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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

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]. DOI: 10.1038/s41598-018-24937-4

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]. DOI: 10.1038/s41398-017-0056-8

Khan, R., Nguyen, T. H., Shisler, J., 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]. DOI: 10.1061/(ASCE)WR.1943-5452.0000929

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. DOI: 10.1016/j.csda.2018.01.007

Berding, K., Holscher, H. D., Arthur, A. E., & Donovan, S. M. (2018). Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake. Journal of Nutritional Biochemistry, 56, 165-174. DOI: 10.1016/j.jnutbio.2018.01.002

Dominguez, V. R., & Malhi, R. S. (2018). Foreword. American Anthropologist, 120(2), 328-329. DOI: 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. DOI: 10.1111/aman.13042

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. DOI: 10.1016/j.reprotox.2018.03.008

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

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., ... Ridlon, J. M. (Accepted/In press). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243T Gut microbes, 1-17. DOI: 10.1080/19490976.2018.1458180

Nievergelt, C. M., Ashley-Koch, A. E., Dalvie, S., Hauser, M. A., Morey, R. A., Smith, A. K., & Uddin, M. (2018). Genomic Approaches to Posttraumatic Stress Disorder: The Psychiatric Genomic Consortium Initiative. Biological Psychiatry, 83(10), 831-839. DOI: 10.1016/j.biopsych.2018.01.020

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252]. DOI: 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]. DOI: 10.1186/s12864-018-4619-8

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

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. DOI: 10.1037/abn0000348

Swaminathan, S., Abeysekara, N. S., Knight, J. M., Liu, M., Dong, J., Hudson, M. E., ... 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. DOI: 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]. DOI: 10.1128/AEM.00235-18

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. DOI: 10.1109/TSG.2016.2593021

Farrell, A. K., Slatcher, R. B., Tobin, E. T., Imami, L., Wildman, D. E., Luca, F., & Zilioli, S. (2018). Socioeconomic status, family negative emotional climate, and anti-inflammatory gene expression among youth with asthma. Psychoneuroendocrinology, 91, 62-67. DOI: 10.1016/j.psyneuen.2018.02.011

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. DOI: 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]. DOI: 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] Association for Computing Machinery. DOI: 10.1145/3190619.3191681

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. DOI: 10.1016/j.ympev.2018.01.007

the STRONG Kids Team (2018). Child body mass index, genotype and parenting in the prediction of restrictive feeding. Pediatric Obesity, 13(4), 239-246. DOI: 10.1111/ijpo.12219

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. DOI: 10.1016/j.reprotox.2018.01.006

Fleming, S. A., Chichlowski, M., Berg, B. M., Donovan, S. M., & Dilger, R. N. (2018). Dietary sialyllactose does not influence measures of recognition memory or diurnal activity in the young pig. Nutrients, 10(4), [395]. DOI: 10.3390/nu10040395

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. DOI: 10.1016/j.jconhyd.2018.03.002

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. DOI: 10.1016/j.jsbmb.2018.01.014

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]. DOI: 10.1128/AEM.02475-17

Vazquez-Bravo, B., Gonçalves, K., Shisler, J. L., & Mariñas, B. J. (2018). Adenovirus Replication Cycle Disruption from Exposure to Polychromatic Ultraviolet Irradiation. Environmental Science and Technology, 52(6), 3652-3659. DOI: 10.1021/acs.est.7b06082

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]. DOI: 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. DOI: 10.1021/acs.est.7b05510

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. DOI: 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. DOI: 10.1016/j.theriogenology.2017.11.010

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. DOI: 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. DOI: 10.1002/ajpa.23395

Duncan, L. E., Ratanatharathorn, A., Aiello, A. E., Almli, L. M., Amstadter, A. B., Ashley-Koch, A. E., ... Koenen, K. C. (2018). Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability. Molecular Psychiatry, 23(3), 666-673. DOI: 10.1038/mp.2017.77

STRONG Kids Team (2018). Predictors and Outcomes of Mealtime Emotional Climate in Families with Preschoolers. Journal of Pediatric Psychology, 43(2), 195-206. DOI: 10.1093/jpepsy/jsx109

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. DOI: 10.1111/1365-2656.12781

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. DOI: 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. DOI: 10.1093/sysbio/syx077

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]. DOI: 10.1128/MMBR.00044-17

Harwood, S. A., Mendenhall, R., Lee, S. S., Riopelle, C., & Huntt, M. B. (Accepted/In press). 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, 1-15. DOI: 10.1080/24694452.2017.1419122

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. DOI: 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. DOI: 10.1073/pnas.1713568115

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]. DOI: 10.1099/jgv.0.001006

Bustamante, A. C., Armstrong, D. L., & Uddin, M. (2018). Epigenetic profiles associated with major depression in the human brain. Psychiatry research, 260, 439-442. DOI: 10.1016/j.psychres.2017.12.010

Nelson, B. W., Allen, N. B., & Laurent, H. (2018). Infant HPA axis as a potential mechanism linking maternal mental health and infant telomere length. Psychoneuroendocrinology, 88, 38-46. DOI: 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. DOI: 10.1016/j.rssm.2017.12.001

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. DOI: 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. DOI: 10.1017/S0954579417000621

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]. DOI: 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]. DOI: 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. DOI: 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]. DOI: 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. DOI: 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. DOI: 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. DOI: 10.1073/pnas.1720554115

Josek, T., Walden, K. K. O., Allan, B. F., Alleyne, M., & Robertson, H. M. (Accepted/In press). 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. DOI: 10.1016/j.ttbdis.2018.05.013

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. DOI: 10.1093/jme/tjx224

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (Accepted/In press). A roadmap for global synthesis of the plant tree of life. American journal of botany. DOI: 10.1002/ajb2.1041

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

Lipscomb, S. T., Becker, D. R., Laurent, H., Neiderhiser, J. M., Shaw, D. S., Natsuaki, M. N., ... Leve, L. D. (Accepted/In press). 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. DOI: 10.1002/icd.2083

Armstrong, D., & Wildman, D. E. (2018). Extracellular vesicles and the promise of continuous liquid biopsies. Journal of Pathology and Translational Medicine, 52(1), 1-8. DOI: 10.4132/jptm.2017.05.21

Bustamante, A. C., Aiello, A. E., Guffanti, G., Galea, S., Wildman, D. E., & Uddin, M. (2018). FKBP5 DNA methylation does not mediate the association between childhood maltreatment and depression symptom severity in the Detroit Neighborhood Health Study. Journal of Psychiatric Research, 96, 39-48. DOI: 10.1016/j.jpsychires.2017.09.016

