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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]. https://doi.org/10.1016/j.cej.2019.122865

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]. https://doi.org/10.1038/s41467-019-10424-5

Fischer-Hwang, I., Ochoa, I., Weissman, T., & Hernaez, M. (2019). Denoising of Aligned Genomic Data. Scientific reports, 9(1), [15067]. https://doi.org/10.1038/s41598-019-51418-z

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]. https://doi.org/10.1038/s41598-019-39134-0

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]. https://doi.org/10.1038/s41598-019-38793-3

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]. https://doi.org/10.1038/s41598-019-53691-4

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]. https://doi.org/10.1038/s41598-019-53925-5

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]. https://doi.org/10.1016/j.pmedr.2019.100993

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]. https://doi.org/10.1016/j.chemosphere.2019.124727

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]. https://doi.org/10.1103/PhysRevB.100.205125

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]. https://doi.org/10.1186/s12859-019-3169-7

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. https://doi.org/10.1021/acs.est.9b03734

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]. https://doi.org/10.1093/molbev/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. https://doi.org/10.1111/mec.15253

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685. https://doi.org/10.1038/s41586-019-1693-2

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]. https://doi.org/10.1093/femsec/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]. https://doi.org/10.1103/PhysRevE.100.040602

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. https://doi.org/10.1021/acs.est.9b03461

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]. https://doi.org/10.1186/s13059-019-1807-z

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. https://doi.org/10.1080/19386389.2019.1652967

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]. https://doi.org/10.1002/ajp.23046

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. https://doi.org/10.1038/s41564-019-0494-6

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]. https://doi.org/10.1002/ajp.23060

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. https://doi.org/10.1002/cpt.1482

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]. https://doi.org/10.1002/ajp.23045

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. https://doi.org/10.1007/s10834-019-09618-2

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]. https://doi.org/10.1016/j.taap.2019.114629

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. https://doi.org/10.1016/j.psyneuen.2019.04.023

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. https://doi.org/10.4230/LIPIcs.WABI.2019.4

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). https://doi.org/10.1073/pnas.1913223116

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]. https://doi.org/10.1126/sciadv.aax3346

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]. https://doi.org/10.1093/bioinformatics/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). https://doi.org/10.1128/mSphere.00271-19

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14]. https://doi.org/10.1186/s13015-019-0151-x

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. https://doi.org/10.1021/acs.est.8b06583

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]. https://doi.org/10.1093/bioinformatics/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. https://doi.org/10.1007/s12687-019-00407-w

Roca, A. L. (2019). African elephant genetics: enigmas and anomalies †. Journal of genetics, 98(3), [83]. https://doi.org/10.1007/s12041-019-1125-y

Yang, R., Chen, X., & Ochoa, I. (2019). MassComp, a lossless compressor for mass spectrometry data. BMC bioinformatics, 20(1), [368]. https://doi.org/10.1186/s12859-019-2962-7

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. https://doi.org/10.1002/ajpa.23842

Shahoei, S. H., & Nelson, E. R. (2019). Nuclear receptors, cholesterol homeostasis and the immune system. Journal of Steroid Biochemistry and Molecular Biology, 191, [105364]. https://doi.org/10.1016/j.jsbmb.2019.04.013

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. https://doi.org/10.1038/s41586-019-1279-z

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.. https://doi.org/10.1109/DSN-S.2019.00018

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. https://doi.org/10.1109/NER.2019.8717057

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.. https://doi.org/10.1109/DCC.2019.00017

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.. https://doi.org/10.1109/DCC.2019.00087

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. https://doi.org/10.1093/jme/tjy215

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]. https://doi.org/10.1128/mBio.00760-19

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. https://doi.org/10.1093/sysbio/syy068

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. https://doi.org/10.1093/bioinformatics/bty833

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. https://doi.org/10.1016/j.jas.2019.02.006

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. https://doi.org/10.1111/aman.13218

Malhi, R. S., Antón, S. C., & Fuentes, A. (2019). Increasing Diversity in Evolutionary Anthropological Sciences—the IDEAS Program. American Anthropologist, 121(2), 478-479. https://doi.org/10.1111/aman.13226

