., Varatharajah, Y., Berry, B. M., Kremen, V., Sperling, M. R., Davis, K. A., ... Kucewicz, M. T. (2019). Unsupervised machine-learning classification of electrophysiologically active electrodes during human cognitive task performance. Scientific reports, 9(1), [17390].

Andrade, F. C. D., Kramer, K. Z., Greenlee, A., Williams, A. N., & Mendenhall, R. (2019). Impact of the Chicago Earned Income Tax Periodic Payment intervention on food security. Preventive Medicine Reports, 16, [100993].

Wu, X., Tang, A., Bi, X., Nguyen, T. H., & Yuan, B. (2019). Influence of algal organic matter of Microcystis aeruginosa on ferrate decay and MS2 bacteriophage inactivation. Chemosphere, 236, [124727].

Mitrano, M., Lee, S., Husain, A. A., Zhu, M., Munoz, G. D. L. P., Sun, S. X. L., ... Abbamonte, P. (2019). Evidence for photoinduced sliding of the charge-order condensate in La1.875Ba0.125CuO4. Physical Review B, 100(20), [205125].

Heldenbrand, J. R., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S. N., Hudson, M. E., ... Mainzer, L. S. (2019). Recommendations for performance optimizations when using GATK3.8 and GATK4. BMC bioinformatics, 20(1), [557].

Samineni, L., Xiong, B., Chowdhury, R., Pei, A., Kuehster, L., Wang, H., ... Velegol, S. (2019). 7 Log Virus Removal in a Simple Functionalized Sand Filter. Environmental Science and Technology, 53(21), 12706-12714.

Moran, R. L., Catchen, J. M., & Fuller, R. C. (Accepted/In press). Genomic resources for darters (Percidae: Etheostominae) provide insight into postzygotic barriers implicated in speciation. Molecular biology and evolution, [msz260].

Rochette, N. C., Rivera-Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular ecology, 28(21), 4737-4754.

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685.

Landesman, W. J., Mulder, K., Page Fredericks, L., & Allan, B. F. (2019). Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load. FEMS microbiology ecology, 95(12), [fiz167].

Chatterjee, P., & Goldenfeld, N. (2019). Three-body interactions drive the transition to polar order in a simple flocking model. Physical Review E, 100(4), [040602].

Fuzawa, M., Araud, E., Li, J., Shisler, J. L., & Nguyen, T. H. (2019). Free Chlorine Disinfection Mechanisms of Rotaviruses and Human Norovirus Surrogate Tulane Virus Attached to Fresh Produce Surfaces. Environmental Science and Technology, 53(20), 11999-12006.

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., ... Knight, R. (2019). Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome biology, 20(1), [201].

Brown, N. M., Mendenhall, R., Black, M., Moer, M. V., Flynn, K., McKee, M., ... Zhai, C. X. (2019). In Search of Zora/When Metadata Isn’t Enough: Rescuing the Experiences of Black Women Through Statistical Modeling. Journal of Library Metadata, 19(3-4), 141-162.

Donohue, M. E., Asangba, A. E., Ralainirina, J., Weisrock, D. W., Stumpf, R. M., & Wright, P. C. (2019). Extensive variability in the gut microbiome of a highly-specialized and critically endangered lemur species across sites. American journal of primatology, 81(10-11), [e23046].

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., ... Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4(10), 1727-1736.

Amato, K. R., & Stumpf, R. M. (2019). Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology. American journal of primatology, 81(10-11), [e23060].

Athreya, A. P., Neavin, D., Carrillo-Roa, T., Skime, M., Biernacka, J., Frye, M. A., ... Bobo, W. V. (2019). Pharmacogenomics-Driven Prediction of Antidepressant Treatment Outcomes: A Machine-Learning Approach With Multi-trial Replication. Clinical Pharmacology and Therapeutics, 106(4), 855-865.

Asangba, A. E., Donohue, M. E., Lamb, A., Wright, P. C., Halajian, A., Leigh, S. R., & Stumpf, R. M. (2019). Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity. American journal of primatology, 81(10-11), [e23045].

Kramer, K., Andrade, F. C. D., Greenlee, A. J., Mendenhall, R., Bellisle, D., & Lemons Blanks, R. (2019). Periodic Earned Income Tax Credit (EITC) Payment, Financial Stress and Wellbeing: A Longitudinal Study. Journal of Family and Economic Issues, 40(3), 511-523.

Rattan, S., Beers, H. K., Kannan, A., Ramakrishnan, A., Brehm, E., Bagchi, I. C., ... Flaws, J. A. (2019). Prenatal and ancestral exposure to di(2-ethylhexyl) phthalate alters gene expression and DNA methylation in mouse ovaries. Toxicology and Applied Pharmacology, 379, [114629].

Roca, A. L. (2019). African elephant genetics: enigmas and anomalies. Journal of genetics, 98.

Kern, S., & Laurent, H. K. (2019). Childhood abuse predicts affective symptoms via HPA reactivity during mother-infant stress. Psychoneuroendocrinology, 107, 19-25.

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2019). Traction: Fast non-parametric improvement of estimated gene trees. In K. T. Huber, & D. Gusfield (Eds.), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 [4] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.

Shpigler, H. Y., Saul, M. C., Corona, F., Block, L., Ahmed, A. C., Zhao, S. D., & Robinson, G. E. (2019). Erratum: Deep evolutionary conservation of autism-related genes (Proceedings of the National Academy of Sciences of the United States of America (2017) 114(9653-9658) Doi: 10.1073/pnas.1708127114). Proceedings of the National Academy of Sciences of the United States of America, 116(35).

Mitrano, M., Lee, S., Husain, A. A., Delacretaz, L., Zhu, M., De La Peña Munoz, G., ... Abbamonte, P. (2019). Ultrafast time-resolved x-ray scattering reveals diffusive charge order dynamics in La2-xBaxCuO4 Science Advances, 5(8), [eaax3346].

Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M., & Weissman, T. (2019). SPRING: A next-generation compressor for FASTQ data. Bioinformatics, 35(15), 2674-2676. [bty1015].

Gomez, A., Sharma, A. K., Mallott, E. K., Petrzelkova, K. J., Jost Robinson, C. A., Yeoman, C. J., ... Mcmahon, K. (2019). Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere, 4(4).

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14].

Bauza, V., Madadi, V., Ocharo, R. M., Nguyen, T. H., & Guest, J. S. (2019). Microbial source tracking using 16S rRNA amplicon sequencing identifies evidence of widespread contamination from young children's feces in an Urban Slum of Nairobi, Kenya. Environmental Science and Technology, 53(14), 8271-8281.

Molloy, E. K., & Warnow, T. (2019). TreeMerge: A new method for improving the scalability of species tree estimation methods. Bioinformatics, 35(14), i417-i426. [btz344].

Fogleman, A. J., Zahnd, W. E., Lipka, A. E., Malhi, R. S., Ganai, S., Delfino, K. R., & Jenkins, W. D. (2019). Knowledge, attitudes, and perceived barriers towards genetic testing across three rural Illinois communities. Journal of Community Genetics, 10(3), 417-423.

Roca, A. L. (2019). African elephant genetics: enigmas and anomalies †. Journal of genetics, 98(3), [83].

Yang, R., Chen, X., & Ochoa, I. (2019). MassComp, a lossless compressor for mass spectrometry data. BMC bioinformatics, 20(1), [368].

Pafčo, B., Sharma, A. K., Petrželková, K. J., Vlčková, K., Todd, A., Yeoman, C. J., ... Gomez, A. (2019). Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors. American journal of physical anthropology, 169(3), 575-585.

Shahoei, S. H., & Nelson, E. R. (2019). Nuclear receptors, cholesterol homeostasis and the immune system. Journal of Steroid Biochemistry and Molecular Biology, 191, [105364].

Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., ... Willerslev, E. (2019). The population history of northeastern Siberia since the Pleistocene. Nature, 570(7760), 182-188.

Banerjee, S. S., Cyriac, J., Jha, S., Kalbarczyk, Z. T., & Iyer, R. K. (2019). Towards a Bayesian Approach for Assessing Fault Tolerance of Deep Neural Networks. In Proceedings - 49th Annual IEEE/IFIP International Conference on Dependable Systems and Networks - Supplemental Volume, DSN-S 2019 (pp. 25-26). [8805761] (Proceedings - 49th Annual IEEE/IFIP International Conference on Dependable Systems and Networks - Supplemental Volume, DSN-S 2019). Institute of Electrical and Electronics Engineers Inc..

Saboo, K. V., Varatharajah, Y., Berry, B. M., Sperling, M. R., Gorniak, R., Davis, K. A., ... Iyer, R. K. (2019). A Computationally Efficient Model for Predicting Successful Memory Encoding Using Machine-Learning-based EEG Channel Selection. In 9th International IEEE EMBS Conference on Neural Engineering, NER 2019 (pp. 323-327). [8717057] (International IEEE/EMBS Conference on Neural Engineering, NER; Vol. 2019-March). IEEE Computer Society.

Ochoa-Alvarez, I., Li, H., Baumgarte, F., Hergenrother, C., Voges, J., & Hernaez, M. (2019). AliCo: A New Efficient Representation for SAM Files. In J. A. Storer, A. Bilgin, J. Serra-Sagrista, & M. W. Marcellin (Eds.), Proceedings - DCC 2019: 2019 Data Compression Conference (pp. 93-102). [8712770] (Data Compression Conference Proceedings; Vol. 2019-March). Institute of Electrical and Electronics Engineers Inc..

Goyal, M., Tatwawadi, K., Chandak, S., & Ochoa, I. (2019). DeepZip: Lossless Data Compression Using Recurrent Neural Networks. In A. Bilgin, J. A. Storer, M. W. Marcellin, & J. Serra-Sagrista (Eds.), Proceedings - DCC 2019: 2019 Data Compression Conference [8712659] (Data Compression Conference Proceedings; Vol. 2019-March). Institute of Electrical and Electronics Engineers Inc..

Parker, A. T., Gardner, A. M., Perez, M., Allan, B. F., & Muturi, E. J. (2019). Container Size Alters the Outcome of Interspecific Competition between Aedes aegypti (Diptera: Culicidae) and Aedes albopictus. Journal of medical entomology, 56(3), 708-715.

Walters, K. A., Zhu, R., Welge, M., Scherler, K., Park, J. K., Rahil, Z., ... Kash, J. C. (2019). Differential effects of influenza virus NA, HA head, and HA stalk antibodies on peripheral blood leukocyte gene expression during human infection. mBio, 10(3), [e00760-19].

Nute, M., Saleh, E., & Warnow, T. (2019). Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets. Systematic biology, 68(3), 396-411.

Shah, N., Nute, M. G., Warnow, T., & Pop, M. (2019). Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics, 35(9), 1613-1614.

Schablitsky, J. M., Witt, K. E., Madrigal, J. R., Ellegaard, M. R., Malhi, R. S., & Schroeder, H. (2019). Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter. Journal of Archaeological Science, 105, 11-18.

Bader, A. C., & Malhi, R. S. (2019). How Subjectivity Strengthens Research: Developing an Integrative Approach to Investigating Human Diet in the Pacific Northwest Coast. American Anthropologist, 121(2), 476-478.

Malhi, R. S., Antón, S. C., & Fuentes, A. (2019). Increasing Diversity in Evolutionary Anthropological Sciences—the IDEAS Program. American Anthropologist, 121(2), 478-479.

Barakat, R., Seymore, T., Lin, P. C. P., Park, C. J., & Ko, C. (2019). Prenatal exposure to an environmentally relevant phthalate mixture disrupts testicular steroidogenesis in adult male mice. Environmental Research, 172, 194-201.

Chung, K., Kalbarczyk, Z. T., & Iyer, R. K. (2019). Availability attacks on computing systems through alteration of environmental control: Smart malware approach. In G. S. Ramachandran, & J. Ortiz (Eds.), ICCPS 2019 - Proceedings of the 2019 ACM/IEEE International Conference on Cyber-Physical Systems (pp. 1-12). (ICCPS 2019 - Proceedings of the 2019 ACM/IEEE International Conference on Cyber-Physical Systems). Association for Computing Machinery, Inc.