Cianzio, S. R., Arelli, P. R., Swaminathan, S., Lundeen, P., Gebhart, G., Rivera-Velez, N., ... Hudson, M. E. (2018). Genetically diverse soybean cyst nematode-resistant full-sib soybean germplasm lines AR4SCN, AR5SCN, AR6SCN, AR7SCN, and AR8SCN. Journal of Plant Registrations, 12(1), 124-131. DOI: 10.3198/jpr2017.03.0015crg

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]. DOI: 10.1371/journal.pone.0192165

Vlčková, K., Shutt-Phillip, K., Heisterman, M., Pafčo, B., Petrželkov, K. J., Todd, A., ... Gomez, A. (2018). Impact of stress on the gut microbiome of free-ranging western lowland gorillas. Microbiology (United Kingdom), 164(1), 40-44. [000587]. DOI: 10.1099/mic.0.000587

Hylemon, P. B., Harris, S. C., & Ridlon, J. M. (Accepted/In press). Metabolism of hydrogen gases and bile acids in the gut microbiome. FEBS Letters. DOI: 10.1002/1873-3468.13064

Hassan, U., Zhu, R., & Bashir, R. (2018). Multivariate computational analysis of biosensor's data for improved CD64 quantification for sepsis diagnosis. Lab on a Chip, 18(8), 1231-1240. DOI: 10.1039/c8lc00108a

Kim, G. S., Smith, A. K., Nievergelt, C. M., & Uddin, M. (Accepted/In press). Neuroepigenetics of Post-Traumatic Stress Disorder. Progress in Molecular Biology and Translational Science. DOI: 10.1016/bs.pmbts.2018.04.001

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P. J., ... Shapiro, D. J. (2018). Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response. Oncotarget, 9(19), 14741-14753. DOI: 10.18632/oncotarget.10819

Halsey, S. J., Allan, B. F., & Miller, J. R. (Accepted/In press). The role of Ixodes scapularis, Borrelia burgdorferi and wildlife hosts in Lyme disease prevalence: A quantitative review. Ticks and Tick-borne Diseases. DOI: 10.1016/j.ttbdis.2018.04.006  

Wickland, D. P., Battu, G., Hudson, K. A., Diers, B. W., & Hudson, M. E. (2017). A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy. BMC Bioinformatics, 18(1), [586]. DOI: 10.1186/s12859-017-2000-6

Xue, C., & Goldenfeld, N. (2017). Coevolution Maintains Diversity in the Stochastic "kill the Winner" Model. Physical Review Letters, 119(26), [268101]. DOI: 10.1103/PhysRevLett.119.268101

Goldenfeld, N., Biancalani, T., & Jafarpour, F. (2017). Universal biology and the statistical mechanics of early life. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 375(2109), [20160341]. DOI: 10.1098/rsta.2016.0341

Nowak, R. A., Bi, J. J., Koohestani, F., Mesquita, F. S., & Erbach, G. T. (2017). Female Reproductive C: Uterine Tumors and the Environment. In Reproductive and Endocrine Toxicology (Vol. 4-15, pp. 438-469). Elsevier Inc.. DOI: 10.1016/B978-0-12-801238-3.95678-2

Dávila, J., Li, Q., & Bagchi, I. C. (2017). Genetic Mouse Models for Female Reproductive Toxicology Studies. In Reproductive and Endocrine Toxicology (Vol. 4-15, pp. 470-494). Elsevier Inc.. DOI: 10.1016/B978-0-12-801238-3.95679-4

Uprety, S., Hong, P. Y., Sadik, N., Dangol, B., Adhikari, R., Jutla, A., ... Nguyen, T. H. (2017). The effect of the 2015 earthquake on the bacterial community compositions in water in Nepal. Frontiers in Microbiology, 8(DEC), [2380]. DOI: 10.3389/fmicb.2017.02380

Weckle, A., McGowen, M. R., Xing, J., Chen, C., Sterner, K. N., Hou, Z. C., ... Wildman, D. E. (2017). Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection. Molecular Phylogenetics and Evolution, 117, 2-9. DOI: 10.1016/j.ympev.2017.09.007

Avalos, A., Pan, H., Li, C., Acevedo-Gonzalez, J. P., Rendon, G., Fields, C. J., ... Zhang, G. (2017). A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nature Communications, 8(1), [1550]. DOI: 10.1038/s41467-017-01800-0

Kim, M. J., Oh, H. J., Kim, G. A., Setyawan, E. M. N., Choi, Y. B., Lee, S. H., ... Lee, B. C. (2017). Birth of clones of the world's first cloned dog. Scientific Reports, 7(1), [15235]. DOI: 10.1038/s41598-017-15328-2

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

Rochette, N. C., & Catchen, J. M. (2017). Deriving genotypes from RAD-seq short-read data using Stacks. Nature Protocols, 12(12), 2640-2659. DOI: 10.1038/nprot.2017.123

Mudd, A. T., Fleming, S. A., Labhart, B., Chichlowski, M., Berg, B. M., Donovan, S. M., & Dilger, R. N. (2017). Dietary sialyllactose influences sialic acid concentrations in the prefrontal cortex and magnetic resonance imaging measures in corpus callosum of young pigs. Nutrients, 9(12), [1297]. DOI: 10.3390/nu9121297

Zimmer, E., & Wildman, D. (2017). Editorial for 25th Anniversary Issue of Molecular Phylogenetics and Evolution. Molecular Phylogenetics and Evolution, 117. DOI: 10.1016/j.ympev.2017.10.024

Andrade, F. C. D., Kramer, K. Z., Monk, J. K., Greenlee, A. J., & Mendenhall, R. (2017). Financial stress and depressive symptoms: the impact of an intervention of the Chicago Earned Income Tax Periodic Payment. Public Health, 153, 99-102. DOI: 10.1016/j.puhe.2017.08.017

Park, C. J., Chen, G., Koo, Y., Lin, P. C. P., Cacioppo, J. A., Prohaska, H., & Ko, C. M. J. (2017). Generation and characterization of an estrogen receptor alpha-iCre knock-in mouse. Genesis, 55(12), [e23084]. DOI: 10.1002/dvg.23084

Cacioppo, J. A., Lin, P. C. P., Hannon, P. R., McDougle, D. R., Gal, A., & Ko, C. (2017). Granulosa cell endothelin-2 expression is fundamental for ovulatory follicle rupture. Scientific Reports, 7(1), [817]. DOI: 10.1038/s41598-017-00943-w

Yu, J., Berga, S. L., Zou, W., Yook, D. G., Pan, J. C., Andrade, A. A., ... Taylor, R. N. (2017). IL-1β Inhibits Connexin 43 and Disrupts Decidualization of Human Endometrial Stromal Cells Through ERK1/2 and p38 MAP Kinase. Endocrinology, 158(12), 4270-4285. DOI: 10.1210/en.2017-00495

