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Hire Dr. Ernest D.

Netherlands

USD 120 /hr

Freelance Bioinformatician and Biostatistician | Expert in R and Python for Biological insight

Profile Summary

As a Postdoctoral Researcher at the University Medical Center Utrecht I have the chance to deal with several types of 'omics datasets (Genomics, Transcriptomics, Epigenetics, scRNAseq), and data-driven questions related to understanding disease pathobiology in atherosclerotic and heart disease, with a special interest in sex-differences.

My previous work at the London School of Hygiene and Tropical Medicine focused in genomic studies in the five main species of Plasmodium causing malaria to determine genomic barcodes to deploy in elimination settings across endemic countries and the application of machine learning approaches leading to several scientific publications.

Also I have been involved as an epidemiologist and data quality manager for a multinational cross-sectional study looking at risk factors for Cardiovascular Disease in Russia and provided data management counsel in other projects.

Other interests include website development (front and back-end) and the study of Microbiome data.

Subject Matter Expertise

Services

Consulting
Data & AI
Product Development

Work Experience

Postdoc

University Medical Center Utrecht

October 2020 - Present

Research Fellow in Bioinformatics and Biostatistics

London School of Hygiene and Tropical Medicine

August 2018 - September 2020

Research Assistant and PhD Student

London School of Hygiene and Tropical Medicine

December 2014 - August 2018

Education

PhD in Malaria Genomics (Pathogen Molecular Biology)

London School of Hygiene and Tropical Medicine

April 2016 - August 2018

MSc in Applied Bioinformatics (Agrifood School)

Cranfield University

October 2013 - September 2014

Agricultural Engineer speciality in Biotechnology (Escuela de Agronomos)

Universidad Politecnica de Valencia

September 2008 - September 2014

Certifications

Certification details not provided.

Publications

JOURNAL ARTICLE

Klaske R Siegersma, Rutger R van de Leur, N Charlotte Onland-Moret, David A Leon, Ernest Diez-Benavente, Liesbeth Rozendaal, Michiel L Bots, Ruben Coronel, Yolande Appelman, Leonard Hofstra, et al. (2022). Deep neural networks reveal novel sex-specific electrocardiographic features relevant for mortality risk . European Heart Journal - Digital Health.

Showering A, Martinez J, Benavente ED, Gezan SA, Jones RT, Oke C, Tytheridge S, Pretorius E, Scott D, Allen RL, et al.(2022). Skin microbiome alters attractiveness to Anopheles mosquitoes . BMC microbiology.

Ernest Diez Benavente, Emilia Manko, Jody Phelan, Monica Campos, Debbie Nolder, Diana Fernandez, Gabriel Velez-Tobon, Alberto Tobón Castaño, Jamille G. Dombrowski, Claudio R. F. Marinho, et al. (2021). Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa . Nature Communications.

Silva-Pinto A, Domingos J, Cardoso M, Reis A, Benavente ED, Caldas JP, Conceição C, Toscano C, Baptista-Fernandes T, Clark TG, et al.(2021). Artemether-lumefantrine treatment failure of uncomplicated Plasmodium falciparum malaria in travellers coming from Angola and Mozambique . International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, Clark TG, Campino S(2021). Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus . Parasites & vectors.

Deelder W, Benavente ED, Phelan J, Manko E, Campino S, Palla L, Clark TG(2021). Using deep learning to identify recent positive selection in malaria parasite sequence data . Malaria journal.

O'Sullivan DM, Doyle RM, Temisak S, Redshaw N, Whale AS, Logan G, Huang J, Fischer N, Amos GCA, Preston MD, et al.(2021). An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities . Scientific reports.

Nolder D, Stewart L, Tucker J, Ibrahim A, Gray A, Corrah T, Gallagher C, John L, O'Brien E, Aggarwal D, et al.(2021). Failure of rapid diagnostic tests in Plasmodium falciparum malaria cases in UK travellers: identification and characterisation of the parasites . International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

Da Veiga Leal S, Ward D, Campino S, Benavente ED, Ibrahim A, Claret T, Isaías V, Monteiro D, Clark TG, Gonçalves L, et al.(2021). Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak . Malaria journal.

Diez Benavente E, Jimenez-Lopez F, Attia ZI et al. Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker [version 1; peer review: 1 approved with reservations] Wellcome Open Res 2021, 6:12 (https://doi.org/10.12688/wellcomeopenres.16499.1) .

Ernest Diez Benavente, Francisco Jimenez-Lopez, Zachi I. Attia, Sofia Malyutina, Alexander Kudryavtsev, Andrew Ryabikov, Paul A. Friedman, Suraj Kapa, Michael Voevoda, Pablo Perel, et al.(2021). Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker . Wellcome Open Research. 6. p. 12. F1000 Research Ltd

Attia IZ, Tseng AS, Benavente ED, Medina-Inojosa JR, Clark TG, Malyutina S, Kapa S, Schirmer H, Kudryavtsev AV, Noseworthy PA, et al.(2021). External validation of a deep learning electrocardiogram algorithm to detect ventricular dysfunction . International journal of cardiology.

Miguel-Blanco C, Murithi JM, Benavente ED, Angrisano F, Sala KA, van Schalkwyk DA, Vanaerschot M, Schwach F, Fuchter MJ, Billker O, et al.(2021). The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957 . Scientific reports.

Plasma Testosterone Levels and Atherosclerotic Plaque Gene Expression in Men With Advanced Atherosclerosis @ARTICLE{10.3389/fcvm.2021.693351, AUTHOR= {Groepenhoff, Floor and Diez Benavente, Ernest and Boltjes, Arjan and Timmerman, Nathalie and Waissi, Farahnaz and Hartman, Robin J. G. and Onland-Moret, N. C. and Pasterkamp, Gerard and Den Ruijter, Hester}, TITLE= {Plasma Testosterone Levels and Atherosclerotic Plaque Gene Expression in Men With Advanced Atherosclerosis}, JOURNAL= {Frontiers in Cardiovascular Medicine}, VOLUME= {8}, PAGES= {584}, YEAR= {2021}, URL= {https://www.frontiersin.org/article/10.3389/fcvm.2021.693351}, DOI= {10.3389/fcvm.2021.693351}, ISSN= {2297-055X}, ABSTRACT= {Aims: Low plasma testosterone levels have been shown to predict worse outcome in men with severe atherosclerotic disease. We hypothesized that a low plasma testosterone level affects disease risk through changes in gene expression in atherosclerotic plaques. Therefore, we studied plasma testosterone levels in relation to gene expression levels in atherosclerotic plaque tissue of men with advanced atherosclerotic disease.Methods: Plasma testosterone levels were measured in 203 men undergoing carotid endarterectomy. The corresponding atherosclerotic plaque tissue was used for RNA sequencing. First, we assessed how often the androgen receptor gene was expressed in the plaque. Second, correlations between plasma testosterone levels and pre-selected testosterone-sensitive genes were assessed. Finally, differences within the RNA expression profile of the plaque as a whole, characterized into gene regulatory networks and at individual gene level were assessed in relation to testosterone levels.Results: Testosterone plasma levels were low with a median of 11.6 nmol/L (IQR: 8.6–13.8). RNA-seq of the plaque resulted in reliable expression data for 18,850 genes to be analyzed. Within the RNA seq data, the androgen-receptor gene was expressed in 189 out of 203 (93%) atherosclerotic plaques of men undergoing carotid endarterectomy. The androgen receptor gene expression was not associated with testosterone plasma levels. There were no significant differences in gene expression of atherosclerotic plaques between different endogenous testosterone levels. This remained true for known testosterone-sensitive genes, the complete transcriptomic profile, male-specific gene co-expression modules as well as for individual genes.Conclusion: In men with severe atherosclerotic disease the androgen receptor is highly expressed in plaque tissue. However, plasma testosterone levels were neither associated with pre-selected testosterone sensitive genes, gene expression profiles nor gene regulatory networks in late-stage atherosclerotic plaques. The effect of testosterone on gene expression of the late-stage atherosclerotic plaque appears limited, suggesting that alternate mechanisms explain its effect on clinical outcomes.}} . Frontiers in Cardiovascular Medicine.

Ernest Diez Benavente, Anna Turkiewicz, Giorgio Sirugo, Emilia Manko, Colin J. Sutherland, Susana Campino, Taane G. Clark (2020). Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance . PLOS Genetics.

Ibrahim A, Diez Benavente E, Nolder D, Proux S, Higgins M, Muwanguzi J, Gomez Gonzalez PJ, Fuehrer HP, Roper C, Nosten F, et al.(2020). Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure . Scientific reports.

Ernest Diez Benavente, Giorgio Sirugo, Monica Campos, Jody Phelan, Debbie Nolder, Jamille G. Dombrowski, Claudio R. F. Marinho, Kanlaya Sriprawat, Aimee R. Taylor, James Watson, et al.(2020). A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria . PLOS Genetics. 16. (2). p. e1008576. Public Library of Science ({PLoS})

Ernest Diez Benavente, Ronan M. Doyle, Denise M. O'Sullivan, Sean D. Aller, Sebastian Bruchmann, Taane Clark, Andreu Coello Pelegrin, Martin Cormican, Matthew J. Ellington, Elaine McGrath, et al.(2020). Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study . Microbial Genomics. 6. (2). Microbiology Society

Ernest Diez Benavente, Matt Ravenhall, Colin J. Sutherland, David A. Baker, Susana Campino, Taane G. Clark(2019). An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene . Scientific Reports. 9. (1). Springer Science and Business Media {LLC}

Ernest Diez Benavente, Ana Rita Gomes, Jeremy Ryan De Silva, Matthew Grigg, Harriet Walker, Bridget E. Barber, Timothy William, Tsin Wen Yeo, Paola Florez de Sessions, Abhinay Ramaprasad, et al.(2019). Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations . Scientific Reports. 9. (1). Springer Science and Business Media {LLC}

(2019). Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data . Frontiers in Genetics.

Mohring F, Hart MN, Rawlinson TA, Henrici R, Charleston JA, Diez Benavente E, Patel A, Hall J, Almond N, Campino S, et al.(2019). Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research . eLife.

Ernest Diez Benavente, Yan He, Luzia Helena Carvalho, Susana Campino, David C. Warhurst, Khalid B. Beshir, Inke Lubis, Ana Rita Gomes, Jun Feng, Wang Jiazhi, et al. (2019). Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area . PLOS ONE.

Ernest Diez Benavente, Sarah Cook, Sofia Malyutina, Alexander V Kudryavtsev, Maria Averina, Natalia Bobrova, Sergey Boytsov, Soren Brage, Taane G. Clark, Anne Elise Eggen, et al.(2018). Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18 . Wellcome Open Research. 3. p. 67. F1000 Research Ltd

Cook S, Malyutina S, Kudryavtsev AV et al. Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18 [version 3; referees: 3 approved] Wellcome Open Res 2018, 3:67 (https://doi.org/10.12688/wellcomeopenres.14619.3) .

Sarah Auburn, Ernest D. Benavente, Olivo Miotto, Richard D. Pearson, Roberto Amato, Matthew J. Grigg, Bridget E. Barber, Timothy William, Irene Handayuni, Jutta Marfurt, et al.(2018). Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics . Nature Communications. 9. (1). Springer Science and Business Media {LLC}

Ernest Diez Benavente, Damilola R. Oresegun, Paola Florez de Sessions, Eloise M. Walker, Cally Roper, Jamille G. Dombrowski, Rodrigo M. de Souza, Claudio R. F. Marinho, Colin J. Sutherland, Martin L. Hibberd, et al.(2018). Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development . Scientific Reports. 8. (1). Springer Nature

Ernest Diez Benavente, Susana Campino, Xin-zhuan Su, Alejandro Marin-Menendez, Alison Kemp, Nadia Cross, Laura Drought, Thomas D. Otto, Matt Ravenhall, Frank Schwach, et al.(2018). A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways . PLOS Pathogens. 14. (11). p. e1007436. Public Library of Science ({PLoS})

Leon LJ, Doyle R, Diez-Benavente E, Clark TG, Klein N, Stanier P, Moore GE(2018). Enrichment of clinically relevant organisms in spontaneous preterm delivered placenta and reagent contamination across all clinical groups in a large UK pregnancy cohort . Applied and environmental microbiology.

