ORCID: https://orcid.org/0000-0002-6245-2622

Resumen de investigación

Me especializo en investigación en genómica y bioinformática. Desarrollo pipelines bioinformáticos para el análisis de datos genómicos, con énfasis en RNA-seq, ChIP-seq y single-cell RNA-seq relacionados con genómica humana y de ratón. Mi trabajo se centra en comprender el papel de los factores de transcripción en el desarrollo y transformación de células sanguíneas, especialmente en la leucemia mieloide aguda (AML). También me he enfocado en la genómica ambiental, desarrollando pipelines para el ensamblaje y anotación de genomas bacterianos y metagenomas. Mi experiencia se extiende desde la biología molecular hasta el análisis de datos en genómica e inteligencia artificial, aplicando estas habilidades en diversos contextos de investigación. Por lo general trabajo con equipos multidisciplinarios.

Proyectos

Proyecto ANID SIA SA77210106. “Estudio de los factores de transcripción ZEB1 y ZEB2 en el desarrollo de células madre leucémicas para descubrir nuevos blancos terapéuticos contra la leucemia mieloide aguda (LMA)” 2022-2024. Responsable

Proyectos de Docencia y Vinculación con el Medio

Publicaciones

2023: Mardones C., Navarrete-Munoz C., Armijo M.E., Salgado K., Rivas-Valdes F., Gonzalez-Pecchi V., Farkas C., Villagra A., Hepp M.I. “Role of HDAC6-STAT3 in immunomodulatory pathways in Colorectal cancer cells”. Molecular Immunology, 164, pp. 98 – 111. DOI: 10.1016/j.molimm.2023.11.007

2023: Amigo R., Raiqueo F., Tarifeño E., Farkas C., Gutiérrez J.L. “Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects”. International Journal of Molecular Sciences, 24 (20), art. no. 15245. DOI: 10.3390/ijms242015245

2023: Farkas C., Retamal-Fredes E., Ávila A., Fehlings M.G., Vidal P.M. “Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice”. Frontiers in Microbiology, 14, art. no. 1229783. DOI: 10.3389/fmicb.2023.1229783

2022: Oviedo M.J., Ramírez E., Cifuentes M., Farkas C., Mella A., Bertinat R., Gajardo R., Ferrada L., Jara N., De Lima I., et al. “Is IIIG9 a New Protein with Exclusive Ciliary Function? Analysis of Its Potential Role in Cancer and Other Pathologies”. Cells, 11 (20), art. no. 3327. DOI: 10.3390/cells11203327

2022: Amigo R., Farkas C., Gidi C., Hepp M.I., Cartes N., Tarifeño E., Workman J.L., Gutiérrez J.L. “The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes”. Biochimica et Biophysica Acta – Gene Regulatory Mechanisms, 1865 (1), art. no. 194781. DOI: 10.1016/j.bbagrm.2021.194781

2022: Farkas C., Recabal A., Mella A., Candia-Herrera D., Olivero M.G., Haigh J.J., Tarifeño-Saldivia E., Caprile T. “annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing”. GigaScience, 11, art. no. giac099. DOI: 10.1093/gigascience/giac099

Productividad Científica anterior a la UCSC

Proyecto MITACS Canada. “Improving Q-RT-PCR screening for COVID-19 by tracking viral variants”. 2020 – 2021. Responsable.

Proyecto ANID – FONDECYT 1110821. “CHARACTERIZATION OF SALL2 TRANSCRIPTION FACTOR AND ITS RELATIOSHIP TO P53 TUMOR SUPPRESSOR”, 2011 – 2015. Colaborador

Proyecto ANID – 1151031, “REGULATION AND FUNCTION OF THE SALL2 TRANSCRIPTION FACTOR DURING CELLULAR STRESS” 2011-2013. Colaborador

2021: Wang J., Farkas C., Benyoucef A., Carmichael C., Haigh K., Wong N., Huylebroeck D., Stemmler M.P., Brabletz S., Brabletz T., Nefzger C.M., Goossens S., Berx G., Polo J.M., Haigh J.J. “Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity”. PLoS Biology, 19 (9), art. no. e3001394. DOI: 10.1371/journal.pbio.3001394