Brinkworth, J. F. (2017). Infectious disease and the diversification of the human genome. Human Biology, 89(1), 47-65. DOI: 10.13110/humanbiology.89.1.03

Sánchez-Tapia, M., Aguilar-López, M., Pérez-Cruz, C., Pichardo-Ontiveros, E., Wang, M., Donovan, S. M., ... Torres, N. (2017). Nopal (Opuntia ficus indica) protects from metabolic endotoxemia by modifying gut microbiota in obese rats fed high fat/sucrose diet. Scientific Reports, 7(1), [4716]. DOI: 10.1038/s41598-017-05096-4

Keck, A. S., Sloane, S., Liechty, J. M., Fiese, B. H., & Donovan, S. M. (2017). Productivity, impact, and collaboration differences between transdisciplinary and traditionally trained doctoral students: A comparison of publication patterns. PLoS ONE, 12(12), [e0189391]. DOI: 10.1371/journal.pone.0189391

VanderWaal, K., Gilbertson, M., Okanga, S., Allan, B. F., & Craft, M. E. (2017). Seasonality and pathogen transmission in pastoral cattle contact networks. Royal Society Open Science, 4(12), [170808]. DOI: 10.1098/rsos.170808

Baek, A. E., Yu, Y. R. A., He, S., Wardell, S. E., Chang, C. Y., Kwon, S., ... Nelson, E. R. (2017). The cholesterol metabolite 27 hydroxycholesterol facilitates breast cancer metastasis through its actions on immune cells. Nature Communications, 8(1), [864]. DOI: 10.1038/s41467-017-00910-z

Warren, W. C., Kuderna, L., Alexander, A., Catchen, J., Pérez-Silva, J. G., López-Otín, C., ... Waterhouse, R. M. (2017). The Novel Evolution of the Sperm Whale Genome. Genome biology and evolution, 9(12), 3260-3264. DOI: 10.1093/gbe/evx187

Ryerson, M. R., Richards, M. M., Kvansakul, M., Hawkins, C. J., & Shisler, J. L. (2017). Vaccinia virus encodes a novel inhibitor of apoptosis that associates with the apoptosome. Journal of Virology, 91(23), [e01385-17]. DOI: 10.1128/JVI.01385-17

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Rustom, L. E., Boudou, T., Nemke, B. W., Lu, Y., Hoelzle, D. J., Markel, M. D., ... Wagoner Johnson, A. J. (2017). Multiscale Porosity Directs Bone Regeneration in Biphasic Calcium Phosphate Scaffolds. ACS Biomaterials Science and Engineering, 3(11), 2768-2778. DOI: 10.1021/acsbiomaterials.6b00632

Goldenfeld, N. (2017). A statistical mechanical phase transition to turbulence in a model shear flow. Journal of Fluid Mechanics, 830, 1-4. DOI: 10.1017/jfm.2017.597

KEESING, F. E. L. I. C. I. A., OSTFELD, R. I. C. H. A. R. D. S., YOUNG, T. R. U. M. A. N. P., & ALLAN, B. R. I. A. N. F. (2017). Cattle and rainfall affect tick abundance in central Kenya. Parasitology, 1-10. DOI: 10.1017/S003118201700155X

Wei, W., Mesquita, A. C. O., Figueiró, A. D. A., Wu, X., Manjunatha, S., Wickland, D. P., ... Clough, S. J. (2017). Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil. BMC Genomics, 18(1), [849]. DOI: 10.1186/s12864-017-4160-1

Mudd, A. T., Berding, K., Wang, M., Donovan, S. M., & Dilger, R. N. (2017). Serum cortisol mediates the relationship between fecal Ruminococcus and brain N-acetylaspartate in the young pig. Gut Microbes, 8(6), 589-600. DOI: 10.1080/19490976.2017.1353849

Lescak, E. A., Wund, M. A., Bassham, S., Catchen, J., Prince, D. J., Lucas, R., ... Cresko, W. A. (2017). Ancient three-spined stickleback (Gasterosteus aculeatus) mtDNA lineages are not associated with phenotypic or nuclear genetic variation. Biological Journal of the Linnean Society, 122(3), 579-588. DOI: 10.1093/biolinnean/blx080

Boyd, B. M., Allen, J. M., Nguyen, N. P., Sweet, A. D., Warnow, T., Shapiro, M. D., ... Johnson, K. P. (2017). Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola). Systematic Biology, 66(6), 896-911. DOI: 10.1093/sysbio/syx027

Cheng, Q., Juen, J., Bellam, S., Fulara, N., Close, D., Silverstein, J. C., & Schatz, B. (2017). Predicting Pulmonary Function from Phone Sensors. Telemedicine and e-Health, 23(11), 913-919. DOI: 10.1089/tmj.2017.0008

Rahman, H., Currier, E., Johnson, M., Goding, R., Johnson, A. W., & Kersh, M. E. (2017). Primary and Secondary Consequences of Rotator Cuff Injury on Joint Stabilizing Tissues in the Shoulder. Journal of Biomechanical Engineering, 139(11), [110801]. DOI: 10.1115/1.4037917

Matthew, L. E., Piedra, L. M., Wu, C. F., Kramer Diaz, A., Wang, H., Straub, A. P., & Nguyen, T. H. (2017). Social work and engineering: Lessons from a water filtration project in Guatemala. International Social Work, 60(6), 1578-1590. DOI: 10.1177/0020872816655869

Yao, L., Li, H., Martin, R. D., Moreau, C. S., & Malhi, R. S. (2017). Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Molecular Phylogenetics and Evolution, 116, 227-238. DOI: 10.1016/j.ympev.2017.08.006

Cole, N. C., Wang, A. A., Donovan, S. M., Lee, S. Y., & Teran-Garcia, M. (2017). Variants in Chemosensory Genes Are Associated with Picky Eating Behavior in Preschool-Age Children. Journal of Nutrigenetics and Nutrigenomics, 10(3-4), 84-92. DOI: 10.1159/000478857

Miller, R. J., Han, A., Gates-Tanzer, L. T., Erdman, J. W., Shisler, J. L., Wallig, M. A., & O'Brien, W. D. (2017). Quantitative ultrasound and the pancreas: Demonstration of early detection capability. In 2017 IEEE International Ultrasonics Symposium, IUS 2017 [8091743] IEEE Computer Society. DOI: 10.1109/ULTSYM.2017.8091743

Martínez, O., Bravo Cruz, A., Santos, S., Ramírez, M., Miranda, E., Shisler, J., & Otero, M. (2017). Vaccination with a codon-optimized A27L-containing plasmid decreases virus replication and dissemination after vaccinia virus challenge. Vaccine, 35(44), 6007-6014. DOI: 10.1016/j.vaccine.2017.05.091

