Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

Acrylonitrile‐Mediated Nascent RNA Sequencing for Transcriptome‐Wide Profiling of Cellular RNA Dynamics

(2020) Yuqi Chen et al.   Advanced Science

RNA Conformation Capture by Proximity Ligation

(2020) Grzegorz Kudla et al.   Annual Review of Genomics and Human Genetics

Real-time RT-PCR in COVID-19 detection: issues affecting the results

(2020) Alireza Tahamtan et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

(2020) Zhaokui Cai et al.   NATURE

The lncRNA LAMP5-AS1 drives leukemia cell stemness by directly modulating DOT1L methyltransferase activity in MLL leukemia

(2020) Wen-Tao Wang et al.   Journal of Hematology & Oncology

SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

(2019) Zhi-Wei Guo et al.   Database-The Journal of Biological Databases and Curation

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

(2019) Roland G. Huber et al.   Nature Communications

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs

(2019) Zhangming Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effects of pH and salts on nucleic acid partitioning during phenol extraction

(2019) Lei Xu et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

(2019) Joana Carlevaro-Fita et al.   MOLECULAR CELL

The Landscape of Circular RNA in Cancer

(2019) Josh N. Vo et al.   CELL

How are circRNAs translated by non-canonical initiation mechanisms?

(2019) Leïla Halidou Diallo et al.   BIOCHIMIE

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Noncoding RNAs in cancer therapy resistance and targeted drug development

(2019) Wen-Tao Wang et al.   Journal of Hematology & Oncology

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

(2019) Jörg Morf et al.   NATURE BIOTECHNOLOGY

CircMYBL2, a circRNA from MYBL2, Regulates FLT3 Translation by Recruiting PTBP1 to Promote FLT3-ITD AML Progression

(2019) Yu-Meng Sun et al.   BLOOD

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

(2019) Carrie Wright et al.   BMC GENOMICS

Decrypting noncoding RNA interactions, structures, and functional networks

(2019) Muller Fabbri et al.   GENOME RESEARCH

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines

(2019) Hang Ruan et al.   Genome Medicine

MALAT1: a druggable long non-coding RNA for targeted anti-cancer approaches

(2018) Nicola Amodio et al.   Journal of Hematology & Oncology

Circular RNAs: a new frontier for cancer diagnosis and therapy

(2018) Miaoci Zhang et al.   Journal of Hematology & Oncology

Long non-coding RNA-SNHG7 acts as a target of miR-34a to increase GALNT7 level and regulate PI3K/Akt/mTOR pathway in colorectal cancer progression

(2018) Yang Li et al.   Journal of Hematology & Oncology

Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling

(2018) Maria D Giraldez et al.   NATURE BIOTECHNOLOGY

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions

(2018) Marisa A P Baptista et al.   NATURE METHODS

Single-cell RNA sequencing for the study of development, physiology and disease

(2018) S. Steven Potter   Nature Reviews Nephrology

HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis

(2018) Wanju Jiao et al.   ONCOGENE

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

circRNA disease: a manually curated database of experimentally supported circRNA-disease associations

(2018) Zheng Zhao et al.   Cell Death & Disease

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

(2018) Chunyan Fan et al.   Database-The Journal of Biological Databases and Curation

tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA

(2018) Siqi Li et al.   Genes

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

(2018) Pavel P Kuksa et al.   BIOINFORMATICS

The Biogenesis, Functions, and Challenges of Circular RNAs

(2018) Xiang Li et al.   MOLECULAR CELL

Small-seq for single-cell small-RNA sequencing

(2018) Michael Hagemann-Jensen et al.   Nature Protocols

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

(2018) Rui Dong et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity

(2018) Pan Li et al.   Cell Host & Microbe

Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies

(2018) Nonthaphat Kent Wong et al.   Journal of Hematology & Oncology

Higher-Order Organization Principles of Pre-translational mRNPs

(2018) Mihir Metkar et al.   MOLECULAR CELL

LncBook: a curated knowledgebase of human long non-coding RNAs

(2018) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers

(2018) Yue Gao et al.   NUCLEIC ACIDS RESEARCH

EVmiRNA: a database of miRNA profiling in extracellular vesicles

(2018) Teng Liu et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma

(2018) Maolei Zhang et al.   Nature Communications

Circular RNAs in cancer: an emerging key player

(2017) Yeping Dong et al.   Journal of Hematology & Oncology

Role of epigenetics-microRNA axis in drug resistance of multiple myeloma

(2017) Nasrin Rastgoo et al.   Journal of Hematology & Oncology

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis

(2017) Paul Schimmel   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CSCD: a database for cancer-specific circular RNAs

