Publications for Carsten Daub

Article

1 Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC genomics 2018 19:1 181-

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2 FANTOM consortium, 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, 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 17:3 308-325

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3 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 2018 31:4 450-457

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4 IIBDGC Consortium, Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS computational biology 2018 14:3 e1005934-

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5 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-

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6 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-

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7 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

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8 FANTOM Consortium, 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, 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

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9 FANTOM Consortium, Ehrlund A, Mejhert N, Bjork C, Andersson R, Kulyte A, Astrom G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y, Sandelin A, Ingelsson E, Ryden M, Laurencikiene J, Arner P, Arner E. Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. DIABETES 2017 66:1 218-230

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10 FANTOM consortium, 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, Kokudo N, Forrest ARR, Kojima S. Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes. EBioMedicine 2017 24: 257-266

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11 FANTOM Consortium, Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS, 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. Nature genetics 2016 48:3 331-5

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12 FANTOM Consortium, 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, Carninci P, Hayashizaki Y, Forrest ARR, Wasserman WW, Detmar M. DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C. JOURNAL OF CELL SCIENCE 2016 129:13 2573-85

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13 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 reports 2016 16:9 2317-26

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14 FANTOM consortium, Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Mar JC. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PloS one 2015 10:12 e0144176-

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15 Fantom Consortium, Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic acids research 2015 43:14 6787-98

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16 Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma QL, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Wasserman WW, Detmar M. DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium. CELL REPORTS 2015 13:7 1493-1504

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17 FANTOM consortium, 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, Baillie JK, 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. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome biology 2015 16: 22-

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18 FANTOM Consortium, Mina M, Magi S, Jurman G, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Furlanello C. Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells. Scientific reports 2015 5: 11999-

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19 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 human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions. Scientific reports 2015 5: 8283-

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20 Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, Kasim V, Simon C, Daub CO, Carninci P, Hayashizaki Y, Masutomi K. Telomerase Reverse Transcriptase Regulates microRNAs. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2015 16:1 1192-208

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21 FANTOM Consortium, Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Ronnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AMN, 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, Hara M, Herlyn M, Ikawa T, Kai CK, 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, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, 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 MJL, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest ARR, Sandelin A, Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. SCIENCE 2015 347:6225 1010-4

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22 FANTOM Consortium, Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y, Khachigian LM, Okada-Hatakeyama M, Semple CA. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS computational biology 2015 11:4 e1004217-

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23 Persson H, Kwon AT, Ramilowski JA, Silberberg G, Söderhäll C, Orsmark-Pietras C, Nordlund B, Konradsen JR, de Hoon MJ, Melén E, Hayashizaki Y, Hedlin G, Kere J, Daub CO. Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles. The Journal of allergy and clinical immunology 2015 136:3 638-48

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24 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 transcription factors on CCL2 production in human white adipose tissue. Diabetes 2014 63:4 1248-58

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25 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, Schwarzfischer L, 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, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014 507:7493 455-461

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26 RIKEN PMI CLST DGT, FANTOM Consortium, Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jorgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JAC, 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, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drablos F, Edge ASB, 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, Furuno M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Sui SJH, 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 A, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, 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 JFJ, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, Morais DAD, 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, Nakazato K, Van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Nozaki T, Ogishima S, Ohkura N, Ohmiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JGD, Rackham OJL, 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, Satoh H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng GJ, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PAC, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyoda H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verardo 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 XB, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. A promoter-level mammalian expression atlas. NATURE 2014 507:7493 462-70

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27 FANTOM consortium, Hurst LD, Sachenkova O, Daub C, Forrest AR, Huminiecki L. A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome biology 2014 15:7 413-

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28 FANTOM consortium, Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F. Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC genomics 2014 15: 120-

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29 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, Daub CO, Rydén M, Horowitz MC, Arner P. Early B cell factor 1 regulates adipocyte morphology and lipolysis in white adipose tissue. Cell metabolism 2014 19:6 981-92

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30 FANTOM consortium, Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, Lassmann T, Daub CO, Forrest AR, Lennartsson A, Ekwall K. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood 2014 123:17 e46-57

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

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32 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, Carninci P, Gustincich S. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in cellular neuroscience 2014 8: 41-

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33 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. A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Frontiers in genetics 2013 4: 209-

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34 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 physiology 2013 54:5 697-710

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35 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 of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins. Biological psychiatry 2013 73:6 583-90

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36 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 aged human brains. Neurobiology of aging 2013 34:7 1825-36

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37 Arner E, Mejhert N, Kulyte A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrian S, Ehrlund A, Laurencikiene J, Heden P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Ryden M, Dahlman I, van Nimwegen E, Daub CO, Arner P. Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity. DIABETES 2012 61:8 1986-93

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38 Schroder K, Irvine KM, Taylor MS, Bokil NJ, Cao KAL, Masterman KA, Labzin LI, 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 and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2012 109:16 E944-53

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39 Kato L, Begum NA, Burroughs AM, Doi T, Kawai J, Daub CO, Kawaguchi T, Matsuda F, Hayashizaki Y, Honjo T. Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2012 109:7 2479-84

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40 Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y. 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. NUCLEIC ACIDS RESEARCH 2012 40:4 1424-37

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41 Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P. Promoter architecture of mouse olfactory receptor genes. GENOME RESEARCH 2012 22:3 486-97

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42 Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO. Deep-sequencing of human argonaute-associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin. RNA BIOLOGY 2011 8:1 158-77

