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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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 17 months 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 2.6 years ago by Pawel Szczesny3.2k • updated 9 months ago by Alex Bel10
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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 3.4 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 3.5 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 3.5 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 3.5 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 3.5 years ago by Pawel Szczesny3.2k • updated 3.5 years ago by Istvan Albert ♦♦ 75k
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Comment: C: Exonerate ** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)
... I would not remove it, unless you require from exonerate 100% agreement (this is not recommended BTW) or mismatch codon can ruin your analysis. ...
written 3.5 years ago by Pawel Szczesny3.2k
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Answer: A: Exonerate ** FATAL ERROR **: Unrecognised symbol 'J' (ascii:74)
... J is a placeholder "used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue." It does not represent a proteinogenic amino acid (but an amibiguity between I and L) and exonerate does not have a translation table for it. ...
written 3.5 years ago by Pawel Szczesny3.2k
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Answer: A: How to generate .sra files from Fastq
... I have never used it but Mothur has a command "make.sra". ...
written 3.5 years ago by Pawel Szczesny3.2k

Latest awards to Pawel Szczesny

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Bioinformatics/Cheminformatics/Biology Games
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Student 2.5 years ago, asked a question with at least 3 up-votes. For Detailed Data On Ph Influence On Km
Commentator 2.8 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 2.8 years ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
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Popular Question 3.4 years ago, created a question with more than 1,000 views. For What Is The Best Pipeline For 16S Rna Metagenome Analysis?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: List Of Bioinformatics Books
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Scholar 3.5 years ago, created an answer that has been accepted. For A: Blacklist for questionable genbank entries
Scholar 3.5 years ago, created an answer that has been accepted. For A: Blacklist for questionable genbank entries
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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: List Of Bioinformatics Books

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