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. https://doi.org/10.1016/j.envres.2019.02.017

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. https://doi.org/10.1145/3302509.3311041

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. https://doi.org/10.1145/3297858.3304019

Laurent, H. (2019). Challenges in Characterizing the “Mommy Brain”. Parenting, 19(1-2), 94-96. https://doi.org/10.1080/15295192.2019.1556007

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]. https://doi.org/10.1128/AEM.00052-19

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]. https://doi.org/10.1038/s12276-019-0237-z

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. https://doi.org/10.1145/3314058.3317292

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. https://doi.org/10.1016/j.cryobiol.2019.02.006

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. https://doi.org/10.1016/j.ttbdis.2019.01.002

Ma, L., & Nelson, E. R. (2019). Oxysterols and nuclear receptors. Molecular and Cellular Endocrinology, 484, 42-51. https://doi.org/10.1016/j.mce.2019.01.016

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. https://doi.org/10.1038/s41559-019-0812-7

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]. https://doi.org/10.1109/TC.2018.2875733

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. https://doi.org/10.1038/s41396-018-0175-0

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. https://doi.org/10.1093/sysbio/syy061

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. https://doi.org/10.2987/18-6782.1

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. https://doi.org/10.1111/aje.12560

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. https://doi.org/10.1016/j.reprotox.2019.01.005

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]. https://doi.org/10.1186/s12864-019-5485-8

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]. https://doi.org/10.1186/s13015-019-0136-9

Nowak, R. A. (2019). An interview with Professor Virendra B. Mahesh. Biology of reproduction, 100(2), 301-304. https://doi.org/10.1093/biolre/ioy239

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. https://doi.org/10.1016/j.canlet.2018.10.041

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. https://doi.org/10.1123/jab.2018-0049

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. https://doi.org/10.1080/10618600.2019.1665535

Khan, F., & Laurent, H. K. (2019). Assessing the Impact of Mindfulness and Life Stress on Maternal Well-Being. Mindfulness, 10(1), 26-35. https://doi.org/10.1007/s12671-018-0943-y

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. https://doi.org/10.1038/s41396-019-0551-4

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. https://doi.org/10.1210/en.2018-00872

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. https://doi.org/10.1007/978-3-030-17938-0_4

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. https://doi.org/10.1007/s10493-018-00338-0

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. https://doi.org/10.1530/ERC-18-0572

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]. https://doi.org/10.1523/ENEURO.0214-18.2018

Tang, X., Bi, X., & Qu, A. (2019). Individualized Multilayer Tensor Learning With an Application in Imaging Analysis. Journal of the American Statistical Association. https://doi.org/10.1080/01621459.2019.1585254

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. https://doi.org/10.2217/pgs-2019-0119

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. https://doi.org/10.1080/10618600.2019.1677244

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. https://doi.org/10.1016/j.bbi.2019.05.010

Rustom, L. E., Poellmann, M. J., & Wagoner Johnson, A. J. (2019). Mineralization in micropores of calcium phosphate scaffolds. Acta Biomaterialia, 83, 435-455. https://doi.org/10.1016/j.actbio.2018.11.003

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. https://doi.org/10.1210/en.2019-00131

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. https://doi.org/10.1007/978-3-030-18174-1_1

Duffy, D. M., Ko, C., Jo, M., Brannstrom, M., & Curry, T. E. (2019). Ovulation: Parallels with inflammatory processes. Endocrine reviews, 40(2), 369-416. https://doi.org/10.1210/er.2018-00075

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. https://doi.org/10.1177/0002764219859613

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. https://doi.org/10.1111/risa.13426

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. https://doi.org/10.1534/genetics.119.302261

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]. https://doi.org/10.3389/fgene.2019.00736

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. https://doi.org/10.1111/rssb.12323

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. https://doi.org/10.1210/en.2019-00025

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. https://doi.org/10.1074/jbc.RA119.009390

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. https://doi.org/10.1074/jbc.RA119.007695

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. https://doi.org/10.1177/0886260519844274

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. https://doi.org/10.1080/19490976.2019.1618173

