QuestOmics

Bioinformatician · Human gut microbiome

Sandro Valenzuela

I turn complex sequencing data into the human gut microbiome.

I am a bioinformatician with deep expertise in the human gut microbiome, and I love turning complex sequencing data into clear biological insight. On top of a solid foundation in computer science and next-generation sequencing, I work fluently with SQL, several programming languages, and a broad range of bioinformatics tools. Analytical, proactive, and a genuine team player, I stay effective under pressure and enjoy building things that people actually rely on.

years in bioinformatics
10+
years in bioinformatics
peer-reviewed papers
7
peer-reviewed papers
samples benchmarked
1,300+
samples benchmarked
research roles
6
research roles
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Sandro Valenzuela
sandro@microbiome — bash
$

What I work with

Skills & toolbox

NGS & metagenomicsQC → assembly → taxa & function
R & tidyverse / Shinyanalysis + interactive dashboards
Pythonpipelines, tooling, ML
Shell & HPC (bash, Slurm)reproducible batch at scale
SQL & databasesPostgres, MySQL, MongoDB
Web / full-stackNext.js, Django, JS/TS
Programming
R · Python · bash · awk · tcl · C++ · JavaScript
Databases
MySQL · PostgreSQL · MongoDB
Frameworks
R Shiny (advanced) · Django (intermediate) · .NET (basic)
Genomics
NGS analysis (QC, abundance, expression, taxa assignment) · de novo assembly · samtools / seqtk / GATK / bedtools · prokaryotic & eukaryotic annotation and visualization

Where I’ve worked

Experience, with a live demo for each role

Every position below pairs the work I did with a small interactive illustration of it. Play with the controls — each one recomputes in your browser.

Mar 2023 – Present Current

PhD Researcher

University of Helsinki

Helsinki, Finland

BashRPythonSlurmML phage detection
  • Assessing how a viral enrichment protocol shapes characterisation of the infant gut virome.
  • Modelling ecological time series to elucidate how bacteriophages regulate bacterial population dynamics.
  • Analysing longitudinal microbiome data — correlating taxon abundance with within-strain SNV frequencies.
  • Benchmarking taxonomic profiling software across a cohort of 1,300 samples.
  • Built questomics.app, a web platform for analysing the human gut microbiome.

Interactive demos

Phage–bacteria dynamics

A predator–prey model of how bacteriophages regulate a bacterial population. Move the sliders and watch the ecosystem oscillate.

Longitudinal abundance × SNV coupling

In time-series data I track whether a taxon's abundance moves together with a within-strain variant's frequency. Pick a pair and read the correlation.

Nov 2020 – Dec 2022

Bioinformatician

Meristem SpA

Chile

DjangoBashRPythonNAMDOxford NanoporeCRISPR
  • Designed and implemented the Viroscope platform and pipeline for viral diagnosis.
  • Wrote a CRISPR guide-design tool that ranks SpCas9 protospacers by predicted on-target efficiency.
  • Built and maintained the company's software infrastructure ahead of base-editing data.
  • Delivered curated datasets, acting as the interface between wet-lab and dry-lab operations.

Interactive demos

Coverage-informed viral diagnosis

Viroscope calls a virus present only when assembly coverage clears an evidence threshold. Drag the threshold and watch the verdict flip.

CRISPR guide designer

Scan a target for SpCas9 protospacers and rank them by predicted on-target efficiency. Filter by score and inspect any guide.

Mar 2020 – Aug 2020

Bioinformatician · Research Assistant, BeatsonLab

University of Queensland

Brisbane, Australia

BWA-MEMNovoAlignSMALTmpileupFreebayesGATK4IQ-Treeggtree
  • Investigated how read aligners and variant callers influence phylogenetic inference across closely and distantly related prokaryotic genomes.
  • Ran read QC and taxonomic classification across 131 sequencing projects from heterogeneous platforms.

Interactive demo

Aligner × caller → tree

The same reads, a different aligner or variant caller, a different tree. Switch the tools and see the topology and branch support shift.

Aug 2019 – Mar 2020

Bioinformatics Contractor

Centro de Investigaciones Biológicas (CIBA)

Puerto Montt, Chile

T-CoffeeIQ-TreerentrezggtreeGATKRAxML
  • Advised on the phylogenetic classification of Piscine orthoreovirus (PRV) using all available NCBI data.
  • Advised on SNP calling and phylogenetic analysis of Renibacterium salmoninarum with local Chilean isolates.

Interactive demo

SNP-distance classifier

Pairwise SNP distances place an unknown isolate into a subgenotype. Hover the matrix; pick a query and watch it snap to its cluster.

Oct 2017 – May 2019

Bioinformatician · Production Analytics

uBiome

Chile

RStudioShinyshinydashboardMongoDBPostgreSQLMySQLBash
  • Generated monthly, quarterly, and semiannual reports tracking processed sequences over time.
  • Built R Shiny dashboards for lab operations, including a sequencer-plate heatmap of per-well read yield.
  • Developed applications to automate data acquisition and improve operational efficiency.
  • Supported lab operations through read QC and multi-source data provisioning.

Interactive demos

Production throughput dashboard

The kind of Shiny dashboard I shipped for operations: sequencing throughput over time. Toggle the reporting cadence.

Sequencer plate QC heatmap

A Shiny heatmap of a 96-well run — colour is total reads per well. Set a QC threshold to flag wells that under-sequenced.

Oct 2015 – Sep 2017

Bioinformatician · Research Assistant

Lab. de Genética Microbiana, CBIB · Universidad Andrés Bello

Santiago, Chile

RStudioShinySlurmBashIllustrator
  • Provided cross-disciplinary support and ran microbiome research across diverse sample sources.
  • Developed pipelines to automate the analysis of heterogeneous microbial samples.
  • Delivered bioinformatics solutions and analyses to other faculty groups.

Interactive demo

Community composition explorer

Taxonomic profiles across sample types. Switch the taxonomic rank and see the community recompose.

2015 – 2016

Undergraduate Thesis · Molecular Dynamics

Universidad de Talca · Center for Bioinformatics & Molecular Simulation

Talca, Chile

NAMDVMDTclBashLinux HPC
  • Ran molecular dynamics simulations of the FOXP2 forkhead domain and the RfaH elongation factor.
  • Showed both proteins reach marked conformational changes after ~100 ns of simulation.
  • Studied domain swapping and the RfaH fold-switching ('protein transformation') mechanism.

Interactive demo

Fold-switching in 3D

The two proteins I simulated, shown as their real Cα backbones (PDB 2A07 & 2OUG). Rotate them, then scrub the trajectory toward 100 ns to watch the conformation drift.

Research output

Publications

Showing 1–10 of 17

Google Scholar
  1. 1
    Impact of phage enrichment on the observed infant gut phageome

    Valenzuela-Diaz S, Dikareva E, Hickman B, Kiljunen S, Kolho KL, de Vos W, Salonen A, Korpela K

    Microbiology Spectrum · 2026First author

  2. 2
    Microbiome and plant cell transformation trigger insect gall induction in cassava

    Gätjens-Boniche O, Jiménez-Madrigal JP, Whetten RW, Valenzuela-Diaz S, Alemán-Gutiérrez A, Hanson PE, Pinto-Tomás AA

    Frontiers in Plant Science · 2023

  3. 3
    Viroscope: plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage

    Valenzuela SL, Norambuena T, Morgante V, García F, Jiménez JC, Núñez C, Fuentes I, Pollak B

    Frontiers in Microbiology · 2022First author

  4. 4
    Viroscope: plant viral diagnosis from NGS data using biologically-informed genome assembly coverage

    Valenzuela SL, Norambuena T, Morgante V, García F, Jiménez JC, et al.

    bioRxiv (preprint) · 2022First author

  5. 5
    Extensive phylogenetic analysis of Piscine orthoreovirus genomic sequences shows the robustness of subgenotype classification

    Godoy M, Medina DA, Suarez R, Valenzuela S, Romero J, Kibenge M, Wang Y, Kibenge F

    Pathogens · 2021

  6. 6
    Evaluation of computational methods for human microbiome analysis using simulated data

    Miossec MJ, Valenzuela SL, Pérez-Losada M, Johnson WE, Crandall KA, Castro-Nallar E

    PeerJ · 2020

  7. 7
    Nasal-related characterization associated with the nose microbiome

    Apte Z, Richman J, Almonacid D, Ugalde J, Vera-Wolf P, Valenzuela S

    US Patent App. 16/642,618 · 2020

  8. 8
    Nasal-related characterization associated with the nose microbiome

    Apte Z, Richman J, Almonacid D, Ugalde J, Vera-Wolf P, Valenzuela S

    US Patent App. 16/124,108 · 2019

  9. 9
    Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3

    Gutierrez-Urrutia I, Miossec MJ, Valenzuela SL, Meneses C, Dos Santos VAPM, Castro-Nallar E, Poblete-Castro I

    Journal of Biotechnology · 2018

  10. 10
    Computational methods for human microbiome analysis

    Miossec MJ, Valenzuela SL, Mendez KN, Castro-Nallar E

    Current Protocols in Microbiology · 2017

Education

  • 2023 – Present

    PhD in Integrative Life Science (ongoing)

    University of Helsinki, Finland

  • 2016

    BSc with Honours in Bioinformatics

    Universidad de Talca, Chile

Languages

  • SpanishNative
  • EnglishProfessional

Strengths

  • Proactive
  • Works well under pressure
  • Responsible

Get in touch

Let’s talk data, microbes, or code

Download CV (PDF) svalenzuela@questomics.app +358 41 328 6682

Also reachable at sandro.valenzuela@helsinki.fi · github.com/sanrrone

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