Collections in this community

Recent Submissions

  • Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles 

    Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David (2013-01)
    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping ...
  • EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles 

    Dittmar, W. James; McIver, Lauren; Michalak, Pawel; Garner, Harold R.; Valdez, Gregorio (2014-07-01)
    The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are ...
  • Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans 

    Quilez, Javier; Guilmatre, Audrey; Garg, Paras; Highnam, Gareth; Gymrek, Melissa; Erlich, Yaniv; Joshi, Ricky S.; Mittelman, David; Sharp, Andrew J. (2016-05-05)
    Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) ...
  • Recurrent chimeric fusion RNAs in non-cancer tissues and cells 

    Babiceanu, Mihaela; Qin, Fujun; Xie, Zhongqiu; Jia, Yuemeng; Lopez, Kevin; Janus, Nick; Facemire, Loryn; Kumar, Shailesh; Pang, Yuwei; Qi, Yanjun; Lazar, Iulia M.; Li, Hui (2016-04-07)
    Gene fusions and their products (RNA and protein) were once thought to be unique features to cancer. However, chimeric RNAs can also be found in normal cells. Here, we performed, curated and analyzed nearly 300 RNA-Seq ...
  • XTALKDB: a database of signaling pathway crosstalk 

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T. M. (2017-01-04)
    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents ...
  • A General Lake Model (GLM 3.0) for linking with high-frequency sensor data from the Global Lake Ecological Observatory Network (GLEON) 

    Hipsey, M.R.; Bruce, L.C.; Boon, C.; Busch, B.; Carey, C.C.; Hamilton, D.P.; Hanson, P.C.; Read, J.S.; De Sousa, E.; Weber, M.; Winslow, L.A. (Copernicus GmbH, 2019-01-29)
    The General Lake Model (GLM) is a one-dimensional open-source code designed to simulate the hydrodynamics of lakes, reservoirs, and wetlands. GLM was developed to support the science needs of the Global Lake Ecological ...
  • Simulating demography, genetics, and spatially explicit processes to inform reintroduction of a threatened char 

    Mims, M.C.; Day, C.C.; Burkhart, J.J.; Fuller, M.R.; Hinkle, J.; Bearlin, A.; Dunham, J.B.; DeHaan, P.W.; Holden, Z.A.; Landguth, E.E. (Wiley-Blackwell, 2019-02-12)
    The success of species reintroductions can depend on a combination of environmental, demographic, and genetic factors. Although the importance of these factors in the success of reintroductions is well-accepted, they are ...
  • Novel reprogramming of neutrophils modulates inflammation resolution during atherosclerosis 

    Geng, S.; Zhang, Y.; Lee, C.; Li, L. (American Association for the Advancement of Science, 2019-02-06)
    Nonresolving inflammation perpetuated by innate leukocytes is involved in the pathogenesis of unstable atherosclerosis. However, the role and regulation of neutrophils related to nonresolving inflammation and atherosclerosis ...
  • Identification of soil bacteria capable of utilizing a corn ethanol fermentation byproduct 

    Packard, H.; Taylor, Z.W.; Williams, S.L.; Guimarães, P.I.; Toth, J.; Jensen, R.V.; Senger, R.S.; Kuhn, D.D.; Stevens, A.M. (Public Library of Science, 2019-03-08)
    A commercial corn ethanol production byproduct (syrup) was used as a bacterial growth medium with the long-term aim to repurpose the resulting microbial biomass as a protein supplement in aquaculture feeds. Anaerobic batch ...
  • Ectosymbionts alter spontaneous responses to the Earth’s magnetic field in a crustacean 

    Landler, L.; Skelton, J.; Painter, M.S.; Youmans, P.W.; Muheim, R.; Creed, R.P.; Brown, B.L.; Phillips, J.B. (Nature Publishing Group, 2019-02-28)
    Magnetic sensing is used to structure every-day, non-migratory behaviours in many animals. We show that crayfish exhibit robust spontaneous magnetic alignment responses. These magnetic behaviours are altered by interactions ...
  • Microfluidic reactors for advancing the MS analysis of fast biological responses 