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. https://doi.org/10.1002/dev.21940

Xue, L., Shu, X., Shi, P., Wu, C. O., & Qu, A. (Accepted/In press). Time-varying feature selection for longitudinal analysis. Statistics in Medicine. https://doi.org/10.1002/sim.8412

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. https://doi.org/10.1007/978-3-030-18174-1_12

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. https://doi.org/10.1111/gbb.12502

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. https://doi.org/10.1016/j.chemosphere.2018.09.065

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.. https://doi.org/10.1109/SmartGridComm.2018.8587462

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]. https://doi.org/10.1186/s12859-018-2539-x

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]. https://doi.org/10.1126/science.aav2621

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]. https://doi.org/10.1002/admi.201801233

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. https://doi.org/10.1073/pnas.1807709115

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. https://doi.org/10.1093/jas/sky372

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]. https://doi.org/10.1038/s41598-018-24937-4

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]. https://doi.org/10.1038/s41467-018-05188-3

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]. https://doi.org/10.1038/s41398-017-0056-8

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]. https://doi.org/10.1038/s41522-018-0063-4

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]. https://doi.org/10.1038/s41522-018-0058-1

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]. https://doi.org/10.1038/s41598-018-30093-6

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). https://doi.org/10.1038/s41588-018-0293-7

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]. https://doi.org/10.1038/s41598-018-26506-1

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]. https://doi.org/10.1098/rspb.2018.1962

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941. https://doi.org/10.1093/bioinformatics/bty495

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. https://doi.org/10.1016/j.scitotenv.2018.05.363

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. https://doi.org/10.1080/19490976.2018.1458180

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. https://doi.org/10.1038/s41588-018-0237-2

Nowak, R. A. (2018). An interview with Dr Patricia A. Martin-DeLeon. Biology of reproduction, 99(5), 899-902. https://doi.org/10.1093/biolre/ioy103

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. https://doi.org/10.1016/j.watres.2018.07.065

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. https://doi.org/10.1016/j.jmva.2018.07.012

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). https://doi.org/10.1186/s13073-018-0586-6

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.. https://doi.org/10.1109/CLUSTER.2018.00072

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. https://doi.org/10.1145/3267809.3275474

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. https://doi.org/10.1016/j.ccell.2018.08.019

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. https://doi.org/10.1038/s41893-018-0149-2

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. https://doi.org/10.5705/ss.202015.0317

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. https://doi.org/10.1016/j.biomaterials.2018.07.017

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. https://doi.org/10.1109/TSG.2018.2870362

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. https://doi.org/10.1080/24694452.2017.1419122

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. https://doi.org/10.1017/S0007114518001952

Brinkworth, J. F., & Babbitt, C. C. (2018). Immune system promiscuity in human and nonhuman primate evolution. Human biology, 90(4), 251-269. https://doi.org/10.13110/humanbiology.90.4.01

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]. https://doi.org/10.1371/journal.pone.0203961

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. https://doi.org/10.1002/ece3.4434

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. https://doi.org/10.1073/pnas.1807598115

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. https://doi.org/10.1145/3233547.3233563

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. https://doi.org/10.1145/3233547.3233582

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]. https://doi.org/10.1126/sciadv.aat5473

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). https://doi.org/10.1093/toxsci/kfy165

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]. https://doi.org/10.1061/(ASCE)WR.1943-5452.0000929

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. https://doi.org/10.4230/LIPIcs.WABI.2018.8

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]. https://doi.org/10.1109/MCI.2018.2840660

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. https://doi.org/10.1039/c8em00047f

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.. https://doi.org/10.1109/DSN-W.2018.00027

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.. https://doi.org/10.1109/DSN.2018.00066

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]. https://doi.org/10.1088/1478-3975/aac4e6

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. https://doi.org/10.1126/science.aao4776

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. https://doi.org/10.1080/19336896.2018.1474671

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]. https://doi.org/10.1002/icd.2083

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. https://doi.org/10.1016/j.ttbdis.2018.05.013

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]. https://doi.org/10.1109/TNB.2018.2851997

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. https://doi.org/10.1534/genetics.117.300610

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]. https://doi.org/10.14814/phy2.13746

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. https://doi.org/10.1016/j.ympev.2018.03.006

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. https://doi.org/10.1016/j.ttbdis.2018.04.006

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. https://doi.org/10.1093/jhered/esy019

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]. https://doi.org/10.1088/1741-2552/aac960

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. https://doi.org/10.1073/pnas.1720770115

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.

