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Posts
Getting Greened
Published:
I started the Green Card process about two years ago, and it’s still ongoing.
This process is extensive, to say the least, and really makes you think about immigration in general. It’s unbelievable how much of your life you put on hold to get permanent residency, but the most shocking part is, I am doing it the fast and easy way.
My t-shirt designs
Published:
Around February 2022, as part of the 10th anniversary of the Institute of Quantitative and Computational Biosciences (QCBio) Collaboratory at UCLA, they called for t-shirt designs to commemorate this occasion. As the name indicates, the QCBio Institute is a partnership of multiple departments at UCLA that perform quantitative and computational research in biology. The Collaboratory, is a component of this institute in charge of providing research support and workshops to researchers.
Trip to Bolivia
Published:
In December, 2019 I went to Bolivia for vacation. I try to return every year for at least 2 weeks to visit my family. That time, I had the opportunity to bring my girlfriend with me. Never before have I felt so much like a tour guide, but it was a great experience to show her my country.
Public transportation in the United States
Published:
I have taken the Metrolink train about 10 times in the past two months, during which three trips were significantly delayed—one with a 90+ minute delay for what is typically a 60-minute trip. I also rode the LA Metro, which is, to say the least, a challenging experience. For instance, I once witnessed a young woman threaten other passengers with a knife after they expressed discomfort about her carrying it.
Llamas and antibodies
Published:
Whenever I talk to non-Bolivian people about my country, I like to mention that we have llamas. Llamas are the national animal of Bolivia and are used for their wool, meat, and as pack animals.
blog
publications
Effectiveness of Antioxidant Gene Therapy in Delaying Retinal Degeneration Permalink
Published in Molecular Therapy, 2015
Recommended citation: Biswal, M.R., Ildefonso, C., Wang, Z., Mao, H., Li, H., Zhu, P., Quinones, G., & Lewin, A.S. (2015). Effectiveness of Antioxidant Gene Therapy in Delaying Retinal Degeneration. Molecular Therapy, 23, S156.
Delaying Retinal Degeneration in a Mouse Model of Geographic Atrophy: An Antioxidant Gene Therapy Approach Permalink
Published in Investigative Ophthalmology & Visual Science, 2015
Recommended citation: Biswal, M.R., Ildefonso, C.J., Rossmiller, B.P., Mao, H., Li, H., Han, P., Zhu, P., Quinones, G., & Lewin, A.S. (2015). Delaying Retinal Degeneration in a Mouse Model of Geographic Atrophy: An Antioxidant Gene Therapy Approach. Investigative Ophthalmology & Visual Science, 56(7), 3189-3189.
RNA editing in nascent RNA affects pre-mRNA splicing Permalink
Published in Genome Research, 2018
Recommended citation: Hsiao, Y.-H. E. et al. RNA editing in nascent RNA affects pre-mRNA splicing. Genome Res. 28, 812–823 (2018).
Regulation of RNA editing by RNA-binding proteins in human cells Permalink
Published in Communications Biology, 2019
Recommended citation: Quinones-Valdez, G., Tran, S.S., Jun, HI. et al. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol 2, 19 (2019). https://doi.org/10.1038/s42003-018-0271-8
Perspectives on ENCODE Permalink
Published in Nature, 2020
Recommended citation: The ENCODE Project Consortium. (2020). Perspectives on ENCODE. Nature, 583, 693–698. https://doi.org/10.1038/s41586-020-2449-8
RNA editing in cancer impacts mRNA abundance in immune response pathways Permalink
Published in Genome Biology, 2020
Recommended citation: Chan, T.F., Bahn, J.H., Jun, H.I., Lee, J.H., Quinones-Valdez, G., Cheng, C., & Xiao, X. (2020). RNA editing in cancer impacts mRNA abundance in immune response pathways. Genome Biology, 21, 268. https://doi.org/10.1186/s13059-020-02171-4
Expanded encyclopaedias of DNA elements in the human and mouse genomes Permalink
Published in Nature, 2020
Recommended citation: Moore, J.E., Purcaro, M.J., Pratt, H.E., et al. (2020). Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710. https://doi.org/10.1038/s41586-020-2493-4
scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq Permalink
Published in Science Advances, 2022
Recommended citation: Quinones-Valdez, G., Fu, T., Chan, T.W., & Xiao, X. (2022). scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq. Science Advances, 8(35), eabn6398. https://doi.org/10.1126/sciadv.abn6398
L-GIREMI uncovers RNA editing sites in long-read RNA-seq Permalink
Published in Genome Biology, 2023
Recommended citation: Liu, Z., Quinones-Valdez, G., Fu, T., Huang, E., Choudhury, M., Reese, F., & Xiao, X. (2023). L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Genome Biology, 24, 171. https://doi.org/10.1186/s13059-023-02999-1
hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing Permalink
Published in Molecular Cell, 2024
Recommended citation: Zheng, R., Dunlap, M., Bobkov, G.O.M., Gonzalez-Figueroa, C., Patel, K.J., Lyu, J., Quinones-Valdez, G., & Xiao, X. (2024). hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing. Molecular Cell. https://doi.org/10.1016/j.molcel.2024.05.010
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing Permalink
Published in bioRxiv, 2024
Recommended citation: Quinones-Valdez, G., Amoah, K., & Xiao, X. (2024). Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. bioRxiv. https://doi.org/10.1101/2024.06.14.599101
Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia Permalink
Published in The American Journal of Human Genetics, 2024
Recommended citation: Hervoso, J.L., Amoah, K., Dodson, J., Choudhury, M., Bhattacharya, A., Quinones-Valdez, G., & Xiao, X. (2024). Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. The American Journal of Human Genetics, 111(8), 1573-1587. https://doi.org/10.1016/j.ajhg.2024.08.012
talks
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
Published:
Selected talk for the International Society for Computational Biology
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
Published:
Plenary talk at the anual meeting of the American Society of Human Genetics.
teaching
Variant Calling with GATK
Technical workshop, UCLA QCBio Collaboratory, 2020
I taught this workshop in the summer of 2020 as temporary instructor for the QCBio Collaboratory. The workshop was held online due to the pandemic. The material consists on a hand-on tutorial on the best practices protocol from GATK for small germline variant calling.
Single cell RNA-sequencing data analysis with R
Technical workshop, UCLA QCBio Collaboratory, 2022
This workshop introduces the basic concepts and algorithms necessary to analyze single-cell RNA-sequencing data using the R package Seurat. The workshop is hands-on and covers both theoretical and computational aspects of the analysis of this type of data. Among the topics covered are: