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I am Rodolfo Antonio Salido Benítez, a scientist, lab automation enthusiast, DIY maker, and open source preacher.

I earned my PhD in Bioengineering from UC San Diego under Professor Rob Knight.

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My academic interests surround the interface between humans and machines in well-being, productivity, rehabilitation, and augmentation. I'm passionate about creatively shaping our shared vision of humanity.

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As an undergraduate, I interned at Calibr, a non-profit biomedical research institute. There, I assisted in operating an automated High Throughput Screening system to identify potential drug candidates for neglected diseases. After earning my B.Sc., I joined the Knight Lab as a Research Associate, working with robotic liquid handling devices for high throughput microbiome analyses. Later, as a Graduate Student Researcher, I studied studied the built environment microbiome and its associations with human health. 

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With over nine years of experience in high throughput systems, I have collaborated with industrial robotic arms and liquid handling devices to conduct both fundamental and targeted research.

Research interests

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  • High throughput sequencing

  • Robotics / Automation

  • Machine learning

  • Open source hardware

  • Frugal innovation

  • Genomics / Microbiome

  • Multi-omics

  • Environmental monitoring

  • Built-environment

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In my free time, I enjoy live music events, exploring great food spots, experiencing visually stimulating environments, and spending time with good company. I practice resistance training through weight lifting; I joined the 1K pound club in 2023 by lifting more than 1,000 pounds across squat, deadlift, and bench press.

 

I also develop my non-verbal communication skills through photography and music. I enjoy portraiture, street, and conceptual photography, and I have a growing music library of over 2,500 songs, which I collect, catalog, and mix.

2019 - 2024

Doctor of Philosophy, Bioengineering - University of California San Diego, La Jolla, CA

EDUCATION

Masters of Science , Bioengineering - University of California San Diego, La Jolla, CA

2019 - 2023

2012 - 2016

Bachelor of Science, Physiology & Neuroscience - University of California San Diego, La Jolla, CA

2010 - 2012

International Baccalaureate Diploma Programme - Preparatoria Federal Lazaro Cardenas, Tijuana BC, Mexico

AWARDS

2023

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2012

Henry Booker Award for Exemplary Ethical Engineering - Jacobs School of Engineering, University of California San Diego

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Bronze Medal National Biology Olympiad - Chihuahua, Mexico

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SELECTED PUBLICATIONS                           5 first/co-first* author, 22 peer-reviewed papers total

  • Salido, R. A.* et al. The International Space Station Has a Unique and Extreme Microbial and Chemical Environment Driven by Use Patterns. Cell (in review, 2024).

  • Fielding-Miller, R. et al. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg. Heal. - Am. 19, (2023).

  • Aksenov, A. A.*; Salido, R. A.* et al. The molecular impact of life in an indoor environment. Sci. Adv. 8, (2022).

  • Cantú, V. J.*; Salido, R. A.* et al. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. mSystems 7, (2022).

  • Salido, R. A.* et al. Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs. mSystems 6, (2021).

  • Salido, R. A.* et al. Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. mSystems 5, (2020).

  • Sanders, J. G. et al. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 20, 1–14 (2019).

  • Minich, J. J. et al. High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems 3, (2018).

EXPERIENCE

Oct. 2016 - Sep. 2019

Knight Lab, UCSD Health Sciences

Staff Research Associate I

  • Developed a highly efficient, miniaturized shotgun sequencing pipeline, yielding substantial reductions in library preparation costs through reduced reagents consumption and parallelization of sample processing. The pipeline, having processed over 50,000 samples for microbiome research, showcases my dedication to automated, cost-effective, and impactful research methodologies.

  • Created sample plating templates and established standardized assay readout output files to contribute to the development of a high-throughput bioinformatic sample information management system.

  • Integrated novel liquid handling technologies into the existing laboratory robotic infrastructure, resulting in a reduction of experimental procedural time from 2.5 hours to just 45 minutes, alongside a fourfold decrease in consumable tip usage.

  • Introduced desktop 3D printer technologies and applied them to develop custom lab equipment, enhancing operational efficiency.

  • Diagnosed and resolved robotic malfunctions while also playing a vital role in orchestrating collaborative efforts for device upgrades with industry providers

Sep. 2019 - Present

Knight Lab, UC San Diego Bioengineering

Graduate Student Researcher

  • Engineered a high-throughput pipeline for shotgun metatranscriptomic sequencing, effectively processing over 4,000 wastewater samples for environmental monitoring of human diseases.

  • Led the analysis of wastewater metatranscriptomic data, exploring the feasibility of training a machine learning classifier to differentiate SARS-CoV-2 detection status by RT-qPCR from metatranscriptome profiles. Correlated bacterial alpha diversity with population size and characterized antimicrobial resistance profiles of different wastewater streams.

  • Enhanced wet-lab protocols for delicate RNA sample handling, and provided comprehensive training to laboratory technicians to ensure reproducibility of metatranscriptomic pipeline methodology.

