Phillipe Loher

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Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types

Rogan Magee, Phillipe Loher, Eric Londin, 2017, Nucleic acids research.

Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells

I. Rigoutsos, Phillipe Loher, Y. Kirino, 2017, Scientific Reports.

The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells

Phillipe Loher, Isidore Rigoutsos, Takuya Kawamura, 2017, Nucleic acids research.

The complex transcriptional landscape of the anucleate human platelet

I. Rigoutsos, P. Fortina, Huang-wen Chen, 2013, BMC Genomics.

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets

I. Rigoutsos, T. Huynh, R. Zhou, 2012, Scientific Reports.

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner

I. Rigoutsos, Rogan Magee, Phillipe Loher, 2020, BMC Biology.

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

Yi Jing, George A Calin, Chad A Shaw, 2015, Proceedings of the National Academy of Sciences.

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

R. Krause, N. Rajewsky, P. Qiu, 2020, Life Science Alliance.

Systems-level Analysis of 32 TCGA Cancers Reveals Disease-dependent tRNA Fragmentation Patterns and Very Selective Associations with Messenger RNAs and Repeat Elements

Aristeidis G. Telonis, I. Rigoutsos, A. Telonis, 2017, bioRxiv.

tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities.

Aristeidis G. Telonis, I. Rigoutsos, A. Telonis, 2019, Cancer research.

The presence or absence alone of miRNA isoforms (isomiRs) successfully discriminate amongst the 32 TCGA cancer types

Aristeidis G. Telonis, I. Rigoutsos, A. Telonis, 2016, bioRxiv.

miRTOP: An open source community project for the development of a unified format file for miRNA data

Karen Eilbeck, Elisa Ficarra, Gianvito Urgese, 2018 .

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

I. Rigoutsos, A. Telonis, Phillipe Loher, 2017, Nucleic acids research.

Single-nucleotide Differences and Cell Type Decide the Subcellular Localization of miRNA Isoforms (isomiRs), tRNA-derived Fragments (tRFs) and rRNA-derived Fragments (rRFs)

I. Rigoutsos, Phillipe Loher, Y. Jing, 2022, bioRxiv.

Sequence Interactive exploration of RNA22 microRNA target predictions

I. Rigoutsos, Phillipe Loher, 2012 .

Unraveling the Role of microRNA and isomiRNA Networks in Multiple Primary Melanoma Pathogenesis

M. Ferracin, M. Negrini, I. Rigoutsos, 2020 .

The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis

I. Rigoutsos, E. Hatzimichael, Phillipe Loher, 2013, Cellular and Molecular Life Sciences.

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

Ke Xu, Thomas Yu, Julio Saez-Rodriguez, 2019, bioRxiv.

Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity

Yi Jing, Phillipe Loher, Eric Londin, 2015, Nucleic acids research.

Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

Yi Jing, Phillipe Loher, Aristeidis G. Telonis, 2015, Oncotarget.

Interactive exploration of RNA22 microRNA target predictions

Isidore Rigoutsos, Phillipe Loher, I. Rigoutsos, 2012, Bioinform..

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Karen Eilbeck, Elisa Ficarra, Gianvito Urgese, 2018, bioRxiv.

IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets

Phillipe Loher, Eric Londin, Venetia Pliatsika, 2021, Bioinform..

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types

Phillipe Loher, Eric R. Londin, Isidore Rigoutsos, 2014, Scientific Reports.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Joshua M. Stuart, Christopher M. Lalansingh, 2019, Nature Biotechnology.

Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma.

Steven J. M. Jones, Benjamin J. Raphael, Mark D. M. Leiserson, 2017, Cancer cell.

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer

Phillipe Loher, Eric Londin, Aristeidis G. Telonis, 2018, Scientific Reports.

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers

Phillipe Loher, Megumi Shigematsu, Isidore Rigoutsos, 2015, Proceedings of the National Academy of Sciences.

Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis

M. Ferracin, M. Negrini, I. Rigoutsos, 2021, Cell Death & Disease.

ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets

I. Rigoutsos, T. Huynh, R. Zhou, 2012, Scientific Reports.

MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects

Isidore Rigoutsos, Rogan Magee, Phillipe Loher, 2017, Nucleic Acids Res..

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data

Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos, 2017, Scientific Reports.

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

Phillipe Loher, Eric R. Londin, Isidore Rigoutsos, 2014, Oncotarget.

Nuclear and mitochondrial tRNA-lookalikes in the human genome

Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos, 2014, Front. Genet..

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

E. Ruppin, E. Bowman, Qingrong Chen, 2021, Nature Communications.

A community effort to create standards for evaluating tumor subclonal reconstruction

Nathan M. Wilson, Ville Mustonen, Salem Malikic, 2019, Nature Biotechnology.

The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis

I. Rigoutsos, E. Hatzimichael, Phillipe Loher, 2012, Cellular and Molecular Life Sciences.

Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data

Phillipe Loher, Nestoras Karathanasis, Phillipe Loher, 2019, bioRxiv.

The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome

C. Shaw, I. Rigoutsos, P. Fortina, 2014, Biology Direct.

The Short and the Long of it: Timing of Mortality for Older Adults in a State Trauma System.

Elinore J. Kaufman, B. Carr, D. Wiebe, 2021, The Journal of surgical research.

Consequential considerations when mapping tRNA fragments

Isidore Rigoutsos, Phillipe Loher, Aristeidis G. Telonis, 2016, BMC Bioinformatics.

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner

I. Rigoutsos, Rogan Magee, Phillipe Loher, 2020, BMC Biology.

MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments

Isidore Rigoutsos, Phillipe Loher, Venetia Pliatsika, 2016, Bioinform..

Comments on: “A comprehensive repertoire of tRNA-derived fragments in prostate cancer”

Aristeidis G. Telonis, I. Rigoutsos, A. Telonis, 2016, bioRxiv.

Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap.

Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos, 2018, Methods in molecular biology.

Threshold-seq: a tool for determining the threshold in short RNA-seq datasets

Isidore Rigoutsos, Rogan Magee, Phillipe Loher, 2017, Bioinform..

Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme

I. Rigoutsos, Phillipe Loher, Y. Kirino, 2019, RNA biology.

Using medicare claims to estimate risk-adjusted performance of Pennsylvania trauma centers

I. Rigoutsos, D. Wiebe, Phillipe Loher, 2023, PLOS digital health.

Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs

Phillipe Loher, Eric Londin, Isidore Rigoutsos, 2015, Proceedings of the National Academy of Sciences.

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

Aristeidis G. Telonis, I. Rigoutsos, Phillipe Loher, 2017, Nucleic acids research.

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

I. Rigoutsos, Phillipe Loher, Eric Londin, 2014, Oncotarget.

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

I. Rigoutsos, Phillipe Loher, Tess Cherlin, 2023, Non-coding RNA.

MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs)

I. Rigoutsos, Phillipe Loher, Tess Cherlin, 2023, Nucleic acids research.

MINTmap: fast and exhaustive profiling of nuclear and MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. mitochondrial tRNA fragments from short RNA-seq data.

Aristeidis G. Telonis, Phillipe Loher, Isidore Rig outsos, 2022 .

The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type

Aristeidis G. Telonis, I. Rigoutsos, Phillipe Loher, 2024, BMC biology.