    Lazar, I.M.; Deng, J.; Stremler, M.A.; Ahuja, S. (Nature Publishing Group, 2019-02-11)
    The response of cells to physical or chemical stimuli is complex, unfolding on time-scales from seconds to days, with or without de novo protein synthesis, and involving signaling processes that are transient or sustained. ...
  • Observations at backyard bird feeders influence the emotions and actions of people that feed birds 

    Dayer, Ashley A.; Rosenblatt, Connor; Bonter, David N.; Faulkner, Holly; Hall, Richard J.; Hochachka, Wesley M.; Phillips, Tina B.; Hawley, Dana M. (British Ecological Society, 2019-03-25)
    1. Backyard bird feeding is one of the most common ways people engage with wildlife in many parts of the world. Given its scale, it can have profound consequences for the ecology of feeder birds and their behaviour. While ...
  • Analysis of global gene expression changes in human bronchial epithelial cells exposed to spores of the allergenic fungus, Alternaria alternata 

    Babiceanu, M. C.; Howard, B. A.; Rumore, A. C.; Kita, H.; Lawrence, C. B. (Frontiers, 2013-07-19)
    Exposure and sensitivity to ubiquitous airborne fungi such as Alternaria alternata have long been implicated in the development, onset, and exacerbation of chronic allergic airway disorders. This present study is the first ...
  • Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem 

    Lee, Charles K.; Laughlin, Daniel C.; Bottos, Eric M.; Caruso, Tancredi; Joy, Kurt; Barrett, John E.; Brabyn, Lars; Nielsen, Uffe N.; Adams, Byron J.; Wall, Diana H.; Hopkins, David W.; Pointing, Stephen B.; McDonald, Ian R.; Cowan, Don A.; Banks, Jonathan C.; Stichbury, Glen A.; Jones, Irfon; Zawar-Reza, Peyman; Katurji, Marwan; Hogg, Ian D.; Sparrow, Ashley D.; Storey, Bryan C.; Green, T.G. Allan; Cary, S. Craig (Springer Nature, 2019-02-15)
    Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a ...
  • Nematodes in a polar desert reveal the relative role of biotic interactions in the coexistence of soil animals 

    Caruso, Tancredi; Hogg, Ian D.; Nielsen, Uffe N.; Bottos, Eric M.; Lee, Charles K.; Hopkins, David W.; Cary, S. Craig; Barrett, John E.; Green, T.G. Allan; Storey, Bryan C.; Wall, Diana H.; Adams, Byron J. (Springer Nature, 2019-02-15)
    Abiotic factors are major determinants of soil animal distributions and their dominant role is pronounced in extreme ecosystems, with biotic interactions seemingly playing a minor role. We modelled co-occurrence and ...
  • Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases 

    Rebollar, Eria A.; Antwis, Rachael E.; Becker, Matthew H.; Belden, Lisa K.; Bletz, Molly C.; Brucker, Robert M.; Harrison, Xavier A.; Hughey, Myra C.; Kueneman, Jordan G.; Loudon, Andrew H.; McKenzie, Valerie; Medina, Daniel; Minbiole, Kevin P. C.; Rollins-Smith, Louise A.; Walke, Jenifer B.; Weiss, Sophie; Woodhams, Douglas C.; Harris, Ried N. (Frontiers, 2016-02-02)
    Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and ...
  • Panamanian frog species host unique skin bacterial communities 

    Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibanez, Roberto; Harris, Reid N. (Frontiers, 2015-10-27)
    Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, ...
  • Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? 

    Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Bemans, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Foey; Salminen, Janne; Newton, Ryan J.; Buergmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Baneras, Lluis; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindstrom, Eva S.; Basiliko, Nathan; Nemergut, Diana R. (Frontiers, 2016-02-24)
    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community ...
  • Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica 

    Buelow, Heather N.; Winter, Ara S.; Van Horn, David J.; Barrett, John E.; Gooseff, Michael N.; Schwartz, Egbert; Takacs-Vesbach, Cristina D. (Frontiers, 2016-07-18)
    The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, ...
  • Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin 

    Medina, Daniel; Walke, Jenifer B.; Gajewski, Zachary; Becker, Matthew H.; Swartwout, Meredith C.; Belden, Lisa K. (Frontiers, 2017-08-24)
    One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the ...

View more