Banerjee, S. S., Kalbarczyk, Z. T., & Iyer, R. K. (2019). AcMC 2: Accelerated Markov Chain Monte Carlo for Probabilistic Models. In ASPLOS 2019 - 24th International Conference on Architectural Support for Programming Languages and Operating Systems (pp. 515-528). (International Conference on Architectural Support for Programming Languages and Operating Systems - ASPLOS). Association for Computing Machinery.

Laurent, H. (2019). Challenges in Characterizing the “Mommy Brain”. Parenting, 19(1-2), 94-96.

Devendran, S., Shrestha, R., Alves, J. M. P., Wolf, P. G., Ly, L., Hernandez, A. G., ... Ridlon, J. M. (2019). Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids. Applied and environmental microbiology, 85(7), [e00052-19].

Kim, D. H., Park, H. J., Park, H. S., Lee, J. U., Ko, C. M., Gye, M. C., & Choi, J. M. (2019). Estrogen receptor α in T cells suppresses follicular helper T cell responses and prevents autoimmunity. Experimental and Molecular Medicine, 51(4), [41].

Chung, K., Cao, P., Wu, Y., Kalbarczyk, Z. T., Iyer, R. K., & Withers, A. (2019). Traction: An infrastructure for trusted alert sharing and collaborative mitigaTION. In Proceedings of the 6th Annual Symposium on Hot Topics in the Science of Security, HotSoS 2019 [a27] (ACM International Conference Proceeding Series). Association for Computing Machinery.

Najafi, A., Daghigh Kia, H., Mehdipour, M., Shamsollahi, M., & Miller, D. J. (2019). Does fennel extract ameliorate oxidative stress frozen-thawed ram sperm? Cryobiology, 87, 47-51.

Landesman, W. J., Mulder, K., Allan, B. F., Bashor, L. A., Keesing, F., LoGiudice, K., & Ostfeld, R. S. (2019). Potential effects of blood meal host on bacterial community composition in Ixodes scapularis nymphs. Ticks and Tick-borne Diseases, 10(3), 523-527.

Ma, L., & Nelson, E. R. (2019). Oxysterols and nuclear receptors. Molecular and Cellular Endocrinology, 484, 42-51.

Kim, B. M., Amores, A., Kang, S., Ahn, D. H., Kim, J. H., Kim, I. C., ... Park, H. (2019). Antarctic blackfin icefish genome reveals adaptations to extreme environments. Nature Ecology and Evolution, 3(3), 469-478.

Banerjee, S. S., El-Hadedy, M., Lim, J. B., Kalbarczyk, Z. T., Chen, D., Lumetta, S. S., & Iyer, R. K. (2019). ASAP: Accelerated Short-Read Alignment on Programmable Hardware. IEEE Transactions on Computers, 68(3), 331-346. [8490591].

Amato, K. R., G. Sanders, J., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L. R., ... R. Leigh, S. (2019). Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME Journal, 13(3), 576-587.

Roch, S., Nute, M., & Warnow, T. (2019). Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods. Systematic biology, 68(2), 281-297.

Parker, A. T., & Allan, B. F. (2019). Do gutter guards affect mosquito production in roof gutter habitats? Journal of the American Mosquito Control Association, 35(1), 67-70.

Welsh, E. C., Keesing, F., & Allan, B. F. (2019). Oxpecker (Buphagus erythrorhynchus, Buphagus africanus) and tick abundances in acaricide-treated livestock areas. African Journal of Ecology, 57(1), 155-159.

Park, C. J., Barakat, R., Ulanov, A., Li, Z., Lin, P. C., Chiu, K., ... Ko, C. M. J. (2019). Sanitary pads and diapers contain higher phthalate contents than those in common commercial plastic products. Reproductive Toxicology, 84, 114-121.

Masonbrink, R., Maier, T. R., Muppirala, U., Seetharam, A. S., Lord, E., Juvale, P. S., ... Baum, T. J. (2019). The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics, 20(1), [119].

Zhang, Q., Rao, S., & Warnow, T. (2019). Constrained incremental tree building: New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms for Molecular Biology, 14(1), [2].

Nowak, R. A. (2019). An interview with Professor Virendra B. Mahesh. Biology of reproduction, 100(2), 301-304.

Yu, L., Wang, L., Mao, C., Duraki, D., Kim, J. E., Huang, R., ... Shapiro, D. J. (2019). Estrogen-independent Myc overexpression confers endocrine therapy resistance on breast cancer cells expressing ERαY537S and ERαD538G mutations. Cancer Letters, 442, 373-382.

Dai, B., Wang, J., Shen, X., & Qu, P. (2019). Smooth neighborhood recommender systems. Journal of Machine Learning Research, 20.

Tisha, A. L., Armstrong, A. A., Wagoner Johnson, A. J., & Lopez-Ortiz, C. (2019). Skeletal Muscle Adaptations and Passive Muscle Stiffness in Cerebral Palsy: A Literature Review and Conceptual Model. Journal of Applied Biomechanics, 35(1), 68-79.

Wang, Y., Bi, X., & Qu, A. (Accepted/In press). A Logistic Factorization Model for Recommender Systems With Multinomial Responses. Journal of Computational and Graphical Statistics.

Khan, F., & Laurent, H. K. (2019). Assessing the Impact of Mindfulness and Life Stress on Maternal Well-Being. Mindfulness, 10(1), 26-35.

Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M., ... Wegener Parfrey, L. (Accepted/In press). Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME Journal.

Neff, A. M., Blanco, S. C., Flaws, J. A., Bagchi, I. C., & Bagchi, M. K. (2019). Chronic Exposure of Mice to Bisphenol-A Alters Uterine Fibroblast Growth Factor Signaling and Leads to Aberrant Epithelial Proliferation. Endocrinology, 160(5), 1234-1246.

Dufort y Álvarez, G., Seroussi, G., Smircich, P., Sotelo, J., Ochoa-Alvarez, I., & Martín, Á. (2019). Compression of Nanopore FASTQ Files. In F. Ortuño, I. Rojas, F. Rojas, O. Valenzuela, & F. Ortuño (Eds.), Bioinformatics and Biomedical Engineering - 7th International Work-Conference, IWBBIO 2019, Proceedings (pp. 36-47). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11465 LNBI). Springer-Verlag.

