E. Arner

发表

An atlas of active enhancers across human cell types and tissues

T. Meehan, C. Mungall, A. Sandelin, 2014, Nature.

Gateways to the FANTOM5 promoter level mammalian expression atlas

Derek W Wright, T. Meehan, A. Diehl, 2015, Genome Biology.

An atlas of human long non-coding RNAs with accurate 5′ ends

Jordan A. Ramilowski, J. Gough, C. Hon, 2017, Nature.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Thomas J. Ha, Kelly J. Morris, Louise N. Winteringham, 2015, Science.

The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease

B. Haas, S. Salzberg, O. White, 2005, Science.

The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi

Piero Carninci, Y. Hayashizaki, C. Daub, 2011, PLoS neglected tropical diseases.

Correcting errors in shotgun sequences.

E. Arner, Ellen Kindlund, M. Tammi, 2003, Nucleic acids research.

Correcting Errors in Shotgun Sequences Using DNPs and a Novel Pattern Matching Algorithm

E. Arner, Ellen Kindlund, M. Tammi, 2002 .

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Andrew M. Waterhouse, 2009, Nature Genetics.

Systematic analysis of transcription start sites in avian development

Piero Carninci, Y. Hayashizaki, T. Lassmann, 2017, PLoS biology.

Dynamics of human adipose lipid turnover in health and metabolic disease

S. Bernard, E. Arner, P. Arner, 2011, Nature.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, Nature Communications.

An integrated expression atlas of miRNAs and their promoters in human and mouse

Jay W. Shin, Thomas J. Ha, Louise N. Winteringham, 2017, Nature Biotechnology.

Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

E. Arner, D. Nilsson, Marcela Ferella, 2007, BMC Genomics.

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Mathieu Blanchette, Nicholas M. Luscombe, Boris Lenhard, 2020, Nature Communications.

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Christopher J. F. Cameron, N. Luscombe, M. Blanchette, 2019, Nature Communications.

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Thomas J. Ha, The Fantom Consortium, Piero Carninci, 2018, The Cerebellum.

Optimization of turn-back primers in isothermal amplification

Y. Hayashizaki, C. Daub, E. Arner, 2011, Nucleic acids research.

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation

Yoshihide Hayashizaki, Erik Arner, Atsutaka Kubosaki, 2009, Genome Biology.

Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis

Harukazu Suzuki, B. Kaczkowski, M. Furuno, 2020, bioRxiv.

Expression of FBN1 during adipogenesis: Relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions

E. Arner, P. Arner, I. Dahlman, 2016, Molecular genetics and metabolism.

Expression of FBN 1 during adipogenesis : relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions

E. Arner, P. Arner, I. Dahlman, 2016 .

A framework for identification of on- and off-target transcriptional responses to drug treatment

Erik Arner, Takahiro Arakawa, Satoshi Takizawa, 2019, Scientific Reports.

Adipocyte lipases and defect of lipolysis in human obesity.

E. Arner, P. Arner, A. Sicard, 2005, Diabetes.

Health and obesity: not just skin deep.

E. Arner, P. Arner, 2013, Science.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Boris Lenhard, Lusy Handoko, Piero Carninci, 2020, Genome research.

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2020 .

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, bioRxiv.

Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019, bioRxiv.

Regional impact of adipose tissue morphology on the metabolic profile in morbid obesity

E. Arner, P. Arner, M. Rydén, 2010, Diabetologia.

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

Thomas J. Ha, Piero Carninci, Y. Hayashizaki, 2019, BMC Genomics.

Correction to: Relatively frequent switching of transcription start sites during cerebellar development

Thomas J. Ha, Piero Carninci, Y. Hayashizaki, 2018, BMC Genomics.

FANTOM5 CAGE profiles of human and mouse samples

Jay W. Shin, Thomas J. Ha, Kelly J. Morris, 2017, Scientific Data.

Comparative transcriptomics of primary cells in vertebrates

Martin S. Taylor, Jordan A. Ramilowski, Robert S. Young, 2020, Genome research.

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β

Ahmad M. N. Alhendi, Piero Carninci, Y. Hayashizaki, 2018, Scientific Reports.

Low early B-cell factor 1 (EBF1) activity in human subcutaneous adipose tissue is linked to a pernicious metabolic profile.

E. Arner, P. Arner, M. Rydén, 2015, Diabetes & metabolism.

regulators of hematopoiesis High-throughput transcription profiling identifies putative epigenetic

T. Lassmann, A. Forrest, M. Itoh, 2014 .

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

T. Lassmann, A. Forrest, M. Itoh, 2014, Blood.

Transcriptional features of genomic regulatory blocks

Y. Hayashizaki, Harukazu Suzuki, B. Lenhard, 2009, Genome Biology.

Ceruloplasmin Is a Novel Adipokine Which Is Overexpressed in Adipose Tissue of Obese Subjects and in Obesity-Associated Cancer Cells

T. Lassmann, A. Forrest, M. Itoh, 2014, PloS one.

Tumor necrosis factor alpha and regulation of adipose tissue.

E. Arner, P. Arner, M. Rydén, 2010, The New England journal of medicine.

Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes

Piero Carninci, T. Olsson, E. Arner, 2022, Science advances.

Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue.

C. Daub, K. Dahlman-Wright, E. Arner, 2014, Cell metabolism.

Changes in Subcutaneous Fat Cell Volume and Insulin Sensitivity After Weight Loss

E. Arner, P. Arner, I. Dahlman, 2014, Diabetes Care.

Dynamics of fat cell turnover in humans

Tom Britton, Peter Arner, Erik Arner, 2008, Nature.

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C

Jay W. Shin, Piero Carninci, Y. Hayashizaki, 2016, Journal of Cell Science.

22nd European Congress on Obesity (ECO2015), Prague, Czech Republic, May 6-9, 2015: Abstracts

J. N. Fidalgo, Jimmy D Bell, L. S. Silveira, 2015, Obesity Facts.

PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment

O. Ohara, A. Iwama, R. Klose, 2022, Nature Communications.

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, EBioMedicine.

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

Yu Li, T. Arakawa, E. Arner, 2021, bioRxiv.

Solving repeat problems in shotgun sequencing

Erik Arner, E. Arner, 2006 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2021, Nature Communications.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Jay W. Shin, C. Hon, Piero Carninci, 2018, bioRxiv.

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

M. Fagiolini, T. Hensch, A. Sandelin, 2015, Epigenetics & Chromatin.

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Robert S. Young, J. Blake, T. Meehan, 2015, PLoS biology.

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

P. Kapranov, Piero Carninci, Y. Hayashizaki, 2016, Nucleic acids research.

Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Christopher J. F. Cameron, N. Luscombe, M. Blanchette, 2021, Nature Communications.

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Vladimir B. Bajic, Sebastian Schmeier, Piero Carninci, 2015, Nucleic acids research.

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

A. Sandelin, Piero Carninci, Y. Hayashizaki, 2014, Blood.

reveal timed changes and dynamic enhancer methylation Analysis of the DNA methylome and transcriptome in granulopoiesis

A. Sandelin, Piero Carninci, Y. Hayashizaki, 2014 .

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment

Ramzan Umarov, Erik Arner, E. Arner, 2020, bioRxiv.

Automatic identification of small molecules that promote cell conversion and reprogramming

Xin Gao, Diego di Bernardo, Akira Hasegawa, 2020, bioRxiv.

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution

A. Sandelin, Piero Carninci, Y. Hayashizaki, 2016, Diabetes.

Inducing human retinal pigment epithelium-like cells from somatic tissue

C. Hon, Piero Carninci, B. Kaczkowski, 2020, bioRxiv.

Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation

C. Wadelius, E. Ingelsson, E. Arner, 2019, iScience.

Discriminative identification of transcriptional responses of promoters and enhancers after stimulus

Panos Kalnis, Vladimir B. Bajic, Erik Arner, 2016, Nucleic acids research.

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

Geoffrey J Faulkner, Piero Carninci, Yoshihide Hayashizaki, 2017, PLoS genetics.

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment

Mariko Okada, Xin Gao, Yi Huang, 2017, Bioinform..

MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis

Piero Carninci, Y. Hayashizaki, E. Arner, 2019, Scientific Reports.

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.

Jay W. Shin, Piero Carninci, Y. Hayashizaki, 2015, Cell reports.

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions

Björn Andersson, Martti T. Tammi, Erik Arner, 2006, BMC Bioinformatics.

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Masaru Tomita, Jun Kawai, Piero Carninci, 2010, BMC Genomics.

Genetic Predisposition for Type 2 Diabetes, but Not for Overweight/Obesity, Is Associated with a Restricted Adipogenesis

U. Smith, E. Arner, P. Arner, 2011, PLoS ONE.

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

V. Bajic, Piero Carninci, Y. Hayashizaki, 2018, Scientific Reports.

The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

D. Hume, J. Severin, A. Lengeling, 2020, Frontiers in Cell and Developmental Biology.

Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.

Jeff E. Mold, S. Bernard, E. Arner, 2015, Cell metabolism.

Optimization of turn-back primers in isothermal amplification

Carsten O. Daub, Yoshihide Hayashizaki, Yuki Kawai, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2018, Open Biology.

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity

Piotr J. Balwierz, E. van Nimwegen, Y. Hayashizaki, 2012, Diabetes.

Adipocyte Turnover: Relevance to Human Adipose Tissue Morphology

S. Bernard, T. Britton, E. Arner, 2009, Diabetes.

TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences

Björn Andersson, Martti T. Tammi, Erik Arner, 2003, Comput. Methods Programs Biomed..

The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells.

Jun Kawai, Yoshihide Hayashizaki, Yuki Hasegawa, 2010, Molecular immunology.

Analysis of Enhancer-Promoter Interactions using CAGE and RADICL-Seq Technologies.

Piero Carninci, E. Arner, A. T. Kwon, 2021, Methods in molecular biology.

Clinical and Translational Report TransplantedBoneMarrow-DerivedCells Contribute to Human Adipogenesis Graphical

Jeff E. Mold, S. Bernard, E. Arner, 2015 .

A framework for identification of on- and off-target transcriptional responses to drug treatment

Harukazu Suzuki, M. Furuno, T. Arakawa, 2019, Scientific Reports.

NGSView: an extensible open source editor for next-generation sequencing data

Y. Hayashizaki, C. Daub, E. Arner, 2009, Bioinform..

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Carsten O. Daub, Mariko Okada, Piero Carninci, 2015, PLoS Comput. Biol..

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

V. Bajic, Piero Carninci, Y. Hayashizaki, 2018, Scientific Reports.

Molecular profiling of high-level athlete skeletal muscle after acute exercise – a systems biology approach

B. Kaczkowski, A. Mardinoğlu, E. Arner, 2023, bioRxiv.

Additive Effects of MicroRNAs and Transcription Factors on CCL2 Production in Human White Adipose Tissue

C. Daub, E. Arner, P. Arner, 2014, Diabetes.

Inducing Human Retinal Pigment Epithelium-like Cells

B. Kaczkowski, T. Kasukawa, E. Arner, 2020 .

xcore: an R package for inference of gene expression regulators

Harukazu Suzuki, B. Kaczkowski, M. Furuno, 2022, bioRxiv.

Additive effects of miRNAs and transcription factors on CCL 2 production in human white adipose tissue

C. Daub, E. Arner, P. Arner, 2013 .

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

Giuseppe Jurman, Piero Carninci, Y. Hayashizaki, 2015, Scientific Reports.

Development of p53 Knockout U87MG Cell Line for Unbiased Drug Delivery Testing System Using CRISPR-Cas9 and Transcriptomic Analysis.

Harukazu Suzuki, B. Kaczkowski, M. Furuno, 2021, Journal of biotechnology.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping 1

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019 .

FANTOM5 CAGE profiles of human and mouse samples.

Jay W. Shin, Thomas J. Ha, Kelly J. Morris, 2017, Scientific data.

ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid

Björn Andersson, Martti T. Tammi, Erik Arner, 2004, Bioinform..

Comparative Genomics of Trypanosomatid Parasitic Protozoa

Daniel Nilsson, Jonathan Crabtree, Neil Hall, 2005, Science.

Edinburgh Explorer The Transcriptional Network that Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

D. Hume, J. Severin, A. Lengeling, 2020 .

Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs

Björn Andersson, Tom Britton, Martti T. Tammi, 2002, Bioinform..

RADICL-seq identifies general and cell type specific principles of genome-wide RNA-chromatin interactions