profile picture

Scott Walmsley, PhD

Big data scientist, bioinformaticist and molecular biologist

Education

Postdoc in Proteome Informatics

University of Michigan Medical School
2011 - 2014

PhD in Cell and Molecular Biology

Colorado State University
2006 - 2011

BSc in Biological Sciences, Minor Biochemistry

Colorado State University
1994 - 1997

Career Profile

Originally a bench scientist in the field of molecular biology, I have developed skills to answer difficult questions of disease and biomarker discovery through computer code. My career has co-evolved with the challenges of mass spectrometry based and clinical data analysis. My technical and leadership skills are transferable to answering any data challenge in most disciplines. I believe in strongly applied fundamentals of code engineering (testing, Agile, clear code).

I am currently seeking a position as a Data Scientist, Bioinformatics Scientist or Computational Scientist at the mid to senior level. I am willing to relocate!


Click on sub titles below to expand.

Work Experience

Consultant, contract analyst, and owner.

2017 - 2018
MetaboSoft LLC, Centennial, Colorado

Performing data analysis of complex clinical cohorts. Custom computational pipeline development. Network analysis for human metabolic pathways.

Scientist - Research Instructor

2015 - 2018
UC Denver-Anschutz, Aurora, Colorado

Lead developer for computational framework to assemble sample specific databases using metabolomics mass spectrometry data. Biomarker discovery using informatics workflows for elucidating the varied treatment response of asthmatic children using metabolomics. Lectures in UCD Comp. Bio. Program core classes and metabolomics workshops.

Scientist - Instructor

2014 - 2015
National Jewish Hospital, Denver, Colorado

Lead developer for computational framework to assemble sample specific databases. Lab transfered to UCD for continuing work.

Postdoctoral Research Fellow

2011 - 2014
University of Michigan Medical School, Ann Arbor, Michigan

Analyzed trypsin digestion efficiencies through mass spectrometry data. Developed Java program to analyze NIST MS data.

Graduate Research Assistant

2006-2011
Colorado State University, Fort Collins, CO

Body of dissertation work completed profiling the renal response to metabolomic acidosis using mass spectrometry based proteomics. Teached biochemistry laboratories to undergraduates.

Science Technologist

1998-2006
Heska Corporation, Loveland, CO

ELISA development, serum biomarker profiling and flea insectiside target identification and expression for molceular and biological contact assay.

Research Assistant

1997-1998
Colorado State University, Dept. of Molecular Biology and Biochemistry, Fort Collins, CO

DNA transcription factor footprinting using manual sequencing techniques. TFIIa affinity purification from Acanthamoeba.

Awards

USHUPO Travel Award
For research of the kinetics of proteolysis of Apolipoprotein-A1 and the implications toward quantitative mass spectrometry.
US Human Proteome Organization. Seattle, Washington. April 2014
MSACL Young Investigator Travel Award
For presenting significant differences in activity for porcine and bovine trypsin digests of human serum albumin.
Association for Mass Spectrometry, Applications to the Clinical Lab. San Diego, California. February 2013.
USHUPO Travel Award
For research on the reproducibility and specificity of trypsin digestion in proteomics.
US Human Proteome Organization. San Fransisco, California. March, 2012
Graduate Research Honors Award
For research detailing the protein modelling of the kidney proximal tubule brush border during metabolic acidosis.
Colorado State University Cell and Molecular Biology Research Symposium. Fort Collins, Colorado. 2010.
Graduate Research High Honors Award
For developing a method to enrich brush border membrane vesicles from kidney proximal tubules.
Colorado State University Cell and Molecular Biology Research Symposium. Fort Collins, Colorado. 2009.

Teaching Experience

Computational Biology Program CCMB7711

2015 - 2018
UC-Denver Anschutz

Lecture in Multiple Sequence Alignment, computational aspects.

Computational Biology Program CCMB7712

2015 - 2018
UC-Denver Anschutz

Lectures in proteome and metabolome informatics.

Hands-on Metabolomics Workshop

2014 - 2017
UC-Denver Anschutz

Lectures and hands-on computer laboratories in 'R for Metabolomics Data Analysis', 'WebTools for Metabolomics Data' and 'Introduction to Statistics'.

Introductory Genetics Laboratory

2006
Colorado State University

Basic hands-on techniques in molecular biology and protein biochemistry.

