Searching journal content for articles similar to Elf and Ehrenberg 13 (11): 2475.

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  1. Research: Enhancer RNA profiling predicts transcription factor activity
    • Joseph G. Azofeifa,
    • Mary A. Allen,
    • Josephina R. Hendrix,
    • Timothy Read,
    • Jonathan D. Rubin,
    • and Robin D. Dowell
    Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
    ...RNA inferred MD-score and the transcription level (FPKM) of the gene encoding the TF (Supplemental Fig. S14B), suggesting that some TFs are themselves regulated at transcription. However, the observed correlations were often weak and complex—typically neither linear or monotonic—consistent with the observation...
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  2. COMMENTARY: Systems Biology Is Taking Off
    • Måns Ehrenberg,
    • Johan Elf,
    • Erik Aurell,
    • Rickard Sandberg,
    • and Jesper Tegnér
    Genome Res. November 2003 13: 2377-2380; doi:10.1101/gr.1763203
    ..., J. and Ehrenberg, M. 2003 . Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res. (this issue). ↵ Elf, J., Nilsson, D., Tenson, T., and Ehrenberg, M. 2003 . Selective charging of tRNA isoacceptors explains patterns of codon usage. Science 300 : 1718...
  3. Preface: The Logic of Life
    • Måns Ehrenberg,
    • Erik Aurell,
    • Johan Elf,
    • Rickard Sandberg,
    • and Jesper Tegnér
    Genome Res. November 2003 13: 2375-2376; doi:10.1101/gr.1765703
    ...maturation. Genome Res. 13 : (this issue). Elf, J., and Ehrenberg, M. 2003 . Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res. 13 : (this issue). Jensen, L.J., Ussery, D.W., and Brunak, S. 2003 . Functionality of system components: Conservation...
  4. Method: Detecting differential growth of microbial populations with Gaussian process regression
    • Peter D. Tonner,
    • Cynthia L. Darnell,
    • Barbara E. Engelhardt,
    • and Amy K. Schmid
    Genome Res. February 2017 27: 320-333; Published in Advance November 18, 2016, doi:10.1101/gr.210286.116
    ...of smooth underlying growth functions through the length-scale parameter, explicitly accounting for experimental noise. This is in contrast to other recent models such as linear spline fitting in generalized additive models (GAMs), which are sensitive to technical variation (Sekse et al. 2012...
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  5. Method: Genome-wide identification of conserved regulatory function in diverged sequences
    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    ...line) alignments; (black dotted line) perfectly separates correct from incorrect alignments. (Inset) The receiver operating characteristic (ROC) curve for the linear SVM classifier separating orthologous from control alignments; the curve profiles the performance in terms of the number of orthologous...
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  6. ARTICLE: The anatomy of microbial cell state transitions in response to oxygen
    • Amy K. Schmid,
    • David J. Reiss,
    • Amardeep Kaur,
    • Min Pan,
    • Nichole King,
    • Phu T. Van,
    • Laura Hohmann,
    • Daniel B. Martin,
    • and Nitin S. Baliga
    Genome Res. October 2007 17: 1399-1413; Published in Advance September 4, 2007, doi:10.1101/gr.6728007
    ...) ( Fig. 3A ) correlated most strongly with the ability to predict its dynamics based upon the changes in the measured oxygen tension levels via a linear model (Supplemental Fig. 2) ( Bonneau et al. 2006 ). We therefore used the values along the PC1 axis to assign the “oxic score” to each cluster, which...
  7. METHODS: Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH
    • José M. Lage,
    • John H. Leamon,
    • Tanja Pejovic,
    • Stefan Hamann,
    • Michelle Lacey,
    • Deborah Dillon,
    • Richard Segraves,
    • Bettina Vossbrinck,
    • Antonio González,
    • Daniel Pinkel,
    • Donna G. Albertson,
    • Jose Costa,
    • and Paul M. Lizardi
    Genome Res. February 1, 2003 13: 294-307; doi:10.1101/gr.377203
    ...are between −0.262 and 0.262 (0.833 and 1.199 when expressed as linear ratios) for the unamplified experiment. The same confidence bounds calculated for the unamplified experiment are replicated in the plot of ratios generated by microarray analysis of amplified DNA. Evaluation of DNA Amplification Bias Using...
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