User: umer.zeeshan.ijaz

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Posts by umer.zeeshan.ijaz

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Job: Bioinformatics PDRA Opportunity in Environmental' Omics Lab (Water & Environment Research Group, University of Glasgow)
... A **post-doctorate research associate position in bioinformatics** is available in my lab (click on Apply button on the following links to submit the credentials rather than emailing me directly): http://www.jobs.ac.uk/job/BEV662/research-associate/ https://www22.i-grasp.com/fe/tpl_glasgow01.asp?n ...
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Job: PhD Studentships @ University of Glasgow [International students can also apply]
... Hi All, I am part of a few interdisciplinary projects where we (have secured/are short-listed for) funding to support PhD students (ideally someone with strong molecular biology/engineering/computational/statistical/bioinformatics background) in numerous research groups I am affiliated with. In som ...
jobs written 2.6 years ago by umer.zeeshan.ijaz1.7k
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Job: EPSRC CASE Bioinformatics studentship: Development of novel statistics to study the human microbiome
... Please apply here: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=63673 Start date 1st October 2015 – 4 years fully funded to UK and EU applicants Principal supervisor: Dr Christopher Quince (Warwick Medical School, University of Warwick) Secondary supervisors: Dr Umer Zeeshan Ijaz (Unive ...
metagenomic job written 3.1 years ago by umer.zeeshan.ijaz1.7k
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Answer: A: How to tell if a RefSeq or UniProt protein identifier is human?
... There is a way to do this using rest-style KEGG API You can convert NCBI gene id or uniprot ID to KEGG gene ID using a query such as (paste these on your browsers): http://rest.kegg.jp/conv/genes/uniprot:Q9XCI8 http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320 Now the process involves NCBI gene ...
written 3.2 years ago by umer.zeeshan.ijaz1.7k
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Answer: A: Retrieve the FASTA transcript sequences of a list of NCBI genes
... Say you are able to extract the identifiers with one identifier/line (perhaps in a file). I am just using the echo to generate the list: $ echo -e "A0QTF8\nA0QTG1\nA0QU63" A0QTF8 A0QTG1 A0QU63 Then you can use the following one-liner to get the sequences: $ echo -e "A0QTF8\nA0QTG1\nA0QU63" | wh ...
written 3.2 years ago by umer.zeeshan.ijaz1.7k
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Answer: A: Pairwise comparisons between multiple groups with DESeq2
... It depends on you, if you want to capture overall differences (obviously skewed by one group being an outlier) then you can pool them together, otherwise you can do pairwise comparisons. I have two scripts NB.R (based on DESeq2) and KW.R (based on Kruskal-Wallis with FDR) that you can use alternati ...
written 3.2 years ago by umer.zeeshan.ijaz1.7k
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Answer: A: K-means for non-spherical (non-globular) clusters
... You can also try Evidence Accumulation Clustering & Dirichlet Process Mean Clustering: Maths here: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/clust_validity.pdf Code here: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/clust_validity.R Usage here: http://userweb.eng.gla.ac.u ...
written 3.2 years ago by umer.zeeshan.ijaz1.7k
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Job: PhD Project – Development of Novel Algorithms and Tools for Integration of Metagenomics and Metabolomics
... Please note that a PhD studentship has become available in my group. Last date of submission of application is Monday, June 15, 2015. To apply, visit the link http://www.findaphd.com/search/ProjectDetails.aspx?PJID=62183 Here are the details from the above link: Microorganisms are ubiquitous and p ...
metagenomics job written 3.2 years ago by umer.zeeshan.ijaz1.7k
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Comment: C: Verify if all the components of a pathway are present in a genomes
... Hi dago, I figured it out by hit and trial method. Bioconductor's KEGGREST could be a good starting point to explore KEGG REST service further. Please also have a look at the HUManN workflow on how they incorporated MinPath. Here are a few more one-liners that you can use on a GENBANK file to under ...
written 3.3 years ago by umer.zeeshan.ijaz1.7k
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Answer: A: Verify if all the components of a pathway are present in a genomes
... You can use MinPath to see if all the enzymes are sufficient for a given Pathway to exist (the other way around). This is what I will do: If I start with contigs or a genome sequence (can be a file with multiple genomes in it), I will use a tool such as PROKKA  to generate a genbank file of my anno ...
written 3.4 years ago by umer.zeeshan.ijaz1.7k

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