CV

Education

Employment

Other Courses / Certification

edX Professional Certificate (HarvardX) : "Data Analysis for Life Sciences " (4 courses, completed 11/27/2021, grades of 93-100%)

Coursera Specialization (Johns Hopkins University) : "Genomic Data Science" (8 courses, completed 3/7/2021, grades of 88-100%)

Coursera Specialization (Johns Hopkins University) : "Biostatistics in Public Health" (4 courses, completed 7/22/2023, grades of 98-100%)




As mentioned above, I have additional completed coursework from the University of Michigan (related to Bioinformatics, 3.81 GPA)

edX (Massachusetts Institute of Technology:  MITx 7.03.1x) : "Genetics: The Fundamentals" (6/14/2024, grade of 92%)

edX (Massachusetts Institute of Technology:  MITx 7.03.2x) : "Genetics: Analysis and Applications" (6/20/2024, grade of 93%)

edX (Massachusetts Institute of Technology:  MITx 7.03.3x) : "Genetics: Population Genetics and Human Traits" (6/17/2024, grade of 96%)

Coursera (Johns Hopkins University) : "Regression Models" (11/27/2019, grade of 100%)

Coursera (Johns Hopkins University) : "Practical Machine Learning" (12/8/2019, grade of 96%)


I also have some more notes as well as (partial) listing other on-line courses in this blog post.



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

*Equal contribution

1) Goto RM*, Warden CD*, Shiina T, Hosomichi K, Zhang J, Kang TH, Wu X, Glass MC, Delany ME, Miller MM (2022) The Gallus gallus RJF reference genome reveals an MHCY haplotype organized in gene blocks that contain 107 loci including 45 specialized, polymorphic MHC class I loci, 41 C-type lectin-like loci, and other loci amid hundreds of transposable elements. G3.  12 (11): jkac218


2) Warden CD, Cholli P, Qin H, Guo C, Wang Y, Kancharla C, Russell AM, Salvatierra S, Mutsvunguma LZ, Higa KK, Wu X, Wilczynski S, Pillai R, Ogembo JG (2022) HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study. Infectious Agents and Cancer.  17 (1): 44


3) Warden CD, Adamson AW, Neuhausen SL, Wu X (2014) Detailed Comparison of Two Popular Variant Calling Packages for Exome and Targeted Exon Studies. PeerJ. 2:600


4) 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


5) 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


6) 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


7) 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 also submitted a 3rd comment.  The NAR staff correctly requested we look into more information before posting, but ultimately did not post the 3rd comment because the mistake was in GEO (not the COHCAP paper).  However, I will convey the main message of that content here (and there is also going to be a Corrigendum for the earlier factual errors):

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

b)     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”

I was previously uncertain which machine was correct.  However, I can now 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 made me comfortable with updating the GEO entries.


8) Warden CD and Lacey SF (2012) Updated Phylogenetic Analysis of Polyomavirus-Host Co-Evolution. J. Bioinfo. Res. 1(4) : 46-49

 

9) 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 has been the following corrigendum:

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).


10) 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

While I mostly emphasize the first author (or equal contribution) papers above, you can see more notes about corrections on my papers here (and corrections that I have pointed out in other papers, where I am not the author, here).  You can also see some of the concerns that I raised for results from genomics companies (again, which have never been my employer) within the set of links in this blog post.


Professional Memberships


 Member, Society for Genome Biology & Technology (2013-2014)

 Member, International Society for Computational Biology (2011-2012)


Selected Honors and Awards

NIH NIGMS Predoctoral Fellowship (2014-2015)

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, F1000 Research (1 article, 2020)

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)