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43 Kimura Y, de Hoon MJL, Aoki S, Ishizu Y, Kawai Y, Kogo Y, Daub CO, Lezhava A, Arner E, Hayashizaki Y. Optimization of turn-back primers in isothermal amplification. NUCLEIC ACIDS RESEARCH 2011 39:9 e59-

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44 Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in next generation sequencing data. BIOINFORMATICS 2011 27:1 130-1

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45 Franzen O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki Y, Aslund L, Andersson B, Daub CO. The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi. PLOS NEGLECTED TROPICAL DISEASES 2011 5:8 e1283-

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46 Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y. Unamplified cap analysis of gene expression on a single-molecule sequencer. GENOME RESEARCH 2011 21:7 1150-9

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47 Kawaji H, Severin J, Lizio M, Forrest ARR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. NUCLEIC ACIDS RESEARCH 2011 39: D856-60

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48 Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO. A comprehensive survey of 3 ' animal miRNA modification events and a possible role for 3 ' adenylation in modulating miRNA targeting effectiveness. GENOME RESEARCH 2010 20:10 1398-410

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49 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 ARR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, Ogawa C, Teasdale RD, Tegner J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, 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 Combinatorial Transcriptional Regulation in Mouse and Man. CELL 2010 140:5 744-52

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50 Vitezic M, Lassmann T, Forrest ARR, Suzuki M, Tomaru Y, Kawai J, Carninci P, Suzuki H, Hayashizaki Y, Daub CO. Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. NUCLEIC ACIDS RESEARCH 2010 38:22 8141-8

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51 Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC GENOMICS 2010 11: 257-

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52 de Hoon MJL, 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 in mature microRNAs in high-throughput sequencing libraries. GENOME RESEARCH 2010 20:2 257-64

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53 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 HE, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. NATURE METHODS 2010 7:7 528-34

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54 Arner E, Hayashizaki Y, Daub CO. NGSView: an extensible open source editor for next-generation sequencing data. BIOINFORMATICS 2010 26:1 125-6

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55 Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJL, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest ARR. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. GENOME BIOLOGY 2009 10:4 R39-

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56 Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MHE, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. GENOME RESEARCH 2009 19:2 255-65

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57 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. GENOME BIOLOGY 2009 10:7 R79-

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58 Takahashi Y, Forrest ARR, Maeno E, Hashimoto T, Daub CO, Yasuda J. MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines. PLOS ONE 2009 4:8 e6677-

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59 Hashimoto T, de Hoon MJL, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ. Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. BIOINFORMATICS 2009 25:19 2613-4

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60 Kawaji H, Hayashizaki Y, Daub CO. SDRF2GRAPH-a visualization tool of a spreadsheet-based description of experimental processes. BMC BIOINFORMATICS 2009 10: 133-

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61 Lassmann T, Hayashizaki Y, Daub CO. TagDust-a program to eliminate artifacts from next generation sequencing data. BIOINFORMATICS 2009 25:21 2839-40

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62 Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest ARR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. GENOME BIOLOGY 2009 10:4 R40-

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63 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 ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotransposon transcriptome of mammalian cells. NATURE GENETICS 2009 41:5 563-71

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64 Riken Omics Sci Ctr, FANTOM Consortium, Suzuki H, Forrest ARR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJL, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom 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, Hornquist 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, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, Laurent GS, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, AWells C, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, 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 transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. NATURE GENETICS 2009 41:5 553-62

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65 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, 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, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS. Tiny RNAs associated with transcription start sites in animals. NATURE GENETICS 2009 41:5 572-8

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66 Akalin A, Fredman D, Arner E, Dong XJ, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B. Transcriptional features of genomic regulatory blocks. GENOME BIOLOGY 2009 10:4 R38-

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67 Daub CO, Sonnhammer ELL. Employing conservation of co-expression to improve functional inference. BMC SYSTEMS BIOLOGY 2008 2: 81-

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68 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 small RNAs. BMC GENOMICS 2008 9: 157-

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69 Abhiman S, Daub CO, Sonnhammer ELL. Prediction of function divergence in protein families using the substitution rate variation parameter alpha. MOLECULAR BIOLOGY AND EVOLUTION 2006 23:7 1406-13

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70 Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R. Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. JOURNAL OF EXPERIMENTAL BOTANY 2005 56:417 1887-96

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71 Daub CO, Steuer R, Selbig J, Kloska S. Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data. BMC BIOINFORMATICS 2004 5: 118-

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72 Daub CO, Kloska S, Selbig J. MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. BIOINFORMATICS 2003 19:17 2332-3

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73 Steuer R, Kurths J, Daub CO, Weise J, Selbig J. The mutual information: Detecting and evaluating dependencies between variables. BIOINFORMATICS 2002 18: S231-40

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74 Abdul-Redah T, Daub C, Streffer F, Chatzidimitriou-Dreismann CA. Anomalous neutron reflectivity at the quartz/H2O-D2O interface. PHYSICA B 2000 291:3-4 314-316

Letter

1 FANTOM Consortium, Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y, Bertin N, Forrest ARR. Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. NATURE BIOTECHNOLOGY 2014 32:3 217-9

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Other

1 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-

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2 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-

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3 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 ARR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegner J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, 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 Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010). CELL 2010 141:2 369-369
4 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, 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, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS. Tiny RNAs associated with transcription start sites in animals (vol 41, pg 572, 2009). NATURE GENETICS 2009 41:7 859-859