2021: Recabal A., Fernández P., López S., Barahona M.J., Ordenes P., Palma A., Elizondo-Vega R., Farkas C., Uribe A., Caprile T., Sáez J.C., García-Robles M.A. “The FGF2-induced tanycyte proliferation involves a connexin 43 hemichannel/purinergic-dependent pathway”. Journal of Neurochemistry, 156 (2), pp. 182 – 199. DOI: 10.1111/jnc.15188

2021: Farkas C., Quiroz A., Alvarez C., Hermosilla V., Aylwin C.F., Lomniczi A., Castro A.F., Hepp M.I., Pincheira R. “Characterization of SALL2 Gene Isoforms and Targets Across Cell Types Reveals Highly Conserved Networks”. Frontiers in Genetics, 12, art. no. 613808. DOI: 10.3389/fgene.2021.613808

2021: Farkas C., Martins C.P., Escobar D., Hepp M.I., Castro A.F., Evan G., Gutiérrez J.L., Warren R., Pincheira R. “Correction: Wild type p53 transcriptionally represses the SALL2 transcription factor under genotoxic stress (PLoS ONE (2013) 8, 9 (e73817) DOI: 10.1371/journal.pone.0073817)”. PLoS ONE, 9 (8), art. no. e104307. DOI: 10.1371/journal.pone.0104307

2020: Farkas C., Fuentes-Villalobos F., Garrido J.L., Haigh J., Barría M.I. “Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions”. PeerJ, 2020 (5), art. no. e9255. DOI: 10.7717/peerj.9255

2020: Farkas C., Donoso R.A., Gárate-Castro C., Villegas P., Durán R.E., Seeger M., Pérez-Pantoja D. “Draft genome sequences of two Pseudomonas strains that are able to use furan derivatives as their sole carbon source”. Microbiology Resource Announcements, 9 (2), art. no. e01131-19. DOI: 10.1128/MRA.01131-19

2019: Farkas C., Fuentes-Villalobos F., Rebolledo-Jaramillo B., Benavides F., Castro A.F., Pincheira R. “Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data”. BMC Genomics, 20 (1), art. no. 131. DOI: 10.1186/s12864-019-5504-9

2019: Fuentes-Villalobos F., Farkas C., Riquelme-Barrios S., Armijo M.E., Soto-Rifo R., Pincheira R., Castro A.F. “DISC1 promotes translation maintenance during sodium arsenite-induced oxidative stress”. Biochimica et Biophysica Acta – Gene Regulatory Mechanisms, 1862 (6), pp. 657 – 669. DOI: 10.1016/j.bbagrm.2019.05.001

2018: E. Hermosilla V., Salgado G., Riffo E., Escobar D., Hepp M.I., Farkas C., Galindo M., Morín V., García-Robles M.A., Castro A.F., Pincheira R. “SALL2 represses cyclins D1 and E1 expression and restrains G1/S cell cycle transition and cancer-related phenotypes”. Molecular Oncology, 12 (7), pp. 1026 – 1046. DOI: 10.1002/1878-0261.12308

2017: Hermosilla V.E., Hepp M.I., Escobar D., Farkas C., Riffo E.N., Castro A.F., Pincheira R. “Developmental SALL2 transcription factor: A new player in cancer”. Carcinogenesis, 38 (7), art. no. bgx036, pp. 680 – 690. DOI: 10.1093/carcin/bgx036

2015: Escobar D., Hepp M.I., Farkas C., Campos T., Sodir N.M., Morales M., Álvarez C.I., Swigart L., Evan G.I., Gutiérrez J.L., Nishinakamura R., Castro A.F., Pincheira R. “Sall2 is required for proapoptotic Noxa expression and genotoxic stress-induced apoptosis by doxorubicin”. Cell Death and Disease, 6 (7), art. no. e1816. DOI: 10.1038/cddis.2015.165

2013: Farkas C., Martins C.P., Escobar D., Hepp M.I., Castro A.F., Evan G., Gutiérrez J.L., Warren R., Donner D.B., Pincheira R. “Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress”. PLoS ONE, 8 (9), art. no. e73817. DOI: 10.1371/journal.pone.0073817