Josek, T., Gardner, A. M., Hedlund, T. J., Parker, A. T., Allmann Updyke, E., & Allan, B. F. (2019). Fatal attraction: lone star ticks (Amblyomma americanum) exhibit preference for human female breath over male breath. Experimental and Applied Acarology, 77(1), 59-64.

He, S., Ma, L., Baek, A. E., Vardanyan, A., Vembar, V., Chen, J. J., ... Nelson, E. (2019). Host CYP27A1 expression is essential for ovarian cancer progression. Endocrine-Related Cancer, 26(7), 659-675.

Kucewicz, M. T., Saboo, K., Berry, B. M., Kremen, V., Miller, L. R., Khadjevand, F., ... Worrell, G. A. (2019). Human verbal memory encoding is hierarchically distributed in a continuous processing stream. eNeuro, 6(1), [e0214-18.2018].

Tang, X., Bi, X., & Qu, A. (2019). Individualized Multilayer Tensor Learning With an Application in Imaging Analysis. Journal of the American Statistical Association.

Athreya, A. P., Iyer, R., Wang, L., Weinshilboum, R. M., & Bobo, W. V. (2019). Integration of machine learning and pharmacogenomic biomarkers for predicting response to antidepressant treatment: Can computational intelligence be used to augment clinical assessments? Pharmacogenomics, 20(14), 983-988.

Kinson, C., Tang, X., Zuo, Z., & Qu, A. (Accepted/In press). Longitudinal Principal Component Analysis With an Application to Marketing Data. Journal of Computational and Graphical Statistics.

Nelson, B. W., Wright, D. B., Allen, N. B., & Laurent, H. K. (2019). Maternal stress and social support prospectively predict infant inflammation. Brain, Behavior, and Immunity.

Rustom, L. E., Poellmann, M. J., & Wagoner Johnson, A. J. (2019). Mineralization in micropores of calcium phosphate scaffolds. Acta Biomaterialia, 83, 435-455.

Nallasamy, S., Kaya Okur, H. S., Bhurke, A., Davila, J., Li, Q., Young, S. L., ... Bagchi, I. C. (2019). Msx Homeobox Genes Act Downstream of BMP2 to Regulate Endometrial Decidualization in Mice and in Humans. Endocrinology, 160(7), 1631-1644.

Warnow, T. (2019). New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 3-21). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag.

Duffy, D. M., Ko, C., Jo, M., Brannstrom, M., & Curry, T. E. (2019). Ovulation: Parallels with inflammatory processes. Endocrine reviews, 40(2), 369-416.

Lewis, J. A., Mendenhall, R., Ojiemwen, A., Thomas, M., Riopelle, C., Harwood, S. A., & Browne Huntt, M. (2019). Racial Microaggressions and Sense of Belonging at a Historically White University. American Behavioral Scientist.

Fuzawa, M., Smith, R. L., Ku, K. M., Shisler, J. L., Feng, H., Juvik, J. A., & Nguyen, T. H. (Accepted/In press). Roles of Vegetable Surface Properties and Sanitizer Type on Annual Disease Burden of Rotavirus Illness by Consumption of Rotavirus-Contaminated Fresh Vegetables: A Quantitative Microbial Risk Assessment. Risk Analysis.

Nelson, T. C., Crandall, J. G., Ituarte, C. M., Catchen, J. M., & Cresko, W. A. (2019). Selection, linkage, and population structure interact to shape genetic variation among threespine stickleback genomes. Genetics, 212(4), 1367-1382.

Kendig, K. I., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S. N., Heldenbrand, J. R., ... Mainzer, L. S. (2019). SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy. Frontiers in Genetics, 10(JUL), [736].

Xiang, D., Zhao, S. D., & Tony Cai, T. (2019). Signal classification for the integrative analysis of multiple sequences of large-scale multiple tests. Journal of the Royal Statistical Society. Series B: Statistical Methodology, 81(4), 707-734.

Shahoei, S. H., Kim, Y. C., Cler, S. J., Ma, L., Anakk, S., Kemper, J. K., & Nelson, E. R. (2019). Small Heterodimer Partner Regulates Dichotomous T Cell Expansion by Macrophages. Endocrinology, 160(7), 1573-1589.

Doden, H. L., Pollet, R. M., Mythen, S. M., Wawrzak, Z., Devendran, S., Cann, I., ... Ridlon, J. M. (2019). Structural and biochemical characterization of 20-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32. Journal of Biological Chemistry, 294(32), 12040-12053.

Dutta, S., Aoki, K., Doungkamchan, K., Tiemeyer, M., Bovin, N., & Miller, D. J. (2019). Sulfated Lewis A trisaccharide on oviduct membrane glycoproteins binds bovine sperm and lengthens sperm lifespan. Journal of Biological Chemistry, 294(36), 13445-13463.

Dawson, D. N., Volpe, V. V., & Laurent, H. K. (2019). Synergistic Effects of Psychological Intimate Partner Violence Exposure and Gender Discrimination on Postnatal Mental Health Trajectories. Journal of interpersonal violence.

Ridlon, J. M., Devendran, S., Alves, J. M., Doden, H., Wolf, P. G., Pereira, G. V., ... Gaskins, H. R. (2019). The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes.

Nelson, B. W., Bernstein, R., Allen, N. B., & Laurent, H. K. (Accepted/In press). The quality of early infant-caregiver relational attachment and longitudinal changes in infant inflammation across 6 months. Developmental psychobiology.

Xue, L., Shu, X., Shi, P., Wu, C. O., & Qu, A. (Accepted/In press). Time-varying feature selection for longitudinal analysis. Statistics in Medicine.

Le, T., Sy, A., Molloy, E. K., Zhang, Q. R., Rao, S., & Warnow, T. (2019). Using INC Within Divide-and-Conquer Phylogeny Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 167-178). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag.

Saul, M. C., Blatti, C., Yang, W., Bukhari, S. A., Shpigler, H. Y., Troy, J. M., ... Sinha, S. (2019). Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. Genes, Brain and Behavior, e12502.

