CHRISTOPHER S. NELSON

San Francisco Bay Area

Phone: 224-***-****

ad3ltc@r.postjobfree.com

https://www.linkedin.com/in/christopher-nelson-5451005 SUMMARY:

PhD trained bioinformatics scientist with expertise in analysis of genetic variation and liquid biopsy. Interested in custom analysis algorithms in Python and R for bioinformatic and genomic projects. EDUCATION:

Univ. of California, Berkeley / Buck Institute, Postdoc, Statistical Genetics 2013 – 2017 Univ. of California, San Francisco, Ph.D. in Biomedical Sciences (Genomics) 2007 – 2013 The University of Chicago, B.A. with Honors in Biological Sciences 2003 – 2007 SKILLS:

• Programming languages: Python, Bash, R, and SQL.

• Next generation sequencing techniques: Analyzing and managing data through high-throughput sequencing technology pipelines. Verification and validation of new assays and sequencers. Liquid biopsy development, genome sequencing, WES, ChIPseq, RNAseq.

• Tools: Linux/UNIX command line pipelines on HPC cluster and cloud computing environments, git, NumPy, SciPy, Pandas, Statsmodels, ggplot2, R survival analysis modules, R/Bioconductor, Google cloud SDK, IGV, VCFtools, Samtools, BEDtools, SRAtoolkit, BWA-mem, Picard, and GATK.

• Statistical genetics methods: genome-wide association studies (GWAS), quantitative trait locus (QTL) and survival analysis.

• Deep background in molecular biology, genetics, bioinformatics, and genomic oncology.

• Strong knowledge of statistical tests application and implementation.

• Excellent verbal and written communication skills. EXPERIENCE:

Staff Bioinformatics Scientist, Process Development and Pipeline Engineering Personalis, Fremont, California 2022- present

• Conducted performance assessments for novel sequencing instruments, including NovaSeqX Plus and Ultima.

• Represented the bioinformatics group in business partner meetings, contributing insights and expertise to foster collaboration and effective communication across interdisciplinary teams.

• Managed and mentored a bioinformatics analyst, conducting 1:1s, providing training on local bioinformatics infrastructure, guiding and reviewing all work, and assisting in career planning.

• Continued analysis and support for operations, process development and R&D teams working on liquid biopsy and immune oncology products.

Senior Bioinformatics Scientist, Process Development and Pipeline Engineering Personalis, Menlo Park, California 2019- 2022

• Led bioinformatics analysis and provided experiment design support for Process Development, OPS, and R&D teams developing liquid biopsy and immune oncology products.

• Independently identified and resolved issues, pushing improvements to pipeline repositories for pipeline engineering projects.

• Iteratively evaluated and enhanced sensitivity and positive predictive value (PPV) of liquid biopsy products.

• Implemented improved fusion sensitivity for RNA and neoantigen pipelines.

• Implemented somatic whole genome sequencing (WGS) small variant calling in pipelines. Enables the development of a tumor-informed NeXT Personal minimal residual disease liquid biopsy product. Bioinformatics Scientist (Staff Scientist), Algorithms and Data Analysis Thermo Fisher Scientific (formerly Affymetrix), Santa Clara, California 2017- 2019

• Work on Bayesian DNA genotyping algorithms for a high-throughput genotyping business unit.

• Deliver accurate genotyping priors and algorithms for hundreds of thousands of samples. o E.g., blood-typing study that has already saved lives by finding rare donors genetically. NRSA Postdoctoral Fellow, Statistical Genetics

Dr. Rachel Brem’s lab, University of California, Berkeley 2013 – 2014, Buck Institute 2014 – 2017

• Developed statistical genetics tools and genomic methods for large-scale studies on model organisms.

• Analyzed next-generation sequencing (NGS) data sets including RNAseq and genome sequencing.

• Discovered novel genes associated with longevity, metabolic health, and gut aging in wild isolates of flies and yeast.

