- Dec 2017
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royalsocietypublishing.org royalsocietypublishing.org
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The natural selection of bad science
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www.sciencedirect.com www.sciencedirect.com
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Transcription factor–DNA binding: beyond binding site motifs
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alleledb.gersteinlab.org alleledb.gersteinlab.orgAlleleDB1
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AlleleDB is a repository, providing genomic annotation of cis-regulatory single nucleotide variants (SNVs) associated with allele-specific binding (ASB) and expression (ASE).
Tags
Annotators
URL
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- Nov 2017
-
www.rittmanmead.com www.rittmanmead.com
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Linux cluster sysadmin -- OS metric monitoring with colmux
SSH keys, pdsh distributed execution, collectl and colmux monitoring
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stackoverflow.com stackoverflow.com
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find . -type d \( -path dir1 -o -path dir2 -o -path dir3 \) -prune -o -print
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rsanderlin.com rsanderlin.com
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BASH: Create User Accounts with Random Password
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www.cyberciti.biz www.cyberciti.biz
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How to Change a USER and GROUP ID on Linux For All Owned Files
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stackoverflow.com stackoverflow.com
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while IFS='=' read -r col1 col2 do echo "$col1" echo "$col2" done <testprop.properties
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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In silico modeling predicts drug sensitivity of patient-derived cancer cells
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www.lrjournal.com www.lrjournal.com
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missense
nonsense?
what about missense mutations of unknown significance?
-
Computational drug treatment simulations on projections of dysregulated protein networks derived from the myelodysplastic mutanome match clinical response in patients
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www.gnu.org www.gnu.org
-
Finding Files
with find
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forums.plex.tv forums.plex.tv
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find /volume1/Movies /volume1/Music /volume1/Photos "/volume1/Home Videos" "/volume1/Music Videos" -type d -exec chmod 755 {} \;
recursively changing permissions with find, specifically for directories versus files
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rafalab.github.io rafalab.github.ioharvardx1
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HarvardX Biomedical Data Science Open Online Training
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www.genome.gov www.genome.gov
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Introduction to Population Genetics
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epigeneticsandchromatin.biomedcentral.com epigeneticsandchromatin.biomedcentral.com
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Genome-wide methylation data mirror ancestry information
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www.nature.com www.nature.com
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Two independent modes of chromatin organization revealed by cohesin removal
Tags
Annotators
URL
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f1000research.com f1000research.com
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RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved]
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genomebiology.biomedcentral.com genomebiology.biomedcentral.com
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MCC
Matthews correlation coefficient
-
novel method developed within the MAQC-III project utilizing the expression distributions, corrected for noise and batch effects, and assisted by random resampling, to compute DEG scores related to the Wilcoxon U test (Magic, see Additional file 1: Supplementary Note 2)
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genome.cshlp.org genome.cshlp.org
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These results suggest that deep sequencing is necessary for accurate determination of the expression level of genes
or better quantification methods
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academic.oup.com academic.oup.com
-
EGR2 peaks overlapped with a SOX10 peak when allowing separation distance as large as 1000 bp and 11.09% of the SOX10 peaks overlapped with an EGR2 peak with the same separation distance
unclear
-
Using 40 sets of randomized peak sequences, the occurrence of the motif never exceeded 74%
unclear
-
MOSAiCS implements a model-based approach where the background distribution for unbound regions take into account systematic biases such as mappability and GC content and the peak regions are described with a two component Negative Binomial mixture model
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-
www.sciencedirect.com www.sciencedirect.com
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pairwise overlaps using Fisher’s test and mutual exclusion (Leiserson et al., 2016xA weighted exact test for mutually exclusive mutations in cancer. Leiserson, M.D.M., Reyna, M.A., and Raphael, B.J. Bioinformatics. 2016; 32: i736–i745Crossref | PubMed | Scopus (4)See all ReferencesLeiserson et al., 2016)
-
