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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Mallott, E. K., Garber, P. A., & Malhi, R. S. (2016). Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus). American Journal of Physical Anthropology. DOI: 10.1002/ajpa.23113
 
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
 
Alemzadeh, H., Chen, D., Li, X., Kesavadas, T., Kalbarczyk, Z. T., & Iyer, R. K. (2016). Targeted attacks on teleoperated surgical robots: Dynamic model-based detection and mitigation. In Proceedings - 46th Annual IEEE/IFIP International Conference on Dependable Systems and Networks, DSN 2016. (pp. 395-406). [7579758] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/DSN.2016.43
 
Li, Y., Adur, M. K., Kannan, A., Davila, J., Zhao, Y., Nowak, R. A., ... Li, Q. (2016). Progesterone alleviates Endometriosis via inhibition of uterine cell proliferation, inflammation and angiogenesis in an immunocompetent mouse model. PLoS One, 11(10), [e0165347]. DOI: 10.1371/journal.pone.0165347
 
Ruiz-Rodriguez, C. T., Ishida, Y., Murray, N. D., O'brien, S. J., Graves, J. A. M., Greenwood, A. D., & Roca, A. L. (2016). Koalas (Phascolarctos cinereus) from Queensland are genetically distinct from 2 populations in Victoria. Journal of Heredity, 107(7), 573-580. DOI: 10.1093/jhered/esw049
 
Burnett, L. A., & Nowak, R. A. (2016). Exosomes mediate embryo and maternal interactions at implantation and during pregnancy. Frontiers in Bioscience - Scholar, 8, 79-96.
 
Gugala, N. A., Ishida, Y., Georgiadis, N. J., & Roca, A. L. (2016). Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis). BMC Research Notes, 9(1), [364]. DOI: 10.1186/s13104-016-2167-3
 
Mendenhall, R., Van Moer, M., McKee, M., Brown, N., Lourentzou, I., Zerai, A., ... Flynn, K. (2016). Rescuing lost history: Using big data to recover black women's lived experiences. In Proceedings of XSEDE 2016: Diversity, Big Data, and Science at Scale. (Vol. 17-21-July-2016). [a56] Association for Computing Machinery. DOI: 10.1145/2949550.2949642
 
Hong, Z., Kalbarczyk, Z., & Iyer, R. K. (2016). A Data-Driven Approach to Soil Moisture Collection and Prediction. In 2016 IEEE International Conference on Smart Computing, SMARTCOMP 2016. [7501673] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/SMARTCOMP.2016.7501673
 
Alfano, N., Michaux, J., Morand, S., Aplin, K., Tsangaras, K., Löber, U., ... Greenwood, A. D. (2016). Endogenous gibbon ape leukemia virus identified in a rodent (Melomys burtoni subsp.) from Wallacea (Indonesia). Journal of Virology, 90(18), 8169-8180. DOI: 10.1128/JVI.00723-16
 
Ishida, Y., Van Coeverden de Groot, P. J., Leggett, K. E. A., Putnam, A. S., Fox, V. E., Lai, J., ... Roca, A. L. (2016). Genetic connectivity across marginal habitats: the elephants of the Namib Desert. Ecology and Evolution, 6(17), 6189-6201. DOI: 10.1002/ece3.2352
 
Nugent, N. R., Goldberg, A., & Uddin, M. (2016). Topical Review: The Emerging Field of Epigenetics: Informing Models of Pediatric Trauma and Physical Health. Journal of Pediatric Psychology, 41(1), 55-64. DOI: 10.1093/jpepsy/jsv018
 
Cook, M. D., Allen, J. M., Pence, B. D., Wallig, M. A., Gaskins, H. R., White, B. A., & Woods, J. A. (2016). Exercise and gut immune function: Evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunology and Cell Biology, 94(2), 158-163. DOI: 10.1038/icb.2015.108
 
Lewis, J. A., Mendenhall, R., Harwood, S. A., & Browne Huntt, M. (2016). "ain't i a Woman?": Perceived Gendered Racial Microaggressions Experienced by Black Women. Counseling Psychologist, 44(5), 758-780. DOI: 10.1177/0011000016641193
 
Varatharajah, Y., Iyer, R. K., Berry, B. M., Worrell, G. A., & Brinkmann, B. H. (2017). Seizure Forecasting and the Preictal State in Canine Epilepsy. International Journal of Neural Systems, 27(1), [1650046]. DOI: 10.1142/S0129065716500465
 
Baker, J. L., Dunn, K. A., Mingrone, J., Wood, B. A., Karpinski, B. A., Sherwood, C. C., ... Bielawski, J. P. (2016). Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution. Genetics, 203(2), 905-922. DOI: 10.1534/genetics.115.183889
 
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
 
Ghosh, U., Kalbarczyk, Z., Dong, X., Yau, D. K. Y., Tan, R., & Iyer, R. K. (2016). A simulation study on smart grid resilience under software-defined networking controller failures. In CPSS 2016 - Proceedings of the 2nd ACM International Workshop on Cyber-Physical System Security, Co-located with Asia CCS 2016. (pp. 52-58). Association for Computing Machinery, Inc. DOI: 10.1145/2899015.2899020
 