• Four papers published.

o Ten additional papers since the end of postdoc [through 2023]. Graduate Student Researcher, Genomics

Dr. Joe DeRisi’s lab, University of California, San Francisco (UCSF) 2007 – 2013

• Discovered first evidence of cell-cycle arrest in Plasmodium falciparum, the parasite that causes malaria.

• Produced comprehensive biophysical measurements of the transcription factor Hac1’s DNA binding preferences. For this purpose, designed and fabricated custom microfluidic devices to assay binding.

• Using in vivo ChIPseq and biophysical data, produced a detailed description of the binding preference of FOXP2, a transcription factor involved in spoken language in humans.

• Published five papers.

ACADEMIC FUNDING:

• Two NIH National Research Service Award (NRSA) F32 fellowships (one declined).

• Ellison Foundation Fellowship to Woods Hole Laboratory.

• Google Cloud Credits Award.

• Howard Hughes Medical Institute Undergraduate Fellow. PUBLICATIONS:

1. Kapahi P, Wilson K, Bar S, Dammer E, Carrera E, Hodge B, Tyler Hilsabeck, Bons J, Brownridge G, Beck J, Rose J, Granath-Panelo M, Nelson C, Qi G, Gerencser A, Lan J, Afenjar A, Chawla G, Brem R, Campeau P, Bellen H, Schilling B, Seyfried N, and Ellerby L. (2024) OXR1 maintains the retromer to delay brain aging under dietary restriction. Nature Communications. 2024 15, 467. 2. Hilsabeck T,Liu-Bryan R, Guo T,Wilson KA, Bose N, Raftery D, Beck JN, Lang S, Jin K, Nelson CS, Oron T, Stoller M, Promislow D, Brem RB, Terkeltaub R, Kapahi P. (2022) A fly GWAS for purine metabolites identifies human FAM214 homolog medusa, which acts in a conserved manner to enhance hyperuricemia-driven pathologies by modulating purine metabolism and the inflammatory response. GeroScience 2022 Apr 6 (44):2195–2211.

3. Khanna A, Sellegounder D, Kumar J, Chamoli M, Vargas M, Chinta SJ, Rane A, Nelson C, Peiris TH, Brem R, Andersen J, Lithgow G, Kapahi P. (2021) Trimethylamine modulates dauer formation, neurodegeneration, and lifespan through tyra-3/daf-11 signaling in Caenorhabditis elegans. Aging Cell. 2021 May;20(5):e13351.

4. Khomtchouk BB, Nelson CS, Vand KA, Palmisano S, Grossman RL. (2020) HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. Database (Oxford). 2020 Dec 31;2020:baaa115. 5. Sharma A, Akagi K, Pattavina B, Wilson KA, Nelson C, Watson M, Maksoud E, Ortega M, Brem RB, Kapahi P. (2020). Musashi expression attenuates radiation-induced decline in intestinal permeability and survival in Drosophila. Scientific Reports. 2020 Nov 5;10(1):19080. 6. Gleadall NS, Veldhuisen B, Gollub J, Butterworth AS, Ord J, Penkett CJ, Timmer TC, Sauer CM, van der Bolt N, Brown C, Brugger K, Dilthey AT, Duarte D, Grimsley S, van den Hurk K, Jongerius JM, Luken J, Megy K, Miflin G, Nelson CS, Prinsze FJ, Sambrook J, Simeoni I, Sweeting M, Thornton N, Trompeter S, Tuna S, Varma R, Walker MR; NIHR BioResource, Danesh J, Roberts DJ, Ouwehand WH, Stirrups KE, Rendon A, Westhoff CM, Di Angelantonio E, van der Schoot CE, Astle WJ, Watkins NA, Lane WJ. (2020) Development and validation of a universal blood donor genotyping platform: a multinational prospective study. Blood Adv. 2020 Aug 11;4(15):3495-3506.