Molto, J. E., Loreille, O., Mallott, E. K., Malhi, R. S., Fast, S., Daniels-Higginbotham, J., ... Parr, R. (2017). Complete mitochondrial genome sequencing of a burial from a Romano-Christian cemetery in the Dakhleh Oasis, Egypt: Preliminary indications. Genes, 8(10), [262]. DOI: 10.3390/genes8100262

Athreya, A. P., Banerjee, S. S., Neavin, D., Kaddurah-Daouk, R., Rush, A. J., Frye, M. A., ... Iyer, R. K. (2017). Data-driven longitudinal modeling and prediction of symptom dynamics in major depressive disorder: Integrating factor graphs and learning methods. In 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2017 [8058559] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/CIBCB.2017.8058559

Banerjee, S. S., El-Hadedy, M., Tan, C. Y., Kalbarczyk, Z. T., Lumetta, S., & Iyer, R. K. (2017). On accelerating pair-HMM computations in programmable hardware. In 2017 27th International Conference on Field Programmable Logic and Applications, FPL 2017 [8056837] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.23919/FPL.2017.8056837

He, S., & Nelson, E. R. (2017). 27-Hydroxycholesterol, an endogenous selective estrogen receptor modulator. Maturitas, 104, 29-35. DOI: 10.1016/j.maturitas.2017.07.014

Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in parameter space: a road map for stacks. Methods in Ecology and Evolution, 8(10), 1360-1373. DOI: 10.1111/2041-210X.12775

Moran, R. L., Zhou, M., Catchen, J. M., & Fuller, R. C. (2017). Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance. Evolution, 71(10), 2428-2444. DOI: 10.1111/evo.13321

Lowe, S. R., Joshi, S., Galea, S., Aiello, A. E., Uddin, M., Koenen, K. C., & Cerdá, M. (2017). Pathways from assaultive violence to post-traumatic stress, depression, and generalized anxiety symptoms through stressful life events: Longitudinal mediation models. Psychological Medicine, 47(14), 2556-2566. DOI: 10.1017/S0033291717001143

Nowak, R. A. (2017). Regression of the male reproductive tract in the female embryo is regulated by the orphan nuclear receptor COUP-TFII. Biology of Reproduction, 97(4), 517-518. DOI: 10.1093/biolre/iox109

Jha, S., Brandt, J., Gentile, A., Kalbarczyk, Z., Bauer, G., Enos, J., ... Kramer, W. (2017). Holistic measurement-driven system assessment. In Proceedings - 2017 IEEE International Conference on Cluster Computing, CLUSTER 2017 (Vol. 2017-September, pp. 797-800). [8049019] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/CLUSTER.2017.124

Titcomb, G., Allan, B. F., Ainsworth, T., Henson, L., Hedlund, T., Pringle, R. M., ... Young, H. S. (2017). Interacting effects of wildlife loss and climate on ticks and tick-borne disease. Proceedings of the Royal Society B: Biological Sciences, 284(1862), [20170475]. DOI: 10.1098/rspb.2017.0475

Athreya, A. P., Armstrong, D., Gundling, W., Wildman, D., Kalbarczyk, Z. T., & Iyer, R. K. (2017). Prediction of adenocarcinoma development using game theory. In 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings (pp. 1668-1671). [8037161] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/EMBC.2017.8037161

Shpigler, H. Y., Saul, M. C., Corona, F., Block, L., Cash Ahmed, A., Zhao, S. D., & Robinson, G. E. (2017). Deep evolutionary conservation of autism-related genes. Proceedings of the National Academy of Sciences of the United States of America, 114(36), 9653-9658. DOI: 10.1073/pnas.1708127114

Brandt, A. L., Grigorev, K., Afanador-Hernández, Y. M., Paulino, L. A., Murphy, W. J., Núñez, A., ... Roca, A. L. (2017). Mitogenomic sequences support a north–south subspecies subdivision within Solenodon paradoxus. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 28(5), 662-670. DOI: 10.3109/24701394.2016.1167891

VA Mid-Atlantic MIRECC Workgroup, & PGC PTSD Epigenetics Workgroup (2017). Epigenome-wide association of PTSD from heterogeneous cohorts with a common multi-site analysis pipeline. American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics, 174(6), 619-630. DOI: 10.1002/ajmg.b.32568

Donovan, S. M. (2017). Human milk oligosaccharides: Potent weapons in the battle against rotavirus infection. Journal of Nutrition, 147(9), 1605-1606. DOI: 10.3945/jn.117.255836

Stanton, S. C. E., Zilioli, S., Briskin, J. L., Imami, L., Tobin, E. T., Wildman, D. E., ... Slatcher, R. B. (2017). Mothers’ Attachment is Linked to Their Children’s Anti-Inflammatory Gene Expression via Maternal Warmth. Social Psychological and Personality Science, 8(7), 796-805. DOI: 10.1177/1948550616687125

Luchini, V., Musaad, S., Lee, S. Y., & Donovan, S. M. (2017). Observed differences in child picky eating behavior between home and childcare locations. Appetite, 116, 123-131. DOI: 10.1016/j.appet.2017.04.021

Allen, J. M., Boyd, B., Nguyen, N. P., Vachaspati, P., Warnow, T., Huang, D. I., ... Johnson, K. P. (2017). Phylogenomics from whole genome sequences using aTRAM. Systematic Biology, 66(5), 786-798. DOI: 10.1093/sysbio/syw105

Armstrong, D. L., McGowen, M. R., Weckle, A., Pantham, P., Caravas, J., Agnew, D., ... Wildman, D. E. (2017). The core transcriptome of mammalian placentas and the divergence of expression with placental shape. Placenta, 57, 71-78. DOI: 10.1016/j.placenta.2017.04.015

Dong, S., Masalha, N., Plewa, M. J., & Nguyen, T. H. (2017). Toxicity of Wastewater with Elevated Bromide and Iodide after Chlorination, Chloramination, or Ozonation Disinfection. Environmental Science and Technology, 51(16), 9297-9304. DOI: 10.1021/acs.est.7b02345

Varatharajah, Y., Berry, B. M., Kalbarczyk, Z. T., Brinkmann, B. H., Worrell, G. A., & Iyer, R. K. (2017). Inter-ictal Seizure Onset Zone localization using unsupervised clustering and Bayesian Filtering. In 8th International IEEE EMBS Conference on Neural Engineering, NER 2017 (pp. 533-539). [8008407] IEEE Computer Society. DOI: 10.1109/NER.2017.8008407

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Campbell-Staton, S. C., Cheviron, Z. A., Rochette, N., Catchen, J., Losos, J. B., & Edwards, S. V. (2017). Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard. Science, 357(6350), 495-498. DOI: 10.1126/science.aam5512

Allan, B. F., Tallis, H., Chaplin-Kramer, R., Huckett, S., Kowal, V. A., Musengezi, J., ... Keesing, F. (2017). Can integrating wildlife and livestock enhance ecosystem services in central Kenya? Frontiers in Ecology and the Environment, 15(6), 328-335. DOI: 10.1002/fee.1501

Dong, S., Nguyen, T. H., & Plewa, M. J. (2017). Comparative mammalian cell cytotoxicity of wastewater with elevated bromide and iodide after chlorination, chloramination, or ozonation. Journal of Environmental Sciences, 58, 296-301. DOI: 10.1016/j.jes.2017.03.030

Sicherer, S. H., Allen, K., Lack, G., Taylor, S. L., Donovan, S. M., & Oria, M. (2017). Critical issues in food allergy: A national academies consensus report. Pediatrics, 140(2), [e20170194]. DOI: 10.1542/peds.2017-0194

Bravo Cruz, A. G., Han, A., Roy, E. J., Guzmán, A. B., Miller, R. J., Driskell, E. A., ... Shisler, J. L. (2017). Deletion of the K1L gene results in a vaccinia virus that is less pathogenic due to muted innate immune responses, yet still elicits protective immunity. Journal of Virology, 91(15), [e00542-17]. DOI: 10.1128/JVI.00542-17

Bayzid, M. S., & Warnow, T. (2017). Gene tree parsimony for incomplete gene trees. In 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 (Vol. 88). [2] Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. DOI: 10.4230/LIPIcs.WABI.2017.2

Biswas, S., & Shisler, J. L. (2017). Molluscum contagiosum virus MC159 abrogates cIAP1- NEMO interactions and inhibits NEMO polyubiquitination. Journal of Virology, 91(15), [e00276-17]. DOI: 10.1128/JVI.00276-17

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2017). Optimal completion of incomplete gene trees in polynomial time using OCTAL. In 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 (Vol. 88). [27] Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. DOI: 10.4230/LIPIcs.WABI.2017.27

Zhao, S. D., Cai, T. T., & Li, H. (2017). Optimal detection of weak positive latent dependence between two sequences of multiple tests. Journal of Multivariate Analysis, 160, 169-184. DOI: 10.1016/j.jmva.2017.06.009

Gaither, K., Gomez, R., Akli, L., Mendenhall, R., Bland, M., Fratkin, S., ... DeStefano, L. (2017). Advanced computing for social change - Educating and engaging our students to compete in a changing workforce∗. In PEARC 2017 - Practice and Experience in Advanced Research Computing 2017: Sustainability, Success and Impact (Vol. Part F128771). [a50] Association for Computing Machinery. DOI: 10.1145/3093338.3093391

Schieltz, J. M., Okanga, S., Allan, B. F., & Rubenstein, D. I. (2017). GPS tracking cattle as a monitoring tool for conservation and management. African Journal of Range and Forage Science, 34(3), 173-177. DOI: 10.2989/10220119.2017.1387175

Zhao, S. D., Cai, T. T., Cappola, T. P., Margulies, K. B., & Li, H. (2017). Sparse Simultaneous Signal Detection for Identifying Genetically Controlled Disease Genes. Journal of the American Statistical Association, 112(519), 1032-1046. DOI: 10.1080/01621459.2016.1270825

Kim, J. H., Fiese, B. H., & Donovan, S. M. (2017). Breastfeeding is Natural but Not the Cultural Norm: A Mixed-Methods Study of First-Time Breastfeeding, African American Mothers Participating in WIC. Journal of Nutrition Education and Behavior, 49(7), S151-S161.e1. DOI: 10.1016/j.jneb.2017.04.003

Duka, T., Collins, Z., Anderson, S. M., Raghanti, M. A., Ely, J. J., Hof, P. R., ... Sherwood, C. C. (2017). Divergent lactate dehydrogenase isoenzyme profile in cellular compartments of primate forebrain structures. Molecular and Cellular Neuroscience, 82, 137-142. DOI: 10.1016/j.mcn.2017.04.007

Newell-Fugate, A. E., Lenz, K., Skenandore, C., Nowak, R. A., White, B. A., & Braundmeier-Fleming, A. (2017). Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs. PLoS ONE, 12(7), [e0179542]. DOI: 10.1371/journal.pone.0179542

West, C. E., Kvistgaard, A. S., Peerson, J. M., Donovan, S. M., Peng, Y. M., & Lönnerdal, B. (2017). Effects of osteopontin-enriched formula on lymphocyte subsets in the first 6 months of life: A randomized controlled trial. Pediatric Research, 82(1), 63-71. DOI: 10.1038/pr.2017.77

Dean, C., Fogleman, A. J., Zahnd, W. E., Lipka, A. E., Malhi, R. S., Delfino, K. R., & Jenkins, W. D. (2017). Engaging rural communities in genetic research: challenges and opportunities. Journal of Community Genetics, 8(3), 209-219. DOI: 10.1007/s12687-017-0304-x

Cooke, P. S., Nanjappa, M. K., Ko, C., Prins, G. S., & Hess, R. A. (2017). Estrogens in male physiology. Physiological Reviews, 97(3), 995-1043. DOI: 10.1152/physrev.00018.2016

Baumgarten, S. C., Armouti, M., Ko, C., & Stocco, C. (2017). IGF1R expression in ovarian granulosa cells is essential for steroidogenesis, follicle survival, and fertility in female mice. Endocrinology, 158(7), 2309-2318. DOI: 10.1210/en.2017-00146

Donovan, S. M., & Salas-Salvadó, J. (2017). Introduction to the fourth global summit on the health effects of yogurt. Journal of Nutrition, 147(7), 1449S-1451S. DOI: 10.3945/jn.116.240994

Tan, R., Nguyen, H. H., Foo, E. Y. S., Yau, D. K. Y., Kalbarczyk, Z., Iyer, R. K., & Gooi, H. B. (2017). Modeling and Mitigating Impact of False Data Injection Attacks on Automatic Generation Control. IEEE Transactions on Information Forensics and Security, 12(7), 1609-1624. [7867825]. DOI: 10.1109/TIFS.2017.2676721

Amato, K. R., Van Belle, S., Di Fiore, A., Estrada, A., Stumpf, R., White, B., ... Leigh, S. R. (2017). Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. Microbial Ecology, 74(1), 250-258. DOI: 10.1007/s00248-017-0938-6

Boyd, B. M., Allen, J. M., Nguyen, N. P., Vachaspati, P., Quicksall, Z. S., Warnow, T., ... Reed, D. L. (2017). Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Molecular biology and evolution, 34(7), 1743-1757. DOI: 10.1093/molbev/msx117

Cross, K. J., Clancy, K. B. H., Mendenhall, R., Imoukhuede, P., & Amos, J. R. (2017). The double bind of race and gender: A look into the experiences of women of color in engineering. ASEE Annual Conference and Exposition, Conference Proceedings, 2017-June.

