User: Habil Zare

gravatar for Habil Zare
Habil Zare170
Reputation:
170
Status:
Trusted
Location:
United States/Austin Area
Website:
http://oncinfo.org/
Scholar ID:
Google Scholar Page
Last seen:
8 months ago
Joined:
4 years, 5 months ago
Email:
z***@u.washington.edu

I am an Adjunct Assistant Professor in the Department of Cell Systems & Anatomy at the University of Texas Health Science Center - San Antonio. I am the Principal Investigator of Oncinfo Lab.

I am a bioinformatician and computational biologist, and my primary interest is focused on developing new machine learning algorithms for analyzing complicated, large size, and rich biological data. I have experience with analyzing data provided by a wide range technologies including, next generation sequencing, ChiP-seq, and flow cytometry. I am interested in combining techniques from a variety of fields such as spectral graph theory, feature extraction, Bayesian statistics, Dynamic Bayesian Networks, and deep learning to develop novel algorithms, which can recognize the patterns in the biological or clinical data missed by state-of-the-art methodologies. I am very eager in interdisciplinary collaborations with smart biologists and clinicians to define and accomplish scientific projects with the goal of making discoveries in areas such as molecular and cell biology, cancer diagnosis and prognosis, phylogenetics, genomics, and epigenomics.

Posts by Habil Zare

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Pigengene : BN network using consensus module
... 1- In the learn.bn function, Labels is a named vector of characters. It can have "0" and "1" values if you prefer that. I am not sure I get your question right. "Disease" is just the name of the variable that has Labels values. The name of the variable does not matter. Modules can be a child of this ...
written 12 months ago by Habil Zare170
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Answer: A: Pigengene : BN network using consensus module
... - The input to the compute.pigengene() function includes data and labels, NOT the eigengenes. They are computed by this function. - The parameters are explained in the manual of each function, e.g., see ?learn.bn. Is there a particular parameter you have a question on? - After you have the BN stru ...
written 12 months ago by Habil Zare170
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Answer: A: Pigengene : BN network using consensus module
... The paper that you mentioned is a general introduction to Pigengene. Our following paper is more focused on Bayesian networks (BNs): Agrahari, Rupesh, et al. "Applications of Bayesian network models in predicting types of hematological malignancies." Scientific Reports 8.1 (2018): 6951. I answer you ...
written 12 months ago by Habil Zare170
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Answer: A: Questions on Pigengene
... Can you run the calculate.beta() function with different values for the RsquaredCut argument, say 0:4/20 +0.6? I recommend you choose the highest value that does not lead to an NA value for beta. In Pigengene version 1.5.9, I added RsquaredCut to one.step.pigengene(), arguments. So, when you find an ...
written 20 months ago by Habil Zare170
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Answer: A: Questions on Pigengene
... WGCNA authors recommend not to exclude any genes from the analysis. I think it is reasonable to filter out the genes with too low coverage and the genes with almost constant expression levels. Using 4,000 genes should be fine. I have not used DESeq normalization before in this context. Please post ...
written 21 months ago by Habil Zare170
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Answer: A: Questions on Pigengene
... Do you use RPKM values from RNA-Seq data? Did you transformed the expression values using, say, log(1+ <RPKM>)? ...
written 21 months ago by Habil Zare170
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Comment: C: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
... You're welcome! I am interested in Clomial performance if you will have a way to assess it. ...
written 23 months ago by Habil Zare170
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Answer: A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
... 1- Two samples are not enough to infer the clonal composition. 2- There are 4 samples in the data you sent me by email. The mutation ratios seem to be very low (~0.01). plot(rowSums(Dc), rowSums(Dt),xlim=c(0,1000), ylim=c(0,30))    Your data has 169 mutations, and with only 4 samples, it's not ...
written 23 months ago by Habil Zare170
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Importing Infinium data files using RnBeads::rnb.execute.import()
... I cannot import beta values using the rnb.execute.import function from the RnBeads package: rnb.execute.import(data.source=c("annotation"=clinicalFile,"beta"=dnamCsvFile), data.type="infinium.data.files",verbose=TRUE) 2016-12-06 10:49:24 3.2 STATUS STA ...
rnbeads written 2.9 years ago by Habil Zare170
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Answer: A: Minfi: estimateCellCounts rgSet
... See this. ...
written 3.0 years ago by Habil Zare170

Latest awards to Habil Zare

Scholar 17 months ago, created an answer that has been accepted. For A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
Scholar 17 months ago, created an answer that has been accepted. For A: Pigengene : BN network using consensus module
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Pigengene : BN network using consensus module
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Pigengene : BN network using consensus module
Scholar 2.9 years ago, created an answer that has been accepted. For A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.

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