Search Results - "Yépez, A"

OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data by Brechtmann, Felix, Mertes, Christian, Matusevičiūtė, Agnė, Yépez, Vicente A., Avsec, Žiga, Herzog, Maximilian, Bader, Daniel M., Prokisch, Holger, Gagneur, Julien

“…RNA sequencing (RNA-seq) is gaining popularity as a complementary assay to genome sequencing for precisely identifying the molecular causes of rare disorders…”
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Detection of aberrant splicing events in RNA-seq data using FRASER by Mertes, Christian, Scheller, Ines F., Yépez, Vicente A., Çelik, Muhammed H., Liang, Yingjiqiong, Kremer, Laura S., Gusic, Mirjana, Prokisch, Holger, Gagneur, Julien

“…Aberrant splicing is a major cause of rare diseases.  However, its prediction from genome sequence alone remains in most cases inconclusive. Recently, RNA…”
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Detection of aberrant gene expression events in RNA sequencing data by Yépez, Vicente A., Mertes, Christian, Müller, Michaela F., Klaproth-Andrade, Daniela, Wachutka, Leonhard, Frésard, Laure, Gusic, Mirjana, Scheller, Ines F., Goldberg, Patricia F., Prokisch, Holger, Gagneur, Julien

“…RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-causing gene regulatory defects in individuals affected by genetically…”
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OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer by Yépez, Vicente A, Kremer, Laura S, Iuso, Arcangela, Gusic, Mirjana, Kopajtich, Robert, Koňaříková, Eliška, Nadel, Agnieszka, Wachutka, Leonhard, Prokisch, Holger, Gagneur, Julien

“…The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. Mitochondrial stress tests…”
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Cellular energy regulates mRNA degradation in a codon-specific manner by Tomaz da Silva, Pedro, Zhang, Yujie, Theodorakis, Evangelos, Martens, Laura D, Yépez, Vicente A, Pelechano, Vicent, Gagneur, Julien

“…Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated…”
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Aberrant splicing prediction across human tissues by Wagner, Nils, Çelik, Muhammed H., Hölzlwimmer, Florian R., Mertes, Christian, Prokisch, Holger, Yépez, Vicente A., Gagneur, Julien

“…Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes is limited to clinically accessible tissues such as skin or…”
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Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index by Scheller, Ines F., Lutz, Karoline, Mertes, Christian, Yépez, Vicente A., Gagneur, Julien

“…Detection of aberrantly spliced genes is an important step in RNA-seq-based rare-disease diagnostics. We recently developed FRASER, a denoising…”
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An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy by Segarra-Casas, Alba, Yépez, Vicente A, Demidov, German, Laurie, Steven, Esteve-Codina, Anna, Gagneur, Julien, Parkhurst, Yolande, Muni-Lofra, Robert, Harris, Elizabeth, Marini-Bettolo, Chiara, Straub, Volker, Töpf, Ana

“…Duchenne and Becker muscular dystrophies, caused by pathogenic variants in , are the most common inherited neuromuscular conditions in childhood. These…”
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Modeling fragment counts improves single-cell ATAC-seq analysis by Martens, Laura D., Fischer, David S., Yépez, Vicente A., Theis, Fabian J., Gagneur, Julien

“…Single-cell ATAC sequencing coverage in regulatory regions is typically binarized as an indicator of open chromatin. Here we show that binarization is an…”
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IL-1β induced methylation of the estrogen receptor ERα gene correlates with EMT and chemoresistance in breast cancer cells by Jiménez-Garduño, Aura M., Mendoza-Rodríguez, Mónica G., Urrutia-Cabrera, Daniel, Domínguez-Robles, María C., Pérez-Yépez, Eloy A., Ayala-Sumuano, Jorge Tonatiuh, Meza, Isaura

“…Inflammation has been recently acknowledged as a key participant in the physiopathology of oncogenesis and tumor progression. The inflammatory cytokine IL-1β…”
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Resource partitioning by evergreen and deciduous species in a tropical dry forest by Álvarez-Yépiz, Juan C., Búrquez, Alberto, Martínez-Yrízar, Angelina, Teece, Mark, Yépez, Enrico A., Dovciak, Martin

“…Niche differentiation can lead to coexistence of plant species by partitioning limiting resources. Light partitioning promotes niche differentiation in…”
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Assessing two decades of landscape greenness in relation to temperature and precipitation in a tropical dry forest of Northwestern Mexico by Verdugo, Leonardo, Bojórquez, Adrián, Galaz, Onésimo, Romo-León, José Raúl, Sánchez-Mejía, Zulia M., Yépez, Enrico A., Álvarez-Yépiz, Juan C.