Mendenhall, R., Brown, N. M., & Black, M. L. (2017). The potential of big data in rescuing and recovering black women’s contributions to the Du Bois-Atlanta School and to American sociology. Ethnic and Racial Studies, 40(8), 1231-1233. DOI: 10.1080/01419870.2017.1285421

Meyer, M., Palkopoulou, E., Baleka, S., Stiller, M., Penkman, K. E. H., Alt, K. W., ... Hofreiter, M. (2017). Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. eLife, 6, [e25413]. DOI: 10.7554/eLife.25413

Comstock, S. S., Li, M., Wang, M., Monaco, M. H., Kuhlenschmidt, T. B., Kuhlenschmidt, M. S., & Donovan, S. M. (2017). Dietary human milk oligosaccharides but not prebiotic oligosaccharides increase circulating natural killer cell and mesenteric lymph node memory T cell populations in noninfected and rotavirus-infected neonatal piglets. Journal of Nutrition, 147(6), 1041-1047. DOI: 10.3945/jn.116.243774

Zhu, R., Zhao, Y. Q., Chen, G., Ma, S., & Zhao, H. (2017). Greedy outcome weighted tree learning of optimal personalized treatment rules. Biometrics, 73(2), 391-400. DOI: 10.1111/biom.12593

Zhao, S. D. (2017). Integrative genetic risk prediction using non-parametric empirical Bayes classification. Biometrics, 73(2), 582-592. DOI: 10.1111/biom.12619

Tuppurainen, E. S. M., Venter, E. H., Shisler, J. L., Gari, G., Mekonnen, G. A., Juleff, N., ... Babiuk, L. A. (2017). Review: Capripoxvirus Diseases: Current Status and Opportunities for Control. Transboundary and Emerging Diseases, 64(3), 729-745. DOI: 10.1111/tbed.12444

Saul, M. C., Seward, C. H., Troy, J. M., Zhang, H., Sloofman, L. G., Lu, X., ... Stubbs, L. (2017). Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice. Genome Research, 27(6), 959-972. DOI: 10.1101/gr.214221.116

Sprabery, R., Estrada, Z. J., Kalbarczyk, Z., Iyer, R., Bobba, R. B., & Campbell, R. (2017). Trustworthy services built on event-based probing for layered defense. In Proceedings - 2017 IEEE International Conference on Cloud Engineering, IC2E 2017 (pp. 215-225). [7923805] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/IC2E.2017.36

Lim, B., Chen, D., An, Y., Kalbarczyk, Z., & Iyer, R. (2017). Attack induced common-mode failures on PLC-based safety system in a nuclear power plant: Practical experience report. In Proceedings - 2017 IEEE 22nd Pacific Rim International Symposium on Dependable Computing, PRDC 2017 (pp. 205-210). [7920614] IEEE Computer Society. DOI: 10.1109/PRDC.2017.34

Parker, C. M., Miller, J. R., Allan, B. F., & Ginsberg, H. (2017). Avian and habitat characteristics influence tick infestation among birds in Illinois. Journal of Medical Entomology, 54(3), 550-558. DOI: 10.1093/jme/tjw235

Goldenfeld, N., & Shih, H. Y. (2017). Erratum to: Turbulence as a Problem in Non-equilibrium Statistical Mechanics (Journal of Statistical Physics, (2017), 167, 3-4, (575-594), 10.1007/s10955-016-1682-x). Journal of Statistical Physics, 167(3-4). DOI: 10.1007/s10955-016-1713-7

Devendran, S., Méndez-García, C., & Ridlon, J. M. (2017). Identification and characterization of a 20β-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058. Journal of Lipid Research, 58(5), 916-925. DOI: 10.1194/jlr.M074914

Silva, E., Frost, D., Li, L., Bovin, N., & Miller, D. J. (2017). Lactadherin is a candidate oviduct Lewis X trisaccharide receptor on porcine spermatozoa. Andrology, 5(3), 589-597. DOI: 10.1111/andr.12340

Wright, D. B., Laurent, H. K., & Ablow, J. C. (2017). Mothers Who Were Neglected in Childhood Show Differences in Neural Response to Their Infant’s Cry. Child Maltreatment, 22(2), 158-166. DOI: 10.1177/1077559516683503

Goldenfeld, N., & Shih, H. Y. (2017). Turbulence as a Problem in Non-equilibrium Statistical Mechanics. Journal of Statistical Physics, 167(3-4), 575-594. DOI: 10.1007/s10955-016-1682-x

Catchen, J. M., Hohenlohe, P. A., Bernatchez, L., Funk, W. C., Andrews, K. R., & Allendorf, F. W. (2017). Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Molecular ecology resources, 17(3), 362-365. DOI: 10.1111/1755-0998.12669

Lindo, J., Achilli, A., Perego, U. A., Archer, D., Valdiosera, C., Petzelt, B., ... Malhi, R. S. (2017). Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity. Proceedings of the National Academy of Sciences of the United States of America, 114(16), 4093-4098. DOI: 10.1073/pnas.1620410114

Estrada, Z. J., Sprabery, R., Yan, L., Yu, Z., Campbell, R., Kalbarczyk, Z., & Iyer, R. K. (2017). Using OS design patterns to provide reliability and security as-a-service for VM-based clouds. In VEE 2017 - Proceedings of the 2017 ACM SIGPLAN/SIGOPS International Conference on Virtual Execution Environments (pp. 157-170). Association for Computing Machinery, Inc. DOI: 10.1145/3050748.3050759

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Bulgari, O., Dong, X., Roca, A. L., Caroli, A. M., & Loor, J. J. (2017). Innate immune responses induced by lipopolysaccharide and lipoteichoic acid in primary goat mammary epithelial cells. Journal of Animal Science and Biotechnology, 8(1), [29]. DOI: 10.1186/s40104-017-0162-8

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Branscomb, E., Biancalani, T., Goldenfeld, N., & Russell, M. (2017). Escapement mechanisms and the conversion of disequilibria; the engines of creation. Physics Reports, 677, 1-60. DOI: 10.1016/j.physrep.2017.02.001

Lan, Z. J., Krause, M. S., Redding, S. D., Li, X., Wu, G. Z., Zhou, H. X., ... Lei, Z. M. (2017). Selective deletion of Pten in theca-interstitial cells leads to androgen excess and ovarian dysfunction in mice. Molecular and Cellular Endocrinology, 444, 26-37. DOI: 10.1016/j.mce.2017.01.043

Jafarpour, F., Biancalani, T., & Goldenfeld, N. (2017). Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality. Physical Review E, 95(3), [032407]. DOI: 10.1103/PhysRevE.95.032407

