Research articles, presentations, and other scholarship

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  • Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana 

    Radakovits, Randor; Jinkerson, Robert E.; Fuerstenberg, Susan I.; Tae, Hongseok; Settlage, Robert E.; Boore, Jeffrey L.; Posewitz, Matthew C. (Springer Nature, 2012-02)
    The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a ...
  • Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations 

    Rouxel, Thierry; Grandaubert, Jonathan; Hane, James K.; Hoede, Claire; van de Wouw, Angela P.; Couloux, Arnaud; Dominguez, Victoria; Anthouard, Veronique; Bally, Pascal; Bourras, Salim; Cozijnsen, Anton J.; Ciuffetti, Lynda M.; Degrave, Alexandre; Dilmaghani, Azita; Duret, Laurent; Fudal, Isabelle; Goodwin, Stephen B.; Gout, Lilian; Glaser, Nicolas; Linglin, Juliette; Kema, Gert H. J.; Lapalu, Nicolas; Lawrence, Christopher B.; May, Kim; Meyer, Michel; Ollivier, Benedicte; Poulain, Julie; Schoch, Conrad L.; Simon, Adeline; Spatafora, Joseph W.; Stachowiak, Anna; Turgeon, B. Gillian; Tyler, Brett M.; Vincent, Delphine; Weissenbach, Jean; Amselem, Joelle; Quesneville, Hadi; Oliver, Richard P.; Wincker, Patrick; Balesdent, Marie-Helene; Howlett, Barbara J. (Springer Nature, 2011-02)
    Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi ...
  • Genome sequences of wild and domestic bactrian camels 

    Jirimutu; Wang, Zhen; Ding, Guohui; Chen, Gangliang; Sun, Yamin; Sun, Zhihong; Zhang, Heping; Wang, Lei; Hasi, Surong; Zhang, Yan; Li, Jianmei; Shi, Yixiang; Xu, Ze; He, Chuan; Yu, Siriguleng; Li, Shengdi; Zhang, Wenbin; Batmunkh, Mijiddorj; Ts, Batsukh; Narenbatu; Unierhu; Bat-Ireedui, Shirzana; Gao, Hongwei; Baysgalan, Banzragch; Li, Qing; Jia, Zhiling; Turigenbayila; Subudenggerile; Narenmanduhu; Wang, Zhaoxia; Wang, Juan; Pan, Lei; Chen, Yongcan; Ganerdene, Yaichil; Dabxilt; Erdemt; Altansha; Altansukh; Liu, Tuya; Cao, Minhui; Aruuntsever; Bayart; Hosblig; He, Fei; Zha-ti, A.; Zheng, Guangyong; Qiu, Feng; Sun, Zikui; Zhao, Lele; Zhao, Wenjing; Liu, Baohong; Li, Chao; Chen, Yunqin; Tang, Xiaoyan; Guo, Chunyan; Liu, Wei; Ming, Liang; Temuulen; Cui, Aiying; Li, Yi; Gao, Junhui; Li, Jing; Wurentaodi; Niu, Shen; Sun, Tao; Zhai, Zhengxiao; Zhang, Min; Chen, Chen; Baldan, Tunteg; Bayaer, Tuman; Li, Yixue; Meng, He (Springer Nature, 2012-11)
    Bactrian camels serve as an important means of transportation in the cold desert regions of China and Mongolia. Here we present a 2.01 Gb draft genome sequence from both a wild and a domestic bactrian camel. We estimate ...
  • Genomic insights into the Ixodes scapularis tick vector of Lyme disease 