Wang, Y., Araud, E., Shisler, J. L., Nguyen, T. H., & Yuan, B. (2019). Influence of algal organic matter on MS2 bacteriophage inactivation by ultraviolet irradiation at 220 nm and 254 nm. Chemosphere, 214, 195-202.

Lin, H., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Impact of Malicious SCADA Commands on Power Grids' Dynamic Responses. In 2018 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids, SmartGridComm 2018 [8587462] (2018 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids, SmartGridComm 2018). Institute of Electrical and Electronics Engineers Inc..

Stephens, Z., Wang, C., Iyer, R. K., & Kocher, J. P. (2018). Detection and visualization of complex structural variants from long reads. BMC bioinformatics, 19, [508].

Víctor Moreno-Mayar, J., Vinner, L., De Barros Damgaard, P., De La Fuente, C., Chan, J., Spence, J. P., ... Willerslev, E. (2018). Early human dispersals within the Americas. Science, 362(6419), [eaav2621].

Pei, Y., Shahoei, S. H., Li, Y., Reece, P. J., Nelson, E. R., Gooding, J. J., & Kilian, K. A. (2018). Vertical Integration of Cell-Laden Hydrogels with Bioinspired Photonic Crystal Membranes. Advanced Materials Interfaces, 5(23), [1801233].

Lee, G., Sherer, N. A., Kim, N. H., Rajic, E., Kaur, D., Urriola, N., ... Kuhlman, T. E. (2018). Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell. Proceedings of the National Academy of Sciences of the United States of America, 115(49), 12465-12470.

Winters, R. A., Hamilton, D. N., Bhatnagar, A. S., Fitzgerald, R., Bovin, N., & Miller, D. J. (2018). Porcine sperm binding to oviduct cells and glycans as supplements to traditional laboratory semen analysis. Journal of animal science, 96(12), 5265-5275.

Tabe-Bordbar, S., Emad, A., Zhao, S. D., & Sinha, S. (2018). A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models. Scientific reports, 8(1), [6620].

Summer internship for INdigenous peoples in Genomics (SING) Consortium (2018). A framework for enhancing ethical genomic research with Indigenous communities. Nature communications, 9(1), [2957].

Liu, D., Ray, B., Neavin, D. R., Zhang, J., Athreya, A. P., Biernacka, J. M., ... Weinshilboum, R. M. (2018). Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: Metabolomics-informed genomics. Translational psychiatry, 8(1), [56].

Sun, P. P., Araud, E. M., Huang, C., Shen, Y., Monroy, G. L., Zhong, S., ... Nguyen, T. H. (2018). Disintegration of simulated drinking water biofilms with arrays of microchannel plasma jets. npj Biofilms and Microbiomes, 4(1), [24].

Shen, Y., Huang, P. C., Huang, C., Sun, P., Monroy, G. L., Wu, W., ... Nguyen, T. H. (2018). Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms. npj Biofilms and Microbiomes, 4(1), [15].

Hernandez, J., Volland, A., Leyshon, B. J., Juda, M., Ridlon, J. M., Johnson, R. W., & Steelman, A. J. (2018). Effect of imidacloprid ingestion on immune responses to porcine reproductive and respiratory syndrome virus. Scientific reports, 8(1), [11615].

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., ... Ming, R. (2018). Erratum to: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. (Nature Genetics, (2018), 50, 11, (1565-1573), 10.1038/s41588-018-0237-2). Nature Genetics, 50(12).

Chen, K. L. A., Liu, X., Zhao, Y. C., Hieronymi, K., Rossi, G., Auvil, L. S., ... Madak-Erdogan, Z. (2018). Long-Term Administration of Conjugated Estrogen and Bazedoxifene Decreased Murine Fecal β-Glucuronidase Activity Without Impacting Overall Microbiome Community. Scientific reports, 8(1), [8166].

Gardner, A. M., Muturi, E. J., & Allan, B. F. (2018). Discovery and exploitation of a natural ecological trap for a mosquito disease vector. Proceedings of the Royal Society B: Biological Sciences, 285(1891), [20181962].

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941.

Xu, J., Huang, C., Shi, X., Dong, S., Yuan, B., & Nguyen, T. H. (2018). Role of drinking water biofilms on residual chlorine decay and trihalomethane formation: An experimental and modeling study. Science of the Total Environment, 642, 516-525.

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., ... Ridlon, J. M. (2018). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243 T Gut Microbes, 9(6), 523-539.

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., ... Ming, R. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, 50(11), 1565-1573.

Nowak, R. A. (2018). An interview with Dr Patricia A. Martin-DeLeon. Biology of reproduction, 99(5), 899-902.

Dong, S., Massalha, N., Plewa, M. J., & Nguyen, T. H. (2018). The impact of disinfection Ct values on cytotoxicity of agricultural wastewaters: Ozonation vs. chlorination. Water Research, 144, 482-490.

Zheng, X., Xue, L., & Qu, P. (2018). Time-varying correlation structure estimation and local-feature detection for spatio-temporal data. Journal of Multivariate Analysis, 168, 221-239.

Hale, V. L., Jeraldo, P., Chen, J., Mundy, M., Yao, J., Priya, S., ... Chia, N. (2018). Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Genome medicine, 10(1).

Jha, S., Brandt, J., Gentile, A., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Characterizing Supercomputer Traffic Networks Through Link-Level Analysis. In Proceedings - 2018 IEEE International Conference on Cluster Computing, CLUSTER 2018 (pp. 562-570). [8514916] (Proceedings - IEEE International Conference on Cluster Computing, ICCC; Vol. 2018-September). Institute of Electrical and Electronics Engineers Inc..

Banerjee, S. S., Athreya, A. P., Kalbarczyk, Z. T., Lumetta, S. S., & Iyer, R. K. (2018). A ML-based runtime system for executing dataflow graphs on heterogeneous processors. In SoCC 2018 - Proceedings of the 2018 ACM Symposium on Cloud Computing (SoCC 2018 - Proceedings of the 2018 ACM Symposium on Cloud Computing). Association for Computing Machinery, Inc.

