Publications

 

Publication databases

 

2017

Zhang PGY,  Yeung J,  Gupta I,  Ramirez M,  Ha T,  Swanson DJ,  Nagao-Sato S,  Itoh M,  Kawaji H,  Lassmann T,  Daub CO,  Arner E,  de Hoon M,  FANTOM consortium,  Carninci P,  Forrest ARR,  Hayashizaki Y,  Goldowitz D. Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection. Cerebellum (London, England) 2018 ;

FANTOM Consortium,  Zhang P,  Dimont E,  Ha T,  Swanson DJ,  Itoh M,  Kawaji H,  Lassmann T,  Daub CO,  Arner E,  Carninci P,  Hayashizaki Y,  Forrest ARR,  Hide W,  Goldowitz D. Relatively frequent switching of transcription start sites during cerebellar development (vol 18, 461, 2017). BMC GENOMICS 2018 19; 39-

Yu NY,  Bieder A,  Raman A,  Mileti E,  Katayama S,  Einarsdottir E,  Fredholm BB,  Falk A,  Tapia-Páez I,  Daub CO,  Kere J. Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth. Scientific reports 2017 7;1 11458-

Baillie JK,  Arner E,  Daub C,  De Hoon M,  Itoh M,  Kawaji H,  Lassmann T,  Carninci P,  Forrest ARR,  Hayashizaki Y,  Consortium F,  Faulkner GJ,  Wells CA,  Rehli M,  Pavli P,  Summers KM,  Hume DA. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLOS GENETICS 2017 13;3 e1006641-

Hon CC,  Ramilowski JA,  Harshbarger J,  Bertin N,  Rackham OJ,  Gough J,  Denisenko E,  Schmeier S,  Poulsen TM,  Severin J,  Lizio M,  Kawaji H,  Kasukawa T,  Itoh M,  Burroughs AM,  Noma S,  Djebali S,  Alam T,  Medvedeva YA,  Testa AC,  Lipovich L,  Yip CW,  Abugessaisa I,  Mendez M,  Hasegawa A,  Tang D,  Lassmann T,  Heutink P,  Babina M,  Wells CA,  Kojima S,  Nakamura Y,  Suzuki H,  Daub CO,  de Hoon MJ,  Arner E,  Hayashizaki Y,  Carninci P,  Forrest AR. An atlas of human long non-coding RNAs with accurate 5' ends. Nature 2017 543;7644 199-204

de Rie D,  Abugessaisa I,  Alam T,  Arner E,  Arner P,  Ashoor H,  Åström G,  Babina M,  Bertin N,  Burroughs AM,  Carlisle AJ,  Daub CO,  Detmar M,  Deviatiiarov R,  Fort A,  Gebhard C,  Goldowitz D,  Guhl S,  Ha TJ,  Harshbarger J,  Hasegawa A,  Hashimoto K,  Herlyn M,  Heutink P,  Hitchens KJ,  Hon CC,  Huang E,  Ishizu Y,  Kai C,  Kasukawa T,  Klinken P,  Lassmann T,  Lecellier CH,  Lee W,  Lizio M,  Makeev V,  Mathelier A,  Medvedeva YA,  Mejhert N,  Mungall CJ,  Noma S,  Ohshima M,  Okada-Hatakeyama M,  Persson H,  Rizzu P,  Roudnicky F,  Sætrom P,  Sato H,  Severin J,  Shin JW,  Swoboda RK,  Tarui H,  Toyoda H,  Vitting-Seerup K,  Winteringham L,  Yamaguchi Y,  Yasuzawa K,  Yoneda M,  Yumoto N,  Zabierowski S,  Zhang PG,  Wells CA,  Summers KM,  Kawaji H,  Sandelin A,  Rehli M,  FANTOM Consortium,  Hayashizaki Y,  Carninci P,  Forrest ARR,  de Hoon MJL. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature biotechnology 2017 35;9 872-878