CRISPR screening has emerged as a powerful method for identifying critical functional dependencies in vitro (Koike-Yusa et al., 2014xGenome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, Mdel.C., and Yusa, K. Nat. Biotechnol. 2014; 32: 267–273Crossref | PubMed | Scopus (285)See all References, Shalem et al., 2014xGenome-scale CRISPR-Cas9 knockout screening in human cells. Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelson, T., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., and Zhang, F. Science. 2014; 343: 84–87Crossref | PubMed | Scopus (936)See all References)
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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EXCAVATOR: detecting copy number variants from whole-exome sequencing data
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www.nature.com www.nature.com
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plasma cells
B cells
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polymorphonuclear (PMN) cell39
granulocyte
-
we determined the number of histologies needed to identify genes with maximal prognostic power
histologies=samples
-
All microarray studies in PRECOG were consistently normalized and pre-processed
no RNA-seq
-
CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Robust enumeration of cell subsets from tissue expression profiles
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bmcbioinformatics.biomedcentral.com bmcbioinformatics.biomedcentral.com
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AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Clone 1 is the founding clone; 12.74% of the tumour cells contain only this set of mutations
derivation unclear; not provided in supplemental information
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-
images.nature.com images.nature.com
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Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing
-
Comparison of SNVs detected in the whole genome sequencing data with SNPs genotyped using arrays
inference of "%diploid coverage"
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gmt.genome.wustl.edu gmt.genome.wustl.edu
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SomaticSniper
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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tier 1 contains all changes in the amino acid coding regions of annotated exons, consensus splice-site regions, and RNA genes (including microRNA genes). Tier 2 contains changes in highly conserved regions of the genome or regions that have regulatory potential. Tier 3 contains mutations in the nonrepetitive part of the genome that does not meet tier 2 criteria, and tier 4 contains mutations in the remainder of the genome
Tags
Annotators
URL
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Gene Set Enrichment Analysis Made Simple
using aggregate t or chi^2 statistic to test if a set of genes is on aggregate differentially expressed
-
-
www.laptop-lcd-screen.co.uk www.laptop-lcd-screen.co.uk
-
UK Based LCD Screen Replacement Experts
Tags
Annotators
URL
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-
onlinelibrary.wiley.com onlinelibrary.wiley.com
-
The background puzzle: how identical mutations in the same gene lead to different disease symptoms
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-
www.larkinweb.co.uk www.larkinweb.co.uk
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Mounting file systems over two SSH hops
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www.nature.com www.nature.com
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To stay young, kill zombie cells
-
- Oct 2017
-
genomebiology.biomedcentral.com genomebiology.biomedcentral.com
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Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
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genome.cshlp.org genome.cshlp.org
-
RNA-sequence analysis of human B-cells
Tags
Annotators
URL
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-
academic.oup.com academic.oup.com
-
Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve
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-
www.sciencedirect.com www.sciencedirect.com
-
Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma
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-
www.nature.com www.nature.com
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The prognostic landscape of genes and infiltrating immune cells across human cancers
Tags
Annotators
URL
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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RNA sequencing of cancer reveals novel splicing alterations
Tags
Annotators
URL
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-
www.nature.com www.nature.com
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Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high-grade serous ovarian cancer that distinguish malignant, tumour-sustaining and chemo-resistant ovarian tumour cells
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Tags
Annotators
URL
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genomebiology.biomedcentral.com genomebiology.biomedcentral.com
-
Using their expression data and the same fold-change categories, we investigated the influence of both affinity and cooperative effects based on GraphProt predictions of Ago2 binding sites in comparison to the available CLIP-seq data.
Could do the same since expression microarray data are available, but they show complete lack of differential expression when over-expressing our proteins of interest.
-
allows the evaluation of putative binding sites with a meaningful score that reflects the biological functionality
score = prediction margin Part of standard GraphProt output?
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Prediction margins
Part of standard GraphProt output?
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TIA-1 has been described as an ARE-binding protein and binds both U-rich and AU-rich elements.
-
logos are a mere visualization aid and do not represent the full extent of the information captured by GraphProt models
-
tenfold cross-validation technique
How do AUROCs look for our proteins of interest compared to the AUROCs for the iCLIP'ed proteins in Additional File 2?
