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Submissions from 2020

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On the expanding roles of tRNA fragments in modulating cell behavior, Rogan Magee and Isidore Rigoutsos

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Complete chemical structures of human mitochondrial tRNAs, Takeo Suzuki, Yuka Yashiro, Ittoku Kikuchi, Yuma Ishigami, Hironori Saito, Ikuya Matsuzawa, Shunpei Okada, Mari Mito, Shintaro Iwasaki, Ding Ma, Xuewei Zhao, Kana Asano, Huan Lin, Yohei Kirino, Yuriko Sakaguchi, and Tsutomu Suzuki

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Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data., Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang Vv Pham, Li Xiaomei, Thuc D Le, Adi L Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, and Pablo Meyer

Submissions from 2019

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Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients., Sunjay Jude Fernandes, Hiromasa Morikawa, Ewoud Ewing, Sabrina Ruhrmann, Rubin Narayan Joshi, Vincenzo Lagani, Nestoras Karathanasis, Mohsen Khademi, Nuria Planell, Angelika Schmidt, Ioannis Tsamardinos, Tomas Olsson, Fredrik Piehl, Ingrid Kockum, Maja Jagodic, Jesper Tegnér, and David Gomez-Cabrero

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Genome-wide identification of short 2',3'-cyclic phosphate-containing RNAs and their regulation in aging., Megumi Shigematsu, Keisuke Morichika, Takuya Kawamura, Shozo Honda, and Yohei Kirino

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Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen., Claire Simonneau, Junning Yang, Xianguo Kong, Robert Kilker, Leonard Edelstein, Paolo Fortina, Eric R. Londin, and Arie Horowitz

Submissions from 2018

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Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer., Rogan G. Magee, Aristeidis G. Telonis, Phillipe Loher, Eric R Londin, and Isidore Rigoutsos

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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., Venetia Pliatsika, Phillipe Loher, Rogan Magee, Aristeidis G. Telonis, Eric R. Londin, Megumi Shigematsu, Yohei Kirino, and Isidore Rigoutsos

Submissions from 2017

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The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells., Shozo Honda; Takuya Kawamura; Phillipe Loher; Keisuke Morichika; Isidore Rigoutsos; and Yohei Kirino, PhD

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Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells., Shozo Honda, Phillipe Loher, Keisuke Morichika, Megumi Shigematsu, Takuya Kawamura, Yoriko Kirino, Isidore Rigoutsos, and Yohei Kirino

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MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data., Phillipe Loher, Aristeidis G. Telonis, and Isidore Rigoutsos

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

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YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs., Megumi Shigematsu, Shozo Honda, Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos, and Yohei Kirino

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5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves., Megumi Shigematsu and Yohei Kirino

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

Submissions from 2016

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Consequential considerations when mapping tRNA fragments., Aristeidis G Telonis; Phillipe Loher; Yohei Kirino, PhD; and Isidore Rigoutsos

Submissions from 2015

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Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences., Shozo Honda and Yohei Kirino

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Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers., Shozo Honda; Phillipe Loher; Megumi Shigematsu; Juan P. Palazzo; Ryusuke Suzuki; Issei Imoto; Isidore Rigoutsos; and Yohei Kirino, PhD

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Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells., Masaya Jimbo; Fernando F Blanco; Yu-Hung Huang; Aristeidis G Telonis; Brad A Screnci; Gabriela L Cosma; Vitali Alexeev; Gregory E Gonye; Charles Yeo; Janet A Sawicki; Jordan M Winter; and Jonathan Brody, MD

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What is translational bioinformatics?, Eric R. Londin and Carol I. Barash

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tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins., Megumi Shigematsu and Yohei Kirino, PhD

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Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity., Aristeidis G Telonis, Phillipe Loher, Yi Jing, Eric R Londin, and Isidore Rigoutsos

Submissions from 2014

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IsomiR Expression Profiles in Human Lymphoblastoid Cell Lines Exhibit Population and Gender Dependencies., Phillipe Loher, Eric R Londin, and Isidore Rigoutsos

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The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome., Eric R Londin, Eleftheria Hatzimichael, Phillipe Loher, Leonard Edelstein, Chad Shaw, Kathleen Delgrosso, Paolo Fortina, Paul Bray, Steven E. McKenzie, and Isidore Rigoutsos

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

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MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells., Honglei Zhou and Isidore Rigoutsos

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The emerging roles of GPRC5A in diseases., Honglei Zhou and Isidore Rigoutsos

Submissions from 2013

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Roles and mechanism of miR-199a and miR-125b in tumor angiogenesis., Jun He, Yi Jing, Wei Li, Xu Qian, Qing Xu, Feng-Shan Li, Ling-Zhi Liu, Bing-Hua Jiang, and Yue Jiang

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The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease., Elena Mogilyansky and Isidore Rigoutsos