Noguchi S,  Arakawa T,  Fukuda S,  Furuno M,  Hasegawa A,  Hori F,  Ishikawa-Kato S,  Kaida K,  Kaiho A,  Kanamori-Katayama M,  Kawashima T,  Kojima M,  Kubosaki A,  Manabe RI,  Murata M,  Nagao-Sato S,  Nakazato K,  Ninomiya N,  Nishiyori-Sueki H,  Noma S,  Saijyo E,  Saka A,  Sakai M,  Simon C,  Suzuki N,  Tagami M,  Watanabe S,  Yoshida S,  Arner P,  Axton RA,  Babina M,  Baillie JK,  Barnett TC,  Beckhouse AG,  Blumenthal A,  Bodega B,  Bonetti A,  Briggs J,  Brombacher F,  Carlisle AJ,  Clevers HC,  Davis CA,  Detmar M,  Dohi T,  Edge ASB,  Edinger M,  Ehrlund A,  Ekwall K,  Endoh M,  Enomoto H,  Eslami A,  Fagiolini M,  Fairbairn L,  Farach-Carson MC,  Faulkner GJ,  Ferrai C,  Fisher ME,  Forrester LM,  Fujita R,  Furusawa JI,  Geijtenbeek TB,  Gingeras T,  Goldowitz D,  Guhl S,  Guler R,  Gustincich S,  Ha TJ,  Hamaguchi M,  Hara M,  Hasegawa Y,  Herlyn M,  Heutink P,  Hitchens KJ,  Hume DA,  Ikawa T,  Ishizu Y,  Kai C,  Kawamoto H,  Kawamura YI,  Kempfle JS,  Kenna TJ,  Kere J,  Khachigian LM,  Kitamura T,  Klein S,  Klinken SP,  Knox AJ,  Kojima S,  Koseki H,  Koyasu S,  Lee W,  Lennartsson A,  Mackay-Sim A,  Mejhert N,  Mizuno Y,  Morikawa H,  Morimoto M,  Moro K,  Morris KJ,  Motohashi H,  Mummery CL,  Nakachi Y,  Nakahara F,  Nakamura T,  Nakamura Y,  Nozaki T,  Ogishima S,  Ohkura N,  Ohno H,  Ohshima M,  Okada-Hatakeyama M,  Okazaki Y,  Orlando V,  Ovchinnikov DA,  Passier R,  Patrikakis M,  Pombo A,  Pradhan-Bhatt S,  Qin XY,  Rehli M,  Rizzu P,  Roy S,  Sajantila A,  Sakaguchi S,  Sato H,  Satoh H,  Savvi S,  Saxena A,  Schmidl C,  Schneider C,  Schulze-Tanzil GG,  Schwegmann A,  Sheng G,  Shin JW,  Sugiyama D,  Sugiyama T,  Summers KM,  Takahashi N,  Takai J,  Tanaka H,  Tatsukawa H,  Tomoiu A,  Toyoda H,  van de Wetering M,  van den Berg LM,  Verardo R,  Vijayan D,  Wells CA,  Winteringham LN,  Wolvetang E,  Yamaguchi Y,  Yamamoto M,  Yanagi-Mizuochi C,  Yoneda M,  Yonekura Y,  Zhang PG,  Zucchelli S,  Abugessaisa I,  Arner E,  Harshbarger J,  Kondo A,  Lassmann T,  Lizio M,  Sahin S,  Sengstag T,  Severin J,  Shimoji H,  Suzuki M,  Suzuki H,  Kawai J,  Kondo N,  Itoh M,  Daub CO,  Kasukawa T,  Kawaji H,  Carninci P,  Forrest ARR,  Hayashizaki Y. FANTOM5 CAGE profiles of human and mouse samples. Scientific data 2017 4; 170112-

Bäckdahl J,  Andersson DP,  Eriksson-Hogling D,  Caidahl K,  Thorell A,  Mileti E,  Daub CO,  Arner P,  Rydén M. Long-term improvement in aortic pulse wave velocity after weight loss can be predicted by white adipose tissue factors. American journal of hypertension 2017 ;

Qin XY,  Hara M,  Arner E,  Kawaguchi Y,  Inoue I,  Tatsukawa H,  Furutani Y,  Nagatsuma K,  Matsuura T,  Wei F,  Kikuchi J,  Sone H,  Daub C,  Kawaji H,  Lassmann T,  Itoh M,  Suzuki H,  Carninci P,  Hayashizaki Y,  FANTOM consortium,  Kokudo N,  Forrest ARR,  Kojima S. Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes. EBioMedicine 2017 24; 257-266

2016

Ehrlund A, Mejhert N, Björk C, Andersson R, Kulyté A, Åström G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, Sandelin A, Ingelsson E, Consortium F, Rydén M, Laurencikiene J, Arner P, Arner E. Transcriptional Dynamics During Human Adipogenesis and its Link to Adipose Morphology and Distribution. Diabetes. 2016 Nov 1. pii: db160631. [Epub ahead of print] PubMed PMID: 27803022.

