551 Matching Annotations
  1. Feb 2019
  2. Jan 2019
  3. Dec 2018
  4. Nov 2018
  5. Oct 2018
  6. Sep 2018
    1. HOMER
    2. Target enhancers are identified by leave-one-ou

      Likelihood ratio test as in ISMARA?

    3. ridge regressio
    4. centered and scale

      Likely centering and scaling (by SD) rows, i.e., across samples.

    5. motifs without any hits in the supplied sequencesand motifs mapping to transcription factors with low expression(default threshold: 1 normalized read per kilobase) are remove

      sensible

    6. motif matrix is centered

      Could mean double-centered, or row- or column-centered. Rows correspond to enhancers, columns to motifs. Centering columns makes sense; rows not so much.

    7. Motif search, calculation of motif activities, and target prediction
    1. Unlike simple k-mer searching, these methods were designed to predict individual RBP binding sites. They go beyond the motif content alone, for instance by taking into account site accessibility (Li et al. 2010; Zhang et al. 2013) or clustering (Akerman et al. 2009; Zhang et al. 2013).

      Suggests that RBPmap is a good choice, provided one uses the weighted rank score accounting for clustering and the conservation filter. mCarts by Zhang et al. applied to the ENCODE CLIP data would complement RBPmap, but what would be even better is if ENCODE had already applied it to their data and can provide the binding site predictions.

    2. Estimating the prevalence of functional exonic splice regulatory information
  7. Aug 2018
    1. RHEL mount hangs: nfs: server [...] not responding, still trying
  8. Jul 2018
    1. repeat expansion at IIL1 leads to increased accumulation of 24-nt siRNAs in a temperature-dependent manner that correlates with the iil phenotype. We show that DCL3 and other components of the RNA-dependent DNA methylation (RdDM) pathway are essential for this siRNA-directed epigenetic gene silencing
  9. Jun 2018
    1. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs

      Queuosine metabolite necessary for DNMT2-induced tRNA modification; salvaged from bacteria of microbiome

  10. May 2018
    1. one level is chosen as the “reference”, and its mean behaviour is represented by the intercept. Each column of the resulting matrix represents the difference between the mean of one level and this reference level
  11. Apr 2018
    1. caffeine caused a significant decrease of PTH secretion and PTH gene expression. This decrease occurred in parallel with a decrease of the intracellular cAMP level, protein kinase A activity, and ADORA1 gene expression
    1. chronic administration of caffeine could lead to negative calcium balance when there is an impaired ability to increase the efficiency of calcium absorption. Such a situation exists in elderly human subjects
    1. Vitamin D concentration among the groups was 16.2±5.3 mL and 80.3% of them were considered to be vitamin D-deficient. All the groups appeared to have deficiencies compared to males who did not consume caffeine
    1. JupyterHub, a multi-user Hub, spawns, manages, and proxies multiple instances of the single-user Jupyter notebook server.
  12. Mar 2018
  13. Feb 2018
    1. Why do some gene and transcript ids start with ENSGR or ENSTR in the GTF/GFF3?