Banerjee, S. S., Athreya, A. P., Mainzer, L. S., Jongeneel, C. V., Hwu, W. M., Kalbarczyk, Z. T., & Iyer, R. K. (2016). Efficient and scalable workflows for genomic analyses. In DIDC 2016 - Proceedings of the ACM International Workshop on Data-Intensive Distributed Computing. (pp. 27-36). Association for Computing Machinery, Inc. DOI: 10.1145/2912152.2912156
 
Tan, R., Nguyen, H. H., Foo, E. Y. S., Dong, X., Yau, D. K. Y., Kalbarczyk, Z., ... Gooi, H. B. (2016). Optimal False Data Injection Attack against Automatic Generation Control in Power Grids. In 2016 ACM/IEEE 7th International Conference on Cyber-Physical Systems, ICCPS 2016 - Proceedings. [7479109] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/ICCPS.2016.7479109
 
Krishna, V. B., Iyer, R. K., & Sanders, W. H. (2016). ARIMA-based modeling and validation of consumption readings in power grids. In Critical Information Infrastructures Security - 10th International Conference, CRITIS 2015, Revised Selected Papers. (Vol. 9578, pp. 199-210). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9578). Springer Verlag. DOI: 10.1007/978-3-319-33331-1_16
 
Alemzadeh, H., Raman, J., Leveson, N., Kalbarczyk, Z., & Iyer, R. K. (2016). Adverse events in robotic surgery: A retrospective study of 14 years of fda data. PLoS One, 11(4), [e0151470]. DOI: 10.1371/journal.pone.0151470
 
Bennett, G., Malone, M., Sauther, M. L., Cuozzo, F. P., White, B., Nelson, K. E., ... Amato, K. R. (2016). Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). American Journal of Primatology, 78(8), 883-892. DOI: 10.1002/ajp.22555
 
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Chambon, C., ... Mosoni, P. (2016). Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics, 17(1), [326]. DOI: 10.1186/s12864-016-2680-8
 
Bhurke, A. S., Bagchi, I. C., & Bagchi, M. K. (2016). Progesterone-Regulated Endometrial Factors Controlling Implantation. American Journal of Reproductive Immunology, 75(3), 237-245. DOI: 10.1111/aji.12473
 
Koohestani, F., Qiang, W., MacNeill, A. L., Druschitz, S. A., Serna, V. A., Adur, M., ... Nowak, R. A. (2016). Halofuginone suppresses growth of human uterine leiomyoma cells in a mouse xenograft model. Human Reproduction, 31(7), 1540-1551. DOI: 10.1093/humrep/dew094
 
Jenkins, W. D., Lipka, A. E., Fogleman, A. J., Delfino, K. R., Malhi, R. S., Hendricks, B., & Cristescu, M. E. (2016). Variance in disease risk: Rural populations and genetic diversity. Genome, 59(7), 519-525. DOI: 10.1139/gen-2016-0077
 
Feinstein, L., Ferrando-Martínez, S., Leal, M., Zhou, X., Sempowski, G. D., Wildman, D. E., ... Aiello, A. E. (2016). Population Distributions of Thymic Function in Adults: Variation by Sociodemographic Characteristics and Health Status. Biodemography and Social Biology, 62(2), 208-221. DOI: 10.1080/19485565.2016.1172199
 
Yu, J., Berga, S. L., Johnston-MacAnanny, E. B., Sidell, N., Bagchi, I. C., Bagchi, M. K., & Taylor, R. N. (2016). Endometrial stromal decidualization responds reversibly to hormone stimulation and withdrawal. Endocrinology, 157(6), 2432-2446. DOI: 10.1210/en.2015-1942
 
Jeraldo, P., Hernandez, A., Nielsen, H. B., Chen, X., White, B. A., Goldenfeld, N., ... Chia, N. (2016). Capturing one of the human gut microbiome's most wanted: Reconstructing the genome of a novel butyrate-producing, clostridial scavenger from metagenomic sequence data. Frontiers in Microbiology, 7(MAY), [783]. DOI: 10.3389/fmicb.2016.00783
 
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Yeoman, C. J., ... Mosoni, P. (2016). Erratum to Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis [BMC Genomics, (2016), 17] DOI: 10.1186/s12864-016-2472-1. BMC Genomics, 17(1), [426]. DOI: 10.1186/s12864-016-2758-3
 
Braundmeier-Fleming, A., Russell, N. T., Yang, W., Nas, M. Y., Yaggie, R. E., Berry, M., ... Klumpp, D. J. (2016). Stool-based biomarkers of interstitial cystitis/bladder pain syndrome. Scientific Reports, 6, [26083]. DOI: 10.1038/srep26083
 
Despres, J., Forano, E., Lepercq, P., Comtet-Marre, S., Jubelin, G., Yeoman, C. J., ... Mosoni, P. (2016). Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics, 17(1), [147]. DOI: 10.1186/s12864-016-2472-1
 
Li, Q., Davila, J., Kannan, A., Flaws, J. A., Bagchi, M. K., & Bagchi, I. C. (2016). Chronic exposure to bisphenol a affects uterine function during early pregnancy in mice. Endocrinology, 157(5), 1764-1774. DOI: 10.1210/en.2015-2031
 