Rydén M, Hrydziuszko O, Mileti E, Raman A, Bornholdt J, Boyd M, Toft E, Qvist V, Näslund E, Thorell A, Andersson DP, Dahlman I, Gao H, Sandelin A, Daub CO, Arner P. The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity. Cell Rep. 2016 Aug 30;16(9):2317-26. doi: 10.1016/j.celrep.2016.07.070. PubMed PMID: 27545890.

Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E; FANTOM consortium.,   Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M. DeepCAGEtranscriptomics identify HOXD10 as a transcription factor regulating lymphaticendothelial responses to VEGF-C. J Cell Sci. 2016 Jul 1;129(13):2573-85. doi:  10.1242/jcs.186767. PubMed PMID: 27199372.  

Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOMConsortium., Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR,  Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct   reprogramming between human cell types. Nat Genet. 2016 Mar;48(3):331-5. doi:  10.1038/ng.3487. PubMed PMID: 26780608. 

2015

Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, CarninciP, Hayashizaki Y, Daub CO; FANTOM consortium., Okada-Hatakeyama M, Mar JC.  Application of Gene Expression Trajectories Initiated from ErbB ReceptorActivation Highlights the Dynamics of Divergent Promoter Usage. PLoS One. 2015Dec 14;10(12):e0144176. doi: 10.1371/journal.pone.0144176. PubMed PMID: 26658111;  PubMed Central PMCID: PMC4682858. 

Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW,   Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P,  Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M. DeepCAGE TranscriptomicsReveal an Important Role of the Transcription Factor MAFB in the LymphaticEndothelium. Cell Rep. 2015 Nov 17;13(7):1493-504. doi:  10.1016/j.celrep.2015.10.002. PubMed PMID: 26549461. 

Mina M, Magi S, Jurman G, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR,  Carninci P, Hayashizaki Y, Daub CO; FANTOM Consortium., Okada-Hatakeyama M,  Furlanello C. Promoter-level expression clustering identifies time development oftranscriptional regulatory cascades initiated by ErbB receptors in breast cancer   cells. Sci Rep. 2015 Jul 16;5:11999. doi: 10.1038/srep11999. PubMed PMID:  26179713; PubMed Central PMCID: PMC4503981. 

Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR;   Fantom Consortium., Hayashizaki Y, Uhlén M, Daub CO. Complementing tissuecharacterization by integrating transcriptome profiling from the Human ProteinAtlas and from the FANTOM5 consortium. Nucleic Acids Res. 2015 Aug18;43(14):6787-98. doi: 10.1093/nar/gkv608. PubMed PMID: 26117540; PubMed CentralPMCID: PMC4538815. 

Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E,   Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium., Khachigian LM,  Okada-Hatakeyama M, Semple CA. Transcriptional dynamics reveal critical roles fornon-coding RNAs in the immediate-early response. PLoS Comput Biol. 2015 Apr17;11(4):e1004217. doi: 10.1371/journal.pcbi.1004217. PubMed PMID: 25885578;  PubMed Central PMCID: PMC4401570. 

Persson H, Kwon AT, Ramilowski JA, Silberberg G, Söderhäll C, Orsmark-PietrasC, Nordlund B, Konradsen JR, de Hoon MJ, Melén E, Hayashizaki Y, Hedlin G, KereJ, Daub CO. Transcriptome analysis of controlled and therapy-resistant childhood   asthma reveals distinct gene expression profiles. J Allergy Clin Immunol. 2015Sep;136(3):638-48. doi: 10.1016/j.jaci.2015.02.026. PubMed PMID: 25863981. 

Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S,  Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, BaillieJK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide   W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli   M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW,  Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; FANTOMconsortium.. Gateways to the FANTOM5 promoter level mammalian expression atlas.  Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6. PubMed PMID:  25723102; PubMed Central PMCID: PMC4310165. 

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F,  Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM,  Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F,  Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L,  Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, HaraM, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S,  Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ,  Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V,  Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S,   Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, WinteringhamLN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, AbugessaisaI, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F,  Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M,  Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S,  Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H,  Summers KM, Wells C; FANTOM Consortium., Hume DA, Forrest AR, Sandelin A,  Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinatedtranscription in transitioning mammalian cells. Science. 2015 Feb27;347(6225):1010-4. doi: 10.1126/science.1259418. PubMed PMID: 25678556; PubMed   Central PMCID: PMC4681433. 

Sakata K, Ohyanagi H, Sato S, Nobori H, Hayashi A, Ishii H, Daub CO, Kawai J,  Suzuki H, Saito T. System-wide analysis of the transcriptional network of humanmyelomonocytic leukemia cells predicts attractor structure andphorbol-ester-induced differentiation and dedifferentiation transitions. Sci Rep.  2015 Feb 6;5:8283. doi: 10.1038/srep08283. PubMed PMID: 25655563; PubMed Central   PMCID: PMC4319166. 

Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, Kasim V, SimonC, Daub CO, Carninci P, Hayashizaki Y, Masutomi K. Telomerase reversetranscriptase regulates microRNAs. Int J Mol Sci. 2015 Jan 6;16(1):1192-208. doi:  10.3390/ijms16011192. PubMed PMID: 25569094; PubMed Central PMCID: PMC4307298. 

2014

Gao H, Mejhert N, Fretz JA, Arner E, Lorente-Cebrián S, Ehrlund A,  Dahlman-Wright K, Gong X, Strömblad S, Douagi I, Laurencikiene J, Dahlman I, DaubCO, Rydén M, Horowitz MC, Arner P. Early B cell factor 1 regulates adipocytemorphology and lipolysis in white adipose tissue. Cell Metab. 2014 Jun3;19(6):981-92. doi: 10.1016/j.cmet.2014.03.032. PubMed PMID: 24856929; PubMedCentral PMCID: PMC4109056. 

Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y; FANTOMConsortium., Bertin N, Forrest AR. Interactive visualization and analysis oflarge-scale sequencing datasets using ZENBU. Nat Biotechnol. 2014Mar;32(3):217-9. doi: 10.1038/nbt.2840. PubMed PMID: 24727769. 

Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, Lassmann T, Daub CO,  Forrest AR, Lennartsson A, Ekwall K; FANTOM consortium.. High-throughputtranscription profiling identifies putative epigenetic regulators of  hematopoiesis. Blood. 2014 Apr 24;123(17):e46-57. doi:  10.1182/blood-2013-02-483537. PubMed PMID: 24671951. 

FANTOM Consortium and the RIKEN PMI and CLST (DGT)., Forrest AR, Kawaji H,  Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M,   Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M,  Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M,  Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D,  Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ,  Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A,  Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, ChenY, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, DohiT, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M,  Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith   MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB,  Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, HaTJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y,  Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F,  Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski   B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS,  Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, KawashimaT, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ,   Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT,  Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, ManabeR, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de LimaMorais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL,  Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, NakazatoK, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, OgishimaS, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, OrlandoV, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S,  Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador   M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H,  Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A,  Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, SugiyamaT, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J,  Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van deWetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW,  Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y,  Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X,  Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, FreemanTC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P,  Hayashizaki Y. A promoter-level mammalian expression atlas. Nature. 2014 Mar27;507(7493):462-70. doi: 10.1038/nature13182. PubMed PMID: 24670764; PubMedCentral PMCID: PMC4529748. 

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen   Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, SchwarzfischerL, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR,  Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E,  Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N,  Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H,  Hayashizaki Y, Müller F; FANTOM Consortium., Forrest AR, Carninci P, Rehli M,  Sandelin A. An atlas of active enhancers across human cell types and tissues.  Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787. PubMed PMID:  24670763.

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F;  FANTOM consortium.. Chromatin states reveal functional associations for globally   defined transcription start sites in four human cell lines. BMC Genomics. 2014Mar 26;15:120. doi: 10.1186/1471-2164-15-120. PubMed PMID: 24669905; PubMedCentral PMCID: PMC3986914. 

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone   R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, CarninciP, Gustincich S. NanoCAGE analysis of the mouse olfactory epithelium identifiesthe expression of vomeronasal receptors and of proximal LINE elements. Front CellNeurosci. 2014 Feb 18;8:41. doi: 10.3389/fncel.2014.00041. PubMed PMID: 24600346;  PubMed Central PMCID: PMC3927265. 

Kulyté A, Belarbi Y, Lorente-Cebrián S, Bambace C, Arner E, Daub CO, Hedén P,  Rydén M, Mejhert N, Arner P. Additive effects of microRNAs and transcriptionfactors on CCL2 production in human white adipose tissue. Diabetes. 2014Apr;63(4):1248-58. doi: 10.2337/db13-0702. PubMed PMID: 24379347. 

2013

Sompallae R, Hofmann O, Maher CA, Gedye C, Behren A, Vitezic M, Daub CO,  Devalle S, Caballero OL, Carninci P, Hayashizaki Y, Lawlor ER, Cebon J, Hide W. Acomprehensive promoter landscape identifies a novel promoter for CD133 inrestricted tissues, cancers, and stem cells. Front Genet. 2013 Oct 29;4:209. doi:  10.3389/fgene.2013.00209. PubMed PMID: 24194746; PubMed Central PMCID:  PMC3810939. 

Ramilowski JA, Sawai S, Seki H, Mochida K, Yoshida T, Sakurai T, Muranaka T,   Saito K, Daub CO. Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals. Plant Cell Physiol. 2013 May;54(5):697-710. doi:  10.1093/pcp/pct057. PubMed PMID: 23589666. 

Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GG, Sanchez JS, Khamis A,  Takahashi H, van de Berg WD, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P,  Heutink P. Regional differences in gene expression and promoter usage in agedhuman brains. Neurobiol Aging. 2013 Jul;34(7):1825-36. doi:  10.1016/j.neurobiolaging.2013.01.005. PubMed PMID: 23428183. 

Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T,  Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I. Molecular networks ofDYX1C1 gene show connection to neuronal migration genes and cytoskeletalproteins. Biol Psychiatry. 2013 Mar 15;73(6):583-90. doi: 10.1016/j.biopsych.2012.08.012. PubMed PMID: 23036959. 

2012

Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M,  Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, TantiJF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P. Adipose   tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes.  2012 Aug;61(8):1986-93. doi: 10.2337/db11-1508. PubMed PMID: 22688341; PubMedCentral PMCID: PMC3402332. 

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, LabzinLI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK,  Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P,  Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ. Conservation anddivergence in Toll-like receptor 4-regulated gene expression in primary humanversus mouse macrophages. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53.   doi: 10.1073/pnas.1110156109. PubMed PMID: 22451944; PubMed Central PMCID:  PMC3341041. 

Kato L, Begum NA, Burroughs AM, Doi T, Kawai J, Daub CO, Kawaguchi T, MatsudaF, Hayashizaki Y, Honjo T. Nonimmunoglobulin target loci of activation-induced  cytidine deaminase (AID) share unique features with immunoglobulin genes. ProcNatl Acad Sci U S A. 2012 Feb 14;109(7):2479-84. doi: 10.1073/pnas.1120791109.  PubMed PMID: 22308462; PubMed Central PMCID: PMC3289292. 

Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, LazarevicD, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S,   Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P. Promoterarchitecture of mouse olfactory receptor genes. Genome Res. 2012Mar;22(3):486-97. doi: 10.1101/gr.126201.111. PubMed PMID: 22194471; PubMedCentral PMCID: PMC3290784. 

Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y. pre-miRNA profilesobtained through application of locked nucleic acids and deep sequencing reveals   complex 5'/3' arm variation including concomitant cleavage and polyuridylationpatterns. Nucleic Acids Res. 2012 Feb;40(4):1424-37. doi: 10.1093/nar/gkr903.  PubMed PMID: 22058130; PubMed Central PMCID: PMC3287202. 

2011

Franzén O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, HayashizakiY, Aslund L, Andersson B, Daub CO. The short non-coding transcriptome of theprotozoan parasite Trypanosoma cruzi. PLoS Negl Trop Dis. 2011 Aug;5(8):e1283.  doi: 10.1371/journal.pntd.0001283. PubMed PMID: 21912713; PubMed Central PMCID:  PMC3166047. 

Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M,  Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y.  Unamplified cap analysis of gene expression on a single-molecule sequencer.  Genome Res. 2011 Jul;21(7):1150-9. doi: 10.1101/gr.115469.110. PubMed PMID:  21596820; PubMed Central PMCID: PMC3129257. 

Kimura Y, de Hoon MJ, Aoki S, Ishizu Y, Kawai Y, Kogo Y, Daub CO, Lezhava A,   Arner E, Hayashizaki Y. Optimization of turn-back primers in isothermalamplification. Nucleic Acids Res. 2011 May;39(9):e59. doi: 10.1093/nar/gkr041.  PubMed PMID: 21310714; PubMed Central PMCID: PMC3089485. 

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO.  Deep-sequencing of human Argonaute-associated small RNAs provides insight intomiRNA sorting and reveals Argonaute association with RNA fragments of diverseorigin. RNA Biol. 2011 Jan-Feb;8(1):158-77. PubMed PMID: 21282978; PubMed CentralPMCID: PMC3127082. 

Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in nextgeneration sequencing data. Bioinformatics. 2011 Jan 1;27(1):130-1. doi:  10.1093/bioinformatics/btq614. PubMed PMID: 21088025; PubMed Central PMCID:  PMC3008642. 

Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, SchroderK, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. Update of the FANTOMweb resource: from mammalian transcriptional landscape to its dynamic regulation.  Nucleic Acids Res. 2011 Jan;39(Database issue):D856-60. doi: 10.1093/nar/gkq1112.  PubMed PMID: 21075797; PubMed Central PMCID: PMC3013704. 

2010

Vitezic M, Lassmann T, Forrest AR, Suzuki M, Tomaru Y, Kawai J, Carninci P,  Suzuki H, Hayashizaki Y, Daub CO. Building promoter aware transcriptionalregulatory networks using siRNA perturbation and deepCAGE. Nucleic Acids Res.  2010 Dec;38(22):8141-8. doi: 10.1093/nar/gkq729. PubMed PMID: 20724440; PubMedCentral PMCID: PMC3001087. 

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, FunakoshiT, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO. A comprehensive survey of 3'  animal miRNA modification events and a possible role for 3' adenylation inmodulating miRNA targeting effectiveness. Genome Res. 2010 Oct;20(10):1398-410.  doi: 10.1101/gr.106054.110. PubMed PMID: 20719920; PubMed Central PMCID:  PMC2945189. 

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic   M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H,  Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO,  Hayashizaki Y, Gustincich S, Carninci P. Linking promoters to functionaltranscripts in small samples with nanoCAGE and CAGEscan. Nat Methods. 2010Jul;7(7):528-34. doi: 10.1038/nmeth.1470. PubMed PMID: 20543846; PubMed CentralPMCID: PMC2906222. 

Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, ArakawaT, Tomita M, Hayashizaki Y, Daub CO. Core promoter structure and genomic context   reflect histone 3 lysine 9 acetylation patterns. BMC Genomics. 2010 Apr21;11:257. doi: 10.1186/1471-2164-11-257. PubMed PMID: 20409305; PubMed CentralPMCID: PMC2867832. 

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A,  Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, GoughJ, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, KawajiH, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A,  Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, NinomiyaN, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y,  Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorialtranscriptional regulation in mouse and man. Cell. 2010 Mar 5;140(5):744-52. doi:  10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov,  Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added];  Radovanovic, Aleksandar [added]; Schwartz, Ariel [added]. PubMed PMID: 20211142;   PubMed Central PMCID: PMC2836267. 

de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M,  Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J,  Suzuki H, Hayashizaki Y. Cross-mapping and the identification of editing sites inmature microRNAs in high-throughput sequencing libraries. Genome Res. 2010Feb;20(2):257-64. doi: 10.1101/gr.095273.109. PubMed PMID: 20051556; PubMedCentral PMCID: PMC2813481. 

Arner E, Hayashizaki Y, Daub CO. NGSView: an extensible open source editorfor next-generation sequencing data. Bioinformatics. 2010 Jan 1;26(1):125-6. doi:  10.1093/bioinformatics/btp611. PubMed PMID: 19855106; PubMed Central PMCID:  PMC2796816. 

2009

Lassmann T, Hayashizaki Y, Daub CO. TagDust--a program to eliminate artifactsfrom next generation sequencing data. Bioinformatics. 2009 Nov 1;25(21):2839-40.   doi: 10.1093/bioinformatics/btp527. PubMed PMID: 19737799; PubMed Central PMCID:   PMC2781754. 

Takahashi Y, Forrest AR, Maeno E, Hashimoto T, Daub CO, Yasuda J. MiR-107 andMiR-185 can induce cell cycle arrest in human non small cell lung cancer celllines. PLoS One. 2009 Aug 18;4(8):e6677. doi: 10.1371/journal.pone.0006677.  PubMed PMID: 19688090; PubMed Central PMCID: PMC2722734. 

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, BeiselC, van Nimwegen E. Methods for analyzing deep sequencing expression data:  constructing the human and mouse promoterome with deepCAGE data. Genome Biol.  2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79. PubMed PMID: 19624849; PubMedCentral PMCID: PMC2728533. 

Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.  Probabilistic resolution of multi-mapping reads in massively parallel sequencing   data using MuMRescueLite. Bioinformatics. 2009 Oct 1;25(19):2613-4. doi:  10.1093/bioinformatics/btp438. PubMed PMID: 19605420. 

Kawaji H, Hayashizaki Y, Daub CO. SDRF2GRAPH: a visualization tool of aspreadsheet-based description of experimental processes. BMC Bioinformatics. 2009May 7;10:133. doi: 10.1186/1471-2105-10-133. PubMed PMID: 19422683; PubMedCentral PMCID: PMC2689195. 

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T,   Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A,  Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, HumeDA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS. Tiny RNAsassociated with transcription start sites in animals. Nat Genet. 2009May;41(5):572-8. doi: 10.1038/ng.312. Erratum in: Nat Genet. 2009 Jul;41(7):859.   PubMed PMID: 19377478. 

Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K,  Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H,  Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM,  Carninci P. The regulated retrotransposon transcriptome of mammalian cells. NatGenet. 2009 May;41(5):563-71. doi: 10.1038/ng.368. PubMed PMID: 19377475. 

FANTOM Consortium., Suzuki H, Forrest AR, van Nimwegen E, Daub CO, BalwierzPJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, SchroderK, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, ArnerE, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N,  Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A,  Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K,  Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto   T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K,  Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji   H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S,  Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M,  Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H,  Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y,  Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J,   Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R,  Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J,  Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ,  Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, ValenE, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K,  Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center., Arakawa T,  Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M,  Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T,   Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y. The transcriptionalnetwork that controls growth arrest and differentiation in a human myeloidleukemia cell line. Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. PubMedPMID: 19377474. 

Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA,  Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. The FANTOM webresource: from mammalian transcriptional landscape to its dynamic regulation.  Genome Biol. 2009;10(4):R40. doi: 10.1186/gb-2009-10-4-r40. PubMed PMID:  19374775; PubMed Central PMCID: PMC2688931. 

Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ,   de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.  FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs,  expression dynamics and regulatory interactions. Genome Biol. 2009;10(4):R39.  doi: 10.1186/gb-2009-10-4-r39. PubMed PMID: 19374773; PubMed Central PMCID:  PMC2688930. 

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO,  Hayashizaki Y, Lenhard B. Transcriptional features of genomic regulatory blocks.   Genome Biol. 2009;10(4):R38. doi: 10.1186/gb-2009-10-4-r38. PubMed PMID:  19374772; PubMed Central PMCID: PMC2688929. 

2008

Daub CO, Sonnhammer EL. Employing conservation of co-expression to improvefunctional inference. BMC Syst Biol. 2008 Sep 22;2:81. doi:  10.1186/1752-0509-2-81. PubMed PMID: 18808668; PubMed Central PMCID: PMC2561017. 

Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO,  Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human smallRNAs. BMC Genomics. 2008 Apr 10;9:157. doi: 10.1186/1471-2164-9-157. PubMed PMID:  18402656; PubMed Central PMCID: PMC2359750. 

2006

Abhiman S, Daub CO, Sonnhammer EL. Prediction of function divergence inprotein families using the substitution rate variation parameter alpha. Mol Biol   Evol. 2006 Jul;23(7):1406-13. PubMed PMID: 16672285. 

2005

Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R. Integrativegene-metabolite network with implemented causality deciphers informational fluxesof sulphur stress response. J Exp Bot. 2005 Jul;56(417):1887-96. PubMed PMID:  15911562. 

2004

Daub CO, Steuer R, Selbig J, Kloska S. Estimating mutual information usingB-spline functions--an improved similarity measure for analysing gene expression   data. BMC Bioinformatics. 2004 Aug 31;5:118. PubMed PMID: 15339346; PubMedCentral PMCID: PMC516800. 

2003

Daub CO, Kloska S, Selbig J. MetaGeneAlyse: analysis of integratedtranscriptional and metabolite data. Bioinformatics. 2003 Nov 22;19(17):2332-3.  PubMed PMID: 14630670. 

2002

Steuer R, Kurths J, Daub CO, Weise J, Selbig J. The mutual information:  detecting and evaluating dependencies between variables. Bioinformatics. 2002;18   Suppl 2:S231-40. PubMed PMID: 12386007.