-
The following describes a typical biological application of computational target detection. A published CLIP-seq experiment for a protein of interest is available for kidney cells, but the targets of that protein are required for liver cells. The original CLIP-seq targets may have missed many correct targets due to differential expression in the two tissues and the costs for a second CLIP-seq experiment in liver cells may not be within the budget or the experiment is otherwise not possible. We provide a solution that uses an accurate protein-binding model from the kidney CLIP-seq data, which can be used to identify potential targets in the entire transcriptome. Transcripts targeted in liver cells can be identified with improved specificity when target prediction is combined with tissue-specific transcript expression data.
use case
-
Peak detection leads to high-fidelity binding sites; however, it again increases the number of false negatives. Therefore, to complete the RBP interactome, computational discovery of missing binding sites is essential.
iCLIP data are not comprehensive
-
GraphProt: modeling binding preferences of RNA-binding proteins
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns
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-
www.purplemath.com www.purplemath.com
-
Solving Quadratic Inequalities
Tags
Annotators
URL
-
-
www.restore.ac.uk www.restore.ac.uk
-
An Introduction to Odds, Odds Ratios and Exponents
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www.biostars.org www.biostars.org
-
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
discussion of tools; recently revived
Tags
Annotators
URL
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asciigenome.readthedocs.io asciigenome.readthedocs.io
-
ASCIIGenome is a command-line genome browser running from terminal window
-
-
www.sanger.ac.uk www.sanger.ac.uk
-
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation
Tags
Annotators
URL
-
-
github.com github.com
-
Genome Maps is a modern and high-performance web-based HTML5 genome browser
Tags
Annotators
URL
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liorpachter.wordpress.com liorpachter.wordpress.com
-
How not to perform a differential expression analysis (or science)
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Salmon provides fast and bias-aware quantification of transcript expression
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Analyzing Copy Number Variation using SNP Array Data: Protocols for Calling CNV and Association Tests
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bmcmedgenomics.biomedcentral.com bmcmedgenomics.biomedcentral.com
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CNVassoc: Association analysis of CNV data using R
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-
zzz.bwh.harvard.edu zzz.bwh.harvard.eduPLINK1
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Rare copy number variant (CNV) data
Tags
Annotators
URL
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journals.plos.org journals.plos.org
-
A New Method for Detecting Associations with Rare Copy-Number Variants
Tags
Annotators
URL
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Chromatin marks and ambient temperature-dependent flowering strike up a novel liaison
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Intragenic Enhancers Attenuate Host Gene Expression
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
A genome-wide analysis of loss of heterozygosity and chromosomal copy number variation in Proteus syndrome using high-density SNP microarrays
Tags
Annotators
URL
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support.illumina.com support.illumina.com
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KaryoStudio
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
CG dinucleotide suppression enables antiviral defence targeting non-self RNA
Tags
Annotators
URL
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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argyle: An R Package for Analysis of Illumina Genotyping Arrays
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-
www.biorxiv.org www.biorxiv.org
-
equal to the frequency of the higher expressed eQTL allele in the population
should be equal to product of frequency of high eQTL allele and major coding allele, though the latter will be close to 1 for the rare coding mutations studied here
-
211,575 rare (MAF < 1%) coding variantsat thousands of genes
not necessarily pathogenic
-
proportiona
inversely proportional?
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Modified penetrance of coding variants by cis-regulatory variation shapes human traits
-
- Sep 2017
-
www.nature.com www.nature.com
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Parental influence on human germline de novo mutations in 1,548 trios from Iceland
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-
www.malacards.org www.malacards.org
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Maternal Uniparental Disomy of Chromosome X
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-
www.malacards.org www.malacards.org
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Paternal Uniparental Disomy of Chromosome X
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-
stackoverflow.com stackoverflow.com
-
Perl script in bash's HereDoc
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-
clubmate.fi clubmate.fi
-
Associative arrays in bash
Tags
Annotators
URL
-
-
www.maketecheasier.com www.maketecheasier.com
-
How to Set Up Bluetooth in Linux
Tags
Annotators
URL
-
-
www.statnews.com www.statnews.com
-
Gut Germs Appear to Play Role in Multiple Sclerosis
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
RNA binding protein CPEB1 remodels host and viral RNA landscapes
remodel = alt splicing
Tags
Annotators
URL
-
-
www.biorxiv.org www.biorxiv.org
-
Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
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-
chronologicaldot.wordpress.com chronologicaldot.wordpress.com
-
Restoring The Menu Panel on Linux Mint Cinnamon
when text has disappeared etc.
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-
bmcbioinformatics.biomedcentral.com bmcbioinformatics.biomedcentral.com
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The projection score - an evaluation criterion for variable subset selection in PCA visualization
"variable" typically means gene or locus in the context of biological data.
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-
www.perlmonks.org www.perlmonks.org
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How can I capture STDERR from an external command?
problem arises when using backticks to execute external commands
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-
www.biorxiv.org www.biorxiv.org
-
Major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data"
re Venter study in PNAS, claiming to be able to identify people based on whole genome data
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-
www.nature.com www.nature.com
-
Plot a course through the genome Inspired by Google Maps, a suite of tools is allowing researchers to chart the complex conformations of chromosomes.
mentioned tools are focused on (capture) Hi-C data
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-
askubuntu.com askubuntu.com
-
Multiple Boot Systems Time Conflicts
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-
raspberrypi.stackexchange.com raspberrypi.stackexchange.com
-
scan all blocks of your partitions
checking an SD card for bad sectors
-
-
www.raymond.cc www.raymond.cc
-
4 Tools to Test and Detect Fake or Counterfeit USB Flash Drives
for Windows
-
-
www.scientificamerican.com www.scientificamerican.com
-
One Test May Spot Cancer, Infections, Diabetes and More
based on cell free DNA fragments in blood; DNA methylation patterns and fragment length distributions can inform on organ of origin.
-
-
www.nature.com www.nature.com
-
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence
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-
www.sciencemag.org www.sciencemag.orgmyIDP1
-
myIDP
collection of articles on why IDPs are useful
Tags
Annotators
URL
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-
biosciences.stanford.edu biosciences.stanford.edu
-
IDP Forms and Documentation
for PhD students
Tags
Annotators
URL
-
-
www.med.upenn.edu www.med.upenn.edu
-
Individual Development Plans (IDPs)
for PhD students
-
- Aug 2017
-
www.springer.com www.springer.com
-
Wood Structure and Environment
impacts of environmental conditions on wood anatomy; not climate reconstruction
Tags
Annotators
URL
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-
iopscience.iop.org iopscience.iop.org
-
Diverse growth trends and climate responses across Eurasia's boreal forest
implies limitations of using macroscopic tree ring features for climate reconstructions, which are influenced by many different factors
-
-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
A Technical Perspective in Modern Tree-ring Research - How to Overcome Dendroecological and Wood Anatomical Challenges
microtome-generated sections along the entire length of wood core samples for anatomical studies
-
- Jul 2017
-
academic.oup.com academic.oup.com
-
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip
better than BMIQ
-
-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
global dye-bias equalization step to control for the different average intensities in the red and green channels. This procedure scales the background-corrected intensities, dividing by the average intensity of the positive control probes in the same channel, red or green, and multiplying by the average intensity of all positive controls in a reference array.
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-
bluishcoder.co.nz bluishcoder.co.nz
-
firefox -ProfileManager
better: firefox --no-remote -ProfileManager
-
-
allanmcrae.com allanmcrae.com
-
Just use SSH’s support for SOCKS5 proxy.
