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Hire Dr. Juan C.
Mexico

Bioinformatician with 10+ years of experience in academia and industry (data analysis, 'omics, compbio)

Profile Summary
Subject Matter Expertise
Services
Writing Technical Writing, Translation
Research Technology Scouting
Consulting Healthcare Consulting, Operations Consulting, Scientific and Technical Consulting
Data & AI Predictive Modeling, Statistical Analysis, Image Processing, Image Analysis, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights
Work Experience

Chief Science Officer

Databiology

December 2015 - Present

Bioinformatician

Centro de Investigación y de Estudios Avanzados Unidad Irapuato

2015 - Present

Proff/Researcher

Universidad Autónoma de Querétaro

2013 - Present

Sr. Software Engineer

European Bioinformatics Institute (EMBL-EBI)

October 2020 - February 2023

Postdoctoral Fellow

Institute for Systems Biology

2008 - 2012

Bioinformatician

IRD

August 2007 - October 2007

Education

PhD Biochemistry Sciences

Escuela Nacional de Ciencias Biológicas

August 2016 - January 2020

Biochemical Eng.

Insituto Tecnologico de Celaya

September 1996 - January 2001

Certifications
Publications
OTHER
Juan Caballero, Harshil Shah(2020). Overview of the expression of key regeneration genes in embryo development and matured tissues in Axolotl (Ambystoma mexicanum) . Cold Spring Harbor Laboratory
Hugo Varela-Rodríguez, Diana G. Abella-Quintana, Luis Varela-Rodríguez, David Gomez-Zepeda, Annie Espinal-Centeno, Juan Caballero-Pérez, José Juan Ordaz-Ortiz, Alfredo Cruz-Ramírez(2020). Functional Characterization of the Lin28/let-7 Circuit during Forelimb Regeneration in Ambystoma mexicanum and its Influence on Metabolic Reprogramming . Cold Spring Harbor Laboratory
Juan Caballero, Yong Zhou, Shizhen Qin, Mingjuan Sun, Li Tang, Xiaowei Yan, Taek-Kyun Kim, Gustavo Glusman, Mary E. Brunkow, Mark J. Soloski, et al.(2019). Measurement of organ-specific and acute-phase blood protein levels in early Lyme disease . Cold Spring Harbor Laboratory
(2013). Diagnostic perspectives in the epoch of next-generation sequencing . Next-Generation Sequencing & Molecular Diagnostics.
JOURNAL ARTICLE
(2020). Analysis of tRNACys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data . F1000Research.
Ting Ting Xiao, Alejandro Aragón Raygoza, Juan Caballero Pérez, Gwendolyn Kirschner, Yanming Deng, Brian Atkinson, Craig Sturrock, Vinicius Lube, Jian You Wang, Gilles Lubineau, et al.(2019). Emergent Protective Organogenesis in Date Palms: A Morpho-Devo-Dynamic Adaptive Strategy during Early Development . The Plant Cell. 31. (8). p. 1751--1766. American Society of Plant Biologists ({ASPB})
(2019). Comparative Analysis of the Soluble Proteome and the Cytolytic Activity of Unbleached and Bleached Millepora complanata (“Fire Coral”) from the Mexican Caribbean . Marine Drugs.
(2019). Evaluation of the presence of Paenibacillus larvae in commercial bee pollen using PCR amplification of the gene for tRNACys . Brazilian Journal of Microbiology.
(2019). Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean . PeerJ.
(2018). Transcriptome profiling of transgenic tobacco (Nicotiana tabacum cv. xanthi nc) expressing CchGLP gene from Capsicum chinense Jacq. reveals gene expression associated with stress tolerance . The Journal of Horticultural Science and Biotechnology.
(2018). Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration . Developmental Biology.
(2018). pMEX01, a 70 kb plasmid isolated from Escherichia coli that confers resistance to multiple β-lactam antibiotics . Brazilian Journal of Microbiology.
(2018). First Report of Cowpea mild mottle virus Infecting Cultivated and Wild Phaseolus in the Central-Western Region of Mexico . Plant Disease.
(2018). Transcriptional landscapes of Axolotl (Ambystoma mexicanum) . Developmental Biology.
(2017). Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome . Cell.
(2017). Identification by MALDI-TOF Mass Spectrometry of Mercury-resistant Bacteria Associated with the Rhizosphere of an Apple Orchard . Geomicrobiology Journal.
(2016). Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients . Journal of Proteome Research.
(2016). miRNAs analysis during prickly pear development . Acta Horticulturae.
(2015). Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris) . Frontiers in Plant Science.
(2015). Influence of Extended Photoperiod on All Male Nile Tilapia (Oreochromis niloticus) Production, Differential Gene Expression and Growth Rate . International Journal of Agriculture and Biology.
(2015). Ancient Origin and Recent Innovations of RNA Polymerase IV and V . Molecular Biology and Evolution.
(2015). Isolation of a conjugative F-like plasmid from a multidrug-resistant Escherichia coli strain CM6 using tandem shock wave-mediated transformation . Journal of Microbiological Methods.
(2015). Cooked common beans ( Phaseolus vulgaris L.) modulate renal genes in streptozotocin-induced diabetic rats . The Journal of Nutritional Biochemistry.
(2015). miRNA expression during prickly pear cactus fruit development . Planta.
(2015). Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes . Genome Biology and Evolution.
(2014). Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia . Genome Announcements.
(2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs . Science.
(2014). Realistic artificial DNA sequences as negative controls for computational genomics . Nucleic Acids Research.
(2014). Accurate and Robust Prediction of Genetic Relationship from Whole-Genome Sequences . PLoS ONE.
(2014). Relationship Estimation from Whole-Genome Sequence Data . PLoS Genetics.
(2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge . Genome Biology.
(2013). Optimal Scaling of Digital Transcriptomes . PLoS ONE.
(2013). Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain . Proceedings of the National Academy of Sciences.
(2012). A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division . Cell.
(2012). Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element . Journal of Experimental Botany.
(2011). Kaviar: an accessible system for testing SNV novelty . Bioinformatics.
(2008). Transcript profiling of Zea mays roots reveals gene responses to phosphate deficiency at the plant- and species-specific levels . Journal of Experimental Botany.
(2008). The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment . Proceedings of the National Academy of Sciences.
(2006). A Family of MicroRNAs Present in Plants and Animals . The Plant Cell.
CONFERENCE PAPER
(2009). Enhancing gene detection with computer generated intergenic regions . 2009 IEEE International Workshop on Genomic Signal Processing and Statistics.