User: ivivek_ngs

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ivivek_ngs4.8k
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Location:
Seattle,WA, USA
Website:
https://github.com/vd4...
Twitter:
@ivivek87
Last seen:
4 weeks ago
Joined:
6 years, 2 months ago
Email:
v*******@gmail.com

I did my PhD in the field of Cancer Computational Medicine employing NGS tools(publicly available) or ad-hoc development and analyzing them. Mostly I did bench-marking of tools till I find the best fit for the heterogeneous cancer data. I worked on integrating multi omics data and briefly ventured in field of single cell which is pretty interesting to me as of now (still working on it as per requirement in the industry).

Battling with two of my worst fears Biology and Computer Science to give life a better meaning. My first fear made me push to get the PhD and my second help me learn to solve problems amassing big-data, in an unbiased data-driven way, thus letting me earn my PhD. Now I want to drive the improvements in the field of healthcare bridging both Biology and Computer Science. I enjoy the interdisciplinary terms Bioinformatics or Computational Biology, but in heart  and mind, I am a Systems Biologist who loves learning data-shapes, distributions , what it provides as features and these can help formulate better biological queries and also address apriori queries or new ones. The challenge in life science and technology drives me and so I am pursuing the research field.

Everyday is a new learning and knowledge is never ending.

Biostars helped me learn all along and now with my experience and learning am happy to help others. 

Creating automated pipeline/workflow scripts for easy usage of different seq technologies. I am passionate about integration of multi-omics data in varied therapeutic areas involving human patients data-sets and leveraging the power of pre-clinical animal models together for target discovery. 

I am interested in Precision and Personalized Medicine and would like to use my skills in the same with translational NGS technologies for addressing problems related to diseases. Currently working in industry in Biomarkers & Target Discovery employing Integrative Computational Systems Medicine approach.

Posts by ivivek_ngs

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Comment: C: How to find out the insert size in RNA seq data
... Yes, I should have updated it, thanks for putting it in the thread. ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Glad it worked out now at your end. I should have pointed out the part of Jeff Leek advice( I was indicating the same but I was not that comprehensive out there), since pre-adjustment is only advisable for a visualization perspective but for model they should be incorporated as covariates to not im ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Wwell, limma is used for DNA methlylation. Should not be an issue, it is just not the voom transformation. Well in voom you will have the difference since it is for RNASeq, while traditionally limma is for array based works so DNAmethylation fits that bill, in that case your query should be valid. T ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Can you show some plots for the scenario. It sounds interesting. However, I also don’t expect a linear model using residuals multifactors for regressing the data giving differential gene expression will exactly match with batch corrected value based on mean expression for the same genes. I have doub ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext
... Apologies for the delayed response, the code you showed should also work, the code I showed gives your SVs and using those residuals you are just fitting them for the batch correction but that does not mean you are performing differential analysis. It is just taking care of the normalized dataset ap ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: Interesting bioinformatics blogs (2017 edition)
... Well there you go the list will need to be edited with your new blog space. I promoted it for a reason that it is very comprehensive for anyone & everyone starting with Bioinformatics. Over the years, I have enjoyed and seen your content grow & mature. If we are listing such blogs yours need ...
written 4 months ago by ivivek_ngs4.8k
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Comment: C: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... Thank you very much for taking time to clarify. Appreciate the detailed explanations. Currently I will not be pursuing this fragment anymore in light of the explanations I have received, if needed for any farther requirements, will reach out to the UniProt helpdesk as advised. ...
written 5 months ago by ivivek_ngs4.8k
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Comment: C: How to create a heatmap of RNA-Seq Data in R?
... 1. Make the annotation of your columns and rows (a.k.a sample list) , 2. use clustering for both of your rows and columns, dendrogram function in the heatmap code is from hclust, or if its pheatmap r function then they have some functions like clustering method 3. label your samples and t ...
written 6 months ago by ivivek_ngs4.8k
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Comment: C: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... A very comprehensive answer . Thanks for taking time to make the interpretations. I agree to your analogy and did have a feeling that it has not been used for gene/transcript annotation. Although I am not an expert in protein annotation so wanted to get insights from experts. Thanks everyone for t ...
written 6 months ago by ivivek_ngs4.8k
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Comment: C: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... Yes, hypothetically it can be a suspected variation of P0DOX7 but cannot be assertive at this point. Not much evidence at transcriptional level though. Thanks again. ...
written 6 months ago by ivivek_ngs4.8k

Latest awards to ivivek_ngs

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Popular Question 4 months ago, created a question with more than 1,000 views. For Discrepancy with MACS2.0 and MACS2.1 broad peaks
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Scholar 7 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Great Question 10 months ago, created a question with more than 5,000 views. For Variant Reduction Using Annovar
Appreciated 11 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: ICGC Variant Calling Pipelines
Scholar 13 months ago, created an answer that has been accepted. For C: KEGG Pathway elements' text color code
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Presenting "Role of genomics in cancer" to graduate students from different fiel
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Popular Question 15 months ago, created a question with more than 1,000 views. For XENA: a new tool for cancer researcher developed by UCSC
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Europe: Non-Paid Bioinformatics Internships/Training
Appreciated 18 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines
Appreciated 18 months ago, created a post with more than 5 votes. For A: ICGC Variant Calling Pipelines

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