Jose Solis-Ruiz

solisruiz.j@gmail.com

Education

Oregon State University - B.Sc
BioResource Research (‘17)
Concentration in Biotechnology and Genomics/Bioinformatics
Minor in Chemistry

Research Data Analyst

OHSU Knights Diagnostics Laboratory (08/11/2022 - Present)

Use Python, R, SQL in Linux to support clinical and research project needs. Provide statistical expertise and data visualization in Python and R.

Research Assistant II

OHSU Knights Diagnostics Laboratory (07/15/2019 - 08/11/2022)

Using Python, R, SQL in Linux to leverage clinical, pathological, ancillary, and genomic data to support diagnostic test development, research, and data reporting at Knights Diagnostic Laboratory. Wrote an internal package named SoaPy to clean and transform clinical, pathological, ancillary, and genomic data.

Bioinformatic Research Specialist

Bayer Crop Sciences (09/04/2018 - 03/29/2019)

Worked as part of a Bioinformatics Team to develop and annotate microbial genome assemblies. Collaborated with scientists to provide genomic and bioinformatic analysis on microbial genomes and genes using Perl, Python and R. Updated a chemical dereplication workflow and collaborated in its development into an in-house web application. Developed and documented relevant scripts/pipelines for genomic/bioinformatic use in Jupyter and R Markdown.

Microbial QA/QC Technician

Agrinos, Inc. (10/16/2017 - 08/31/2018)

Performed quality assurance and quality control to produce high-quality microbial products. Collaborated in research and development of microbial products. Developed a document and signature tracker using Microsoft Power Automate. Assisted in general lab operations and lab maintenance. Ensured the proper documentation of experiments, data, quality assurance and quality control documents.

Laboratory and Bioinformatics Research Technician

Oregon State University Department of Microbiology (12/2013 - 06/10/2017)

Worked in a microbial BSL-2 laboratory to better understand Vibrio cholerae. Performed microbial analysis and co-culture experiments to understand predator-prey relations between protozoans and Vibrio variants. Developed a microbial genome assembly pipeline for microbial read datasets. Developed a bioinformatic tool for the identification of conserved and non-conserved genes in microbial genomes. Wrote a program to perform bulk microbial reference and SRA file downloads from the NCBI website.

Collaborations/Publications

• Li Y, Solis-Ruiz J, Yang F, Long N, Tong CH, Lacbawan FL, Racke FK, Press RD. NGS-defined measurable residual disease (MRD) after initial chemotherapy as a prognostic biomarker for acute myeloid leukemia. Blood Cancer J. 2023 Apr 24;13(1):59. doi: 10.1038/s41408-023-00833-7. PMID: 37088803; PMCID: PMC10123056.
• Post-induction Minimal Residual Disease Defined by Next-Generation Sequencing Predicts Poorer Clinical Outcomes in Patients with Acute Myeloid Leukemia
• IYang F, Long N, Anekpuritanang T, Bottomly D, Savage JC, Lee T, Solis-Ruiz J, Borate U, Wilmot B, Tognon C, Bock AM, Pollyea DA, Radhakrishnan S, Radhakrishnan S, Patel P, Collins RH, Tantravahi S, Deininger MW, Fan G, Druker B, Shinde U, Tyner JW, Press RD, McWeeney S, Agarwal A. Identification and prioritization of myeloid malignancy germline variants in a large cohort of adult patients with AML. Blood. 2022 Feb 24;139(8):1208-1221. doi: 10.1182/blood.2021011354. PMID: 34482403; PMCID: PMC9211447.
• Tauangtham A, et. Al. Reproducibility of Next-Generation Sequencing Results Between Labs and Platforms.

Undergraduate Research Projects

• Predation enhances survival and growth of pathogenic and non-pathogenic isolates of Vibrio cholerae
• Assembler Optimization of Microbial Genome Read Datasets
• Development of Bioinformatics Tool for the Identification of Conserved and Non-conserved Genes in Microbial Genomes
• Thermostable Human Carbonic Anhydrase II Kinetic Study of F93 and Site-Directed Mutagenesis on Residue Position 93 using Non-conical Amino Acids

Computer Knowledge

• C/C++, Perl, Python, R, BASH, Unix, MySQL, PostgresSQL, AirBnB Knowledge Repo, Jupyter, JIRA, GIT

Genomics and Bioinformatics Tool Knowledge

• Velvet, SPAdes, IDBA-UD, PEAR, FLASh, Sickle, AntiSMASH, CLC Genomics Workbench, iTol, FastTree, QIIME, Muthor, QUAST, Phylosift, ANI, AAI, IGV, Mummer, Diamond, NCBI Toolkit, SRA Toolkit, Cytoscape, Bowtie2, BEDtools, SamTools, BCFtools, Cuflinks, Tophat, Glimmer, KEGG, Parnsp, MUSCLE, Geneious, freebayes, Mauve, Hammer, Pfam