Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 75 /hr

★★★★★

☆☆☆☆☆

Hire Dr. Javier Q.

Spain

USD 75 /hr

Bioinformatician with +10 years of experience in data science applied to genomics.

Profile Summary

Bioinformatician with over 10 years of experience in data science: management and analysis of large-scale genomic datasets generated with SNP/methylation microarrays and high-throughput sequencing (whole-genome, targeted, RNA and ChIP sequencing, Hi-C). Expertise in genome-wide association studies (GWAS), variant calling (SNPs, indels and larger structural variants), differential expression analysis and ChIP-sequencing peak calling. Involvement from data acquisition and quality control to statistical analysis, data visualization and reporting, integrating both existing bioinformatics tools and custom scripts into high-performance computing systems. I program in Python, Bash, R, Perl and use IPython notebooks, GitHub (@jaquol), Markdown and SQL databases. I am particularly interested in the implementation of pipelines for data analysis, integration of multiple OMICs data and metadata, the use of visualization to effectively present the data and in helping colleagues with their data analysis needs.

Subject Matter Expertise

• ☆ Genetics
• ☆ Microarrays
• ☆ Omics
• ☆ Genomics
• ☆ DNA Sequencing
• ☆ RNA Sequencing
• ☆ Data Analysis
• ☆ Data Visualization
• ☆ Bioinformatics
• ☆ Visual Communication
• ☆ SQL
• ☆ Technical & Scientific Writing

Services

• Writing
• Consulting
• Data & AI
• Product Development

Work Experience

Bioinformatician

Centre for Genomic Regulation (CRG)

April 2015 - January 2018

Postdoctoral Researcher

Icahn School of Medicine at Mount Sinai

November 2013 - March 2015

Postdoctoral Researcher

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)

October 2012 - October 2012

Education

PhD in Animal Genetics

Universitat Autonoma de Barcelona

September 2008 - September 2012

Master of Science in Biomedical Research

Universitat Pompeu Fabra

September 2007 - September 2008

Bachelor of Science in Biotechnology

Universitat Autonoma de Barcelona

September 2002 - June 2007

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Enrique Vidal, François le Dily, Javier Quilez, Ralph Stadhouders, Yasmina Cuartero, Thomas Graf, Marc A Marti-Renom, Miguel Beato, Guillaume J Filion(2018). {OneD}: increasing reproducibility of Hi-C samples with abnormal karyotypes . Nucleic Acids Research. Oxford University Press ({OUP})

Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero, et al.(2018). Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming . Nature Genetics. 50. (2). p. 238--249. Springer Science and Business Media {LLC}

Javier Quilez, Enrique Vidal, François Le Dily, François Serra, Yasmina Cuartero, Ralph Stadhouders, Thomas Graf, Marc A Marti-Renom, Miguel Beato, Guillaume Filion(2017). Parallel sequencing lives, or what makes large sequencing projects successful . {GigaScience}. 6. (11). p. 1--6. Oxford University Press ({OUP})

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, dummy-AUTHOR_name, Godoy JA, Genome biology, 2016, vol. 17, no. 1, pp. 251, 2016 .

Nacht AS, Pohl A, Zaurin R, Soronellas D, Quilez J, Sharma P, Wright RH, Beato M, Vicent GP, The EMBO journal, 2016, vol. 35, no. 16, pp. 1822-1843, 2016 .

Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, Joshi RS, Mittelman D, Sharp AJ, Nucleic acids research, 2016, vol. 44, no. 8, pp. 3750-3762, 2016 .

Berglund J, Quilez J, Arndt PF, Webster MT, Genome biology and evolution, 2015, vol. 7, no. 2, pp. 522-530, 2015 .

Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, dummy-AUTHOR_name, Warren WC, Proceedings of the National Academy of Sciences of the United States of America, 2014, vol. 111, no. 48, pp. 17230-17235, 2014 .

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, dummy-AUTHOR_name, Gibbs RA, Nature, 2014, vol. 513, no. 7517, pp. 195-201, 2014 .

Brahmachary M, Guilmatre A, Quilez J, Hasson D, Borel C, Warburton P, Sharp AJ, PLoS genetics, 2014, vol. 10, no. 6, pp. e1004418, 2014 .

Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, dummy-AUTHOR_name, Lalueza-Fox C, Nature, 2014, vol. 507, no. 7491, pp. 225-228, 2014 .

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, dummy-AUTHOR_name, Warren WC, Nature, 2014, vol. 505, no. 7482, pp. 174-179, 2014 .

Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, dummy-AUTHOR_name, O'Brien SJ, GigaScience, 2014, vol. 3, pp. 13, 2014 .

Ramirez O, Olalde I, Berglund J, Lorente-Galdos B, Hernandez-Rodriguez J, Quilez J, Webster MT, Wayne RK, Lalueza-Fox C, Vilà C, Marques-Bonet T, BMC genomics, 2014, vol. 15, pp. 465, 2014 .

Quilez J, Martínez V, Woolliams JA, Sanchez A, Pong-Wong R, Kennedy LJ, Quinnell RJ, Ollier WE, Roura X, Ferrer L, Altet L, Francino O, PloS one, 2012, vol. 7, no. 4, pp. e35349, 2012 .

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, Karlsson EK, LUPA Consortium, Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, dummy-AUTHOR_name, Webster MT, PLoS genetics, 2011, vol. 7, no. 10, pp. e1002316, 2011 .

Quilez J, Short AD, Martínez V, Kennedy LJ, Ollier W, Sanchez A, Altet L, Francino O, BMC genomics, 2011, vol. 12, pp. 339, 2011 .

Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, dummy-AUTHOR_name, Lindblad-Toh K, PLoS genetics, 2011, vol. 7, no. 3, pp. e1001332, 2011 .

Martínez V, Quilez J, Sanchez A, Roura X, Francino O, Altet L, Parasites & vectors, 2011, vol. 4, pp. 57, 2011 .

OTHER

Enrique Vidal, François le Dily, Javier Quilez, Ralph Stadhouders, Yasmina Cuartero, Thomas Graf, Marc A. Martí-Renom, Miguel Beato, Guillaume J. Filion(2017). {OneD}: increasing reproducibility of Hi-C Samples with abnormal karyotypes . Cold Spring Harbor Laboratory

Javier Quilez, Enrique Vidal, François Le Dily, François Serra, Yasmina Cuartero, Ralph Stadhouders, Thomas Graf, Marc A. Marti-Renom, Miguel Beato, Guillaume Filion(2017). Parallel sequencing lives, or what makes large sequencing projects successful . Cold Spring Harbor Laboratory