simple alternative to (open)VPN for web content
Tags
Annotators
URL
-
-
pubs.acs.org pubs.acs.org
-
Mass Spectrometry of Structurally Modified DNA
extensive review
Tags
Annotators
URL
-
-
wiki2.dovecot.org wiki2.dovecot.org
-
Welcome to the Dovecot Wiki
Tags
Annotators
URL
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
The ISMARA client
-
-
genome.cshlp.org genome.cshlp.org
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ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
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-
askubuntu.com askubuntu.com
-
Create a script in your encrypted home directory: ~/scripts/mount_storage.sh
How to auto-mount LUKS encrypted drive upon login
-
-
www.napoleome.ch www.napoleome.ch
-
Napoleon oak genome sequencing project web site: example of public engagement in tree genomics
Tags
Annotators
URL
-
-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Quercus robur Genome sequencing and assembly
data (not yet live) associated with https://hyp.is/4DerrmIaEeehDPNBqsRcxQ/www.biorxiv.org/content/biorxiv/early/2017/06/13/149203.full.pdf
Tags
Annotators
URL
-
-
www.edx.org www.edx.org
-
Introduction to R for Data Science
Data analysis course using R
-
-
www.datacamp.com www.datacamp.com
-
Learn Data Science Online
Data analysis courses using R and Python
Tags
Annotators
URL
-
-
runestoneinteractive.org runestoneinteractive.org
-
Runestone Interactive
Interactive textbooks on programming
-
- Jun 2017
-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs
Cordycepin, a modified adenosin produced by a species of fungus, inhibits polyA tail elongation; the RNA-seq data in this paper do NOT include cordycepin-treated samples
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molossinus.lab.nig.ac.jp molossinus.lab.nig.ac.jp
-
Takada et al. 2013
NIG Mouse Genome Database: JF1 and MSM SNPs; effective genome browser
Tags
Annotators
URL
-
-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
Disruption of a novel imprinted zinc-finger gene, ZNF215, in Beckwith-Wiedemann syndrome
demonstrates imprinted expression, but ICR is unknown
Tags
Annotators
URL
-
-
journals.plos.org journals.plos.org
-
Fig 5. Highest ranked ASE genes from (A) brain and (B) liver.
observation of allele-specific expression in brain
-
-
www.placentajournal.org www.placentajournal.org
-
CHURC1
expression is sensitive to tobacco smoke exposure
-
-
eprints.bbk.ac.uk eprints.bbk.ac.uk
-
CLLU1OS
associated with ASM
Tags
Annotators
URL
-
-
genome.cshlp.org genome.cshlp.org
-
SERPINB10
triple-hit: H3K4me2, DNAm and CTCF. skew in SERPINB10 expression consistent with parental allele-specific expression.
Tags
Annotators
URL
-
-
journals.plos.org journals.plos.org
-
SERPINB10
haplotype imbalance of expression observed for SERPINB10, but not MEST (imprinted)
Tags
Annotators
URL
-
- Apr 2017
-
www.biostars.org www.biostars.org
-
I'm the developer of pyGeno. Here's a little script that does just that for the Gene TPST2, by using segment trees
recipe for merging transcripts of a gene into a single compound transcript
-
- Sep 2016
-
www.nature.com www.nature.com
-
78% coding density
MAC genome
-
-
journals.plos.org journals.plos.org
-
The P. tetraurelia MAC genome [1] was assembled from 13× Sanger sequencing reads from different insert size librairies of strain d4-2 DNA. Strain d4-2 only differs from strain 51 at a few loci.
SRA accession ERR138952
Tags
Annotators
URL
-
-
software.broadinstitute.org software.broadinstitute.org
-
You must quit IGV and restart for this preference to take effect. The genome should appear in the drop-down list.
restart may be insufficient; had to modify prefs.properties in ~/igv (removing old cached genome values) before i could see my genomes
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-
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
-
MACS2, an updated version of MACS that is specifically designed to process mixed signal types
Tags
Annotators
URL
-
-
ccb.jhu.edu ccb.jhu.eduHISAT24
-
--novel-splicesite-outfile
use to collect coordinates of identified IES
-
--max-intronlen
set to 1000: max IES length <1000bp
-
--min-intronlen
default acceptable: 26bp is minimal IES length, 20bp is minimal intron length
-
--pen-noncansplice
set to zero
Tags
Annotators
URL
-
-
www.asmscience.org www.asmscience.org
-
90,000 tiny introns (between 20 and 34 nt in length)
-
MIC and MAC determination during the P. tetraurelia sexual cycle
def. maternal: recipient of gametic nucleus
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-
onlinelibrary.wiley.com onlinelibrary.wiley.com
-
Paramecium IESs are unique sequence elements between 26 and 882 bp in length
-
hypothetical pathways for scnRNA-mediated recruitment of the endonuclease in Paramecium
nucleotide modifications: possibly 6mA
-
The “genome-scanning” model, as envisioned in Paramecium
subtraction of MAC RNA from MIC small RNA = targets (IES) for excision
-
Nuclear dimorphism and DNA rearrangements in the ciliates Paramecium tetraurelia
tetraurelia: imprecise repeat v precise (splicing-like) IES excision
-
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thomas-cokelaer.info thomas-cokelaer.info
-
conda and bioconda channel
channel configuration, including for specific python version
-
-
www.cell.com www.cell.com
-
Detection of 6mA Peaks from 6mA-IP-Seq
bowtie (v1), MACS
-
- Aug 2016
-
Local file Local file
-
One currentproject in Dr Schulz’s lab is to characterise a selection of interesting loci in detailusingisoform specific primers and qRT-PCR.
Would be better to end with making an explicit connection between the ENCODE tissue-specific RNAseq data and the Setd2 knock-down RNAseq data. Would it make sense to focus on loci showing evidence for tissue-specific polyA as well as being dependent on Setd2 for correct splicing?
-
not significant (<0.0274)
I would call that marginally significant
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in
as
-
whereupon
but
-
Also these DNA damages as
DNA damage like
-
damages
damage
-
evinced
exhibited
-
remarkable
substantial
-
For some loci even the used tissues can differ in terms of strainand developmental stage between the qRT-PCRand bisulfite sequencing.
German sentence structure: splitting the predicate (differ ... between). Not done in English. very awkward to read.
-
a different and relatively unclear pattern
different and inconsistent patterns
-
Presumed that themechanism of poly(A) site selection/alternative polyadenylation may operate genome-wide in a tissue-specificmanner,and thus, contribute to the complexity of the mammalian transcriptome,
use of very long prepositional phrases at the start of sentences makes reading difficult. stick to simple subject- predicate- object sentence structure.
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Presumed
Hypothesising
-
. This is seen in a different way
-
really low
no or low (<10%)
-
Thedata displayedthat it is roughly possible to
My data suggest that it is possible to qualitatively
-
a totally reliable method
considered quantitative
-
from
determined using
-
Assuming the
The
-
AAA indicates poly(A) site
nice and useful figure but: you primed the cDNA synthesis with random hexamers. the qRT-PCR results are therefore not specific to polyadenylated transcripts. so, above figure shows models consistent with the data rather than summarisations of the data (you did not directly measure polyA).
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random hexamers
beware that this implies non-polyadenylated transcripts also are represented in the sample
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of
for the
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in detail in drafted simplified images
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s
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directs
based on direct
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normalised tissue
reference tissue
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unexpected based on theRNA-seq data
not if you look at the UCSC data (see comment above)
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a
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for example
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Based on the RNA-seq data
depends in this case on whether you look at the scatter plot or the UCSC genome browser: they are not telling the same story for some reason. my corrections below reflect what UCSC shows, which results in flipping of placenta and thymus.
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Thymus
Placenta
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placenta
thymus
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placenta
thymus
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thymus
placenta
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Thymus
Placenta
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placenta
thymus
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, compromised
resulted in
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liver adult
adult liver
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different
the different
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opposed to liver adult
relative to adult liver
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and stretched
:
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moretranscripts terminate across
see above; will stop pointing this out
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conversion rate was calculated as72.55%
low conversion rate leads to over-estimation of methylation, which could explain the 45% methylation seen in placenta
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used for measurements ofheart
primer sets are not tissue-specific; you used them for all tissues; only the measurements themselves are tissue-specific
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arose from
for
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Adck2 encodes for a kinase
The host transcript of the CGI is non-coding. Your upstream primers amplify both the coding transcript and the non-coding host transcript. That is a limitation. Could explain the inconsistencies re the RNAseq data.
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the expression of transcripts
transcription
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qRT-PCR
qRT-PCR cannot show transcription termination: all it can do is verify the RNAseq data, i.e., more relatively more transcription upstream of an active CGI compared to transcription across the CGI. It is important to be precise about what qRT-PCR can and cannot do.
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transcripts terminating
transcription
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transcripts terminateacross
transcription extends across
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transcripts terminating
transcription
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1) Tissue with high CGI activity and more transcripts terminating upstream than across and 2) Tissue with lowCGI activity and more transcripts terminating across than upstream, as described in the chapter ‘Loci selection’.
The data do not show transcripts terminating upstream or downstream of the CGI, they are merely consistent with the hypothesis.
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s a
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