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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. https://doi.org/10.1126/science.aar6851

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]. https://doi.org/10.1088/1361-6463/aac379

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]. https://doi.org/10.1128/genomeA.00624-18

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]. https://doi.org/10.1093/gigascience/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. https://doi.org/10.1016/j.compenvurbsys.2018.05.010

Miller, D. J. (2018). Review: The epic journey of sperm through the female reproductive tract. Animal, 12(s1), s110-s120. https://doi.org/10.1017/S1751731118000526

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. https://doi.org/10.1016/j.csda.2018.01.007

Dominguez, V. R., & Malhi, R. S. (2018). Foreword. American Anthropologist, 120(2), 328-329. https://doi.org/10.1111/aman.13041

Bortolini, M. C., Dominguez, V. R., & Malhi, R. S. (2018). Interview with Maria Cátira Bortolini, Anthropological Geneticist. American Anthropologist, 120(2), 343-344. https://doi.org/10.1111/aman.13042

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. https://doi.org/10.1002/1873-3468.13064

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. https://doi.org/10.1016/j.reprotox.2018.03.008

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]. https://doi.org/10.1002/ajp.22867

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]. https://doi.org/10.1371/journal.pone.0199556

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. https://doi.org/10.1021/acs.est.7b06562

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252]. https://doi.org/10.1186/s12864-018-4621-1

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]. https://doi.org/10.1186/s12864-018-4619-8

Nelson, E. (2018). The significance of cholesterol and its metabolite, 27-hydroxycholesterol in breast cancer. Molecular and Cellular Endocrinology, 466, 73-80. https://doi.org/10.1016/j.mce.2017.09.021

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. https://doi.org/10.1093/jme/tjx232

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. https://doi.org/10.1016/j.ajhg.2018.03.008

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. https://doi.org/10.1210/en.2017-03000

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. https://doi.org/10.1210/en.2018-00011

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. https://doi.org/10.2135/cropsci2017.07.0445

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. https://doi.org/10.1007/s00122-018-3057-y

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]. https://doi.org/10.1128/AEM.00235-18

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. https://doi.org/10.1037/abn0000348

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. https://doi.org/10.1002/ece3.4062

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. https://doi.org/10.1109/TSG.2016.2593021

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. https://doi.org/10.1126/science.aaq1131

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]. https://doi.org/10.1186/s12859-018-2151-0

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. https://doi.org/10.1145/3190619.3191681

Nowak, R. A. (2018). An interview with Dr Linda C. Giudice. Biology of reproduction, 98(4), 437-439. https://doi.org/10.1093/biolre/ioy022

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]. https://doi.org/10.1128/AEM.02475-17

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. https://doi.org/10.1016/j.ympev.2018.01.007

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. https://doi.org/10.1016/j.reprotox.2018.01.006

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. https://doi.org/10.1016/j.jconhyd.2018.03.002

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. https://doi.org/10.1016/j.dcn.2018.01.002

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. https://doi.org/10.1016/j.jsbmb.2018.01.014

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. https://doi.org/10.1021/acs.est.7b06082

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. https://doi.org/10.1016/j.physrep.2017.02.001

Potter, B. A., Beaudoin, A. B., Haynes, C. V., Holliday, V. T., Holmes, C. E., Ives, J. W., ... Surovell, T. (2018). Arrival routes of first Americans uncertain. Science, 359(6381), 1224-1225. https://doi.org/10.1126/science.aar8233

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2018). OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms for Molecular Biology, 13(1), [6]. https://doi.org/10.1186/s13015-018-0124-5

Massalha, N., Dong, S., Plewa, M. J., Borisover, M., & Nguyen, T. H. (2018). Spectroscopic Indicators for Cytotoxicity of Chlorinated and Ozonated Effluents from Wastewater Stabilization Ponds and Activated Sludge. Environmental Science and Technology, 52(5), 3167-3174. https://doi.org/10.1021/acs.est.7b05510

