Browsing HMS Scholarly Articles by Author "Klitgord, Niels"

Now showing items 1-7 of 7

    • A Genome-Wide Gene Function Prediction Resource for Drosophila melanogaster 

      Yan, Han; Venkatesan, Kavitha; Beaver, John E.; Klitgord, Niels; Yildirim, Muhammed; Hao, Tong; Hill, David E.; Cusick, Michael E.; Perrimon, Norbert; Roth, Frederick P.; Vidal, Marc; Provart, Nicholas James (Public Library of Science, 2010)
      Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. Here we present a resource for Drosophila melanogaster gene function predictions. We trained function-specific ...

    • 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 ...

    • Edgetic Perturbation Models of Human Inherited Disorders 

      Simonis, Nicolas; Li, Qian-Ru; Heuze, Fabien; Klitgord, Niels; Tam, Stanley; Venkatesan, Kavitha; Mou, Danny; Swearingen, Venus; Yildirim, Muhammed; Dricot, Amélie; Szeto, David; Lin, Chenwei; Hao, Tong; Fan, Changyu; Milstein, Stuart; Dupuy, Denis; Brasseur, Robert; Zhong, Quan; Charloteaux, Benoit; Yu, Haiyuan; Yan, Han; Hill, David E.; Cusick, Michael; Vidal, Marc (Nature Publishing Group, 2009)
      Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in interactome models as ‘nodes' and ‘edges', respectively. Better ...

    • Host-Pathogen Interactome Mapping for HTLV-1 and -2 Retroviruses 

      Simonis, Nicolas; Rual, Jean-François; Lemmens, Irma; Boxus, Mathieu; Hirozane-Kishikawa, Tomoko; Gatot, Jean-Stéphane; Dricot, Amélie; Hao, Tong; Vertommen, Didier; Legros, Sébastien; Daakour, Sarah; Klitgord, Niels; Martin, Maud; Willaert, Jean-François; Dequiedt, Franck; Navratil, Vincent; Burny, Arsène; Van Lint, Carine; Tavernier, Jan; Kettmann, Richard; Twizere, Jean-Claude; Cusick, Michael; Hill, David E.; Vidal, Marc (BioMed Central, 2012)
      Background: Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, ...

    • Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes 

      Haynes, Chad; Oldfield, Christopher J; Ji, Fei; Klitgord, Niels; Cusick, Michael; Radivojac, Predrag; Uversky, Vladimir N; Vidal, Marc; Iakoucheva, Lilia M (Public Library of Science, 2006)
      Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted ...

    • Novel Insights into RNAi Off-Target Effects Using C. elegans Paralogs 

      Rual, Jean-Francois; Klitgord, Niels; Achaz, Guillaume (BioMed Central, 2007)
      Background: In the few years since its discovery, RNAi has turned into a very powerful tool for the study of gene function by allowing post-transcriptional gene silencing. The RNAi mechanism, which is based on the introduction ...

    • A Rapid Molecular Approach for Chromosomal Phasing 

      Regan, John F.; Kamitaki, Nolan; Legler, Tina; Cooper, Samantha; Klitgord, Niels; Karlin-Neumann, George; Wong, Catherine; Hodges, Shawn; Koehler, Ryan; Tzonev, Svilen; McCarroll, Steven A. (Public Library of Science, 2015)
      Determining the chromosomal phase of pairs of sequence variants – the arrangement of specific alleles as haplotypes – is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ...