K. Wyatt McMahon, Ph.D.

Ludwig Center for Cancer Genetics and Therapeutics

Sidney Kimmel Cancer Center Johns Hopkins Medical Institutes

**** ******* **. ****** ******** Building 1 Baltimore, MD 21287

Cell: 806-***-**** Email: acvgkb@r.postjobfree.com

Candidate Summary

Rare combination of substantial wet-bench experience with extensive computational/programming experience.

13 years of combined computational biology and oncology bioinformatics experience – 20 years total wet-bench and computational research experience.

Independent and collaborative problem-solver answering imperative biological questions leading to 18 peer-reviewed publications, mostly using bioinformatics to glean insight into biological processes.

Experience

January 2014- Present

Faculty Research Associate

Ludwig Center for Cancer Genetics and Therapeutics, Department of Oncology Johns Hopkins Medical Institutes

Directors: Drs. Bert Vogelstein & Kenneth W. Kinzler

Focused on cancer-personalized medicine

Collaboratively developed the group’s bioinformatics suite/pipeline (“X-mansion”: seven custom programs which run on a 12-node Sun Grid Engine-powered cluster complete with automated data transfer and SQL upload) for handling confidential patient data.

Worked in a team-oriented environment on projects that led to publication in high-impact journals

Trained junior team members in computer programming and other aspects of bioinformatics

May 2013-Dec 2013

Co-Founder & CSO

NextGen-Bioinformatics/ Labease Products

Founded a bioinformatics consulting firm to improve cancer genomics pipelines

Initial client was Ludwig Center (Hired to work full-time in January 2014)

May 2011-April 2013

Bioinformaticist

Data Analysis Core - Virginia Bioinformatics Institute at Virginia Tech

Developed novel methods to analyze “omics” data using R, perl, and Linux-based programs to create bioinformatic solutions to genomic and functional genomic problems (including DNA- and RNA-Seq, Affy microarray, transcriptome and genome assembly in a client-facing academic center)

Developed publication-ready reports & figures on the biological implications of analysis results

February 2008-May 2011

Postdoctoral Research Associate

Department of Internal Medicine – Texas Tech University Health Sciences Center

Utilized distributed computing (Condor) with R, Windows, and perl – using the gene expression omnibus (GEO) and novel algorithm development – to use animal models to better understand the molecular mechanisms of diabetic kidney disease

Laboratory supervisor for diabetic nephrology laboratory. Mentored medical & graduate students, and nephrology fellows in wet-bench experiments. Led team to win multiple awards and recognition at local and national meetings for presentation of novel research.

May 2007- February 2008

Postdoctoral Research Associate

Center for Functional Genomics – Texas Tech University

Used Agilent microarray, Bioconductor, R, GeneSpring, and perl to analyze functional genomic data created in-house and for clients

Education and Training

2007 Texas Tech University Health Sciences Center – Ph.D. – Cellular and Molecular Biology

2003 Cold Spring Harbor Scholarship and Course in Bioinformatics

1999 Baylor University – B.S. – Biology

1996-98 Howard Hughes Medical Institute undergraduate research scholar at Texas Tech University

Skills and Expertise

Programming: Expert: R, perl, bash, SGE scripting. Proficient: C#, SQL, MySQL, Linux/Windows interactions, Visual Studio/Winforms. Intermediate: C++, python, htseq, HTML. Novice: Java, JS, CSS

Linux bioinformatics: Expert: Samtools, bioconductor, Tuxedo package, isPCR, netMHC. Intermediate: BWA

Windows bioinformatics: Expert: CLCbio, GeneSpring, Ingenuity Pathway Analysis

Web bioinformatics: Expert: EGA sequence uploads, UCSC CustomTrack creation, DAVID, STRING, PANTHERdb. Intermediate: COSMIC, TCGA

Wet-bench: Expert: Tissue culture, sub-cloning, PCR, qRT-PCR, primer design, RT-PCR, restriction enzymes, bacterial culture, reporter assays, diabetic rat model, survival surgery, necropsy, DNA purification with kit and CsCl. Proficient: Sanger Sequencing (automated and S35), Southern, northern and western blotting, immunoprecipitation, recombinant protein expression. Coomassie blue stain, fluorescence microscopy, immunocytochemistry, RNase Protection Assay, immunohistochemistry.

References

Ken Kinzler, Ph.D. Co-Director of the Ludwig Center (acvgkb@r.postjobfree.com - 410-***-****)

Bert Vogelstein, MD. Co-Director of the Ludwig Center (acvgkb@r.postjobfree.com - 410-***-****)

Others and publications on request

Contact this candidate