Yuan, J., Hu, Z., Mahal, B. A., Zhao, S. D., Kensler, K. H., Pi, J., ... Zhang, L. (2018). Integrated Analysis of Genetic Ancestry and Genomic Alterations across Cancers. Cancer Cell, 34(4), 549-560.e9.

Keesing, F., Ostfeld, R. S., Okanga, S., Huckett, S., Bayles, B. R., Chaplin-Kramer, R., ... Allan, B. F. (2018). Consequences of integrating livestock and wildlife in an African savanna. Nature Sustainability, 1(10), 566-573.

Bi, X., & Qu, P. (2018). A mixed-effects estimating equation approach to nonignorable missing longitudinal data with Refreshment samples. Statistica Sinica, 28(4), 1653-1675.

Ho-Shui-Ling, A., Bolander, J., Rustom, L. E., Johnson, A. W., Luyten, F. P., & Picart, C. (2018). Bone regeneration strategies: Engineered scaffolds, bioactive molecules and stem cells current stage and future perspectives. Biomaterials, 180, 143-162.

Lin, H., Kalbarczyk, Z. T., & Iyer, R. K. (Accepted/In press). RAINCOAT: RAndomization of Network Communication in Power Grid Cyber INfrastructure to Mislead Attackers. IEEE Transactions on Smart Grid.

Harwood, S. A., Mendenhall, R., Lee, S. S., Riopelle, C., & Huntt, M. B. (2018). Everyday Racism in Integrated Spaces: Mapping the Experiences of Students of Color at a Diversifying Predominantly White Institution. Annals of the American Association of Geographers, 108(5), 1245-1259.

Alexander, C., Cross, T. W. L., Devendran, S., Neumer, F., Theis, S., Ridlon, J. M., ... Swanson, K. S. (2018). Effects of prebiotic inulin-Type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs. Clay Minerals, 120(6), 711-720.

Brinkworth, J. F., & Babbitt, C. C. (2018). Immune system promiscuity in human and nonhuman primate evolution. Human biology, 90(4), 251-269.

Gassen, J., Prokosch, M. L., Makhanova, A., Eimerbrink, M. J., White, J. D., Proffitt Leyva, R. P., ... Hill, S. E. (2018). Behavioral immune system activity predicts downregulation of chronic basal inflammation. PloS one, 13(9), [e0203961].

Moran, R. L., Zhou, M., Catchen, J. M., & Fuller, B. C. (2018). Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles. Ecology and Evolution, 8(18), 9282-9294.

Löber, U., Hobbs, M., Dayaram, A., Tsangaras, K., Jones, K., Alquezar-Planas, D. E., ... Greenwood, A. D. (2018). Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proceedings of the National Academy of Sciences of the United States of America, 115(34), 8609-8614.

Pattabiraman, S., & Warnow, T. (2018). Are Profile Hidden Markov Models Identifiable? In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 448-456). (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc.

Stephens, Z. D., & Iyer, R. K. (2018). Measuring the Mappability Spectrum of Reference Genome Assemblies. In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 47-52). (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc.

Potter, B. A., Baichtal, J. F., Beaudoin, A. B., Fehren-Schmitz, L., Haynes, C. V., Holliday, V. T., ... Surovell, T. A. (2018). Current evidence allows multiple models for the peopling of the Americas. Science Advances, 4(8), [eaat5473].

Barakat, R., Lin, P. C., Park, C. J., Best-Popescu, C., Bakry, H. H., Abosalem, M. E., ... Ko, C. M. (2018). Corrigendum to "Prenatal Exposure to DEHP Induces Neuronal Degeneration and Neurobehavioral Abnormalities in Adult Male Mice". Toxicological sciences : an official journal of the Society of Toxicology, 164(2).

Khan, R., Nguyen, T. H., Shisler, J. L., Lin, L. S., Jutla, A., & Colwell, R. (2018). Evaluation of risk of cholera after a natural disaster: Lessons learned from the 2015 Nepal earthquake. Journal of Water Resources Planning and Management, 144(8), [04018044].

Zhang, Q., Rao, S., & Warnow, T. (2018). New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. In L. Parida, & E. Ukkonen (Eds.), 18th International Workshop on Algorithms in Bioinformatics, WABI 2018 [8] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 113). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.

Athreya, A., Iyer, R., Neavin, D., Wang, L., Weinshilboum, R., Kaddurah-Daouk, R., ... Bobo, W. (2018). Augmentation of physician assessments with multi-omics enhances predictability of drug response: A case study of major depressive disorder. IEEE Computational Intelligence Magazine, 13(3), 20-31. [8416980].

Nelson, K. L., Boehm, A. B., Davies-Colley, R. J., Dodd, M. C., Kohn, T., Linden, K. G., ... Zepp, R. G. (2018). Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches. Environmental Science: Processes and Impacts, 20(8), 1089-1122.

Jha, S., Banerjee, S. S., Cyriac, J., Kalbarczyk, Z. T., & Iyer, R. K. (2018). AVFI: Fault Injection for Autonomous Vehicles. In Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2018 (pp. 55-56). [8416212] (Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2018). Institute of Electrical and Electronics Engineers Inc..

Banerjee, S. S., Jha, S., Cyriac, J., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Hands off the wheel in autonomous vehicles? A systems perspective on over a million miles of field data. In Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2018 (pp. 586-597). [8416518] (Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2018). Institute of Electrical and Electronics Engineers Inc..

Shih, H. Y., Mickalide, H., Fraebel, D. T., Goldenfeld, N., & Kuehn, S. (2018). Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Physical Biology, 15(6), [065003].

Leathlobhair, M. N., Perri, A. R., Irving-Pease, E. K., Witt, K. E., Linderholm, A., Haile, J., ... Frantz, L. A. F. (2018). The evolutionary history of dogs in the Americas. Science, 361(6397), 81-85.

Brandt, A. L., Green, M. L., Ishida, Y., Roca, A. L., Novakofski, J., & Mateus-Pinilla, N. E. (2018). Influence of the geographic distribution of prion protein gene sequence variation on patterns of chronic wasting disease spread in white-tailed deer (Odocoileus virginianus). Prion, 12(3-4), 204-215.