Sepúlveda N, Phelan J, Diez-Benavente E, Campino S, Clark TG, Hopkins H, Sutherland C, Drakeley CJ, Beshir KB(2018). Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis . Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Benavente ED, de Sessions PF, Moon RW, Grainger M, Holder AA, Blackman MJ, Roper C, Drakeley CJ, Pain A, Sutherland CJ, et al.(2018). A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line . International journal for parasitology.

Sepúlveda, N., Phelan, J., Diez-Benavente, E., Campino, S., Clark, T.G., Hopkins, H., Sutherland, C., Drakeley, C.J., Beshir, K.B.(2018). Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis . Infection, Genetics and Evolution. 62. p. 211-219.

Leon, L.J., Doyle, R., Diez-Benavente, E., Clark, T.G., Klein, N., Stanier, P., Moore, G.E.(2018). Enrichment of clinically relevant organisms in spontaneous preterm-delivered placentas and reagent contamination across all clinical groups in a large pregnancy cohort in the United Kingdom . Applied and Environmental Microbiology. 84. (14).

Gomes AR, Ravenhall M, Benavente ED, Talman A, Sutherland C, Roper C, Clark TG, Campino S(2017). Corrigendum to "Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes" [Int. J. Parasitol. Drugs and Drug Resist. 7 (2017) 174-180] . International journal for parasitology. Drugs and drug resistance.

Ernest Diez Benavente, Paola Florez de Sessions, Robert W. Moon, Anthony A. Holder, Michael J. Blackman, Cally Roper, Christopher J. Drakeley, Arnab Pain, Colin J. Sutherland, Martin L. Hibberd, et al.(2017). Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations . PLOS Genetics. 13. (9). p. e1007008. Public Library of Science ({PLoS})

Ernest Diez Benavente, Jona Walk, Isaie J. Reuling, Marije C. Behet, Lisette Meerstein-Kessel, Wouter Graumans, Geert-Jan van Gemert, Rianne Siebelink-Stoter, Marga van de Vegte-Bolmer, Thorsten Janssen, et al.(2017). Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial . BMC Medicine. 15. (1). Springer Nature

Ernest Diez Benavente, Ana Rita Gomes, Matt Ravenhall, Arthur Talman, Colin Sutherland, Cally Roper, Taane G. Clark, Susana Campino(2017). Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes . International Journal for Parasitology: Drugs and Drug Resistance. 7. (2). p. 174--180. Elsevier {BV}

Ernest Diez Benavente, Zoe Ward, Wilson Chan, Fady R. Mohareb, Colin J. Sutherland, Cally Roper, Susana Campino, Taane G. Clark, Georges Snounou(2017). Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure . PLOS ONE. 12. (5). p. e0177134. Public Library of Science ({PLoS})

Hidayat Trimarsanto, Ernest D. Benavente, Rintis Noviyanti, Retno Ayu Setya Utami, Leily Trianty, Zuleima Pava, Sisay Getachew, Jung-Yeon Kim, Youn-Kyoung Goo, Sonam Wangchuck, et al.(2017). VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations . PLOS Neglected Tropical Diseases. 11. (3). p. e0005465. Public Library of Science ({PLoS})

Walk, J., Reuling, I.J., Behet, M.C., Meerstein-Kessel, L., Graumans, W., van Gemert, G.-J., Siebelink-Stoter, R., van de Vegte-Bolmer, M., Janssen, T., Teelen, K., et al.(2017). Modest heterologous protection after Plasmodium falciparum sporozoite immunization: A double-blind randomized controlled clinical trial . BMC Medicine. 15. (1).