7. Wilson KA, Beck JN, Nelson CS, Hilsabeck TA, Promislow D, Brem RB, Kapahi P (2020) GWAS for Lifespan and Decline in Climbing Ability in Flies upon Dietary Restriction Reveal decima as a Mediator of Insulin-like Peptide Production. Curr Biol. 2020 Jul 20;30(14):2749-2760 8. Jin K, Wilson KA, Beck JN, Nelson CS, Brownridge GW 3rd, Harrison BR, Djukovic D, Raftery D, Brem RB, Yu S, Drton M, Shojaie A, Kapahi P, Promislow D. (2020) Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila. PLoS Genet. 2020 Jul 9;16(7):e1008835. doi: 10.1371/journal.pgen.1008835. 9. Khomtchouk B. B., Vand K.A., Koehler W.C., Tran D-T, Middlebrook K., Sudhakaran S., Nelson CS, Gozani O, Assimes T.L. An Internet-of-Omics for Human Cardiovascular Disease Data. (2019). Circulation: Genomic and Precision Medicine. 1 Apr 2019;12 10. Peters T.W.*, Nelson C.S.*, Gerencser A.A., Dumas K.J., Tavshanjian B., Chang K.C., Lithgow G.J., Brem R.B., Hughes R.E. Natural Genetic Variation in Yeast Reveals that NEDD4 is a Conserved Modifier of Mutant Polyglutamine Aggregation. (2018). G3 (Bethesda). 2018 Nov 6;8(11):3421-3431

11. Nelson C.S.*, Beck J.N.*, Wilson K.A.*, Pilcher E.R., Kapahi P., and Brem R.B. (2016). Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila. BMC Genomics. 2016 Nov 4;17(1):867.

12. Khanna* A., Kumar* J., Vargas* M., McCloskey T., Barrett L., Katewa S., P. Li, Sharma A., Naudé N., Nelson C.S., Brem R., Killilea D.W., Mooney S., Gill M. and Kapahi P. (2016). A genome-wide screen of bacterial mutants to assess the influence on dauer formation in C. elegans. Scientific Reports. 2016; 6: 38764.

13. Katewa S.D., Akagi K., Bose N., Rakshit K. Camarella T., Zheng X., Hall D., Davies S., Nelson C., Brem R.B., Ramanathan A., Sehgal A., Giebultowicz J.M., Kapahi P. (2016). Peripheral circadian clocks modulate nutrient dependent changes in lifespan and fat metabolism. Cell Metabolism. 2016 Jan 12;23(1):143-54.

14. Ornstein J.S., Nelson C.S., DeRisi J.L., Weissman J.S., El-Samad H. (2013). Low Affinity and Stoichiometry Allows Msn2 to Provide Proportional Homeostatic Regulation. Curr Biol. Nov 6. pii: S0960-9822(13)01190-1.

15. Nelson C.S., Fuller C., Fordyce P., Greninger A., Li H., DeRisi J.L. (2013). Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2 binding motif in chimp and human, which enables the detection of evolutionarily novel regulatory targets. Nucleic Acids Research. 41(12):5991-6004. 16. Abromaitis S.*, Nelson C.S.*, Previte D., Clark J., DeRisi J.L., Koehler J.E. (2013). Bartonella quintana deploys host and vector temperature-specific transcriptomes. PLoS ONE 8(3): e58773. 17. Fordyce P.F., Pincus D., Kimmig P., Nelson C.S., DeRisi J.L., El-Samad H., and Walter P.H. (2012). The basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proc Natl Acad Sci U S A. 2012 November 6; 109(45): E3084- E3093. 18. Kim C.C., Nelson C.S., Wilson E.B., Hou B., DeFranco A. L., DeRisi J.L. (2012). Splenic Red Pulp Macrophages Produce Type I Interferons as Early Sentinels of Malaria Infection but are Dispensable for Control. PLoS ONE. 7(10): e48126.

19. Lam Y.W., Nelson C.S., Sherman S.M. (2006). Mapping of the functional interconnections between thalamic reticular neurons using photostimulation. Journal of Neurophysiology, 96: 2593-2600.

(*co-first author)

Contact this candidate