Lipscomb, S. T., Becker, D. R., Laurent, H. K., Neiderhiser, J. M., Shaw, D. S., Natsuaki, M. N., ... Leve, L. D. (2018). Examining morning HPA axis activity as a moderator of hostile, over-reactive parenting on children's skills for success in school. Infant and Child Development, 27(4), [e2083].

Josek, T., Walden, K. K. O., Allan, B. F., Alleyne, M., & Robertson, H. M. (2018). A foreleg transcriptome for Ixodes scapularis ticks: Candidates for chemoreceptors and binding proteins that might be expressed in the sensory Haller's organ. Ticks and Tick-borne Diseases, 9(5), 1317-1327.

Athreya, A. P., Gaglio, A. J., Cairns, J., Kalari, K. R., Weinshilboum, R. M., Wang, L., ... Iyer, R. K. (2018). Machine learning helps identify new drug mechanisms in triple-negative breast cancer. IEEE Transactions on Nanobioscience, 17(3), 251-259. [8401331].

Bassham, S., Catchen, J., Lescak, E., von Hippel, F. A., & Cresko, W. A. (2018). Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling in stickleback. Genetics, 209(3), 921-939.

Zhou, W., Davis, E. A., Li, K., Nowak, R. A., & Dailey, M. J. (2018). Sex differences influence intestinal epithelial stem cell proliferation independent of obesity. Physiological Reports, 6(13), [e13746].

Vachaspati, P., & Warnow, T. (2018). SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution, 124, 122-136.

Halsey, S. J., Allan, B. F., & Miller, J. R. (2018). The role of Ixodes scapularis, Borrelia burgdorferi and wildlife hosts in Lyme disease prevalence: A quantitative review. Ticks and Tick-borne Diseases, 9(5), 1103-1114.

Brandt, J. R., De Groot, P. J. V. C., Witt, K. E., Engelbrektsson, P. K., Helgen, K. M., Malhi, R. S., ... Roca, A. L. (2018). Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis). Journal of Heredity, 109(5), 553-565.

Varatharajah, Y., Berry, B., Cimbalnik, J., Kremen, V., Van Gompel, J., Stead, M., ... Worrell, G. (2018). Integrating artificial intelligence with real-time intracranial EEG monitoring to automate interictal identification of seizure onset zones in focal epilepsy. Journal of Neural Engineering, 15(4), [046035].

Karig, D., Michael Martini, K., Lu, T., DeLateur, N. A., Goldenfeld, N., & Weiss, R. (2018). Stochastic Turing patterns in a synthetic bacterial population. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6572-6577.

Mendenhall, R., Cross, K. J., Amos, J. R., Clancy, K. B. H., Imoukhuede, P. U. II., & Cromley, J. G. (2018). Intersecting identities of women in engineering. ASEE Annual Conference and Exposition, Conference Proceedings, 2018-June.

Vlčková, K., Pafčo, B., Petrželková, K. J., Modrý, D., Todd, A., Yeoman, C. J., ... Gomez, A. (2018). Relationships between gastrointestinal parasite infections and the fecal microbiome in free-ranging western lowland gorillas. Frontiers in Microbiology, 9(JUN), [1202].

Scheib, C. L., Li, H., Desai, T., Link, V., Kendall, C., Dewar, G., ... Kivisild, T. (2018). Ancient human parallel lineages within North America contributed to a coastal expansion. Science, 360(6392), 1024-1027.

Dong, S., Li, J., Kim, M. H., Cho, J., Park, S. J., Nguyen, T. H., & Eden, J. G. (2018). Deactivation of Legionella Pneumophila in municipal wastewater by ozone generated in arrays of microchannel plasmas. Journal of Physics D: Applied Physics, 51(25), [255501].

Showmaker, K. C., Walden, K. K. O., Fields, C. J., Lambert, K. N., & Hudson, M. E. (2018). Genome sequence of the soybean cyst nematode (Heterodera glycines) endosymbiont "Candidatus Cardinium hertigii" strain cHgTN10. Genome Announcements, 6(26), [e00624-18].

Grigorev, K., Kliver, S., Dobrynin, P., Komissarov, A., Wolfsberger, W., Krasheninnikova, K., ... Oleksyk, T. K. (2018). Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. GigaScience, 7(6), [giy025].

Soliman, A., MacKay, A. J., Schmidt, A., Allan, B., & Wang, S. (Accepted/In press). Quantifying the geographic distribution of building coverage across the US for urban sustainability studies. Computers, Environment and Urban Systems.

Miller, D. J. (2018). Review: The epic journey of sperm through the female reproductive tract. Animal, 12(s1), s110-s120.

Biscarri, W., Zhao, S. D., & Brunner, R. J. (2018). A simple and fast method for computing the Poisson binomial distribution function. Computational Statistics and Data Analysis, 122, 92-100.

Dominguez, V. R., & Malhi, R. S. (2018). Foreword. American Anthropologist, 120(2), 328-329.

Bortolini, M. C., Dominguez, V. R., & Malhi, R. S. (2018). Interview with Maria Cátira Bortolini, Anthropological Geneticist. American Anthropologist, 120(2), 343-344.

Hylemon, P. B., Harris, S. C., & Ridlon, J. M. (2018). Metabolism of hydrogen gases and bile acids in the gut microbiome. FEBS Letters, 592(12), 2070-2082.

Tucker, E. K., & Nowak, R. A. (2018). Methylmercury alters proliferation, migration, and antioxidant capacity in human HTR8/SV-neo trophoblast cells. Reproductive Toxicology, 78, 60-68.

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., ... Johnson, T. J. (2018). The gut microbiome of nonhuman primates: Lessons in ecology and evolution. American journal of primatology, 80(6), [e22867].

Mallott, E. K., Garber, P. A., & Malhi, R. S. (2018). Trnl outperforms rbcl as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (cebus capucinus, primates). PloS one, 13(6), [e0199556].

Araud, E., Shisler, J. L., & Nguyen, T. H. (2018). Inactivation Mechanisms of Human and Animal Rotaviruses by Solar UVA and Visible Light. Environmental Science and Technology, 52(10), 5682-5690.

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252].

