Academic
| Sections | Description | N |
|---|---|---|
| Articles | Peer-reviewed publications in biomedical and computational sciences. | 33 |
| Talks | Presentations at national and international conferences. | 7 |
| Poster | Research posters displayed at academic national and international conferences. | 13 |
| Teaching | Courses and mentorship in bioinformatics and biostatistics. | - |
| Certificates | Professional qualifications and certifications earned. | - |
Articles
♠ : This symbol denotes that the authors consider that the two first authors should be regarded as “joint first authors”.
Published
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Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package
- C Ruiz-Arenas, …, C Hernandez-Ferrer, …, JR Gonzalez
- Epigenetics (2023-07-06)
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Patterns of heterochromatin transitions linked to changes in the expression of Plasmodium falciparum clonally variant genes
- L Michel-Todó, C Bancells, …, C Hernandez-Ferrer, …, JR González, A Cortés
- Microbiology Spectrum (2022-12-14)
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Multi-omics signatures of the human early life exposome
- L Maitre, M Bustamante, C Hernandez-Ferrer, …, HC Keun, M Vrijheid
- Nature Communications (2022-11-21)
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Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood
- C Ruiz-Arenas, C Hernandez-Ferrer, …, JR Gonzalez, M Bustamante
- eLife (2022-03-18)
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The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases
- S Laurie, …, C Hernandez-Ferrer, …, S Beltran
- Human Mutation (2022-02-17)
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Variability of multi-omics profiles in a population-based child cohort
- M Gallego-Paüls, C Hernandez-Ferrer, …, M Vrijheid, L Maitre
- BMC Medicine (2021-07-22)
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The early-life exposome and epigenetic age acceleration in children
- P Prado-Bert, C Ruiz-Arenas, …, C Hernandez-Ferrer, … M Vrijheid, M Bustamante
- Environmental International (2021-06-15)
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Solving patients with rare diseases through programmatic reanalysis of genome-phenome data
- L Matalonga, C Hernandez-Ferrer, …, H Graessner, S Beltran
- European Journal of Human Genetics (2021-06-01)
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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 (2021-05-24)
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WEScover: selection between clinical whole exome sequencing and gene panel testing
- IH Lee, Y Lin, …, C Hernandez-Ferrer, KD Mandl, SW Kong
- BMC Bioinformatics (2021-05-20)
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Early-life environmental exposure determinants of child behavior in Europe: a longitudinal, population-based study
- L Maitre, J Julvez, …, C Hernandez-Ferrer, …, J Wright, M Vrijheid
- Environment International (2021-03-25)
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In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children
- M Vives-Usano, C Hernandez-Ferrer, …, M Vrijheid, M Bustamante
- BMC Medicine (2020-08-19)
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A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: building a Treatabolome
- A Atalaia, R Thompson, …, C Hernandez-Ferrer, …, S Beltran, G Bonne
- Orphanet Journal of Rare Diseases (2020-08-12)
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Association between the pregnancy exposome and fetal growth
- L Agier, X Basagaña, C Hernandez-Ferrer, …, M Vrijheid, R Slama
- International Journal of Epidemiology (2020-03-13)
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Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform
- SW Kong, C Hernandez-Ferrer
- Pacific Symposium on Biocomputing (2020-01-01)
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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, …, KD Mandl, SW Kong
- Human Mutation (2019-11-06)
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Dose and time effects of solar simulated ultraviolet radiation on the in vivo human skin transcriptome
- M Bustamante ♠, C Hernandez-Ferrer ♠, …, M Nieuwenhuijsen, AR Young
- The British Journal of Dermatology (2019-09-16)
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Early-Life Environmental Exposures and Blood Pressure in Children
- C Warembourg, L Maitre, …, C Hernandez-Ferrer, …, M Vrijheid, X Basagaña
- Journal of the American College of Cardiology (2019-09-10)
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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)
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Prenatal Particulate Air Pollution and DNA Methylation in Newborns: An Epigenome-Wide Meta-Analysis
- O Gruzieva, C Xu, …, C Hernandez-Ferrer, …, AA Baccarelli, E Melén
- Environmental Health Perspectives (2019-05-31)
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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)
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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)
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A systemic approach to identify signaling pathways activated during short-term exposure to traffic-related urban air pollution from human blood
- JE Vargas, N Kubesch, C Hernandez-Ferrer, …, M Nieuwenhuijsen, JR Gonzalez
- Environmental Science and Pollution Research (2018-08-23)
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CTDquerier: a bioconductor R package for Comparative Toxicogenomics Database (TM) data extraction, visualization and enrichment of environmental and toxicological studies
- C Hernandez-Ferrer, JR Gonzalez
- Bioinformatics (2018-04-24)
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Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk
- M Rubio, M Bustamante, C Hernandez-Ferrer, …, JR Gonzalez, A Mayor
- PloS ONE (2018-03-05)
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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)
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The acute effects of ultraviolet radiation on the blood transcriptome are independent of plasma 25OHD3
- M Bustamante ♠, C Hernandez-Ferrer ♠, …, M Nieuwenhuij, AR Younge
- Environmental Research (2017-11-01)
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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)
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The Pregnancy Exposome: Multiple Environmental Exposures in the INMA-Sabadell Birth Cohort
- O Robinson, X Basagaña, …, C Hernandez-Ferrer, …, R Slama, M Vrijheid
- Environmental Science & Technology (2015-07-13)
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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, …, LA Pérez-Jurado, JR Gonzalez
- BMC Bioinformatics (2015-05-20)
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The PAU camera and the PAU survey at the William Herschel Telescope
- FJ Castander, O Ballester, …, C Hernandez-Ferrer, …, N Tonello; J de Vicente
- SPIE, Ground-based and Airborne Instrumentation for Astronomy IV (2012-09-24)
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A motion control networked solution for the PAUCam slow control
- O Ballester, C Pio, C Hernandez-Ferrer, M Albareda-Sirvent
- SPIE, Software and Cyberinfrastructure for Astronomy II (2012-09-24)
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Design and implementation of a distributed system for the PAUCam camera control system
- O Ballester, C Pio, C Hernandez-Ferrer, S Serrano, N Tonello
- SPIE, Software and Cyberinfrastructure for Astronomy II (2012-09-24)
Accepted or Submitted
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
- F Pardo-Palacios, …, C Hernandez-Ferrer, …, Rene Maehr
- Nature Methods (Submitted: 2021-07-02)
In preparation
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A review of federated processing for model training and inference in biomedical research environments
- M Chavero-Díez, C Hernandez-Ferrer, …, S Capella-Gutierrez, JL Gelpí
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Treatabolome DB: a knowledge platform on treatments and interventions for genetic-based diseases
- C Hernandez-Ferrer, …, S Beltran
Aknowledged
- A two-step gas chromatography-tandem mass spectrometry method for measurement of multiple environmental pollutants in human plasma
- CL Johnson, E Jazan, SW Kong, KD Pennell
- Environmental Science and Pollution Research (2020-09-10)
Talks
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New RD-Connect GPAP features implemented in collaboration with Solve-RD, EJP-RD and ELIXIR enable the diagnosis of rare disease patients with previously negative WES/WGS.
- L Matalonga, D Piscia, …, C Hernandez-Ferrer, …, I Gut, S Beltran (conductor: L Matalonga)
- European Human Genetics Conference 2022 | Hybrid Conference (program)
- from 2022-06-11 to 2022-06-14 (pending)
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El re-análisis sistemático de datos genómicos y fenotípicos de mas de 4000 pacientes con enfermedades raras no diagnosticadas contribuye a resolver más de un 8% de los casos
- L Matalonga Borrel, C Hernandez-Ferrer, …, A Hoischen, S Beltran (conductor: L Matalonga)
- III Congreso Interdisciplinar de Genética Humana (program)
- from 2021-11-03 to 2021-11-05 (performed: 2021-11-03)
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Treatabolome database: towards enhancing Rare Diseases' treatment visibility
- C Hernandez-Ferrer, A Corvó, …, G Bonne, S Beltran (conductor: C Hernandez-Ferrer)
- Solve-RD Annual Meeting 2021 (program)
- from 2021-04-19 to 2021-04-21 (performed: 2021-04-21)
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Exposome-Wide Association Study in Autism Spectrum Disorder Using Targeted and Untargeted Metabolomics Platforms
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Extending Bioconductor To Exposome Data Analysis
- C Hernandez-Ferrer, JR Gonzalez (conductor: C Hernandez-Ferrer)
- BioC 2017: Where Software and Biology Connect (program)
- from 2017-07-26 to 2017-07-28 (performed: 2017-07-26)
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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 (conductor: C Hernandez-Ferrer)
- Bioconductor European Developers’ Workshop (program)
- from 2016-12-06 to 2016-12-07 (performed: 2016-12-06)
