User: endre.sebestyen

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Posts by endre.sebestyen

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Efficient read mapping and alignment to reference set
... Hi! I have an alignment/mapping question for the following dataset. I have ~1 million different reference sequences with an average of 110 nucleotides, and an actual sequencing of 50 million reads, where one read completely covers a reference sequence (the theoretical Illumina read length is longer ...
alignment sequencing written 5 months ago by endre.sebestyen10
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Normalization for comparing expression statistics across sample and gene groups
... Hi, What would be the current best practice for normalizing gene expression counts, if I want to compare different characteristics of genes and particluarly gene groups (min, max, mean, sd of expression) between two conditions? I'm interested in questions like: "Is the variance of expression means ...
normalization gene sets rna-seq written 6 months ago by endre.sebestyen10 • updated 7 weeks ago by kristoffer.vittingseerup3.4k
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Job: PhD position in cancer systems biology (Budapest, Hungary)
... **Transcriptome noise as an alternative mutator phenotype in cancer** Are you interested in analyzing terabytes of experimental data? Do you want to work on a project, where you need to combine biology, statistics, programming and answer challenging, interdisciplinary research questions? You think ...
cancer job phd rna-seq budapest transcriptomics written 9 months ago by endre.sebestyen10
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Job: Stipendium Hungaricum Fellowship with the Computational Biology Group of Semmelweis University
... Stipendium Hungaricum - Call for Applications 2019/2020 ------------------------------------------------------- ---------- **Role of chromatin structure and expression variance in cancer mutation patterns and signatures** *Call for expression of interest to submit a Stipendium Hungaricum Fellowsh ...
bioinformatics budapest job genomics cancer written 22 months ago by endre.sebestyen10
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Comment: C: kallisto/sleuth for single sample pathway enrichment
... I would like to know both the common upregulated pathways and the individual ones. I know the second one will give shaky results with any tool, but I'd like to give it a try anyway, as the mutated samples have different chromatin structural changes, and I'd like to know if this leads to different ge ...
written 2.6 years ago by endre.sebestyen10
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Comment: C: kallisto/sleuth for single sample pathway enrichment
... Yes, that's one of the questions. How to aggregate when a gene belongs to many pathways? :) Lior Pachter wrote some tweets a while ago, that they used kallisto/sleuth for pathway level analysis. Later they had a [preprint][1], where they aggregated transcript level data to do GO enrichment analysis, ...
written 2.6 years ago by endre.sebestyen10
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kallisto/sleuth for single sample pathway enrichment
... Hi, I'm trying to do a single sample pathway enrichment analysis with Kallisto/Sleuth. I have 3 control samples, and 3 mutated samples. I have good reasons to believe that the mutated samples have a larger number of genes/pathways differentially expressed in each sample individually, which masks a ...
sleuth kallisto rna-seq pathway enrichment written 2.6 years ago by endre.sebestyen10 • updated 2.6 years ago by Rik Verdonck50
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Job: PhD student positions in computational biology at IFOM, Milan, Italy
... ***Position: PhD students in computational biology.*** **About the positions:** We are looking for 2 PhD students to join our lab at IFOM. One PhD student will be working on the computational reconstruction and analysis of enhancer-gene regulatory networks altered in cancer. The second PhD studen ...
bioinformatics ifom milan job genomics written 3.3 years ago by endre.sebestyen10

Latest awards to endre.sebestyen

Popular Question 22 months ago, created a question with more than 1,000 views. For PhD student positions in computational biology at IFOM, Milan, Italy
Popular Question 2.6 years ago, created a question with more than 1,000 views. For PhD student positions in computational biology at IFOM, Milan, Italy

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