Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
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http://jkh1.github.io/
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7 years, 6 months ago
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Posts by Jean-Karim Heriche

<prev • 2,146 results • page 1 of 215 • next >
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Answer: A: Fields with biggest demand for bioinformatics?
... From my point of view, bioimage informatics is the growing field at the moment. There's more demand now from omics people with single cell technologies. You want to know what the cell you sequenced was doing when you harvested it: take some fluorescence images before doing the sequencing. You want t ...
written 16 minutes ago by Jean-Karim Heriche17k
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Comment: C: What are best physicians in Canada?
... How does this relate to bioinformatics ? ...
written 1 day ago by Jean-Karim Heriche17k
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Comment: C: how to combine standard deviations and mean for each group?
... If I understand correctly, you want to sort the rows based on some summary statistics but you're worried about different rows having different distributions. First you should look at the distribution of the data. If the data is not unimodal, measures of central tendency (mean, median, mode) may not ...
written 5 days ago by Jean-Karim Heriche17k
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Comment: C: Relation between GO terms of homologous genes in different organisms.
... I wouldn't know without seeing a phylogenetic tree but I certainly wouldn't make the inference based on name. Also I don't think one can infer orthology for groups as distant as mammals and bacteria. If interested in bacterial genes then look for other bacterial species. But generally, this is the i ...
written 9 days ago by Jean-Karim Heriche17k
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Comment: C: Relation between GO terms of homologous genes in different organisms.
... Transferring annotations between orthologs is commonly done. You don't have to limit yourself to a closely related species but can transfer annotations from any ortholog. For example yeast and Drosophila annotations are routinely used to annotate human genes. Depending on which organisms you're deal ...
written 9 days ago by Jean-Karim Heriche17k
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Answer: A: What's your preferred pathway enrichment analysis tool after DEG analysis and wh
... An alternative approach: [Finding New Order in Biological Functions from the Network Structure of Gene Annotations][1] [1]: http://europepmc.org/articles/PMC4654495/ ...
written 11 days ago by Jean-Karim Heriche17k
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Answer: A: Plotting two ROC curves
... Try with the R [pROC package][1]: library(pROC) roc1 <- plot.roc(outcome1, prediction1, main="ROC comparison", percent=TRUE, col= "red") roc2 <- lines.roc(outcome2, prediction2, percent=TRUE, col="blue") [1]: https://cran.r-project.org/package=pROC ...
written 11 days ago by Jean-Karim Heriche17k
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Comment: C: Essential proteins in PPI network
... From this link, the data corresponds to only one publication testing ~11000 genes and essentiality is defined as embryonic lethality or sterility. You can get this also from Wormbase by selecting the relevant phenotypes in the way I explained above. The difference is that WormBase data is collected ...
written 12 days ago by Jean-Karim Heriche17k
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Answer: A: Essential proteins in PPI network
... Assuming that for you essential means loss of function is lethal, here is how you can go: - On the WormBase site, go to Tools > Ontology browser - In the phenotype ontology (bottom of the page) look for phenotype "lethal" (variant > development variant > organism development variant > ...
written 12 days ago by Jean-Karim Heriche17k
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Comment: C: Essential proteins in PPI network
... I am not sure I understand the problem. WBGene00000040 has no phenotype and lethal phenotypes are reported as not observed for WBGene00000018. However, WBGene00000066 is reported as embryonic lethal. See my answer below for a way of doing it. ...
written 12 days ago by Jean-Karim Heriche17k

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Scholar 10 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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Scholar 22 days ago, created an answer that has been accepted. For A: Finding the right GO annotation flat file for human build GCRh37
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