“…•We analyzed two decades of anomalies of NDVI, precipitation and temperature.•Temperature and precipitation exert positive effects on vegetation…”
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Diagnostic Odyssey in an Adult Patient with Ophthalmologic Abnormalities and Hearing Loss: Contribution of RNA-Seq to the Diagnosis of a PEX1 Deficiency by Muñoz-Pujol, Gerard, Alforja-Castiella, Socorro, Casaroli-Marano, Ricardo, Morales-Romero, Blai, García-Villoria, Judit, Yépez, Vicente A., Gagneur, Julien, Gusic, Mirjana, Prokisch, Holger, Tort, Frederic, Ribes, Antonia

“…Peroxisomal biogenesis disorders (PBDs) are a heterogeneous group of genetic diseases. Multiple peroxisomal pathways are impaired, and very long chain fatty…”
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Technical note: Application of geophysical tools for tree root studies in forest ecosystems in complex soils by Rodríguez-Robles, Ulises, Arredondo, Tulio, Huber-Sannwald, Elisabeth, Ramos-Leal, José Alfredo, Yépez, Enrico A

“…While semiarid forests frequently colonize rocky substrates, knowledge is scarce on how roots garner resources in these extreme habitats. The Sierra San…”
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Coupled plant traits adapted to wetting/drying cycles of substrates co‐define niche multidimensionality by Rodríguez‐Robles, Ulises, Arredondo, J. Tulio, Huber‐Sannwald, Elisabeth, Yépez, Enrico A., Ramos‐Leal, José Alfreso

“…Theories attempting to explain species coexistence in plant communities have argued in favour of species' capacities to occupy a multidimensional niche with…”
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Bi-Allelic UQCRFS1 Variants Are Associated with Mitochondrial Complex III Deficiency, Cardiomyopathy, and Alopecia Totalis by Gusic, Mirjana, Schottmann, Gudrun, Feichtinger, René G., Du, Chen, Scholz, Caroline, Wagner, Matias, Mayr, Johannes A., Lee, Chae-Young, Yépez, Vicente A., Lorenz, Norbert, Morales-Gonzalez, Susanne, Panneman, Daan M., Rötig, Agnès, Rodenburg, Richard J.T., Wortmann, Saskia B., Prokisch, Holger, Schuelke, Markus

“…Isolated complex III (CIII) deficiencies are among the least frequently diagnosed mitochondrial disorders. Clinical symptoms range from isolated myopathy to…”
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Eco-efficiency assessment of disease-infected shrimp farming in Mexico using environmental impact assessment tools by Flores-Pérez, Maria B., Yépez, Enrico A., Robles-Morúa, Agustín, Villa-Ibarra, Martín, Bórquez-López, Rafael, Gil-Núñez, Juan Carlos, Lares-Villa, Fernando, Casillas-Hernández, Ramón

“…Mexico ranks second in shrimp (Litopenaeus vannamei) production of in Latin America with significant annual growth, however, during 2011 shrimp production fell…”
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Author Correction: Detection of aberrant splicing events in RNA-seq data using FRASER by Mertes, Christian, Scheller, Ines F., Yépez, Vicente A., Çelik, Muhammed H., Liang, Yingjiqiong, Kremer, Laura S., Gusic, Mirjana, Prokisch, Holger, Gagneur, Julien

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How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data by Schlieben, Lea D, Prokisch, Holger, Yépez, Vicente A

“…Rare diseases, although individually rare, collectively affect approximately 350 million people worldwide. Currently, nearly 6,000 distinct rare disorders with…”
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Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes by Cao, Xueqi, Huber, Sandra, Ahari, Ata Jadid, Traube, Franziska R, Seifert, Marc, Oakes, Christopher C, Secheyko, Polina, Vilov, Sergey, Scheller, Ines F, Wagner, Nils, Yépez, Vicente A, Blombery, Piers, Haferlach, Torsten, Heinig, Matthias, Wachutka, Leonhard, Hutter, Stephan, Gagneur, Julien

“…Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large…”
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