Hughes, C. E., Hunter, C. D., Vargas, P. T., Schlosser, M. D., & Malhi, R. S. (2016). Police Endorse Color-Blind Racial Beliefs More Than Laypersons. Race and Social Problems, 8(2), 160-170. DOI: 10.1007/s12552-016-9170-0
 
Stumpf, R. M., Gomez, A., Amato, K. R., Yeoman, C. J., Polk, J. D., Wilson, B. A., ... Leigh, S. R. (2016). Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biological Conservation, 199, 56-66. DOI: 10.1016/j.biocon.2016.03.035
 
Estrada, Z. J., Pham, C., Deng, F., Kalbarczyk, Z., Iyer, R. K., & Yan, L. (2016). Dynamic VM Dependability Monitoring Using Hypervisor Probes. In Proceedings - 2015 11th European Dependable Computing Conference, EDCC 2015. (pp. 61-72). [7371955] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/EDCC.2015.9
 
Cui, P., Löber, U., Alquezar-Planas, D. E., Ishida, Y., Courtiol, A., Timms, P., ... Greenwood, A. D. (2016). Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. PeerJ, 2016(3), [1847]. DOI: 10.7717/peerj.1847
 
Darfour-Oduro, K. A., Megens, H. J., Roca, A. L., Groenen, M. A. M., & Schook, L. B. (2016). Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae. BMC Evolutionary Biology, 16(1), [602]. DOI: 10.1186/s12862-016-0602-7
 
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
 
Darfour-Oduro, K. A., Megens, H. J., Roca, A., Groenen, M. A. M., & Schook, L. B. (2016). Evidence for adaptation of porcine Toll-like receptors. Immunogenetics, 68(3), 179-189. DOI: 10.1007/s00251-015-0892-8
 
Alfano, N., Kolokotronis, S. O., Tsangaras, K., Roca, A. L., Xu, W., Eiden, M. V., & Greenwood, A. D. (2016). Eepisodic diversifying selection shaped the genomes of gibbon ape leukemia virus and related gammaretroviruses. Journal of Virology, 90(4), 1757-1772. DOI: 10.1128/JVI.02745-15
 
Alfano, N., Kolokotronis, S. O., Tsangaras, K., Roca, A. L., Xu, W., Eiden, M. V., & Greenwood, A. D. (2016). Erratum to Episodic diversifying selection shaped the genomes of gibbon ape leukemia virus and related gammaretroviruses [J Virol, 90, 4 (2016) 1757-1772]. Journal of Virology, 90(8), 4254. DOI: 10.1128/JVI.00210-16
 
Chung, K., Kamhoua, C. A., Kwiat, K. A., Kalbarczyk, Z. T., & Iyer, R. K. (2016). Game Theory with Learning for Cyber Security Monitoring. In Proceedings - 17th IEEE International Symposium on High Assurance Systems Engineering, HASE 2016. (Vol. 2016-March, pp. 1-8). [7423125] IEEE Computer Society. DOI: 10.1109/HASE.2016.48
 
Aiello, A. E., Dowd, J. B., Jayabalasingham, B., Feinstein, L., Uddin, M., Simanek, A. M., ... Pawelec, G. (2016). PTSD is associated with an increase in aged T cell phenotypes in adults living in Detroit. Psychoneuroendocrinology, 67, 133-141. DOI: 10.1016/j.psyneuen.2016.01.024
 
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
 
Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., ... Blekhman, R. (2016). Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Reports, 14(9), 2142-2153. DOI: 10.1016/j.celrep.2016.02.013
 
Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., ... Leigh, S. R. (2016). Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia, 180(3), 717-733. DOI: 10.1007/s00442-015-3507-z
 
Okur, H. S. K., Das, A., Taylor, R. N., Bagchi, I. C., & Bagchi, M. K. (2016). Roles of estrogen receptor-α and the coactivator MED1 during human endometrial decidualization. Molecular Endocrinology, 30(3), 302-313. DOI: 10.1210/me.2015-1274
 
Bhurke, A. S., Bagchi, I. C., & Bagchi, M. K. (2016). Progesterone-Regulated Endometrial Factors Controlling Implantation. American Journal of Reproductive Immunology. DOI: 10.1111/aji.12473
 
Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., ... Leigh, S. R. (2016). Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME Journal, 10(2), 514-526. DOI: 10.1038/ismej.2015.146
 
Eerkens, J. W., Carlson, T., Malhi, R. S., Blake, J., Bartelink, E. J., Barfod, G. H., ... Marshall, C. K. (2016). Isotopic and genetic analyses of a mass grave in central California: Implications for precontact hunter-gatherer warfare. American Journal of Physical Anthropology, 159(1), 116-125. DOI: 10.1002/ajpa.22843
 
Lipovich, L., Hou, Z. C., Jia, H., Sinkler, C., Mcgowen, M., Sterner, K. N., ... Wildman, D. E. (2016). High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. Journal of Comparative Neurology, 524(2), 288-308. DOI: 10.1002/cne.23843