(2017) Siyu Xia et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

(2017) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Venetia Pliatsika et al.   NUCLEIC ACIDS RESEARCH

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

(2017) Laura E. Ritchey et al.   NUCLEIC ACIDS RESEARCH

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

(2017) Dimitra Karagkouni et al.   NUCLEIC ACIDS RESEARCH

LncATLAS database for subcellular localization of long noncoding RNAs

(2017) David Mas-Ponte et al.   RNA

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

(2017) Pornchai Kaewsapsak et al.   eLife

lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes

(2016) Yining Liu et al.   BIOINFORMATICS

Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations

(2016) Jlenia Guarnerio et al.   CELL

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

CircRNA-derived pseudogenes

(2016) Rui Dong et al.   CELL RESEARCH

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

(2016) Dario Veneziano et al.   HUMAN MUTATION

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

The biogenesis and emerging roles of circular RNAs

(2016) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

YM500v3: a database for small RNA sequencing in human cancer research

(2016) I-Fang Chung et al.   NUCLEIC ACIDS RESEARCH

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers

(2016) Zhen Yang et al.   NUCLEIC ACIDS RESEARCH

tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers

(2016) Ling-Ling Zheng et al.   NUCLEIC ACIDS RESEARCH

Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer

(2016) Yuri Pekarsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

(2016) Lesca M. Holdt et al.   Nature Communications

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

(2016) Tri C. Nguyen et al.   Nature Communications

miRNA Deregulation in Cancer Cells and the Tumor Microenvironment

(2016) R. Rupaimoole et al.   Cancer Discovery

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

(2016) Yajing Hao et al.   Database-The Journal of Biological Databases and Curation

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer

(2015) Jun Li et al.   CANCER RESEARCH

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

The emerging role of lncRNAs in cancer

(2015) Maite Huarte   NATURE MEDICINE

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions

(2015) Anindya Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Regulation of circRNA biogenesis

(2015) Ling-Ling Chen et al.   RNA Biology

miRGate: a curated database of human, mouse and rat miRNA–mRNA targets

(2015) Eduardo Andrés-León et al.   Database-The Journal of Biological Databases and Curation

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The emerging landscape of small nucleolar RNAs in cell biology

(2015) Fabien Dupuis-Sandoval et al.   Wiley Interdisciplinary Reviews-RNA

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Non-coding RNA: what is functional and what is junk?

(2015) Alexander F. Palazzo et al.   Frontiers in Genetics

FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data

(2014) Youri Hoogstrate et al.   BIOINFORMATICS

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

(2014) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

Genomic analysis of RNA localization

(2014) J Matthew Taliaferro et al.   RNA Biology

Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts

(2014) Laurence Josset et al.   RNA Biology

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Technical Variations in Low-Input RNA-seq Methodologies

(2014) Vipul Bhargava et al.   Scientific Reports

Non-coding RNA: a new frontier in regulatory biology

(2014) Xiang-Dong Fu   National Science Review

miRCancer: a microRNA-cancer association database constructed by text mining on literature

(2013) B. Xie et al.   BIOINFORMATICS

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data

(2013) Sören Müller et al.   BIOINFORMATICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Quantitative Transcriptomics using Designed Primer-based Amplification

(2013) Vipul Bhargava et al.   Scientific Reports

Correction: Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits

(2013) Suman Ghosal et al.   Frontiers in Genetics

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin

(2012) Thomas Schubert et al.   MOLECULAR CELL

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

(2012) Zhihua Li et al.   NUCLEIC ACIDS RESEARCH

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

The research strategies for probing the function of long noncoding RNAs

(2011) Biao Yan et al.   GENOMICS

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Transcriptome-wide discovery of circular RNAs in Archaea

(2011) Miri Danan et al.   NUCLEIC ACIDS RESEARCH

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic 5S rRNA biogenesis

(2011) Martin Ciganda et al.   Wiley Interdisciplinary Reviews-RNA

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

Regeneration of total RNA purification silica-based columns

(2010) Aldo Nicosia et al.   BIOMEDICAL CHROMATOGRAPHY

Characterization of the RNA content of chromatin

(2010) T. Mondal et al.   GENOME RESEARCH

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

MicroRNA profiling: separating signal from noise

(2010) Monya Baker   NATURE METHODS

Subcellular fractionation methods and strategies for proteomics

(2010) Yie Hou Lee et al.   PROTEOMICS

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Evidence for human microRNA-offset RNAs in small RNA sequencing data

(2009) D. Langenberger et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo

(2009) Zhen Wang et al.   METHODS

Metabolic tagging and purification of nascent RNA: implications for transcriptomics

(2009) Caroline C. Friedel et al.   Molecular BioSystems

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circulating miRNA and cancer diagnosis

(2009) Yi Tie et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology