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About me

I am an Associate Professor (“Docent” in the Swedish academic system) and group leader for the Clinical Transcriptomics research group at the Department of Biosciences and Nutrition at Karolinska Institutet. My educational background is in Chemistry (Masters in 2000 at Technical University Berlin) and Bioinformatics (PhD in 2004 at Max-Planck-Institute in Golm). I spent two years as postdoc with Erik Sonnhammer at Karolinska Institutet 2004-2006 after which I went to work with Yoshihide Hayashizaki at RIKEN Yokohama. In 2007 I became Team Leader at RIKEN Omics Science Center (OSC) and was also leading the Bioinformatics Core Facility at RIKEN OSC as Facility Director since 2008. In 2012, I moved back to Karolinska Institutet to lead the Clinical Transcriptomics research group to improve the understanding of gene regulation underlying diseases. 

Research description

Publication summary
Total number of peer-reviewed publications: 56, first author: 4, last author: 13
H-index: 30 (Google scholar)
Total number of citations: >4000 (Google scholar)

Teaching portfolio



Since 2014, Niyaz Yoosuf, postdoc
Since 2015, Enrichetta Mileti, PhD student
Since 2015, Tahmina Akhter, PhD student
Since 2015, Abdul Kadir Mukarram, PhD student (to be registered 2015-11-30)
Since 2015, Matthias Hörtenhuber, PhD student (to be registered 2015-11-30)


2012-2014, Olga Hrydziuszko, postdoc
2012-2014, Nancy Yu, postdoc
2012-2013, Andrew Kwon, postdoc, RIKEN Yokohama
2011-2013, Jordan Ramilowski, postdoc, RIKEN Yokohama
2009-2011, Max Burroughs, postdoc, RIKEN Yokohama
2009-2013 Morana Vitezic, Karolinska Institutet PhD student with Carsten Daub as main supervisor, working at RIKEN Yokohama, financed by RIKEN IPA program 




Characterization of the human RFX transcription factor family by regulatory and target gene analysis
Sugiaman-trapman D, Vitezic M, Jouhilahti Em, Mathelier A, Lauter G, Misra S, et al
BMC genomics 2018;19(1):181-

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection
Fantom Consortium, Zhang Pgy, Yeung J, Gupta I, Ramirez M, Ha T, et al
Cerebellum (London, England) 2018;17(3):308-325

Long-Term Improvement in Aortic Pulse Wave Velocity After Weight Loss Can Be Predicted by White Adipose Tissue Factors
Bäckdahl J, Andersson Dp, Eriksson-hogling D, Caidahl K, Thorell A, Mileti E, et al
American journal of hypertension 2018;31(4):450-457

Relatively frequent switching of transcription start sites during cerebellar development (vol 18, 461, 2017)
Fantom Consortium, Zhang P, Dimont E, Ha T, Swanson Dj, Itoh M, et al
BMC GENOMICS 2018;:39-

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease
Iibdgc Consortium, Baillie Jk, Bretherick A, Haley Cs, Clohisey S, Gray A, et al
PLoS computational biology 2018;14(3):e1005934-

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth
Yu Ny, Bieder A, Raman A, Mileti E, Katayama S, Einarsdottir E, et al
Scientific reports 2017;7(1):11458-

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease
Baillie Jk, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, et al
PLOS GENETICS 2017;13(3):e1006641-

An atlas of human long non-coding RNAs with accurate 5' ends
Hon Cc, Ramilowski Ja, Harshbarger J, Bertin N, Rackham Oj, Gough J, et al
Nature 2017;543(7644):199-204

An integrated expression atlas of miRNAs and their promoters in human and mouse
Fantom Consortium, De Rie D, Abugessaisa I, Alam T, Arner E, Arner P, et al
Nature biotechnology 2017;35(9):872-878

FANTOM5 CAGE profiles of human and mouse samples
Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, et al
Scientific data 2017;4():170112-

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution
Fantom Consortium, Ehrlund A, Mejhert N, Bjork C, Andersson R, Kulyte A, et al
DIABETES 2017;66(1):218-230

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes
Fantom Consortium, Qin Xy, Hara M, Arner E, Kawaguchi Y, Inoue I, et al
EBioMedicine 2017;24():257-266

A predictive computational framework for direct reprogramming between human cell types
Fantom Consortium, Rackham Oj, Firas J, Fang H, Oates Me, Holmes Ml, et al
Nature genetics 2016;48(3):331-5

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C
Fantom Consortium, Klein S, Dieterich Lc, Mathelier A, Chong C, Sliwa-primorac A, et al
JOURNAL OF CELL SCIENCE 2016;129(13):2573-85

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity
Rydén M, Hrydziuszko O, Mileti E, Raman A, Bornholdt J, Boyd M, et al
Cell reports 2016;16(9):2317-26

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage
Fantom Consortium, Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, et al
PloS one 2015;10(12):e0144176-

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium
Fantom Consortium, Yu Ny, Hallström Bm, Fagerberg L, Ponten F, Kawaji H, et al
Nucleic acids research 2015;43(14):6787-98

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium
Dieterich Lc, Klein S, Mathelier A, Sliwa-primorac A, Ma Ql, Hong Yk, et al
CELL REPORTS 2015;13(7):1493-1504

Gateways to the FANTOM5 promoter level mammalian expression atlas
Fantom Consortium, Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, et al
Genome biology 2015;16():22-

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells
Fantom Consortium, Mina M, Magi S, Jurman G, Itoh M, Kawaji H, et al
Scientific reports 2015;5():11999-

System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions
Sakata K, Ohyanagi H, Sato S, Nobori H, Hayashi A, Ishii H, et al
Scientific reports 2015;5():8283-

Telomerase Reverse Transcriptase Regulates microRNAs
Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, et al

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Fantom Consortium, Arner E, Daub Co, Vitting-seerup K, Andersson R, Lilje B, et al
SCIENCE 2015;347(6225):1010-4

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response
Fantom Consortium, Aitken S, Magi S, Alhendi Am, Itoh M, Kawaji H, et al
PLoS computational biology 2015;11(4):e1004217-

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles
Persson H, Kwon At, Ramilowski Ja, Silberberg G, Söderhäll C, Orsmark-pietras C, et al
The Journal of allergy and clinical immunology 2015;136(3):638-48

Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue
Kulyté A, Belarbi Y, Lorente-cebrián S, Bambace C, Arner E, Daub Co, et al
Diabetes 2014;63(4):1248-58

An atlas of active enhancers across human cell types and tissues
Andersson R, Gebhard C, Miguel-escalada I, Hoof I, Bornholdt J, Boyd M, et al
Nature 2014;507(7493):455-461

A promoter-level mammalian expression atlas
Riken Pmi Clst Dgt, Fantom Consortium, Forrest Arr, Kawaji H, Rehli M, Baillie Jk, et al
NATURE 2014;507(7493):462-70

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators
Fantom Consortium, Hurst Ld, Sachenkova O, Daub C, Forrest Ar, Huminiecki L
Genome biology 2014;15(7):413-

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
Fantom Consortium, Rye M, Sandve Gk, Daub Co, Kawaji H, Carninci P, et al
BMC genomics 2014;15():120-

Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue
Gao H, Mejhert N, Fretz Ja, Arner E, Lorente-cebrián S, Ehrlund A, et al
Cell metabolism 2014;19(6):981-92

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis
Fantom Consortium, Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, et al
Blood 2014;123(17):e46-57

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
Fantom Consortium, Severin J, Lizio M, Harshbarger J, Kawaji H, Daub Co, et al

MOIRAI: a compact workflow system for CAGE analysis
Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T
BMC bioinformatics 2014;15():144-

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements
Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, et al
Frontiers in cellular neuroscience 2014;8():41-

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells
Sompallae R, Hofmann O, Maher Ca, Gedye C, Behren A, Vitezic M, et al
Frontiers in genetics 2013;4():209-

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals
Ramilowski Ja, Sawai S, Seki H, Mochida K, Yoshida T, Sakurai T, et al
Plant & cell physiology 2013;54(5):697-710

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins
Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin Tr, Ohman T, et al
Biological psychiatry 2013;73(6):583-90

Regional differences in gene expression and promoter usage in aged human brains
Pardo Lm, Rizzu P, Francescatto M, Vitezic M, Leday Gg, Sanchez Js, et al
Neurobiology of aging 2013;34(7):1825-36

Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity
Arner E, Mejhert N, Kulyte A, Balwierz Pj, Pachkov M, Cormont M, et al
DIABETES 2012;61(8):1986-93

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages
Schroder K, Irvine Km, Taylor Ms, Bokil Nj, Cao Kal, Masterman Ka, et al

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes
Kato L, Begum Na, Burroughs Am, Doi T, Kawai J, Daub Co, et al

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns
Burroughs Am, Kawano M, Ando Y, Daub Co, Hayashizaki Y
NUCLEIC ACIDS RESEARCH 2012;40(4):1424-37

Promoter architecture of mouse olfactory receptor genes
Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, et al
GENOME RESEARCH 2012;22(3):486-97

Deep-sequencing of human argonaute-associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin
Burroughs Am, Ando Y, De Hoon Mjl, Tomaru Y, Suzuki H, Hayashizaki Y, et al
RNA BIOLOGY 2011;8(1):158-77

Optimization of turn-back primers in isothermal amplification
Kimura Y, De Hoon Mjl, Aoki S, Ishizu Y, Kawai Y, Kogo Y, et al

SAMStat: monitoring biases in next generation sequencing data
Lassmann T, Hayashizaki Y, Daub Co
BIOINFORMATICS 2011;27(1):130-1

The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi
Franzen O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, et al

Unamplified cap analysis of gene expression on a single-molecule sequencer
Kanamori-katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, et al
GENOME RESEARCH 2011;21(7):1150-9

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji H, Severin J, Lizio M, Forrest Arr, Van Nimwegen E, Rehli M, et al

A comprehensive survey of 3 ' animal miRNA modification events and a possible role for 3 ' adenylation in modulating miRNA targeting effectiveness
Burroughs Am, Ando Y, De Hoon Mjl, Tomaru Y, Nishibu T, Ukekawa R, et al
GENOME RESEARCH 2010;20(10):1398-410

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi T, Suzuki H, Cannistraci Cv, Katayama S, Bajic Vb, Tan K, et al
CELL 2010;140(5):744-52

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010)
Ravasi T, Suzuki H, Cannistraci Cv, Katayama S, Bajic Vb, Tan K, et al
CELL 2010;141(2):369-369

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Vitezic M, Lassmann T, Forrest Arr, Suzuki M, Tomaru Y, Kawai J, et al
NUCLEIC ACIDS RESEARCH 2010;38(22):8141-8

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, et al
BMC GENOMICS 2010;:257-

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
De Hoon Mjl, Taft Rj, Hashimoto T, Kanamori-katayama M, Kawaji H, Kawano M, et al
GENOME RESEARCH 2010;20(2):257-64

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, et al
NATURE METHODS 2010;7(7):528-34

NGSView: an extensible open source editor for next-generation sequencing data
Arner E, Hayashizaki Y, Daub Co
BIOINFORMATICS 2010;26(1):125-6

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Severin J, Waterhouse Am, Kawaji H, Lassmann T, Van Nimwegen E, Balwierz Pj, et al
GENOME BIOLOGY 2009;10(4):R39-

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, et al
GENOME RESEARCH 2009;19(2):255-65

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
Balwierz Pj, Carninci P, Daub Co, Kawai J, Hayashizaki Y, Van Belle W, et al
GENOME BIOLOGY 2009;10(7):R79-

MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines
Takahashi Y, Forrest Arr, Maeno E, Hashimoto T, Daub Co, Yasuda J
PLOS ONE 2009;4(8):e6677-

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite
Hashimoto T, De Hoon Mjl, Grimmond Sm, Daub Co, Hayashizaki Y, Faulkner Gj
BIOINFORMATICS 2009;25(19):2613-4

SDRF2GRAPH-a visualization tool of a spreadsheet-based description of experimental processes
Kawaji H, Hayashizaki Y, Daub Co

TagDust-a program to eliminate artifacts from next generation sequencing data
Lassmann T, Hayashizaki Y, Daub Co
BIOINFORMATICS 2009;25(21):2839-40

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine Km, et al
GENOME BIOLOGY 2009;10(4):R40-

The regulated retrotransposon transcriptome of mammalian cells
Faulkner Gj, Kimura Y, Daub Co, Wani S, Plessy C, Irvine Km, et al
NATURE GENETICS 2009;41(5):563-71

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Riken Omics Sci Ctr, Fantom Consortium, Suzuki H, Forrest Arr, Van Nimwegen E, Daub Co, et al
NATURE GENETICS 2009;41(5):553-62

Tiny RNAs associated with transcription start sites in animals
Taft Rj, Glazov Ea, Cloonan N, Simons C, Stephen S, Faulkner Gj, et al
NATURE GENETICS 2009;41(5):572-8

Tiny RNAs associated with transcription start sites in animals (vol 41, pg 572, 2009)
Taft Rj, Glazov Ea, Cloonan N, Simons C, Stephen S, Faulkner Gj, et al
NATURE GENETICS 2009;41(7):859-859

Transcriptional features of genomic regulatory blocks
Akalin A, Fredman D, Arner E, Dong Xj, Bryne Jc, Suzuki H, et al
GENOME BIOLOGY 2009;10(4):R38-

Employing conservation of co-expression to improve functional inference
Daub Co, Sonnhammer Ell

Hidden layers of human small RNAs
Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, et al
BMC GENOMICS 2008;:157-

Prediction of function divergence in protein families using the substitution rate variation parameter alpha
Abhiman S, Daub Co, Sonnhammer Ell

Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response
Nikiforova Vj, Daub Co, Hesse H, Willmitzer L, Hoefgen R

Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data
Daub Co, Steuer R, Selbig J, Kloska S

MetaGeneAlyse: analysis of integrated transcriptional and metabolite data
Daub Co, Kloska S, Selbig J
BIOINFORMATICS 2003;19(17):2332-3

The mutual information: Detecting and evaluating dependencies between variables
Steuer R, Kurths J, Daub Co, Weise J, Selbig J

Anomalous neutron reflectivity at the quartz/H2O-D2O interface
Abdul-redah T, Daub C, Streffer F, Chatzidimitriou-dreismann Ca
PHYSICA B 2000;291(3-4):314-316

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