Donovan, S. M. (2017). Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health. Gut Microbes, 8(2), 75-81. DOI: 10.1080/19490976.2017.1299309

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Uddin, M., Jansen, S., & Telzer, E. H. (2017). Adolescent depression linked to socioeconomic status? Molecular approaches for revealing premorbid risk factors. BioEssays, 39(3), [1600194]. DOI: 10.1002/bies.201600194

Di Martino, C., Sarkar, S., Ganesan, R., Kalbarczyk, Z. T., & Iyer, R. K. (2017). Analysis and diagnosis of SLA violations in a production SaaS cloud. IEEE Transactions on Reliability, 66(1), 54-75. [7835304]. DOI: 10.1109/TR.2016.2635033

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Laurent, H. K., Duncan, L. G., Lightcap, A., & Khan, F. (2017). Mindful parenting predicts mothers' and infants' hypothalamic-pituitary-adrenal activity during a dyadic stressor. Developmental Psychology, 53(3), 417-424. DOI: 10.1037/dev0000258

Barakat, R., Lin, P. C. P., Rattan, S., Brehm, E., Canisso, I. F., Abosalum, M. E., ... Ko, C. M. (2017). Prenatal exposure to DEHP induces premature reproductive senescence in male mice. Toxicological Sciences, 156(1), 96-108. DOI: 10.1093/toxsci/kfw248

Chung, K., Formicola, V., Kalbarczyk, Z. T., Iyer, R. K., Withers, A., & Slagell, A. J. (2017). Attacking supercomputers through targeted alteration of environmental control: A data driven case study. In 2016 IEEE Conference on Communications and Network Security, CNS 2016 (pp. 406-410). [7860528] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/CNS.2016.7860528

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Pham, C., Wang, L., Tak, B. C., Baset, S., Tang, C., Kalbarczyk, Z., & Iyer, R. K. (2017). Failure Diagnosis for Distributed Systems Using Targeted Fault Injection. IEEE Transactions on Parallel and Distributed Systems, 28(2), 503-516. [7484300]. DOI: 10.1109/TPDS.2016.2575829

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Polk, J. D., Stumpf, R. M., & Rosengren, K. S. (2017). Limb dominance, foot orientation and functional asymmetry during walking gait. Gait and Posture, 52, 140-146. DOI: 10.1016/j.gaitpost.2016.11.028

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Mendenhall, R., Linear, T. I. A., McKee, M. W., Lamers, N. A., & Mouawad, M. B. (2017). Chicago African American mothers' power of resistance: Designing Spaces of Hope in global contexts. Advances in Education in Diverse Communities: Research, Policy and Praxis, 12, 409-428. DOI: 10.1108/S1479-358X20140000012019

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Korczak, R., Kamil, A., Fleige, L., Donovan, S. M., & Slavin, J. L. (2017). Dietary fiber and digestive health in children. Nutrition Reviews, 75(4), 241-259. DOI: 10.1093/nutrit/nuw068

Armstrong, A., Alleyne, A., & Johnson, A. W. (2017). Easy-to-use 3D printer for fabrication of biological scaffolds. In Mechatronics; Estimation and Identification; Uncertain Systems and Robustness; Path Planning and Motion Control; Tracking Control Systems; Multi-Agent and Networked Systems; Manufacturing; Intelligent Transportation and Vehicles; Sensors and Actuators; Diagnostics and Detection; Unmanned, Ground and Surface Robotics; Motion and Vibration Control Applications (Vol. 2). American Society of Mechanical Engineers. DOI: 10.1115/DSCC2017-5147

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Dong, S., Li, J., Kim, M. H., Park, S. J., Eden, J. G., Guest, J. S., & Nguyen, T. H. (2017). Human health trade-offs in the disinfection of wastewater for landscape irrigation: Microplasma ozonation: Vs. chlorination. Environmental Science: Water Research and Technology, 3(1), 106-118. DOI: 10.1039/c6ew00235h

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Han, K. A., Shin, W. H., Jung, S., Seol, W., Seo, H., Ko, C. M., & Chung, K. C. (2017). Leucine-rich repeat kinase 2 exacerbates neuronal cytotoxicity through phosphorylation of histone deacetylase 3 and histone deacetylation. Human molecular genetics, 26(1), 1-18. DOI: 10.1093/hmg/ddw363

Randrianandrasana, M., Wu, W. Y., Carney, D. A., Johnson, A. J. W., & Berenbaum, M. R. (2017). Structural and mechanical properties of cocoons of Antherina suraka (Saturniidae, Lepidoptera), an endemic species used for silk production in Madagascar. Journal of Insect Science, 17(1). DOI: 10.1093/jisesa/iew112

Li, X., Alemzadeh, H., Chen, D., Kalbarczyk, Z., Iyer, R. K., & Kesavadas, T. (2017). Surgeon Training in Telerobotic Surgery via a Hardware-in-the-Loop Simulator. Journal of Healthcare Engineering, 2017, [6702919]. DOI: 10.1155/2017/6702919

Chen, S., McCutchen, M., Cao, P., Qadeer, S., & Iyer, R. K. (2017). SVAuth – A single-sign-on integration solution with runtime verification. In Runtime Verification - 17th International Conference, RV 2017, Proceedings (Vol. 10548 LNCS, pp. 349-358). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10548 LNCS). Springer Verlag. DOI: 10.1007/978-3-319-67531-2_21

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Lucas, T., Wegner, R., Pierce, J., Lumley, M. A., Laurent, H. K., & Granger, D. A. (2017). Perceived discrimination, racial identity, and multisystem stress response to social evaluative threat among African American men and women. Psychosomatic Medicine, 79(3), 293-305. DOI: 10.1097/PSY.0000000000000406

Shoaib, T., Carmichael, A., Corman, R. E., Shen, Y., Nguyen, T. H., Ewoldt, R. H., & Espinosa-Marzal, R. M. (2017). Self-adaptive hydrogels to mineralization. Soft Matter, 13(32), 5469-5480. DOI: 10.1039/c7sm01058c

Bauza, V., Ocharo, R. M., Nguyen, T. H., & Guest, J. S. (2017). Soil ingestion is associated with child diarrhea in an urban slum of Nairobi, Kenya. American Journal of Tropical Medicine and Hygiene, 96(3), 569-575. DOI: 10.4269/ajtmh.16-0543

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

Min, E., Kandel, M. E., Ko, C. J., Popescu, G., Jung, W., & Best-Popescu, C. (2016). Label-free, multi-scale imaging of ex-vivo mouse brain using spatial light interference microscopy. Scientific Reports, 6, [39667]. DOI: 10.1038/srep39667

Small, C. M., Bassham, S., Catchen, J., Amores, A., Fuiten, A. M., Brown, R. S., ... Cresko, W. A. (2016). The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biology, 17(1), [258]. DOI: 10.1186/s13059-016-1126-6

