Browsing Faculty of Arts and Sciences by Keyword "Computational Biology"

Now showing items 1-20 of 34

    • The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum 

      Harcombe, William R.; Delaney, Nigel F.; Leiby, Nicholas; Klitgord, Niels; Marx, Christopher J. (Public Library of Science, 2013)
      The most powerful genome-scale framework to model metabolism, flux balance analysis (FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed optimality criterion in order to predict the set of ...

    • Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells 

      McCole, Ruth B.; Fonseka, Chamith Y.; Koren, Amnon; Wu, C.-ting (Public Library of Science, 2014)
      Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian ...

    • Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents 

      Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D.; Lewis, James D.; Bushman, Frederic D. (Public Library of Science, 2013)
      Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses ...

    • Bayesian Inference of Spatial Organizations of Chromosomes 

      Hu, Ming; Deng, Ke; Qin, Zhaohui; Dixon, Jesse; Selvaraj, Siddarth; Fang, Jennifer; Ren, Bing; Liu, Jun (Public Library of Science, 2013)
      Knowledge of spatial chromosomal organizations is critical for the study of transcriptional regulation and other nuclear processes in the cell. Recently, chromosome conformation capture (3C) based technologies, such as ...

    • Can You Sequence Ecology? Metagenomics of Adaptive Diversification 

      Marx, Christopher J (Public Library of Science, 2013)
      Few areas of science have benefited more from the expansion in sequencing capability than the study of microbial communities. Can sequence data, besides providing hypotheses of the functions the members possess, detect the ...

    • Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi 

      Zeiner, Carolyn A.; Purvine, Samuel O.; Zink, Erika M.; Paša-Tolić, Ljiljana; Chaput, Dominique L.; Haridas, Sajeet; Wu, Si; LaButti, Kurt; Grigoriev, Igor V.; Henrissat, Bernard; Santelli, Cara M.; Hansel, Colleen M. (Public Library of Science, 2016)
      Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the ...

    • Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC 

      Jaratlerdsiri, Weerachai; Deakin, Janine; Godinez, Ricardo M.; Shan, Xueyan; Peterson, Daniel G.; Marthey, Sylvain; Lyons, Eric; McCarthy, Fiona M.; Isberg, Sally R.; Higgins, Damien P.; Chong, Amanda Y.; John, John St; Glenn, Travis C.; Ray, David A.; Gongora, Jaime (Public Library of Science, 2014)
      The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes ...

    • A Comprehensive Reference Transcriptome Resource for the Common House Spider Parasteatoda tepidariorum 

      Posnien, Nico; Zeng, Victor; Schwager, Evelyn E.; Pechmann, Matthias; Hilbrant, Maarten; Keefe, Joseph D.; Damen, Wim G. M.; Prpic, Nikola-Michael; McGregor, Alistair P.; Extavour, Cassandra G. (Public Library of Science, 2014)
      Parasteatoda tepidariorum is an increasingly popular model for the study of spider development and the evolution of development more broadly. However, fully understanding the regulation and evolution of P. tepidariorum ...

    • Computing Complex Visual Features with Retinal Spike Times 

      Gütig, Robert; Gollisch, Tim; Sompolinsky, Haim I; Meister, Markus (Public Library of Science, 2013)
      Neurons in sensory systems can represent information not only by their firing rate, but also by the precise timing of individual spikes. For example, certain retinal ganglion cells, first identified in the salamander, ...

    • Conservation Weighting Functions Enable Covariance Analyses to Detect Functionally Important Amino Acids 

      Colwell, Lucy J.; Brenner, Michael P.; Murray, Andrew W. (Public Library of Science, 2014)
      The explosive growth in the number of protein sequences gives rise to the possibility of using the natural variation in sequences of homologous proteins to find residues that control different protein phenotypes. Because ...