Ferrando, D., Toubiana, D., Kandiyote, N. S., Nguyen, T. H., Nejidat, A., & Herzberg, M. (2018). Ambivalent role of calcium in the viscoelastic properties of extracellular polymeric substances and the consequent fouling of reverse osmosis membranes. Desalination, 429, 12-19. https://doi.org/10.1016/j.desal.2017.12.006

Keesing, F., Ostfeld, R. S., Young, T. P., & Allan, B. F. (2018). Cattle and rainfall affect tick abundance in central Kenya. Parasitology, 145(3), 345-354. https://doi.org/10.1017/S003118201700155X

Kannan, A., Bhurke, A., Sitruk-Ware, R., Lalitkumar, P. G., Gemzell-Danielsson, K., Williams, A. R. W., ... Bagchi, I. C. (2018). Characterization of Molecular Changes in Endometrium Associated With Chronic Use of Progesterone Receptor Modulators: Ulipristal Acetate Versus Mifepristone. Reproductive Sciences, 25(3), 320-328. https://doi.org/10.1177/1933719117746764

Winters, R. A., Nettenstrom, L. M., Lopez, D. G., Willenburg, K. L., Vishwanath, R., Bovin, N. V., & Miller, D. J. (2018). Effect of sorting boar spermatozoa by sex chromosomes on oviduct cell binding. Theriogenology, 108, 22-28. https://doi.org/10.1016/j.theriogenology.2017.11.010

Hu, R., Morley, M. P., Brandimarto, J., Tucker, N. R., Parsons, V. A., Zhao, S. D., ... Cappola, T. P. (2018). Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects. Circulation. Genomic and precision medicine, 11(3), e001901. https://doi.org/10.1161/CIRCGEN.117.001901

Vidimar, V., Chakravarti, D., Bulun, S. E., Yin, P., Nowak, R., Wei, J. J., & Kim, J. J. (2018). The AKT/BCL-2 Axis Mediates Survival of Uterine Leiomyoma in a Novel 3D Spheroid Model. Endocrinology, 159(3), 1453-1462. https://doi.org/10.1210/en.2017-03191

Molloy, E. K., & Warnow, T. (2018). To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic biology, 67(2), 285-303. https://doi.org/10.1093/sysbio/syx077

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (2018). A roadmap for global synthesis of the plant tree of life. American journal of botany, 105(3), 614-622. https://doi.org/10.1002/ajb2.1041

Harris, S. C., Devendran, S., Alves, J. M. P., Mythen, S. M., Hylemon, P. B., & Ridlon, J. M. (2018). Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, 1863(3), 276-283. https://doi.org/10.1016/j.bbalip.2017.12.001

Mallott, E. K., Amato, K. R., Garber, P. A., & Malhi, R. S. (2018). Influence of fruit and invertebrate consumption on the gut microbiota of wild white-faced capuchins (Cebus capucinus). American journal of physical anthropology, 165(3), 576-588. https://doi.org/10.1002/ajpa.23395

Raulo, A., Ruokolainen, L., Lane, A., Amato, K., Knight, R., Leigh, S., ... Tecot, S. R. (2018). Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. Journal of Animal Ecology, 87(2), 388-399. https://doi.org/10.1111/1365-2656.12781

Greenwood, A. D., O'Brien, S. P., Roca, A. L., & Eiden, M. V. (2018). Transmission, evolution, and endogenization: Lessons learned from recent retroviral invasions. Microbiology and Molecular Biology Reviews, 82(1), [e00044-17]. https://doi.org/10.1128/MMBR.00044-17

Ryerson, M. R., & Shisler, J. L. (2018). Characterizing the effects of insertion of a 5.2 kb region of a VACV genome, which contains known immune evasion genes, on MVA immunogenicity. Virus Research, 246, 55-64. https://doi.org/10.1016/j.virusres.2018.01.004

