User: Jelena Aleksic

gravatar for Jelena Aleksic
Reputation:
900
Status:
Trusted
Location:
Cambridge, UK
Website:
http://www.sciencewrit...
Scholar ID:
Google Scholar Page
Last seen:
3 years, 9 months ago
Joined:
6 years, 10 months ago
Email:
j********@gen.cam.ac.uk

I'm a bioinformatics postdoc working in Michaela Frye's lab at the Stem Cell Institute, University of Cambridge. My current project focuses on the role of RNA methylation in genome regulation, and uses data from a range of methods including mRNA-seq, sRNA-seq, bisulfite sequencing, CLIP, and most recently, ribosomal profiling. More broadly, I am interested in studying different levels of genome regulation, and how they interact to determine developmental outcomes. I also do freelance science writing.

Posts by Jelena Aleksic

<prev • 57 results • page 1 of 6 • next >
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Answer: A: Where to download In-vitro RNA-seq published experiments?
... The Cancer Genome Atlas has a large selection of data from tumours: http://cancergenome.nih.gov/ ...
written 4.5 years ago by Jelena Aleksic900
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Answer: A: identifying miRNA in RNAseq
... You might pick some up, but really, an mRNA-seq experiment is designed to pick up protein coding genes. If you are interested in a detailed look at miRNA expression, it is better to do a dedicated sRNA-seq experiment. As Lorena already mentioned, the protocol is different, and different size selecti ...
written 4.5 years ago by Jelena Aleksic900
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Answer: A: Sinking into the swamp by Using DESeq without replicates !!
... You just can't do a statistical analysis of differential expression without replicates. Basically all you can do is calculate the ratio between your sample and control, and then rank these, but it gives you no measure of confidence in the results, for obvious reasons. You can use DEseq to perform th ...
written 4.5 years ago by Jelena Aleksic900
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Comment: C: list of genes with associated histone marks
... Which organism? Which developmental point? Which tissue?  ...
written 4.5 years ago by Jelena Aleksic900
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Answer: A: Any Term To Descripe Protein Having No Go Term Annotated
... "of unknown function" "the function has not been annotated" "function as yet unknown" ...
written 5.3 years ago by Jelena Aleksic900
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Answer: A: Rrna Removal In Rna-Seq Data
... I personally use option b) when doing this. The reason is that it allows me to use multiply matching reads in subsequent analysis, while making sure that these definitely do not map to rRNA. But the other options you suggest also seem valid to me. ...
written 5.3 years ago by Jelena Aleksic900
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Comment: C: Tophat - Htseq Count? How Can I Improve The Mapping Percentage For Single End R
... What's the experiment? Is it RNA-seq? What RNA sizes did you select for? ...
written 5.4 years ago by Jelena Aleksic900
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Answer: A: What Makes A Dna Sequence Motif A Dna Sequence Motif?
... It's an interesting question, with I think a not particularly well defined answer. When searching for them, we define a motif as a DNA sequence (or DNA position weight matrix) that is found at a frequency higher than would be expected based on the sequence background model. A motif can in theory be ...
written 5.4 years ago by Jelena Aleksic900
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Comment: C: Csv File Parsing With Perl
... Looks good to me! However, just to be on the paranoid side, I tend to write that function slightly differently, so that it still returns something even if there are no quotes found (on the off-chance bits of the dataset are inconsistent): sub extractQuote { my $sentence = $_[0]; if ($senten ...
written 5.4 years ago by Jelena Aleksic900
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Answer: A: Need Help Writing A Perl Script For Extracting Sequences Based On A List
... In case it's helpful, here's how I would solve this. Feel free to ask questions about anything that doesn't make sense :) use v5.10.0; use strict; use warnings; # checks that you have input files unless ($ARGV[0] and $ARGV[1]) { die "Missing input file\nUsage: $0 list.txt seq.fa\n"; } # open ...
written 5.4 years ago by Jelena Aleksic900

Latest awards to Jelena Aleksic

Appreciated 5.2 years ago, created a post with more than 5 votes. For Intermine: A Flexible Data Warehouse System For Biological Data
Good Answer 5.2 years ago, created an answer that was upvoted at least 5 times. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Scholar 5.2 years ago, created an answer that has been accepted. For A: Is Any Database Provide Human Genes' Conservation Scores ?
Supporter 5.2 years ago, voted at least 25 times.
Commentator 5.2 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 5.2 years ago, created an answer with at least 3 up-votes. For A: Good Methodology To Name Rna-Seq Files
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: How To Convert A Plain Squence In A Perl String Variable To Fasta Format
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Is Any Database Provide Human Genes' Conservation Scores ?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: What Makes A Dna Sequence Motif A Dna Sequence Motif?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Trimming Adapters
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Microarray Expression For Genes With Multiple Probes
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Pointers To Learn About Functional Enrichment And Go Analysis
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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