    Gulia-Nuss, Monika; Nuss, Andrew B.; Meyer, Jason M.; Sonenshine, Daniel E.; Roe, R. Michael; Waterhouse, Robert M.; Sattelle, David B.; de la Fuente, Jose; Ribeiro, Jose M.; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R.; Walenz, Brian P.; Koren, Sergey; Hostetler, Jessica B.; Thiagarajan, Mathangi; Joardar, Vinita S.; Hannick, Linda I.; Bidwell, Shelby; Hammond, Martin P.; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L.; Almeida, Francisca C.; Ayllon, Nieves; Bhide, Ketaki; Bissinger, Brooke W.; Bonzon-Kulichenko, Elena; Buckingham, Steven D.; Caffrey, Daniel R.; Caimano, Melissa J.; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J.; Giraldo-Calderon, Gloria I.; Grabowski, Jeffrey M.; Jiang, David; Khalil, Sayed M. S.; Kim, Donghun; Kocan, Katherine M.; Koci, Juraj; Kuhn, Richard J.; Kurtti, Timothy J.; Lees, Kristin; Lang, Emma G.; Kennedy, Ryan C.; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D.; Sakamoto, Joyce M.; Sanchez-Gracia, Alejandro; Severo, Maiara S.; Silverman, Neal; Simo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P.; Vazquez, Jesus; Vieira, Filipe G.; Villar, Margarita; Wespiser, Adam R.; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V.; Barker, Stephen C.; Shao, Renfu; Zdobnov, Evgeny M.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H. F.; Nelson, David R.; Unger, Maria F.; Tubio, Jose M. C.; Tu, Zhijian; Robertson, Hugh M.; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R.; Lawson, Daniel; Wikel, Stephen K.; Nene, Vishvanath M.; Fraser, Claire M.; Collins, Frank H.; Birren, Bruce; Nelson, Karen E.; Caler, Elisabet; Hill, Catherine A. (Springer Nature, 2016-02)
    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic ...
  • Overlap microtubules link sister k-fibres and balance the forces on bi-oriented kinetochores 

    Kajtez, Janko; Solomatina, Anastasia; Novak, Maja; Polak, Bruno; Vukusic, Kruno; Ruediger, Jonas; Cojoc, Gheorghe; Milas, Ana; Sestak, Ivana Sumanovac; Risteski, Patrik; Tavano, Federica; Klemm, Anna H.; Roscioli, Emanuele; Welburn, Julie; Cimini, Daniela; Gluncic, Matko; Pavin, Nenad; Tolic, Iva M. (Springer Nature, 2016-01)
    During metaphase, forces on kinetochores are exerted by k-fibres, bundles of microtubules that end at the kinetochore. Interestingly, non-kinetochore microtubules have been observed between sister kinetochores, but their ...
  • Age-related variations in the methylome associated with gene expression in human monocytes and T cells 

    Reynolds, Lindsay M.; Taylor, Jackson R.; Ding, Jingzhong; Lohman, Kurt; Johnson, Craig; Siscovick, David; Burke, Gregory; Post, Wendy; Shea, Steven; Jacobs, David R., Jr.; Stunnenberg, Hendrik; Kritchevsky, Stephen B.; Hoeschele, Ina; McCall, Charles E.; Herrington, David M.; Tracy, Russell P.; Liu, Yongmei (Springer Nature, 2014-11)
    Age-related variations in DNA methylation have been reported; however, the functional relevance of these differentially methylated sites (age-dMS) are unclear. Here we report potentially functional age-dMS, defined as ...
  • An analytical framework for optimizing variant discovery from personal genomes 

    Highnam, Gareth; Wang, Jason J.; Kusler, Dean; Zook, Justin; Vijayan, Vinaya; Leibovich, Nir; Mittelman, David (Springer Nature, 2015-02)
    The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the ...
  • Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis 

    Liu, Yongmei; Reynolds, Lindsay M.; Ding, Jingzhong; Hou, Li; Lohman, Kurt; Young, Tracey; Cui, Wei; Huang, Zhiqing; Grenier, Carole; Wan, Ma; Stunnenberg, Hendrik G.; Siscovick, David; Hou, Lifang; Psaty, Bruce M.; Rich, Stephen S.; Rotter, Jerome I.; Kaufman, Joel D.; Burke, Gregory L.; Murphy, Susan; Jacobs, David R., Jr.; Post, Wendy; Hoeschele, Ina; Bell, Douglas A.; Herrington, David; Parks, John S.; Tracy, Russell P.; McCall, Charles E.; Stein, James H. (Springer Nature, 2017-08-30)
    Little is known regarding the epigenetic basis of atherosclerosis. Here we present the CD14+ blood monocyte transcriptome and epigenome signatures associated with human atherosclerosis. The transcriptome signature includes ...
  • Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates 

    Yablonovitch, Arielle L.; Fu, Jeremy; Li, Kexin; Mahato, Simpla; Kang, Lin; Rashkovetsky, Eugenia; Korol, Abraham B.; Tang, Hua; Michalak, Pawel; Zelhof, Andrew C.; Nevo, Eviatar; Li, Jin Billy (Springer Nature, 2017-11-17)
    Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust ...
  • RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes 

