Search Results - "Telonis, Aristeidis G"

Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types by Telonis, Aristeidis G, Magee, Rogan, Loher, Phillipe, Chervoneva, Inna, Londin, Eric, Rigoutsos, Isidore

“…Isoforms of human miRNAs (isomiRs) are constitutively expressed with tissue- and disease-subtype-dependencies. We studied 10 271 tumor datasets from The Cancer…”
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YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs by Shigematsu, Megumi, Honda, Shozo, Loher, Phillipe, Telonis, Aristeidis G, Rigoutsos, Isidore, Kirino, Yohei

“…Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To…”
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Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs by Londin, Eric, Loher, Phillipe, Telonis, Aristeidis G., Quann, Kevin, Clark, Peter, Jing, Yi, Hatzimichael, Eleftheria, Kirino, Yohei, Honda, Shozo, Lally, Michelle, Ramratnam, Bharat, Comstock, Clay E. S., Knudsen, Karen E., Gomella, Leonard, Spaeth, George L., Hark, Lisa, Katz, L. Jay, Witkiewicz, Agnieszka, Rostami, Abdolmohamad, Jimenez, Sergio A., Hollingsworth, Michael A., Yeh, Jen Jen, Shaw, Chad A., McKenzie, Steven E., Bray, Paul, Nelson, Peter T., Zupo, Simona, Van Roosbroeck, Katrien, Keating, Michael J., Calin, George A., Yeo, Charles, Jimbo, Masaya, Cozzitorto, Joseph, Brody, Jonathan R., Delgrosso, Kathleen, Mattick, John S., Fortina, Paolo, Rigoutsos, Isidore

“…Significance MicroRNAs (miRNAs) are small ∼22-nt RNAs that are important regulators of posttranscriptional gene expression. Since their initial discovery, they…”
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The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content by Telonis, Aristeidis G, Rigoutsos, Isidore

“…Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic…”
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MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia by Telonis, Aristeidis G., Yang, Qin, Huang, Hsuan-Ting, Figueroa, Maria E.

“…DNMT3A and IDH1/2 mutations combinatorically regulate the transcriptome and the epigenome in acute myeloid leukemia; yet the mechanisms of this interplay are…”
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N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration by Rigoutsos, Isidore, Lee, Sang Kil, Nam, Su Youn, Anfossi, Simone, Pasculli, Barbara, Pichler, Martin, Jing, Yi, Rodriguez-Aguayo, Cristian, Telonis, Aristeidis G, Rossi, Simona, Ivan, Cristina, Catela Ivkovic, Tina, Fabris, Linda, Clark, Peter M, Ling, Hui, Shimizu, Masayoshi, Redis, Roxana S, Shah, Maitri Y, Zhang, Xinna, Okugawa, Yoshinaga, Jung, Eun Jung, Tsirigos, Aristotelis, Huang, Li, Ferdin, Jana, Gafà, Roberta, Spizzo, Riccardo, Nicoloso, Milena S, Paranjape, Anurag N, Shariati, Maryam, Tiron, Aida, Yeh, Jen Jen, Teruel-Montoya, Raul, Xiao, Lianchun, Melo, Sonia A, Menter, David, Jiang, Zhi-Qin, Flores, Elsa R, Negrini, Massimo, Goel, Ajay, Bar-Eli, Menashe, Mani, Sendurai A, Liu, Chang Gong, Lopez-Berestein, Gabriel, Berindan-Neagoe, Ioana, Esteller, Manel, Kopetz, Scott, Lanza, Giovanni, Calin, George A

“…Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes…”
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The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type by Cherlin, Tess, Jing, Yi, Shah, Siddhartha, Kennedy, Anne, Telonis, Aristeidis G, Pliatsika, Venetia, Wilson, Haley, Thompson, Lily, Vlantis, Panagiotis I, Loher, Phillipe, Leiby, Benjamin, Rigoutsos, Isidore

