Submissions from 2024
Recurrent Inflammatory Myofibroblastic Tumor of Larynx Harboring a Novel THBS1::ALK Fusion, Namra Ajmal, Stacey Gargano, Ujwala Gosavi, and Madalina Tuluc
The Subcellular Distribution of miRNA Isoforms, tRNA-Derived Fragments, and rRNA-Derived Fragments Depends on Nucleotide Sequence and Cell Type, Tess Cherlin, Yi Jing, Siddhartha Shah, Anne Kennedy, Aristeidis Telonis, Venetia Pliatsika, Haley Wilson, Lily Thompson, Panagiotis Vlantis, Phillipe Loher, Benjamin Leiby, and Isidore Rigoutsos
Immunostimulatory Short Non-Coding RNAs in the Circulation of Patients with Tuberculosis Infection, Justin Gumas, Takuya Kawamura, Megumi Shigematsu, and Yohei Kirino
The tRNAVal Half: A Strong Endogenous Toll-Like Receptor 7 Ligand with a 5′-Terminal Universal Sequence Signature, Kamlesh Ganesh Pawar, Takuya Kawamura, and Yohei Kirino
MINRbase: A Comprehensive Database of Nuclear- and Mitochondrial-Ribosomal-RNA-Derived Fragments (rRFs), Venetia Pliatsika, Tess Cherlin, Phillipe Loher, Panagiotis Vlantis, Parth Nagarkar, Stepan Nersisyan, and Isidore Rigoutsos
Immunoactive Signatures of Circulating tRNA- And rRNA-Derived RNAs in Chronic Obstructive Pulmonary Disease, Megumi Shigematsu, Takuya Kawamura, Deepak Deshpande, and Yohei Kirino
Submissions from 2023
The Typical tRNA Co-Expresses Multiple 5' tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease, Robert Akins, Kayleigh Ostberg, Tess Cherlin, Nikolas Tsiouplis, Phillipe Loher, and Isidore Rigoutsos
The Role of Non-Coding RNAs in Myelodysplastic Neoplasms, Vasileios Georgoulis, Epameinondas Koumpis, and Eleftheria Hatzimichael
Examining pi3K-Signaling-Dependent Regulation of Lens Organelle Free Zone Formation via Immunolocalization and Immunoblotting in Chick Embryos, Rifah Gheyas and A. Sue Menko
Extracellular tRNA-Derived RNAs as Emerging Activators of Endosomal Toll-like Receptors: A Narrative Review, Justin Gumas and Yohei Kirino
Structural Insights Into RNA Bridging Between HIV-1 Vif and Antiviral Factor APOBEC3G, Takahide Kouno, Satoshi Shibata, Megumi Shigematsu, Jaekyung Hyun, Tae Gyun Kim, Hiroshi Matsuo, and Matthias Wolf
Immune Cells Localize to Sites of Corneal Erosions in C57BL/6 Mice., Phuong M. Le, Sonali Pal-Ghosh, A. Menko, and Mary Ann Stepp
Emphysematous pyelonephritis necessitating bilateral radical nephrectomy: A case report and literature review., Christine E Wamsley, Arianna Morton, Christopher G Roth, Joseph K Izes, and Li Li
Using Medicare Claims to Estimate Risk-Adjusted Performance of Pennsylvania Trauma Centers, Alexis M Zebrowski, Phillipe Loher, David G Buckler, Isidore Rigoutsos, Brendan G Carr, and Douglas J Wiebe
Submissions from 2022
ANGEL2 Phosphatase Activity is Required for Non-Canonical Mitochondrial RNA Processing, Paula Clemente, Javier Calvo-Garrido, Sarah F. Pearce, Florian A. Schober, Megumi Shigematsu, Stefan J. Siira, Isabelle Laine, Henrik Spåhr, Christian Steinmetzger, Katja Petzold, Yohei Kirino, Rolf Wibom, Oliver Rackham, Aleksandra Filipovska, Joanna Rorbach, Christoph Freyer, and Anna Wredenberg
Challenges Inherent to the Sequencing and Quantification of Short Non-Coding RNAs and How to Address Them, Justin Gumas and Yohei Kirino
Reproducibility Efforts as a Teaching Tool: A Pilot Study, Nestoras Karathanasis, Daniel Hwang, Vibol Heng, Rimal Abhimannyu, Phillip Slogoff-Sevilla, Gina Buchel, Victoria Frisbie, Peiyao Li, Dafni Kryoneriti, and Isidore Rigoutsos
Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations, Megumi Shigematsu and Yohei Kirino
Submissions from 2021
MicroRNA Isoforms Contribution to Melanoma Pathogenesis, Elisabetta Broseghini, Emi Dika, Eric Londin, and Manuela Ferracin
Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis., Emi Dika, Elisabetta Broseghini, Elisa Porcellini, Martina Lambertini, Mattia Riefolo, Giorgio Durante, Phillipe Loher, Roberta Roncarati, Cristian Bassi, Cosimo Misciali, Massimo Negrini, Isidore Rigoutsos, Eric R. Londin, Annalisa Patrizi, and Manuela Ferracin
Input-output signal processing plasticity of vagal motor neurons in response to cardiac ischemic injury., Jonathan Gorky, Alison Moss, Marina Balycheva, Rajanikanth Vadigepalli, and James S. Schwaber
Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data., Phillipe Loher and Nestoras Karathanasis
IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets., Phillipe Loher, Nestoras Karathanasis, Eric R Londin, Paul Bray, Venetia Pliatsika, Aristeidis G. Telonis, and Isidore Rigoutsos
STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans van der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, and David Gomez-Cabrero
RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors, Megumi Shigematsu, Takuya Kawamura, Keisuke Morichika, Natsuko Izumi, Takashi Kiuchi, Shozo Honda, Venetia Pliatsika, Ryuma Matsubara, Isidore Rigoutsos, Susumu Katsuma, Yukihide Tomari, and Yohei Kirino
The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content., Aristeidis G. Telonis and Isidore Rigoutsos
A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients., Adriana Zingone, Sanju Sinha, Michael Ante, Cu Nguyen, Dalia Daujotyte, Elise D. Bowman, Neelam Sinha, Khadijah A Mitchell, Qingrong Chen, Chunhua Yan, Phillipe Loher, Daoud Meerzaman, Eytan Ruppin, and Bríd M. Ryan
Submissions from 2020
Long-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs., Angelica Giuliani, Eric Londin, Manuela Ferracin, Emanuela Mensà, Francesco Prattichizzo, Deborah Ramini, Fiorella Marcheselli, Rina Recchioni, Maria Rita Rippo, Massimiliano Bonafè, Isidore Rigoutsos, Fabiola Olivieri, and Jacopo Sabbatinelli
On the expanding roles of tRNA fragments in modulating cell behavior, Rogan Magee and Isidore Rigoutsos
Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7., Kamlesh Pawar, Megumi Shigematsu, Soroush Sharbati, and Yohei Kirino
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
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
Modulation of Aub-TDRD interactions elucidates piRNA amplification and germplasm formation., Nicholas Vrettos; Manolis Maragkakis; Panagiotis Alexiou; Paraskevi Sgourdou; Fadia Ibrahim; Daniel Palmieri; Yohei Kirino, PhD; and Zissimos Mourelatos
Submissions from 2019
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
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
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
Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer., Rogan G. Magee, Aristeidis G. Telonis, Phillipe Loher, Eric R Londin, and Isidore Rigoutsos
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
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
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
MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data., Phillipe Loher, Aristeidis G. Telonis, and Isidore Rigoutsos
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
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
5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves., Megumi Shigematsu and Yohei Kirino
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
Consequential considerations when mapping tRNA fragments., Aristeidis G Telonis; Phillipe Loher; Yohei Kirino, PhD; and Isidore Rigoutsos
Submissions from 2015
Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences., Shozo Honda and Yohei Kirino
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
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
What is translational bioinformatics?, Eric R. Londin and Carol I. Barash
tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins., Megumi Shigematsu and Yohei Kirino, PhD
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
IsomiR Expression Profiles in Human Lymphoblastoid Cell Lines Exhibit Population and Gender Dependencies., Phillipe Loher, Eric R Londin, and Isidore Rigoutsos
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
Nuclear and mitochondrial tRNA-lookalikes in the human genome., Aristeidis G Telonis, Phillipe Loher, Yohei Kirino, and Isidore Rigoutsos
MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells., Honglei Zhou and Isidore Rigoutsos
The emerging roles of GPRC5A in diseases., Honglei Zhou and Isidore Rigoutsos
Submissions from 2013
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
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
