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Hire Dr. Rubén J.

Norway

USD 100 /hr

Microbial Genomics & Bioinformatics Specialist | PhD | Genome Assembly, Metagenomics, Microbiome, RNA-seq

Profile Summary

About Me I'm a bioinformatician with a PhD in Microbiology from the University of Bergen and 9 peer-reviewed publications in microbial genomics and multi-omics analysis. I specialize in solving complex problems with bacterial, archaeal, and fungal genomic data using cutting-edge computational methods. Research Focus: My expertise spans the full bioinformatics pipeline—from raw NGS data to publication-quality insights. I've published work on comparative genomics, transcriptomics, and proteomics in high-impact journals, demonstrating my commitment to rigorous, reproducible science. What I Do: Microbial Genome Assembly & Annotation: Multi-platform NGS (Illumina, PacBio, Nanopore, hybrid), genome assembly (SPAdes, Flye, Canu), and comprehensive annotation (Prokka, PGAP, RAST) Quality Assurance: Contamination detection (CheckM), assembly metrics, purity assessment, genome binning Functional Analysis: KEGG pathway mapping, enzyme characterization, phylogenetic analysis (16S, custom trees, TYGS) Transcriptomics & Differential Expression: Complete RNA-seq pipelines with DESeq2, publication-quality figures Metagenomics & Microbiome: Taxonomic profiling (QIIME2, DADA2, Kaiju), diversity analysis, MAG recovery, binning Custom Problem-Solving: Design multi-method strategies to answer biological questions (e.g., "Is this sample pure or mixed?"), not just "run tools" Why Work With Me: ✓ PhD-level expertise with publication track record ✓ Specialized focus on microbial genomics (bacteria, archaea, fungi only) ✓ Publication-ready deliverables with detailed methods & visualizations ✓ Problem-solving mindset—I design strategies, not just pipelines ✓ International collaboration experience, responsive communication Tools & Skills: NGS: Illumina, PacBio, Oxford Nanopore | Assembly: SPAdes, Flye, metaSPADES, Canu | Annotation: Prokka, PGAP, RAST, Roary | Functional: KEGG, EggNog, COG, InterPro | Transcriptomics: DESeq2, Kallisto, Trinity | Metagenomics: QIIME2, DADA2, Kraken2, Kaiju | Phylogenetics: IQ-TREE, RAxML, TYGS | Programming: R, Python, Bash/Linux | Visualization: ggplot2, iTol, KEGG maps Recent Projects: - Comprehensive genome purity assessment using multi-pipeline validation - Metagenomic assembly and binning for complex microbial communities - RNA-seq differential expression analysis with publication figures - Phylogenetic placement of novel bacterial isolates - Comparative genomics and functional annotation I'm committed to delivering results that meet publication standards and can withstand peer review. Let's discuss your project and how I can help unlock insights from your data.

Subject Matter Expertise

• ★ Microbiology
• ★ Genomics
• ★ Bioinformatics
• ☆ Computational Biology
• ☆ Microbiome Research
• ☆ Genetics
• ☆ Transcriptomics
• ☆ Comparative Genomics
• ☆ Molecular Evolution
• ☆ Next Generation Sequencing (NGS)
• ☆ DNA Sequencing
• ☆ Genome Sequencing
• ☆ RNA Sequencing
• ☆ Food Microbiology
• ☆ Phylogenetics

Services

• Writing
• Research
• Consulting

Writing General Proofreading & Editing

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Work Experience

Bioinformatic Scientist

Tailoredomics

April 2025 - Present

Bioinformatician

Tailoredomics

April 2025 - Present

PhD fellow

University of Bergen

August 2021 - August 2024

Researcher

University of Bergen

September 2019 - December 2020

Researcher

University of Bergen

September 2018 - January 2020

Research assistant

University of Bergen

September 2018 - June 2019

Education

PhD

University of Bergen

August 2021 - August 2024

Certifications

• PhD

  University of Bergen

  https://bora.uib.no/bora-xmlui/handle/11250/3174973

  February 2024 - Present

Publications

JOURNAL ARTICLE

Rubén Javier-López, Mélodie Kielbasa, Jean Armengaud, Nils-Kåre Birkeland (2025). Transcriptomic and proteomic insights into feather keratin degradation by Fervidobacterium . Frontiers in Microbiology.

Rubén Javier-López, Natia Geliashvili, Nils-Kåre Birkeland (2024). Comparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes . BMC Genomics.

Akzhigit Mashzhan, Aida Kistaubayeva, Rubén Javier-López, Akerke Bissenbay, Nils-Kåre Birkeland (2024). Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile . Microorganisms.

Akzhigit Mashzhan, Aida Kistaubayeva, Rub&#233;n Javier-L&#243;pez, Akerke Bissenbay, Nils-K&#229;re Birkeland (2024). <i>Caldanaerobacter subterraneus</i> subsp. <i>keratinolyticus</i> subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile . Microorganisms.

Akzhigit Mashzhan, Aida Kistaubayeva, Rub&#233;n Javier-L&#243;pez, Ulzhan Bissenova, Akerke Bissenbay, Nils-K&#229;re Birkeland (2024). Polycladomyces zharkentensis sp. nov., a novel thermophilic cellulose- and starch-degrading member of the Bacillota from a geothermal aquifer in Kazakhstan . International Journal of Systematic and Evolutionary Microbiology.

Akzhigit Mashzhan, Ruben Javier-Lopez, Aizhan Talipova, Aida Kistaubayeva (2024). Degradation of keratin compound residues by thermophilic bacteria with keratinase activity . Experimental Biology.

Rub&#233;n Javier-Lopez, Edoardo Mandolini, Munavvara Dzhuraeva, Khursheda Bobodzhanova, Nils-K&#229;re Birkeland (2022). Fervidobacterium pennivorans subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile . Microorganisms.

Nazar Mohamed, Jorunn Litlekals&#248;y, Israa Abdulrahman Ahmed, Einar Marius Hjellestad Martinsen, Jessica Furriol, Ruben Javier-Lopez, Mariam Elsheikh, Nuha Mohamed Gaafar, Luis Morgado, Sunil Mundra, et al.(2021). Analysis of Salivary Mycobiome in a Cohort of Oral Squamous Cell Carcinoma Patients From Sudan Identifies Higher Salivary Carriage of Malassezia as an Independent and Favorable Predictor of Overall Survival . Frontiers in Cellular and Infection Microbiology. 11. Frontiers Media {SA}

Akzhigit Mashzhan, Rub&#233;n Javier-L&#243;pez, Aida Kistaubayeva, Irina Savitskaya, Nils-K&#229;re Birkeland(2021). Metagenomics and Culture-Based Diversity Analysis of the Bacterial Community in the Zharkent Geothermal Spring in Kazakhstan . Current Microbiology. 78. (8). p. 2926--2934. Springer Science and Business Media {LLC}

BOOK CHAPTER

Akzhigit Mashzhan, Rub&#233;n Javier-L&#243;pez, Aida Kistaubayeva, Irina Savitskaya, Nils-K&#229;re Birkeland(2021). Analysis and Characteristics of Thermal Springs in Kazakhstan . Microorganisms for Sustainability. p. 97--114. Springer Singapore