Introductory Cell Biology Laboratory

2007
Colorado State University

Basic hands-on techniques in cell biology.

Publications

A prototypic small molecule database for bronchoalveolar lavage-based metabolomics.
Walmsley S, Cruickshank-Quinn C, Quinn K, Zhang X, Petrache I, Bowler RP, Reisdorph R, Reisdorph N.
Scientific data. 2018; 5:180060.
Performance of a High-Pressure Liquid Chromatography-Ion Mobility-Mass Spectrometry System for Metabolic Profiling.
Zhang X, Kew K, Reisdorph R, Sartain M, Powell R, Armstrong M, Quinn K, Cruickshank-Quinn C, Walmsley S, Bokatzian S, Darland E, Rain M, Imatani K, Reisdorph N.
Analytical chemistry. 2017; 89(12):6384-6391.
Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.
Chen G, Walmsley S, Cheung GCM, Chen L, Cheng CY, Beuerman RW, Wong TY, Zhou L, Choi H.
Analytical chemistry. 2017; 89(9):4897-4906.
Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.
Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.
Journal of proteome research. 2013; 12(12):5666-80.
LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.
Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI.
Molecular & cellular proteomics : MCP. 2013; 12(11):3409-19.
Proteomic profiling of the effect of metabolic acidosis on the apical membrane of the proximal convoluted tubule.
Walmsley SJ, Freund DM, Curthoys NP.
American journal of physiology. Renal physiology. 2012; 302(11):F1465-77.
Proteomic analysis of brush-border membrane vesicles isolated from purified proximal convoluted tubules.
Walmsley SJ, Broeckling C, Hess A, Prenni J, Curthoys NP.
American journal of physiology. Renal physiology. 2010; 298(6):F1323-31.
Identification of serum biomarkers for canine B-cell lymphoma by use of surface-enhanced laser desorption-ionization time-of-flight mass spectrometry.
Gaines PJ, Powell TD, Walmsley SJ, Estredge KL, Wisnewski N, Stinchcomb DT, Withrow SJ, Lana SE.
American journal of veterinary research. 2007; 68(4):405-10.
Identification of two cDNAs encoding synaptic vesicle protein 2 (SV2)-like proteins from epithelial tissues in the cat flea, Ctenocephalides felis.
Walmsley SJ, Gaines PJ.
Insect molecular biology. 2004; 13(3):225-30
Cloning and characterization of five cDNAs encoding peritrophin-A domains from the cat flea, Ctenocephalides felis.
Gaines PJ, Walmsley SJ, Wisnewski N.
Insect biochemistry and molecular biology. 2003; 33(11):1061-73.

Oral Presentations

Unlocking the Computational Toolbox for Metabolomics Success
MS Users Group Meeting, UC Denver Department of Pharmaceutical Sciences; Aurora, Colorado September 2015
Challenges in Clinical Metabolomics Database Development
Agency for Science, Technology and Research; Singapore, December 2014
Kinetic Evaluation of Trypsin Digests of Apolipoprotein-A1: Implications for Quantitative Mass Spectrometry
US-Human Proteome Organization Lightning Talks; Seattle, Washington, April 2014
Profiling of Apolipoprotein-A1 by Peptide Mass Spectrometry
National Institutes of Health, NHLBI; Bethesda MD. February 2014
Analysis of Peptide Ion Signatures for Characterization of Porcine and Bovine Trypsin Digestion
Mass Spectrometry: Applications to the Clinical Lab; San Diego, California, February 2013
Proteomic analysis of the Effect of Metabolic Acidosis on the Apical Membrane of the Proximal Convoluted Tubule
Colorado State University; Fort Collins, Colorado, February 2011
Effect of chronic metabolic acidosis on the proteome of the brush border membrane of the proximal convoluted tubule (PCT)
American Society of Nephrology Renal Week; Denver Colorado, November 2010
To LTQ or to QTOF?
Departmental Seminar, Department of Biochemistry and Molecular Biology; Colorado State University; Fort Collins, Colorado, March 2010
“Dirty Nephrons!”
Departmental Seminar, Department of Biochemistry and Molecular Biology; Colorado State University; Fort Collins, Colorado, November 2008
Flea Peritrophin-like Proteins: Cloning, Characterization, and In-Vivo Challenge
International Symposium for Ectoparasites on Pets; League City, Texas, April 2003

