Section Description
Articles List of publiched, acepted, submitted and scientific articles in preparation.
Talks (Scientific-) Talks I gave during the last years.
Poster (Scientific-) Posters I presented or I participated in the presented research.
Teaching Summary of my experience in teaching.

Articles

Published & Accepted

  • WEScover: selection between clinical whole exome sequencing and gene panel testing

    • IH Lee, Y Lin, WJ Alvarez, C Hernandez-Ferrer, KD Mandl, S Kong
    • BMC Bioinformtics (accepted: 2021-05-07)
  • Early-life environmental exposure determinants of child behavior in Europe: a longitudinal, population-based study

  • Solving patients with rare diseases through programmatic reanalysis of genome-phenome data

    • L Matalonga, Carles Hernandez-Ferrer, D Piscia, …, H Graessner, S Beltran
    • European Journal of Human Genetics (accepted: 2020-11-13)
  • In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children

    • M Vives-Usano, C Hernandez-Ferrer, L Maitre, …, M Vrijheid, M Bustamante
    • BMC Medicine (2020-08-19)
  • A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: building a Treatabolome

  • Association between the pregnancy exposome and fetal growth

  • Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform

  • The Clinical Genome and Ancestry Report (CGAR): An Interactive Web Application for Prioritizing Clinically-implicated Variants from Genome Sequencing Data with Ancestry Composition

    • IH Lee, JA Negron, C Hernandez‐Ferrer, W Jefferson Alvarez, KD Mandl, SW Kong
    • Human Mutation (2019-11-06)
  • Dose and time effects of solar simulated ultraviolet radiation on the in vivo human skin transcriptome

    • M Bustamante*, C Hernandez‐Ferrer*, A Tewari, Y Sarria, GI Harrison, E Puigdecanet, L Nonell, W Kang, MR Friedländer, X Estivill, JR González, M Nieuwenhuijsen, AR Young
    • The British Journal of Dermatology (2019-09-16)
  • Early-Life Environmental Exposures and Blood Pressure in Children

  • Comprehensive study of the exposome and omic data using rexposome Bioconductor packages

    • C Hernandez-Ferrer, G A Wellenius, I Tamayo, X Basagaña, J Sunyer, M Vrijheid, JR Gonzalez
    • Bioinformatics (2019-06-27)
  • Prenatal Particulate Air Pollution and DNA Methylation in Newborns: An Epigenome-Wide Meta-Analysis

  • Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings

    • K Hwang, IH Lee, H Li, DG Won, C Hernandez-Ferrer, JA Negron, SW Kong
    • Scientific reports (2019-03-01)
  • Human Early Life Exposome (HELIX) study: a European population-based exposome cohort

    • L Maitre, J de Bont, …, C Hernandez-Ferrer, …, J Wright, M Vrijheid
    • BMJ open (2018-09-10)
  • A systemic approach to identify signaling pathways activated during short-term exposure to traffic-related urban air pollution from human blood

  • CTDquerier: a bioconductor R package for Comparative Toxicogenomics Database (TM) data extraction, visualization and enrichment of environmental and toxicological studies

  • Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

    • M Rubio, M Bustamante, C Hernandez-Ferrer, D Fernandez-Orth, L Pantano, Y Sarria, M Piqué-Borras, K Vellve, S Agramunt, R Carreras, X Estivill, JR Gonzalez, A Mayor
    • PloS ONE (2018-03-05)
  • psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes

    • A Gutiérrez-Sacristán*, C Hernandez-Ferrer*, JR Gonzalez, LI Furlong
    • Bioinformatics (2017-12-15)
  • The acute effects of ultraviolet radiation on the blood transcriptome are independent of plasma 25OHD3

    • M Bustamante*, C Hernandez-Ferrer*, Y Sarria, GI Harrison, L Nonell, W Kang, MR Friedländer, X Estivill, JR González, M Nieuwenhuij, AR Younge
    • Environmental Research (2017-11-01)
  • MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration

    • C Hernandez-Ferrer, C Ruiz-Arenas, A Beltran-Gomila, JR González
    • BMC Bioinformatics (2017-01-17)
  • The Pregnancy Exposome: Multiple Environmental Exposures in the INMA-Sabadell Birth Cohort

    • O Robinson, X Basagaña, L Agier, M de Castro, C Hernandez-Ferrer, JR Gonzalez, J Grimalt, M Nieuwenhuijsen, J Sunyer, R Slama, M Vrijheid
    • Environmental Science & Technology (2015-07-13)
  • affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

    • C Hernandez-Ferrer, I Quintela Garcia, K Danielski, A Carracedo, LA Pérez-Jurado, JR Gonzalez
    • BMC Bioinformatics (2015-05-20)

