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Charles Warden
PeerJ Author
375 Points

Contributions by role

Author 270
Preprint Author 105
Preprint Feedback 30
Questions 5

Contributions by subject area

Bioinformatics
Computational Biology
Genomics
Cell Biology
Molecular Biology
Genetics
Medical Genetics
Ethical Issues
Science and Medical Education
Oncology

By Q&A topic

Bioinformatics
Cell-biology
Computational-biology
Genetics
Oncology

Charles D Warden

PeerJ Author

Summary

I am currently a Bioinformatics Specialist in the Integrative Genomics Core at City of Hope. I assist scientists with next-generation sequencing (and sometimes microarray) analysis. As needed, I also develop algorithms for genomic analysis.

My work mostly currently focuses on cancer research, but I also assist with basic biology and virology research. I also have published evolutionary genomics papers.

Bioinformatics Biotechnology Computational Biology Genetics Genomics Oncology Translational Medicine Virology

Editing Journals

Past or current institution affiliations

University of Michigan

Work details

Bioinformatics Specialist

City of Hope
Integrative Genomics Core, Department of Molecular and Cellular Biology

Websites

  • Google Scholar
  • Blog

PeerJ Contributions

  • Articles 2
  • Preprints 1
  • Feedback 7
  • Questions 2
September 30, 2014
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Charles D. Warden, Aaron W. Adamson, Susan L. Neuhausen, Xiwei Wu
https://doi.org/10.7717/peerj.600 PubMed 25289185
September 12, 2013
BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways
Charles D. Warden, Noriko Kanaya, Shiuan Chen, Yate-Ching Yuan
https://doi.org/10.7717/peerj.159 PubMed 24058887
June 12, 2014 - Version: 3
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Charles D Warden, Aaron W Adamson, Susan L Neuhausen, Xiwei Wu
https://doi.org/10.7287/peerj.preprints.403v3

Provided feedback on

1 vote
06 Jul 2013

Nine simple ways to make it easier to (re)use your data

Interesting editorial! It looks like this article doesn't currently mention standard high-throughput databases. Although most scientists should be aware of these, data depositi...

1 vote
09 Oct 2013

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Interesting paper - I've noticed that exon coverage has been low in exosome RNA-Seq experiments, and it was interesting to see how much non-coding reads specifically aligned to rRN...

1 vote
28 Mar 2014

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Interesting paper! 1) My understanding was that the population frequencies (75%, 90%, and 99%) were used to try and estimate the specificity of the SNP calls (so, variants fou...

14 Nov 2013

spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

This sounds like an interesting package. A Bioconductor package for alternative splicing analysis would certainly be useful to the community. However, I think it would help to...

02 Jan 2014

A simple scaling normalization for comparing ChIP-Seq samples

This paper looks like it has the potential to be quite useful. However, it seems a bit short and I think it would help to expand on the following details: 1) Do you provide a...

12 Feb 2014

Direct-to-consumer genetic testing in the college classroom: Knowledge, attitudes, and concerns of introductory biology students

Interesting paper. In table 1, maybe it would help to show the same answer frequencies for before and after taking class? At first, I was confused how 82/116 could answer "YES"...

15 Apr 2014

scikit-image: Image processing in Python

Cool paper! Perhaps it would help to provide a link to the software (e.g. https://github.com/scikit-image/scikit-image) in the abstract? I eventually figured it out from link...

2 Questions

1
Standard Data Deposition
about Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
0
Biomarker Application?
about Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing