Moderator: Pawel Szczesny

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Pawel Szczesny3.2k
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Bioinformatics, genomics, systems biology and teaching.

Posts by Pawel Szczesny

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Comment: C: Number of Transcripts in GRCh38
... On the archives of Ensembl (https://www.ensembl.org/info/website/archives/index.html ) you can find old versions. In each case you can find under "More information and statistics" link for human genome detailed breakdown of the number of different features in particular assembly. An example from Jul ...
written 8 months ago by Pawel Szczesny3.2k
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Comment: C: literature mining for genes and mutations
... I would be more specific with the goal of your task. What kind of mutations you want to extract? All variations or only those related to diseases? Any diseases? Any kind of mutation (SNP, indels, structural variants, etc.)? Also, it's worth to know the scale of the task (how many genes you have), an ...
written 8 months ago by Pawel Szczesny3.2k
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How to create bimap with getAnnMap using ENSEMBL ids instead of ENTREZ?
... I was using `Org.hs.eg.db`-type objects to create an annotation map with `annotate` package in a following way: `symbol.bimap <- getAnnMap("SYMBOL", "org.hs.eg.db")`. By default, the returned bimap uses ENTREZ ids as keys. I want to use ENSEMBL ids as keys, but apparently `getAnnMap` does not all ...
R bioconductor annotation written 8 months ago by Pawel Szczesny3.2k
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Model (database) for recurrent regulatory network in human
... I'm looking for a recurrent model of human regulatory network. By recurrent I mean something along the lines: 1. You introduce change (SNP, whole gene deletion, whatever) 2. This intervention induces changes in the transcription of several other genes. 3. This genes induce changes in the transcript ...
regulation network human written 2.4 years ago by Pawel Szczesny3.2k
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Where to find canonical versions of 18S sequences?
... I'm doing an analysis of sequence features in 18S rRNA sequences. I have downloaded data from SILVA database. Unfortunately, typical vertebrate has more than a single 18S sequence. I know that most of them are considered pseudogenes, but unless I check them one by one, there's no way to guess which ...
18s rrna databases written 3.5 years ago by Pawel Szczesny3.2k • updated 20 months ago by Alex Bel30
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Comment: C: Which software can be used to visualize phylogenetic trees with a large number o
... Pointers are in similar question: https://www.biostars.org/p/2438/  ...
written 4.4 years ago by Pawel Szczesny3.2k
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Comment: C: "An Explosion Of Bioinformatics Careers" - from Science Careers
... I didn't notice that. I didn't buy the main thesis (see my comment to Pierre's reply), but I thought it is a regular article, not an advertisement. ...
written 4.4 years ago by Pawel Szczesny3.2k
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Comment: C: "An Explosion Of Bioinformatics Careers" - from Science Careers
... I tell my students that it's a "bleeding edge science" and it will become "avant-garde science" next ;).  ...
written 4.4 years ago by Pawel Szczesny3.2k
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Comment: C: "An Explosion Of Bioinformatics Careers" - from Science Careers
... My impression was that the article in Science creates reality rather than describes it. On the other hand, one created position a year is 100% more than one position created every two years, isn't it? ...
written 4.4 years ago by Pawel Szczesny3.2k
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Forum: "An Explosion Of Bioinformatics Careers" - from Science Careers
... I'm not sure if that was already posted, but I had found it interesting, especially with the growing amount of questions "should I get to bioinformatics". Last paragraph of this piece from Science: Data scientists can expect the field to change and evolve in novel ways in the near future. But the b ...
career forum written 4.4 years ago by Pawel Szczesny3.2k • updated 4.4 years ago by Istvan Albert ♦♦ 78k

Latest awards to Pawel Szczesny

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Where to find canonical versions of 18S sequences?
Great Question 2.4 years ago, created a question with more than 5,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Parsing Jackhmmer Output
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Detailed Data On Ph Influence On Km
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For "An Explosion Of Bioinformatics Careers" - from Science Careers
Popular Question 3.1 years ago, created a question with more than 1,000 views. For What Biological Problems Can Be Gamified Using Bioinformatics Tools?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Converting Taxonomic Lineages Into A Common Tree
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Bioinformatics/Cheminformatics/Biology Games
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Raw Data For Soil Metagenomes?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Converting Taxonomic Lineages Into A Common Tree
Student 3.4 years ago, asked a question with at least 3 up-votes. For Detailed Data On Ph Influence On Km
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How To Estimate Sequencing Depth Needed To Fully Capture Metagenomic Data?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?

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