    • Early Warning Signals of Ecological Transitions: Methods for Spatial Patterns 

      Kéfi, Sonia; Guttal, Vishwesha; Brock, William A.; Carpenter, Stephen R.; Ellison, Aaron M.; Livina, Valerie N.; Seekell, David A.; Scheffer, Marten; van Nes, Egbert H.; Dakos, Vasilis (Public Library of Science, 2014)
      A number of ecosystems can exhibit abrupt shifts between alternative stable states. Because of their important ecological and economic consequences, recent research has focused on devising early warning signals for ...

    • The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium 

      van Gestel, Jordi; Nowak, Martin A.; Tarnita, Corina (Public Library of Science, 2012)
      Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation. However, over the last decades cell-to-cell communication has been found to be ubiquitous. By secreting molecular ...

    • Exploring the miRNA Regulatory Network Using Evolutionary Correlations 

      Obermayer, Benedikt; Levine, Erel (Public Library of Science, 2014)
      Post-transcriptional regulation by miRNAs is a widespread and highly conserved phenomenon in metazoans, with several hundreds to thousands of conserved binding sites for each miRNA, and up to two thirds of all genes under ...

    • Ferristatin II Promotes Degradation of Transferrin Receptor-1 In Vitro and In Vivo 

      Byrne, Shaina L.; Buckett, Peter D.; Kim, Jonghan; Luo, Flora; Sanford, Jack; Chen, Juxing; Enns, Caroline; Wessling-Resnick, Marianne (Public Library of Science, 2013)
      Previous studies have shown that the small molecule iron transport inhibitor ferristatin (NSC30611) acts by down-regulating transferrin receptor-1 (TfR1) via receptor degradation. In this investigation, we show that another ...

    • The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 

      Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen (Public Library of Science, 2014)
      Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...

    • FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations 

      Chubiz, Lon M; Lee, Ming-Chun; Delaney, Nigel Francis; Marx, Christopher J (Public Library of Science, 2012)
      Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina ...

    • GW8510 Increases Insulin Expression in Pancreatic Alpha Cells through Activation of p53 Transcriptional Activity 

      Fomina-Yadlin, Dina; Kubicek, Stefan; Vetere, Amedeo; He, Kaihui Hu; Schreiber, Stuart L.; Wagner, Bridget K. (Public Library of Science, 2012)
      Background: Expression of insulin in terminally differentiated non-beta cell types in the pancreas could be important to treating type-1 diabetes. Previous findings led us to hypothesize involvement of kinase inhibition ...

    • An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology 

      Fernandes de Abreu, Diana Andrea; Caballero, Antonio; Fardel, Pascal; Stroustrup, Nicholas; Chen, Zhunan; Lee, KyungHwa; Keyes, William D.; Nash, Zachary M.; López-Moyado, Isaac F.; Vaggi, Federico; Cornils, Astrid; Regenass, Martin; Neagu, Anca; Ostojic, Ivan; Liu, Chang; Cho, Yongmin; Sifoglu, Deniz; Shen, Yu; Fontana, Walter; Lu, Hang; Csikasz-Nagy, Attila; Murphy, Coleen T.; Antebi, Adam; Blanc, Eric; Apfeld, Javier; Zhang, Yun; Alcedo, Joy; Ch'ng, QueeLim (Public Library of Science, 2014)
      Insulin-like peptides (ILPs) play highly conserved roles in development and physiology. Most animal genomes encode multiple ILPs. Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse ...

    • Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks 

      Gjorgjieva, Julijana; Mease, Rebecca A.; Moody, William J.; Fairhall, Adrienne L. (Public Library of Science, 2014)
      Diverse ion channels and their dynamics endow single neurons with complex biophysical properties. These properties determine the heterogeneity of cell types that make up the brain, as constituents of neural circuits tuned ...

    • MARIS: Method for Analyzing RNA following Intracellular Sorting 

      Hrvatin, Siniša; Deng, Francis; O'Donnell, Charles W.; Gifford, David K.; Melton, Douglas A. (Public Library of Science, 2014)
      Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method ...