“…MicroRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), and rRNA-derived fragments (rRFs) represent most of the small non-coding RNAs (sncRNAs) found in…”
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Plasma metabolomic profiling suggests early indications for predisposition to latent insulin resistance in children conceived by ICSI by Gkourogianni, Alexandra, Kosteria, Ioanna, Telonis, Aristeidis G, Margeli, Alexandra, Mantzou, Emilia, Konsta, Maria, Loutradis, Dimitrios, Mastorakos, George, Papassotiriou, Ioannis, Klapa, Maria I, Kanaka-Gantenbein, Christina, Chrousos, George P

“…There have been increasing indications about an epigenetically-based elevated predisposition of assisted reproductive technology (ART) offspring to insulin…”
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Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer by Telonis, Aristeidis G, Rigoutsos, Isidore

“…Triple-negative breast cancer (TNBC) is a breast cancer subtype characterized by marked differences between White and Black/African-American women. We…”
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MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data by Loher, Phillipe, Telonis, Aristeidis G., Rigoutsos, Isidore

“…Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing…”
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Assessment of isomiR Discrimination Using Commercial qPCR Methods by Magee, Rogan, Telonis, Aristeidis G, Cherlin, Tess, Rigoutsos, Isidore, Londin, Eric

“…We sought to determine whether commercial quantitative polymerase chain reaction (qPCR) methods are capable of distinguishing isomiRs: variants of mature…”
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Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells by Jimbo, Masaya, Blanco, Fernando F, Huang, Yu-Hung, Telonis, Aristeidis G, Screnci, Brad A, Cosma, Gabriela L, Alexeev, Vitali, Gonye, Gregory E, Yeo, Charles J, Sawicki, Janet A, Winter, Jordan M, Brody, Jonathan R

“…Post-transcriptional regulation is a powerful mediator of gene expression, and can rapidly alter the expression of numerous transcripts involved in…”
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Response to: Comment on Genetic Ancestry-Specific Molecular and Survival Differences in Admixed Breast Cancer Patients by Hernandez, Alexandra E, Mahal, Brandon, Telonis, Aristeidis G, Figueroa, Maria, Goel, Neha

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Nuclear and mitochondrial tRNA-lookalikes in the human genome by Telonis, Aristeidis G, Loher, Phillipe, Kirino, Yohei, Rigoutsos, Isidore

“…We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this…”
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MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects by Pliatsika, Venetia, Loher, Phillipe, Magee, Rogan, Telonis, Aristeidis G, Londin, Eric, Shigematsu, Megumi, Kirino, Yohei, Rigoutsos, Isidore

“…Abstract MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments ('tRFs') found in multiple human tissues. The original…”
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Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity by Telonis, Aristeidis G, Loher, Phillipe, Jing, Yi, Londin, Eric, Rigoutsos, Isidore

“…Here we describe our study of miRNA isoforms (isomiRs) in breast cancer (BRCA) and normal breast data sets from the Cancer Genome Atlas (TCGA) repository. We…”
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tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities by Telonis, Aristeidis G, Loher, Phillipe, Magee, Rogan, Pliatsika, Venetia, Londin, Eric, Kirino, Yohei, Rigoutsos, Isidore

“…tRNA-derived fragments (tRF) are a class of potent regulatory RNAs. We mined the datasets from The Cancer Genome Atlas (TCGA) representing 32 cancer types with…”
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MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments by Pliatsika, Venetia, Loher, Phillipe, Telonis, Aristeidis G, Rigoutsos, Isidore

“…It has been known that mature transfer RNAs (tRNAs) that are encoded in the nuclear genome give rise to short molecules, collectively known as tRNA fragments…”
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Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies by Telonis, Aristeidis G, Loher, Phillipe, Honda, Shozo, Jing, Yi, Palazzo, Juan, Kirino, Yohei, Rigoutsos, Isidore

“…We analyzed transcriptomic data from 452 healthy men and women representing five different human populations and two races, and, 311 breast cancer samples from…”
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Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap by Loher, Phillipe, Telonis, Aristeidis G, Rigoutsos, Isidore

“…There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell…”
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