Submmited

  • Variability of multi-omics profiles in a population-based child cohort

    • M Gallego-Paüls, C Hernandez-Ferrer, M Bustamente, M Vrijheid, L Maitre
    • BMC Medicine (2021-03-30)
  • The early-life exposome and epigenetic age acceleration in children

    • P Prado-Bert, M Vives-Usano, …, C Hernandez-Ferrer, … M Vrijheid, M Bustamante
    • Environmental International (2021-02-10)
  • Multi-omics signatures of the human early life exposome

    • L Maitre, M Bustamante, C Hernandez-Ferrer, D Thiel, …, M Coen, JR González, HC Keun, M Vrijheid
    • Cell (2021-02-03) · medRxiv (2021-06-07)
  • Identification of blood autosomal cis-expression quantitative trait methylation (cis-eQTM) in children

    • C Ruiz-Arenas, C Hernandez-Ferrer, M Vives-Usano, …, M Vrijheid, JR Gonzalez, M Bustamante
    • eLife (2020-11-05) · bioRxiv (2020-11-05)
  • Early Life Multiple Exposures and Child Cognitive Function: A Multi-Centric Birth Cohort Study in Six European Countries

    • J Julvez, M López-Vicente, …, C Hernandez-Ferrer, …, X Basagaña, M Vrijheid
    • Environmental Pollution (2020-10-23)

In preparation

No articles in preparation at this moment.

Talks

  • Treatabolome database: towards enhancing Rare Diseases' treatment visibility

    • C Hernandez-Ferrer, A Corvó, L Matalonga, …, H Lochmuller, G Bonne, S Beltran
    • Solve-RD Annual Meeting 2021 (program)
    • from 2021-04-19 to 2021-04-21 (performed: 2021-04-21)
  • Exposome-Wide Association Study in Autism Spectrum Disorder Using Targeted and Untargeted Metabolomics Platforms

    • C Hernandez-Ferrer, DI Walker, CC Johnson, MK Chung, IH Lee, WJ Alvarez, CJ Patel, KD Pennell, DP Jones, SW Kong
    • 2019 International Society for Autism Research Annual Meeting (INSAR 2019) (program, abstracts)
    • from 2019-05-01 to 2019-05-04 (performed: 2019-05-02)
  • Extending Bioconductor To Exposome Data Analysis

    • C Hernandez-Ferrer, JR Gonzalez
    • BioC 2017: Where Software and Biology Connect (program)
    • from 2017-07-26 to 2017-07-28 (performed: 2017-07-26)
  • rexposome: a Bioconductor package for characterizing multiple environmental factors and its association with different omics biomarkers and diseases

    • C Hernandez-Ferrer, M Vrijheid, JR Gonzalez
    • Bioconductor European Developers’ Workshop (program)
    • from 2016-12-06 to 2016-12-07 (performed: 2016-12-06)
  • rexposome: a bioinformatic tool for characterizing multiple environmental factors and its association with different omics biomarkers and diseases

    • C Hernandez-Ferrer, M Vrijheid, JR Gonzalez
    • The Emory Exposome Summer Course (highlights, agenda)
    • to 2016-06-17 (performed: 2016-06-12)

Posters

  • Treatabolome database: towards enhancing Rare Diseases' treatment visibility

    • C Hernandez-Ferrer, A Corvó, L Matalonga, …, H Lochmuller, G Bonne, S Beltran (conductor: S Beltran)
    • European Human Genetics Conference Virtual Conference 2021 (program)
  • Treatabolome: a rare diseases treatment awareness project

    • A Atalaia, R Thompson, …, C Hernandez-Ferrer, …, S Beltran, G Bonne (conductor: A Atalaia)
    • European Conference on Rare Diseases (ECRD2020) (program, poster)
  • Improving the RD-Connect GPAP usability to facilitate rare disease diagnosis and gene discovery

    • A Corvò, L Matalonga, D Piscia, S Laurie, G Bullich, M Fernandez, D Picó, C Hernandez-Ferrer, A Papakonstantinou, I Gut, S Beltran (conductor: A Corvò)
    • VII Jornada de Bioinformàtica i Genòmica (program)
  • MEAL: Methylation and Expression AnaLyzer

    • C Ruiz Arenas, C Hernandez-Ferrer, JR Gonzalez (conductor: C Ruiz Arenas)
    • XIII Symposium on Bioinformatics
  • rexposome: A bioinformatic tool for characterizing multiple environmental factors and its association with different omics biomarkers and disease

