Carlos Farkas Pool - Universidad Católica de la Santísima Concepción

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.

Líneas de investigación

Cáncer con énfasis en leucemias/linfomas
Genómica del cáncer, metagenómica y genómica ambiental
Inteligencia artificial aplicada a sistemas biológicos

Publicaciones académicas

A Haplotype-Resolved Genome Assembly of the Long-Spined Sea Urchin Diadema antillarum, a Keystone Caribbean Reef Herbivore. Genes. https://doi.org/10.3390/genes17080876.
A draft de novo assembly of Diadema antillarum , a keystone herbivore of the Caribbean reefs. https://doi.org/10.64898/2026.05.24.727502.
Antimicrobial Effect of Cellulose Nanofibrils (CNFs) and Biobased Additives in Polyvinyl Alcohol Nanocomposite Materials for Sustainable Food Packaging Application. Polymers. https://doi.org/10.3390/polym18070846.
Antimicrobial Effect of Cellulose Nanofibrils (CNFs) and Biobased Additives in Polyvinyl Alcohol Nanocomposite Materials for Sustainable Food Packaging Application. https://doi.org/10.20944/preprints202603.0458.v1.
Extracellular vesicles from glycolytic mesenchymal stromal cells restrain arthritis progression via IL-10–Producing T and B cells. Theranostics. https://doi.org/10.7150/THNO.123898.

SALL2-Mediated Suppression of WNT Signaling Through Transcriptional Control of AXIN2 in Colorectal Cancer Cells. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms26167896.
Early-Onset Versus Late-Onset Preeclampsia in Bogotá, Colombia: Differential Risk Factor Identification and Evaluation Using Traditional Statistics and Machine Learning. Biomedicines. https://doi.org/10.3390/biomedicines13081958.
Safety and efficacy of mesenchymal stromal cells mitochondria transplantation as a cell-free therapy for osteoarthritis. Journal of Translational Medicine. https://doi.org/10.1186/S12967-024-05945-7.
The medial amygdala’s neural circuitry: Insights into social processing and sex differences. Frontiers in Neuroendocrinology. https://doi.org/10.1016/J.YFRNE.2025.101190.

The Role of Epithelial-to-Mesenchymal Transition Transcription Factors (EMT-TFs) in Acute Myeloid Leukemia Progression. Biomedicines. https://doi.org/10.3390/biomedicines12081915.
Deciphering the Complexities of Acute Myeloid Leukemia: Emerging Roles of Epithelial to Mesenchymal Transition Transcription Factors (EMT-TFs) in Disease Progression. https://doi.org/10.20944/preprints202407.1231.v1.
Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells. Cell Death & Disease. https://doi.org/10.1038/S41419-024-06591-Z.
Neuromotor decline is associated with gut dysbiosis following surgical decompression for Degenerative Cervical Myelopathy. Neurobiology of Disease. https://doi.org/10.1016/J.NBD.2024.106640.
Tracking SARS-CoV-2 variants in wastewater in San Pedro de la Paz, Chile. Journal of Water and Health. https://doi.org/10.2166/WH.2024.284.
Uncovering the role of the subcommissural organ in early brain development through transcriptomic analysis. Biological Research. https://doi.org/10.1186/S40659-024-00524-Y.

Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice. Frontiers in Microbiology. https://doi.org/10.3389/FMICB.2023.1229783.
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. https://doi.org/10.3390/IJMS242015245.

annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing. GigaScience. https://doi.org/10.1093/gigascience/giac099.
Is IIIG9 a New Protein with Exclusive Ciliary Function? Analysis of Its Potential Role in Cancer and Other Pathologies. Cells. https://doi.org/10.3390/CELLS11203327.
The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. https://doi.org/10.1016/J.BBAGRM.2021.194781.

Interplay between the EMT transcription factors ZEB1 and ZEB2 regulates hematopoietic stem and progenitor cell differentiation and hematopoietic lineage fidelity. PLOS Biology. https://doi.org/10.1371/journal.pbio.3001394.
A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Frontiers in Microbiology. https://doi.org/10.3389/FMICB.2021.665041.
Characterization of SALL2 Gene Isoforms and Targets Across Cell Types Reveals Highly Conserved Networks. Frontiers in Genetics. https://doi.org/10.3389/FGENE.2021.613808.
The FGF2‐induced tanycyte proliferation involves a connexin 43 hemichannel/purinergic‐dependent pathway. Journal of Neurochemistry. https://doi.org/10.1111/JNC.15188.

Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.00905-19.
Draft Genome Sequences of Two Pseudomonas Strains That Are Able To Use Furan Derivatives as Their Sole Carbon Source. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.01131-19.
Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions. PeerJ. https://doi.org/10.7717/PEERJ.9255.

DISC1 promotes translation maintenance during sodium arsenite-induced oxidative stress. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. https://doi.org/10.1016/J.BBAGRM.2019.05.001.
Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data. BMC Genomics. https://doi.org/10.1186/S12864-019-5504-9.

A Trichostatin A (TSA)/Sp1-mediated mechanism for the regulation of SALL2 tumor suppressor in Jurkat T cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. https://doi.org/10.1016/J.BBAGRM.2018.05.002.
Genome sequencing and characterization of novel proteobacterial strains having the ability to use furan aldehydes as only carbon source. New Biotechnology. https://doi.org/10.1016/J.NBT.2018.05.924.
SALL2 represses cyclins D1 and E1 expression and restrains G1/S cell cycle transition and cancer‐related phenotypes. Molecular Oncology. https://doi.org/10.1002/1878-0261.12308.

Developmental SALL2 transcription factor: a new player in cancer. Carcinogenesis. https://doi.org/10.1093/CARCIN/BGX036.

Abstract B17: Role of Sall2 transcription factor under genotoxic stress: A transcriptomic approach. Cancer Research. https://doi.org/10.1158/1538-7445.FBCR15-B17.

Sall2 is required for proapoptotic Noxa expression and genotoxic stress-induced apoptosis by doxorubicin. Cell Death & Disease. https://doi.org/10.1038/CDDIS.2015.165.

The Sall2 transcription factor is involved in cellular stress responses. The FEBS Journal.
Correction: Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress. PLoS ONE. https://doi.org/10.1371/JOURNAL.PONE.0104307.

Wild Type p53 Transcriptionally Represses the SALL2 Transcription Factor under Genotoxic Stress. PLoS ONE. https://doi.org/10.1371/JOURNAL.PONE.0073817.
Abstract LB-51: p53 transcriptionally represses the SALL2 transcription factor under genotoxic stress.. Cancer Research. https://doi.org/10.1158/1538-7445.AM2013-LB-51.