Nute, M., Chou, J., Molloy, E. K., & Warnow, T. (2018). The performance of coalescent-based species tree estimation methods under models of missing data. BMC genomics, 19, [286].

Nelson, E. (2018). The significance of cholesterol and its metabolite, 27-hydroxycholesterol in breast cancer. Molecular and Cellular Endocrinology, 466, 73-80.

Josek, T., Allan, B. F., & Alleyne, M. (2018). Morphometric Analysis of Chemoreception Organ in Male and Female Ticks (Acari: Ixodidae). Journal of medical entomology, 55(3), 547-552.

Lindo, J., Rogers, M., Mallott, E. K., Petzelt, B., Mitchell, J., Archer, D., ... DeGiorgio, M. (2018). Patterns of Genetic Coding Variation in a Native American Population before and after European Contact. American Journal of Human Genetics, 102(5), 806-815.

Li, Q., Lawrence, C. R., Nowak, R. A., Flaws, J. A., Bagchi, M. K., & Bagchi, I. C. (2018). Bisphenol A and phthalates modulate peritoneal macrophage function in female mice involving SYMD2-H3K36 dimethylation. Endocrinology, 159(5), 2216-2228.

Lee-Thacker, S., Choi, Y., Taniuchi, I., Takarada, T., Yoneda, Y., Ko, C., & Jo, M. (2018). Core binding factor b expression in ovarian granulosa cells is essential for female fertility. Endocrinology, 159(5), 2094-2109.

Akpertey, A., Singh, R. J., Diers, B. W., Graef, G. L., Mian, M. A. R., Shannon, J. G., ... Nelson, R. L. (2018). Genetic introgression from Glycine tomentella to soybean to increase seed yield. Crop Science, 58(3), 1277-1291.

Swaminathan, S., Abeysekara, N. S., Knight, J. M., Liu, M., Dong, J., Hudson, M., ... Cianzio, S. R. (2018). Mapping of new quantitative trait loci for sudden death syndrome and soybean cyst nematode resistance in two soybean populations. Theoretical and Applied Genetics, 131(5), 1047-1062.

Doden, H., Sallam, L. A., Devendran, S., Ly, L., Doden, G., Daniel, S. L., ... Ridlon, J. M. (2018). Metabolism of oxo-bile acids and characterization of recombinant 12α- hydroxysteroid dehydrogenases from bile acid 7α-dehydroxylating human gut bacteria. Applied and environmental microbiology, 84(10), [e00235-18].

Laurent, H., Goodman, S. H., Stowe, Z. N., Halperin, M., Khan, F., Wright, D., ... Knight, B. (2018). Course of ante-and postnatal depressive symptoms related to mothers' HPA axis regulation. Journal of abnormal psychology, 127(4), 404-416.

Ishida, Y., Gugala, N. A., Georgiadis, N. J., & Roca, A. L. (2018). Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis). Ecology and Evolution, 8(10), 4919-4931.

Lin, H., Chen, C., Wang, J., Qi, J., Jin, D., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Self-healing attack-resilient PMU network for power system operation. IEEE Transactions on Smart Grid, 9(3), 1551-1565.

Bardill, J., Bader, A. C., Garrison, N. A., Bolnick, D. A., Raff, J. A., Walker, A., & Malhi, R. S. (2018). Advancing the ethics of paleogenomics. Science, 360(6387), 384-385.

Ren, Y., Reddy, J. S., Pottier, C., Sarangi, V., Tian, S., Sinnwell, J. P., ... Asmann, Y. W. (2018). Identification of missing variants by combining multiple analytic pipelines. BMC bioinformatics, 19(1), [139].

Chung, K., Kalbarczyk, Z. T., & Iyer, R. K. (2018). Poster: Indirect cyber attacks by perturbation of environment control: A data driven attack model. In Proceedings of the 5th Annual Symposium and Bootcamp on Hot Topics in the Science of Security, HoTSoS 2018 [3191681] (ACM International Conference Proceeding Series). Association for Computing Machinery.

Nowak, R. A. (2018). An interview with Dr Linda C. Giudice. Biology of reproduction, 98(4), 437-439.

Mythen, S. M., Devendran, S., Méndez-García, C., Cann, I., & Ridlon, J. M. (2018). Targeted synthesis and characterization of a gene cluster encoding NAD(P)H-dependent 3α-, 3β-, and 12α-hydroxysteroid dehydrogenases from Eggerthella CAG:298, a gut metagenomic sequence. Applied and environmental microbiology, 84(7), [e02475-17].

Springer, M. S., Murphy, W. J., & Roca, A. L. (2018). Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution, 121, 158-165.

Richardson, K. A., Hannon, P. R., Johnson-Walker, Y. J., Myint, M. S., Flaws, J. A., & Nowak, R. A. (2018). Di (2-ethylhexyl) phthalate (DEHP) alters proliferation and uterine gland numbers in the uteri of adult exposed mice. Reproductive Toxicology, 77, 70-79.

Liang, X., Lu, N., Chang, L. C., Nguyen, T. H., & Massoudieh, A. (2018). Evaluation of bacterial run and tumble motility parameters through trajectory analysis. Journal of Contaminant Hydrology, 211, 26-38.

Laurent, H. K., Wright, D., & Finnegan, M. (2018). Mindfulness-related differences in neural response to own infant negative versus positive emotion contexts. Developmental Cognitive Neuroscience, 30, 70-76.

Pomatto, V., Cottone, E., Cocci, P., Mozzicafreddo, M., Mosconi, G., Nelson, E. R., ... Bovolin, P. (2018). Plasticizers used in food-contact materials affect adipogenesis in 3T3-L1 cells. Journal of Steroid Biochemistry and Molecular Biology, 178, 322-332.

Vazquez-Bravo, B., Gonçalves, K., Shisler, J. L., & Marinas, B. J. (2018). Adenovirus Replication Cycle Disruption from Exposure to Polychromatic Ultraviolet Irradiation. Environmental Science and Technology, 52(6), 3652-3659.

Branscomb, E., Biancalani, T., Goldenfeld, N., & Russell, M. (2018). Escapement mechanisms and the conversion of disequilibria; the engines of creation. Physics Reports, 677, 1-60.

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