Gernat, T., Rao, V. D., Middendorf, M., Dankowicz, H., Goldenfeld, N., & Robinson, G. E. (2018). Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks. Proceedings of the National Academy of Sciences of the United States of America, 115(7), 1433-1438. https://doi.org/10.1073/pnas.1713568115

de Flamingh, A., Roca, A. L., & van Aarde, R. J. (2018). Origin and phylogeography of African savannah elephants (Loxodonta africana) in Kruger and nearby parks in southern Africa. Conservation Genetics, 19(1), 155-167. https://doi.org/10.1007/s10592-017-1005-z

Delker, B. C., Bernstein, R. E., & Laurent, H. K. (2018). Out of harm's way: Secure versus insecure-disorganized attachment predicts less adolescent risk taking related to childhood poverty. Development and Psychopathology, 30(1), 283-296. https://doi.org/10.1017/S0954579417000621

Biswas, S., Smith, G. L., Roy, E. J., Ward, B., & Shisler, J. L. (2018). A comparison of the effect of molluscum contagiosum virus MC159 and MC160 proteins on vaccinia virus virulence in intranasal and intradermal infection routes. Journal of General Virology, 99(2), 246-252. [001006]. https://doi.org/10.1099/jgv.0.001006

Nelson, B. W., Allen, N. B., & Laurent, H. K. (2018). Infant HPA axis as a potential mechanism linking maternal mental health and infant telomere length. Psychoneuroendocrinology, 88, 38-46. https://doi.org/10.1016/j.psyneuen.2017.11.008

Mendenhall, R., Kramer, K. Z., & Bellisle, D. (2018). Low- and moderate-income families’ avenues to mobility: Overcoming threats to asset accumulation and remaining in undesirable neighborhoods. Research in Social Stratification and Mobility, 53, 26-39. https://doi.org/10.1016/j.rssm.2017.12.001

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., ... Welch, L. (2018). The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS computational biology, 14(2), [e1005772]. https://doi.org/10.1371/journal.pcbi.1005772

Bayzid, M. S., & Warnow, T. (2018). Gene tree parsimony for incomplete gene trees: Addressing true biological loss. Algorithms for Molecular Biology, 13(1), [1]. https://doi.org/10.1186/s13015-017-0120-1

Moreno-Mayar, J. V., Potter, B. A., Vinner, L., Steinrücken, M., Rasmussen, S., Terhorst, J., ... Willerslev, E. (2018). Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature, 553(7687), 203-207. https://doi.org/10.1038/nature25173

Pence, B. D., Ryerson, M. R., Cruz, A. G. B., Woods, J. A., & Shisler, J. L. (2018). Voluntary wheel running does not alter mortality to or immunogenicity of vaccinia virus in mice: A pilot study. Frontiers in Physiology, 8(JAN), [1123]. https://doi.org/10.3389/fphys.2017.01123

de Flamingh, A., Mallott, E. K., Roca, A. L., Boraas, A. S., & Malhi, R. S. (2018). Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska. Mitochondrial DNA Part B: Resources, 3(1), 409-411. https://doi.org/10.1080/23802359.2018.1456371

Mapes, J., Anandan, L., Li, Q., Neff, A., Clevenger, C. V., Bagchi, I. C., & Bagchi, M. K. (2018). Aberrantly high expression of the CUB and zona pellucida-like domain-containing protein 1 (CUZD1) in mammary epithelium leads to breast tumorigenesis. Journal of Biological Chemistry, 293(8), 2850-2864. https://doi.org/10.1074/jbc.RA117.000162

Palkopoulou, E., Lipson, M., Mallick, S., Nielsen, S., Rohland, N., Baleka, S., ... Reich, D. (2018). A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences of the United States of America, 115(11), E2566-E2574. https://doi.org/10.1073/pnas.1720554115

Updyke, E. A., & Allan, B. F. (2018). An experimental evaluation of cross-vane PanelTraps for the collection of SylvaticTriatomines (Hemiptera: Reduviidae). Journal of medical entomology, 55(2), 485-489. https://doi.org/10.1093/jme/tjx224

Nowak, R. A. (2018). An interview with Dr R. Michael Roberts. Biology of reproduction, 98(6), 739-741. https://doi.org/10.1093/biolre/ioy053