Athreya, A. P., Ngiam, K. Y., Luo, Z., Tai, E. S., Kalbarczyk, Z., & Iyer, R. K. (2016). Towards longitudinal analysis of a population's electronic health records using factor graphs. In Proceedings - 3rd IEEE/ACM International Conference on Big Data Computing, Applications and Technologies, BDCAT 2016 (pp. 79-86). Association for Computing Machinery, Inc. DOI: 10.1145/3006299.3006309

Castro, J. J., Gomez, A., White, B. A., Mangian, H. J., Loften, J. R., & Drackley, J. K. (2016). Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 1. Effects of prebiotic supplementation depend on site and age. Journal of Dairy Science, 99(12), 9682-9702. DOI: 10.3168/jds.2016-11006

Castro, J. J., Gomez, A., White, B., Loften, J. R., & Drackley, J. K. (2016). Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age. Journal of Dairy Science, 99(12), 9703-9715. DOI: 10.3168/jds.2016-11007

Oakley, O. R., Kim, K. J., Lin, P. C., Barakat, R., Cacioppo, J. A., Li, Z., ... Ko, C. M. (2016). Estradiol synthesis in gut-associated lymphoid tissue: Leukocyte regulation by a sexually monomorphic system. Endocrinology, 157(12), 4579-4587. DOI: 10.1210/en.2016-1391

Bustamante, A. C., Aiello, A. E., Galea, S., Ratanatharathorn, A., Noronha, C., Wildman, D. E., & Uddin, M. (2016). Glucocorticoid receptor DNA methylation, childhood maltreatment and major depression. Journal of Affective Disorders, 206, 181-188. DOI: 10.1016/j.jad.2016.07.038

Wildman, D. E. (2016). IFPA award in placentology lecture: Phylogenomic origins and evolution of the mammalian placenta. Placenta, 48, S31-S39. DOI: 10.1016/j.placenta.2016.04.004

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Yu, N., Lee, T. G., Rosa, D. P., Hudson, M., & Diers, B. W. (2016). Impact of Rhg1 copy number, type, and interaction with Rhg4 on resistance to Heterodera glycines in soybean. Theoretical and Applied Genetics, 129(12), 2403-2412. DOI: 10.1007/s00122-016-2779-y

Feng, Z., Lu, R., Yuan, B., Zhou, Z., Wu, Q., & Nguyen, T. H. (2016). Influence of solution chemistry on the inactivation of particle-associated viruses by UV irradiation. Colloids and Surfaces B: Biointerfaces, 148, 622-628. DOI: 10.1016/j.colsurfb.2016.09.025

Kruger Ben Shabat, S., Sasson, G., Doron-Faigenboim, A., Durman, T., Yaacoby, S., Berg Miller, M. E., ... Mizrahi, I. (2016). Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME Journal, 10(12), 2958-2972. DOI: 10.1038/ismej.2016.62

Durgam, S. S., Stewart, A. A., Sivaguru, M., Wagoner Johnson, A. J., & Stewart, M. C. (2016). Tendon-derived progenitor cells improve healing of collagenase-induced flexor tendinitis. Journal of Orthopaedic Research, 34(12), 2162-2171. DOI: 10.1002/jor.23251

Li, X., Alemzadeh, H., Chen, D., Kalbarczyk, Z., Iyer, R. K., & Kesavadas, T. (2016). A hardware-in-the-loop simulator for safety training in robotic surgery. In IROS 2016 - 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems (Vol. 2016-November, pp. 5291-5296). [7759778] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/IROS.2016.7759778

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Lindo, J., Huerta-Sánchez, E., Nakagome, S., Rasmussen, M., Petzelt, B., Mitchell, J., ... Malhi, R. S. (2016). A time transect of exomes from a Native American population before and after European contact. Nature Communications, 7, [13175]. DOI: 10.1038/ncomms13175

Nelson, E. R., & Habibi, H. R. (2016). Thyroid hormone regulates vitellogenin by inducing estrogen receptor alpha in the goldfish liver. Molecular and Cellular Endocrinology, 436, 259-267. DOI: 10.1016/j.mce.2016.08.045

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Nguyen, N. P., Nute, M., Mirarab, S., & Warnow, T. (2016). HIPPI: Highly accurate protein family classification with ensembles of HMMs. BMC Genomics, 17, [765]. DOI: 10.1186/s12864-016-3097-0

Nute, M., & Warnow, T. (2016). Scaling statistical multiple sequence alignment to large datasets. BMC Genomics, 17, [764]. DOI: 10.1186/s12864-016-3101-8

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Dong, S., Lu, J., Plewa, M. J., & Nguyen, T. H. (2016). Comparative Mammalian Cell Cytotoxicity of Wastewaters for Agricultural Reuse after Ozonation. Environmental Science and Technology, 50(21), 11752-11759. DOI: 10.1021/acs.est.6b04796

Vlčková, K., Gomez, A., Petrželková, K. J., Whittier, C. A., Todd, A. F., Yeoman, C. J., ... Leigh, S. R. (2016). Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla). Microbial Ecology, 72(4), 943-954. DOI: 10.1007/s00248-016-0745-5

Brannon, P. M., Weaver, C. M., Anderson, C. A. M., Donovan, S. M., Murphy, S. P., & Yaktine, A. L. (2016). Scanning for new evidence to prioritize updates to the Dietary Reference Intakes: Case studies for thiamin and phosphorus1,2. American Journal of Clinical Nutrition, 104(5), 1366-1377. DOI: 10.3945/ajcn.115.128256

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Comstock, S. S., & Donovan, S. M. (2016). Human Milk Oligosaccharides as Modulators of Intestinal and Systemic Immunity. In Prebiotics and Probiotics in Human Milk: Origins and Functions of Milk-Borne Oligosaccharides and Bacteria (pp. 223-248). Elsevier Inc.. DOI: 10.1016/B978-0-12-802725-7.00008-7

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Zhu, R., Zhao, Q., Zhao, H., & Ma, S. (2016). Integrating multidimensional omics data for cancer outcome. Biostatistics, 17(4), 605-618. DOI: 10.1093/biostatistics/kxw010

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Bravo Cruz, A. G., & Shisler, J. L. (2016). Vaccinia virus K1 ankyrin repeat protein inhibits NF-κB activation by preventing RelA acetylation. Journal of General Virology, 97(10), 2691-2702. [000576]. DOI: 10.1099/jgv.0.000576

Krishna, V. B., Lee, K., Weaver, G. A., Iyer, R. K., & Sanders, W. H. (2016). F-DETA: A framework for detecting electricity theft attacks in smart grids. In Proceedings - 46th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2016 (pp. 407-418). [7579759] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/DSN.2016.44

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