  • Successfully implemented the metatranscriptomic pipeline on fecal samples, generating both shotgun metatranscriptomic and metagenomic data from a single nucleic acid extraction per sample for hundreds of samples. This pipeline is expected to process tens of thousands of fecal samples.

  • Spearheaded the development and implementation of a novel environmental monitoring system, enabling the detection of SARS-CoV-2 in San Diego County public schools. Managed the processing of tens of thousands of surface samples to bolster pandemic response measures in high-risk communities.

  • Evaluated, validated, and integrated new liquid handling technologies into UC San Diego's Expedited COVID IdenTification Environment (EXCITE) Lab, significantly enhancing critical infrastructure redundancy and minimizing consumable costs for SARS-CoV-2 clinical tests.

  • Designed and manufactured tailor-made, 3D-printed sample collection devices to support both UC San Diego's Return To Learn initiative and the collaborative 3D Microbial Mapping project with the Jet Propulsion Laboratory (JPL).

  • Mentored an accomplished group of bioengineering undergraduates in the development of an award- winning frugal innovation project. This project enabled affordable SARS-CoV-2 detection with minimal laboratory infrastructure, showcasing innovation and practical problem-solving skills.

  • Contributed significant enhancements to the wet-lab sample information management repository, including new functionalities, visualizations, and their associated unit tests for continuous integration.

Director of Laboratory Automation                                               appointed April 2023

  • Led procurement evaluation of an automated liquid handling device for precious reagent dispensing, minimizing dead volumes and reducing reagent consumable costs. Justified the instrument purchase with a cost analysis that estimated a return on investment after processing nine thousand samples compared to the established infrastructure.

  • Developed a sequencing library normalization method based on read count distributions from shallow sequencing, improving cost efficiency of highly multiplexed library pools by producing more even sequencing depth among samples and achieving higher average reads per sample.

  • Collaborated in the adoption of a standardized, barcoded sample collection device for high throughput microbiome sample accession and nucleic acid extraction, with the potential for tandem small molecule metabolite extraction. This standardized device minimizes well-to-well contamination, shortens processing time, and facilitates sample tracking, sample randomization, and integration with automation compared to the established pipeline.

  • Contributed to and maintained a GitHub-based sample information management repository (LIMS-like system) that enables Quality Control (QC) of automated wet lab pipelines and semi-automation of sample tracking, from sample accession to deposition in a public database (Qiita, an open-source microbial study management platform)

  • Designed and implemented Preventative Maintenance (PM) procedures for automated infrastructure, including custom PM tracking forms specific to different instrument types.

Apr. 2014 - Aug. 2016

California Institute for Biomedical Research (Calibr)

Lab Automation Intern, ultra High Throughput Screening (uHTS)

  • Optimized automation protocols to maximize throughput and ease of screening for biochemical and cell based assays. 

  • Coordinated the utilization of automated liquid handling devices to efficiently screen up to four distinct projects simultaneously, offering real-time troubleshooting when required.

  • Assisted scientists in miniaturizing their assays and optimizing them for high-throughput platforms.

  • Designed systematic procedures to obtain measurable accuracy and precision quality control data of liquid handling devices in order to guarantee institute standards. 

  • Led multiple personal manufacturing projects aimed towards upgrading the lab space and instrumentation. 

  • Trained and managed new interns to ensure proper working condition of the uHTS lab while maximizing their learning experience. 

TEACHING EXPERIENCE

Sep. 2015 - Dec. 2015

Division of Biological Sciences, UC San Diego

Teaching Assistant - Cellular Neurobiology with Professors Nicholas Spitzer and Chih-Ying Su  

  • Led weekly discussions and implemented creative approaches to teach complex material promoting deeper understanding of underlying biological mechanisms.

  • Participated in weekly meetings with Professors and other TA’s to discuss teaching strategies, review problem sets, and go over class logistics.

Mar. 2015 - Jun. 2015

Division of Biological Sciences, UC San Diego

Instructional Apprentice - The Cell with Professor Stephanie Mel

  • Led weekly discussions and experimented with varied teaching styles to help students grasp the introductory concepts of a class on The Cell. Participated in grading and other class logistics.

Jan. 2021 - Mar. 2021

Shu Chien-Gene Lay Department of Bioengineering, UC San Diego

Introduction to Bioengineering                                                         Winter Quarter 2021

  • Led bioengineering tele-laboratory projects, imparting principles of problem definition, imaging data analysis, prototyping, additive manufacturing, and device testing to undergraduate students.

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Applied Genomic Technologies                                                        Winter Quarter 2020

  • Facilitated weekly discussion sections to address student queries regarding course content.

  • Crafted problem sets for homework assignments and participated in grading.

  • Assessed student performance in final presentations and delivered constructive feedback.

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Principles of Bioinstrumentation Design                                              Fall Quarter 2020

  • Conducted weekly discussion sections to provide guidance on homework assignments.

  • Collaborated in weekly meetings with Professor and fellow TAs to review problem sets and assess student work.

Contact Me

rsalidob<at>ucsd.edu

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