    • C Hernandez-Ferrer, M Vrijheid, JR Gonzalez (conductor: C Hernandez-Ferrer)
    • XIII Symposium on Bioinformatics (poster)
  • Analyzing SNPs, CNVs, inversions and mosaicisms association studies using Affymetrix CytoScan

    • C Hernandez-Ferrer, I Quintela Garcia, K Danielski, A Carracedo Alvarez, LA Perez-Jurado, JR Gonzalez (conductor: C Hernandez-Ferrer)
    • Molecular Targets for Predictive and Personalized Medicine of Cancer (program, poster)
  • The correlation structure of the Pregnancy Exposome: multiple environmental exposures in the INMA-Sabadell Birth Cohort

    • O Robinson, M Casas, X Basagaña, C Hernandez-Ferrer, M Vrijheid (conductor: M Casas)
    • Prenatal Programming and Toxicity Summit (PPTOX IV)
  • Analyzing SNPs, CNVs, inversions and mosaicisms association studies using Affymetrix CytoScan

    • C Hernandez-Ferrer, I Quintela Garcia, K Danielski, A Carracedo Alvarez, LA Perez-Jurado, JR Gonzalez (conductor: C Hernandez-Ferrer)
    • XII Symposium on Bioinformatics (program, poster)
  • Detection of cancer signatures by integrating different features from omics data combining multi-block and path modelling methods

    • JR Gonzalez, M Esnaola, A Caceres, C Hernandez-Ferrer, M Lopez-Sanchez, LA Perez-Jurado (conductor: JR Gonzalez)
    • Integrative and Computational Biology Joint Symposium

Teaching

Direction of master thesis in bioinformatics

Acting as final master thesis director:

  • Analyzing glioma samples to identify glimoa-specific expression biomarkers; by Aitor Gómez Osuna and being conducted during 2nd semester of 2020
  • Análisis de integración en la asociación de datos omicos con la exposición a aire contaminado (diésel); by Laura Pauner Sotes and being conducted during 2nd semester of 2020
  • Implementación de un paquete de python para el análisis de datos genómicos en enfermedades raras; by Irene Sánchez López and conducted during 1st semester of 2020 (grade: A; score of 9.2/10)
  • Búsqueda de correlaciones entre metilación de sitios CpG y expresión de genes a lo largo del genoma humano; by Óscar Crespo and conducted during 1st semester of 2020 (grade: A; score of 9.4/10)
  • Impacto de la polución ambiental aérea en la metilación del DNA y microRNAs en ictus isquémico; by Carolina Soriano and conducted during 2nd semester of 2019 (grade: B; score of 8.97/10)
  • Multi-Omic Data clustering in Brain Cancer; by Paula Fernández and conducted during 1st semester of 2019 (grade: A; score of 9.16/10)

Biotools for biostatistics and bioinformatics (1st edition)

  • Barcelona Institute for Global Health // Bioinformatic Research Group in Epidemiology
  • 2017-05 as Instructor

4’5h: Code management using GIT repositories

Tutorship of high school research projects

  • Barcelona Institute for Global Health
  • From 2016-06 to 2018-01 as Tutor and/or supervisor

The institution was collaborating with the regional government in order to host some students in an internship during their last year of high school, allowing them to conduct a research project.

  • Aproximació als TADs com unitat funcional i la seva associació amb malalties humanes; by David Morón and Maria Solà, from INS Estany de la Ricarda, and conducted during summer of 2017 (grade: A+; a score of 10/10)
  • Relació entre desenvolupament cognitiu i metilació genética: Una anàlisi exploratòria; by Alba Cabús, from IES Can Puig, and conducted during summer of 2016 (grade: A; score of 10/10)

Statistical analysis of omic data in R (3th edition)

  • Barcelona Institute for Global Health // Bioinformatic Research Group in Epidemiology
  • 2016-05 as Instructor

6h: RNASeq data analysis using R and Bioconductor packages

Statistical analysis of omic data in R (2nd edition)

  • Barcelona Institute for Global Health // Bioinformatic Research Group in Epidemiology
  • 2015-05 as Instructor

2h: Genomic data visualization

Introduction to python for bioinformatics

  • Centre for Research in Agricultural Genomics // Statistical and population genomics
  • 2013-06 as Instructor

8h: Basic introduction to python programming for non-programmers in bioinformatics in the field of plant and animal genomics. The session covered from languages description to small bioinformatics exercises.

Fonaments dels Computadors (subject 102765)

100h: Computer laboratory sessions covering the three main blocks of the subject (Combinational Circuits, Sequential Circuits, and Process Unit-Control Unit architecture and processors) as well as individual tutorship on student’s demand.