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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 (conductor: C Hernandez-Ferrer)
- The Emory Exposome Summer Course (highlights)
- to 2016-06-17 (performed: 2016-06-12)
Posters
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Orchestrating federated processing within a federation of cancer data nodes - The EUCAIM perspective
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OpenEBench 2024 update: Capturing the new perspectives and current needs of communities and scientific projects for scientific benchmarking
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OpenEBench 2024 update: Updating web widgets and introducing users intranet
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OpenEBench 2023 update: better support and deeper interactions with benchmarking scientific communities
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Federated Learning: General Review and Future Directions
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Treatabolome database: towards enhancing Rare Diseases' treatment visibility
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Treatabolome: a rare diseases treatment awareness project
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Improving the RD-Connect GPAP usability to facilitate rare disease diagnosis and gene discovery
- A Corvò, L Matalonga, …, C Hernandez-Ferrer, …, I Gut, S Beltran (conductor: A Corvò)
- VII Jornada de Bioinformàtica i Genòmica (program)
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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)
- Emory Exposome Summer Course · 2016 (poster, Highlights)
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MEAL: Methylation and Expression AnaLyzer
- C Ruiz Arenas, C Hernandez-Ferrer, JR Gonzalez (conductor: C Ruiz Arenas)
- XIII Symposium on Bioinformatics
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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)
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Analyzing SNPs, CNVs, inversions and mosaicisms association studies using Affymetrix CytoScan
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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)
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Analyzing SNPs, CNVs, inversions and mosaicisms association studies using Affymetrix CytoScan
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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
Formal Teaching
Associate/Substitute Teacher
- Artificial Vision // Master in Artificial Intelligence // Universitat de Barcelona // 2023-2024
Direction of master thesis in bioinformatics
- Open University of Catalonia // Master in Bioinformatics and Biostatistics
- from 2019-09 to 07-2023 as External Collaborator
Acting as final master thesis director:
- Federated machine learning applied to biomedical analysis; a bibliographic review; by María Chavero and conducted during 2nd semester of 2022-2023 (grade: A+; score of
10/10) - Enhanced production of Monoclonal Antibodies with Artificial Intelligence and data-driven modelling; by Irene Martínez and conducted during 2nd semester of 2022-2023 (grade: B; score of
8.5/10) - Caracterización de paneles génicos para la clasificación de pacientes en Glioblastoma; by Olatz Sanz and conducted during 2nd semester of 2022-2023 (grade: A; score of
9.7/10) - Identificación de biomarcadores de la expresión génica específicos de glioma y clasificación de pacientes por machine learning; by Aitor Gómez and conducted during 2nd semester of 2020-2021 (grade: B; score of
8.7/10) - Estudio sobre la repercusión de la contaminación ambiental en general y de las emisiones diésel en particular sobre el transcriptoma humano; by Laura Pauner and conducted during 2nd semester of 2020-2021 (grade: B, score:
8.8/10) - 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 2020-2021 (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 2020-2021 (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 2019-2020 (grade: B; score of
8.9/10) - Multi-Omic Data clustering in Brain Cancer; by Paula Fernández and conducted during 1st semester of 2019-2020 (grade: A; score of
9.2/10)
Informal Teaching
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 (2 days)
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 (1 day)
2h: Genomic data visualization
Introduction to R
- Barcelona Institute for Global Health
- 2014-04 as Instructor (1 day)
4h: Algorithms and programming structures
Introduction to python for bioinformatics
- Centre for Research in Agricultural Genomics // Statistical and population genomics
- 2013-06 as Instructor (2 days)
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)
- Universitat Autonoma de Barcelona // Bachelor’s Degree in Computer Engineering
- From 2010-09 to 2011-06 as Teaching Assistant
100h: Computer laboratory sessions covering the three main blocks of the subject (Combinatorial Circuits, Sequential Circuits, and Process Unit-Control Unit architecture and processors) as well as individual tutorship on student’s demand.
Certificates
- Associate Professor (Professor lector), AQU (Catalan Government), January 2023