Abstracts

Rapid MS1 Formulae to Isotope Pattern Matching Using a Novel MS1 Search Engine for Metabolomics
Scott Walmsley*, Nichole Samantha Bokatzian, Hyungwon Choi, Richard Reisdorph, Nichole Reisdorph
American Society For Mass Spectrometry, San Antonio,Texas, June 2016
A Novel Method for Theoretically Determining the Success Rate of Identification by MS1 Using a Human Metabolome Database
Scott Walmsley*, Nichole Reisdorph
American Society For Mass Spectrometry, St Louis Missouri, June 2015
Kinetic Evaluation of Trypsin Digests of Apolipoprotein-A1: Implications for Quantitative Mass Spectrometry
Scott Walmsley*, Xinjian Yan,Yuxue Liang, Stephen Stein, Alexey Nesvizhskii
US Human Proteome Organization annual meeting; Seattle, Washington, April 6-9, 2014
Analysis of Peptide Ion Signatures for Characterization of Porcine and Bovine Trypsin Digestion
Scott Walmsley*, Paul Rudnick, Yuxue Liang, Steve Stein and Alexey Nesvizhskii
Mass Spectrometry: Applications to the Clinical Lab; San Diego, California, February 9-13, 2013
Mechanistic Investigations of Hydrostatic Pressure Effects on Trypsin Digestion
Alexander Lazarev*, Vera Gross, Alexander Ivanov, Scott Walmsley, Alexey Nesvizhskii
Mass Spectrometry, Applications to the Clinical Lab; San Diego, California, February 2013
Evaluation of Different Porcine and Bovine Trypsins Yield Different Cleavage Results
Scott Walmsley*,Paul Rudnick, Yuxue Liang, Steve Stein and Alexey Nesvizhskii
American Society For Mass Spectrometry, Vancouver, British Columbia, June 2012
THOR: an Algorithm for Determining the Minimal Variance Cutoff in Proteomics Spectral Count Data
Scott Walmsley*, Hyungwon Choi, Damian Fermin, Alexey Nesvizhskii
American Society For Mass Spectrometry, Minneapolis Minnesota, June 2013
Use of Spectral Counting and AMT to Quantify changes in Renal Proximal Convoluted Tubules During Metabolic Acidosis
Scott Walmsley* and Norman Curthoys
American Society For Mass Spectrometry; Denver, CO, June 2011
Evaluation of LCMS QTOF and AMT Technologies for the Quantitative Analysis of the Response to Metabolic Acidosis by the Proximal Convoluted Tubule Brush Border Membrane
Scott Walmsley* and Norman Curthoys
Colorado Biological Mass Spectrometry Society Summer Meeting; Boulder Colorado, August, 2010
Reducing Tissue Heterogeneity for the Specific Proteomic Analysis of Proximal Convoluted Tubule Apical Membranesv
Scott Walmsley*, Corey Broeckling, Jessica Prenni, Norman Curthoys
American Society For Mass Spectrometry; Philadelphia Pennsylvania, June 2009
Improving the Value of Corn Proteins Via Reforming with Anaerobic Bacteria
Tim Eggeman*, Dan Verser, Shirley Hunter, Scott Walmsley
28th Symposium on Biotechnology for Fuels and Chemicals; Nashville Tennessee, May, 2006
Cloning and characterization of a family of peritrophin-like cDNAs from the cat flea, Ctenocephalides felis
Pat Gaines*, Scott Walmsley, Kevin Brandt, Nancy Wisnewski
Entomological Society of America Annual Meeting; Montreal, Canada, December 3-6, 2000
Ctenocephalides felis GABA receptor subunit Rdl: Cloning and survey of the cyclodiene resistance allele in fleas
Kevin Brandt*, Pat Gaines, Scott Walmsley, Gary Silver, Nancy Wisnewski
2000 Entomological Society of America Annual Meeting; Montreal, Canada, December 3-6, 2000

Skills & Proficiency

R & statistical analysis

Pattern recognition and machine learning

SQL databases (SQL/PHP)

Coding (Java & C)

Algorithms

noSQL databases (MongoDB, Neo4J)

Molecular Biology

Protein Biochemistry