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A., III; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang (Springer Nature, 2015-02-10)
    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features ...
  • Antimicrobial Resistance Prediction in PATRIC and RAST 

    Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; Kenyon, Ronald W.; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R.; Will, Rebecca; Xia, Fangfang; Stevens, Rick (Springer Nature, 2016-06-14)
    The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic ...
  • Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts 

    Al Dahouk, Sascha; Koehler, Stephan; Occhialini, Alessandra; Jimenez de Bagues, Maria Pilar; Hammerl, Jens Andre; Eisenberg, Tobias; Vergnaud, Gilles; Cloeckaert, Axel; Zygmunt, Michel S.; Whatmore, Adrian M.; Melzer, Falk; Drees, Kevin P.; Foster, Jeffrey T.; Wattam, Alice R.; Scholz, Holger C. (Springer Nature, 2017-03-16)
    Twenty-one small Gram-negative motile coccobacilli were isolated from 15 systemically diseased African bullfrogs (Pyxicephalus edulis), and were initially identified as Ochrobactrum anthropi by standard microbiological ...
  • Transient ALT activation protects human primary cells from chromosome instability induced by low chronic oxidative stress 

    Coluzzi, Elisa; Buonsante, Rossella; Leone, Stefano; Asmar, Anthony J.; Miller, Kelley L.; Cimini, Daniela; Sgura, Antonella (Springer Nature, 2017-02-27)
    Cells are often subjected to the effect of reactive oxygen species (ROS) as a result of both intracellular metabolism and exposure to exogenous factors. ROS-dependent oxidative stress can induce 8-oxodG within the GGG ...
  • Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons 

    Hixson, James E.; Jun, Goo; Shimmin, Lawrence C.; Wang, Yizhi; Yu, Guoqiang; Mao, Chunhong; Warren, Andrew S.; Howard, Timothy D.; Vander Heide, Richard S.; Van Eyk, Jennifer; Wang, Yue; Herrington, David M. (Springer Nature, 2017-06-22)
    We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified ...
  • Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems 

    Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Avezedo, Vasco; Ghosh, Preetam; Viana, Marcus; Wattam, Alice R. (Springer Nature, 2017-08-18)
    In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other ...
  • Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis 

    Kale, Shiv D.; Ayubi, Tariq; Chung, Dawoon; Tubau-Juni, Nuria; Leber, Andrew; Dang, Ha X.; Karyala, Saikumar; Hontecillas, Raquel; Lawrence, Christopher B.; Cramer, Robert A.; Bassaganya-Riera, Josep (Springer Nature, 2017-12-06)
    Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon ...
  • Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma 

    Connolly, Nina P.; Shetty, Amol C.; Stokum, Jesse A.; Hoeschele, Ina; Siegel, Marni B.; Miller, C. Ryan; Kim, Anthony J.; Ho, Cheng-Ying; Davila, Eduardo; Simard, J. Marc; Devine, Scott E.; Rossmeisl, John H.; Holland, Eric C.; Winkles, Jeffrey A.; Woodworth, Graeme F. (Springer Nature, 2018-01-19)
    Glioma is a unique neoplastic disease that develops exclusively in the central nervous system (CNS) and rarely metastasizes to other tissues. This feature strongly implicates the tumor-host CNS microenvironment in gliomagenesis ...
  • Cell Cycle Model System for Advancing Cancer Biomarker Research 

    Lazar, Iulia M.; Hoeschele, Ina; de Morais, Juliana; Tenga, Milagros J. (Springer Nature, 2017-12-21)
    Progress in understanding the complexity of a devastating disease such as cancer has underscored the need for developing comprehensive panels of molecular markers for early disease detection and precision medicine applications. ...
  • Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems 

    Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Vaz, Aline; Goes-Neto, Aristoteles; Tiwari, Sandeep; Ghosh, Preetam; Wattam, Alice R.; Azevedo, Vasco (Springer Nature, 2018-07-25)
    The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing ...
  • A virtual look at Epstein-Barr virus infection: Biological interpretations 

    Duca, Karen A.; Shapiro, Michael; Delgado-Eckert, Edgar; Hadinoto, Vey; Jarrah, Abdul S.; Laubenbacher, Reinhard; Lee, Kichol; Luzuriaga, Katherine; Polys, Nicholas F.; Thorley-Lawson, David A. (PLOS, 2007-10-19)
    The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention. However, it is as yet unclear to what extent these techniques ...

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