Nowak, R. A. (2018). An interview with Dr Sudhansu K. Dey. Biology of reproduction, 98(1), 1-3. https://doi.org/10.1093/biolre/iox153

Gates-Tanzer, L. T., & Shisler, J. L. (2018). Cellular FLIP long isoform (cFLIP l )-IKKα interactions inhibit IRF7 activation, representing a new cellular strategy to inhibit IFNα expression Journal of Biological Chemistry, 293(5), 1745-1755. https://doi.org/10.1074/jbc.RA117.000541

Zhu, X., & Qu, A. (2018). Cluster analysis of longitudinal profiles with subgroups. Electronic Journal of Statistics, 12(1), 171-193. https://doi.org/10.1214/17-EJS1389

Manjunath, M., Zhang, Y., Kim, Y., Yeo, S. H., Sobh, O., Russell, N., ... Song, J. S. (2018). ClusterEnG: An interactive educational web resource for clustering and visualizing high-dimensional data. PeerJ Computer Science, 2018(5), [e155]. https://doi.org/10.7717/peerj-cs.155

Dávila, J., Li, Q., & Bagchi, I. C. (2018). Genetic Mouse Models for Female Reproductive Toxicology Studies. In Reproductive and Endocrine Toxicology (Vol. 4-15, pp. 470-494). Elsevier Inc.. https://doi.org/10.1016/B978-0-12-801238-3.95679-4

Viana, J. P. G., Siqueira, M. V. B. M., Araujo, F. L., Grando, C., Sujii, P. S., De Aguiar Silvestre, E., ... Zucchi, M. I. (2018). Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw. PloS one, 13(3), [e0192165]. https://doi.org/10.1371/journal.pone.0192165

Armstrong, A., Wagoner Johnson, A. J., & Alleyne, A. G. (2018). Improved cross-coupled iterative learning control for contouring NURBS curves. In Control and Optimization of Connected and Automated Ground Vehicles; Dynamic Systems and Control Education; Dynamics and Control of Renewable Energy Systems; Energy Harvesting; Energy Systems; Estimation and Identification; Intelligent Transportation and Vehicles; Manufacturing; Mechatronics; Modeling and Control of IC Engines and Aftertreatment Systems; Modeling and Control of IC Engines and Powertrain Systems; Modeling and Management of Power Systems (Vol. 2). American Society of Mechanical Engineers (ASME). https://doi.org/10.1115/DSCC2018-9145

Peng, J., Milenkovic, O., & Ochoa, I. (2018). METHCOMP: A special purpose compression platform for DNA methylation data. Bioinformatics, 34(15), 2654-2656. https://doi.org/10.1093/bioinformatics/bty143

Rong, Y., Zhao, S. D., Zhu, J., Yuan, W., Cheng, W., & Li, Y. (2018). More accurate semiparametric regression in pharmacogenomics. Statistics and its Interface, 11(4), 573-580. https://doi.org/10.4310/SII.2018.v11.n4.a2

Bi, X., Qu, A., & Shen, X. (2018). Multilayer tensor factorization with applications to recommender systems. Annals of Statistics, 46(6B), 3308-3333. https://doi.org/10.1214/17-AOS1659

Molloy, E. K., & Warnow, T. (2018). NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees. In A. Ouangraoua, & M. Blanchette (Eds.), Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings (pp. 260-276). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11183 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-030-00834-5_15

Park, C. J., Kim, H., Jin, J., Barakat, R., Lin, P. C., Choi, J. M., & Ko, C. M. J. (2018). Porcine intestinal lymphoid tissues synthesize estradiol. Journal of Veterinary Science, 19(4), 477-482. https://doi.org/10.4142/jvs.2018.19.4.477

Barakat, R., Lin, P. C., Park, C. J., Best, C., Bakry, H. H., Abosalem, M. E., ... Ko, C. (2018). Prenatal exposure to DEHP induces neuronal degeneration and neurobehavioral abnormalities in adult male mice. Toxicological Sciences, 164(2), 439-452. https://doi.org/10.1093/toxsci/kfy103

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