Diez Benavente, E., Florez de Sessions, P., Moon, R.W., Holder, A.A., Blackman, M.J., Roper, C., Drakeley, C.J., Pain, A., Sutherland, C.J., Hibberd, M.L., et al.(2017). Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations . PLoS Genetics. 13. (9).

Ernest Diez Benavente, Matt Ravenhall, Mwapatsa Mipando, Anja T. R. Jensen, Colin J. Sutherland, Cally Roper, Nuno Sepúlveda, Dominic P. Kwiatkowski, Jacqui Montgomery, Kamija S. Phiri, et al.(2016). Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi . Malaria Journal. 15. (1). Springer Nature

Ernest Diez Benavente, Hifzur Rahman Ansari, Thomas J. Templeton, Amit Kumar Subudhi, Abhinay Ramaprasad, Jianxia Tang, Feng Lu, Raeece Naeem, Yasmeen Hashish, Mary C. Oguike, et al.(2016). Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species . International Journal for Parasitology. 46. (11). p. 685--696. Elsevier {BV}

Ernest Diez Benavente, Susana Campino, Samuel Assefa, Eloise Thompson, Laura G. Drought, Catherine J. Taylor, Zaria Gorvett, Celine K. Carret, Christian Flueck, Al C. Ivens, et al.(2016). Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines . Malaria Journal. 15. (1). Springer Nature

Ernest D Benavente, Francesc Coll, Nick Furnham, Ruth McNerney, Judith R Glynn, Susana Campino, Arnab Pain, Fady R Mohareb, Taane G Clark(2015). PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis . BMC Bioinformatics. 16. (1). Springer Nature

PREPRINT

SCOTT DAV, BENAVENTE ED, LIBISELLER-EGGER J, FEDEROV D, PHELAN J, ILINA E, TIKHONOVA P, KUDRYAVSTEV A, GALEEVA J, CLARK T, et al.(2022). Bayesian Compositional Regression with Microbiome Features via Variational Inference .

Aherrahrou R, Lue D, Perry RN, Aberra YT, Khan MD, Soh JY, Örd T, Singha P, Gilani H, Benavente ED, et al.(2022). Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes .

Mokry M, Boltjes A, Cui K, Slenders L, Mekke JM, Depuydt MA, Timmerman N, Waissi F, Verwer MC, Turner AW, et al.(2021). Transcriptomic-based clustering of advanced atherosclerotic plaques identifies subgroups of plaques with differential underlying biology that associate with clinical presentation .

Getting close to nature – <i>Plasmodium knowlesi</i> reference genome sequences from contemporary clinical isolates @article{PPR:PPR421696, title = {Getting close to nature – <i>Plasmodium knowlesi</i> reference genome sequences from contemporary clinical isolates}, author = {Oresegun DR and Thorpe P and Benavente ED and Campino S and Muh F and Moon R and Clark TG and Cox-Singh J}, doi = {10.1101/2021.11.16.468780} } .

Leal SdV, Ward D, Campino S, Benavente ED, Ibrahim A, Andrade T, Varela I, Monteiro D, Clark TG, Gonçalves L, et al.(2021). Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: The 2017 malaria outbreak .

Leal SdV, Ward D, Campino S, Benavente ED, Ibrahim A, Andrade T, Varela I, Clark TG, Monteiro D, Gonçalves L, et al.(2020). Drug Resistance Profile and Clonality of Plasmodium Falciparum Parasites in Cape Verde: The 2017 Malaria Outbreak .

OTHER

Ernest Diez Benavente, Francisco Lopez-Jimenez, Olena Iakunchykova, Sofia Malyutina, Alexander Kudryavtsev, Andrew Ryabikov, Paul A. Friedman, Suraj Kapa, Pablo Perel, Tom Wilsgaard, et al.(2021). Capturing population differences in rates of vascular aging using a deep learning electrocardiogram algorithm: a cross-sectional study . Cold Spring Harbor Laboratory