CV

Education

 8/2007-9/2009MA, Molecular Biology Princeton University, Princeton, NJ
(scanned transcript)
(Master's Thesis - at least what I have saved...)
 8/2003-5/2007BS, Applied Biology
    -Highest Honor
    -Research Option
 Georgia Institute of Technology, Atlanta, GA
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Employment


 2016-Bioinformatics Specialist
City of Hope National Medical Center, Duarte, CA
 2015-2015Research Associate, Chinnaiyan Lab,  Michigan Center for Translational Pathology
University of Michigan, Ann Arbor, MI
 2014-2015Graduate Student, Department of Computational Medicine and Bioinformatics
University of Michigan, Ann Arbor, MI
 2010-2014Bioinformatics Specialist
City of Hope National Medical Center, Duarte, CA
 2009-2010Research and Teaching Specialist V
University of Medicine and Dentistry of New Jersey, Newark, NJ


First-Author Publications (See Google Scholar for Full Publication List)

*Equal contribution
 
1) Warden CD, Adamson AW, Neuhausen SL, Wu X (2014) Detailed Comparison of Two Popular Variant Calling Packages for Exome and Targeted Exon StudiesPeerJ. 2:600

2) Warden CD, Yuan YC, Wu X (2013) Optimal Calculation of RNA-Seq Fold-Change Values. Int J Comput Bioinfo In Silico Model. 2(6): 285-292


3) Brown CE*, Warden CD*, Starr R, Deng X, Badie B, Yuan YC, Forman SJ, Barish ME (2013) Glioma IL13Rα2 Is Associated with Mesenchymal Signature Gene Expression and Poor Patient Prognosis. PLOS ONE. 8(10): e77769


4) Warden CD, Kanaya N, Chen S, and Yuan YC (2013) BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PeerJ. 1:e159

5) Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. (2013) COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res. 41 (11): e117

 
I have also submitted a 3rd comment, but NAR staff is correctly requesting we look into more information before posting.  However, in the meantime, I will convey the main message of that content here:

I didn’t add this under the previous comments because I don’t know what is correct (and I am still not 100% certain).  However, I thought I should mention one more discrepancy that I knew about:

1)     The Supplemental Methods say “After washing, the stained beadchip was coated with XC4 buffer and scanned using Illumina’s HiScanSQ scanner.

2)     The “Data Processing” in 450k “HCT116 Mutant Comparison” GEO entry (GSE42308, when viewing individual sample like GSM1038308) says “Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

While I have some more details to work out before an official corrigendum is published, I believe I now have enough evidence to conclude that the HiScanSQ was the machine that was actually used (and I have updated the GEO entries).  Illlumina has confirmed that the BeadArray can't scan the 450k array (so, it can't be correct), and Illumina also confirmed that City of Hope didn't have any Illumina scanners before February 2011 (which is when the HiScanSQ was installed, and approximately when these samples were processed).  So, that is what makes me comfortable with updating the GEO entries.


6) Warden CD and Lacey SF (2012) Updated Phylogenetic Analysis of Polyomavirus-Host Co-EvolutionJ. Bioinfo. Res. 1(4) : 46-49
 
7) Warden C, Tang Q, and Zhu H. (2011) Herpesvirus BACs: Past, Present, and Future Journal of Biomedicine and Biotechnology Volume 2011, Article ID 124595
 
There will be the following correction:

Current"For example, AD169, Towne, and TB40 are considered the “clinical” BAC strains whereas Toledo, FIX, PH, and TR are considered to be the “laboratory” BAC strains [28]."
Corrected:"For example, AD169, Towne, and TB40 are considered the “laboratory” BAC strains whereas Toledo, FIX, PH, and TR are considered to be the “clinical” BAC strains [28]."

I would like to thank Kalpana Dulal for pointing out this error.

More important than this minor error, I think the most important lesson to upcoming scientists is that the amount of time I had working in this area (~6 months as an RTS V) was not sufficient to have enough of an intuition about the field (beyond what you can read in the literature) to represent my knowledge with a review.  For example, I have never created a viral BAC (and, even at that point, I would say I had more of an emphasis on the data analysis side).

I very much appreciate the goal of having fair overall credit (in terms of being able to have at least one 1st author paper while working in a lab), but I think my work on Zhang et al. 2010 ("Statistical analysis of mutant growth kinetics" in "Materials and Methods" and - I believe - analysis of the functional annotations in Figure 3) and Huang et al. 2013 ("Tiling Array Analysis" scripts on this website, as well as relatively larger portion of the paper writing than the PLOS Pathogens paper) better reflect my bioinformatics skills from that time.

I was also occasionally an assistant for the in vivo mouse experiments, but I think that was more a matter of realizing my limits for certain experimental protocols (although, strictly speaking, that was also a contribution to the PLOS Pathogens paper).

8) Warden CD, Kim S-H., and Yi S. (2008) Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PLoS One 3(2): e1559

Professional Memberships

 2013-2014 Member, Society for Genome Biology & Technology
 2011-2012 Member, International Society for Computational Biology

Selected Honors and Awards
NSF Graduate Research Fellowship (2008-2009) 
Cherry L. Emerson Research Award (awarded Spring 2007) 
Marshall Fellowship Finalist (Fall 2006 – Southeast Region) 
President’s Undergraduate Research Award (Spring 2006)
 
 
Editorial Review
Article Reviewer, BMC Bioinformatics (1 article, 2016)
Article Reviewer, Breast Cancer Research (3 articles, 2013-2016)
Article Reviewer, Cancer Informatics (4 articles, 2014)
Article Reviewer, BMC Medical Genomics (2012)
 
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