Publications for Carsten Daub

Article

1	Akhter T, Mileti E, Kere MM, Kolmert J, Konradsen JR, Hedlin G, Melen E, Daub CO. Enhancers regulate genes linked to severe and mild childhood asthma. HELIYON 2024 10:14 e34386- View record in PubMed®
2	Emanuelsson EB, Arif M, Reitzner SM, Perez S, Lindholm ME, Mardinoglu A, Daub C, Sundberg CJ, Chapman MA. Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training. ISCIENCE 2024 27:1 108638- View record in PubMed®
3	Hörtenhuber M, Hytönen MK, Mukarram AK, Arumilli M, Araujo CL, Quintero I, Syrjä P, Airas N, Kaukonen M, Kyöstilä K, Niskanen J, Jokinen TS, Mottaghitalab F, Takan I, Salokorpi N, Raman A, Stevens I, Iivanainen A, Yoshihara M, Gusev O, Bannasch D, Sukura A, Schoenebeck JJ, Ezer S, Katayama S, Daub CO, Kere J, Lohi H, DoGA Consortium. The DoGA consortium expression atlas of promoters and genes in 100 canine tissues. Nature communications 2024 15:1 9082- View record in PubMed®
4	Arora A, Becker M, Marques C, Oksanen M, Li D, Mastropasqua F, Watts ME, Arora M, Falk A, Daub CO, Lanekoff I, Tammimies K. Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics. Scientific reports 2023 13:1 10519- View record in PubMed®
5	Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature genetics 2022 54:7 1037-1050 View record in PubMed®
6	Sahu B, Hartonen T, Pihlajamaa P, Wei B, Dave K, Zhu F, Kaasinen E, Lidschreiber K, Lidschreiber M, Daub CO, Cramer P, Kivioja T, Taipale J. Sequence determinants of human gene regulatory elements. Nature genetics 2022 54:3 283-294 View record in PubMed®
7	Ezer S, Yoshihara M, Katayama S, Daub C, Lohi H, Krjutskov K, Kere J, DoGA consortium. Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog. STAR protocols 2021 2:4 100995- View record in PubMed®
8	Mileti E, Kwok KHM, Andersson DP, Mathelier A, Raman A, Bäckdahl J, Jalkanen J, Massier L, Thorell A, Gao H, Arner P, Mejhert N, Daub CO, Rydén M. Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State. Diabetes 2021 70:7 1486-1497 View record in PubMed®
9	Chireh A, Grankvist R, Sandell M, Mukarram AK, Arnberg F, Lundberg J, Daub CO, Holmin S. Micro-biopsy for detection of gene expression changes in ischemic swine myocardium: A pilot study. PloS one 2021 16:4 e0250582- View record in PubMed®
10	Corral-Vazquez C, Blanco J, Aiese Cigliano R, Sarrate Z, Rivera-Egea R, Vidal F, Garrido N, Daub C, Anton E. The RNA content of human sperm reflects prior events in spermatogenesis and potential post-fertilization effects. Molecular human reproduction 2021 27:6 View record in PubMed®
11	Kaukonen M, Quintero IB, Mukarram AK, Hytönen MK, Holopainen S, Wickström K, Kyöstilä K, Arumilli M, Jalomäki S, Daub CO, Kere J, Lohi H, DoGA Consortium. A putative silencer variant in a spontaneous canine model of retinitis pigmentosa. PLoS genetics 2020 16:3 e1008659- View record in PubMed®
12	Hörtenhuber M, Mukarram AK, Stoiber MH, Brown JB, Daub CO. -DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. GigaScience* 2020 9:3 View record in PubMed®
13	Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO. Identification and transfer of spatial transcriptomics signatures for cancer diagnosis. Breast cancer research : BCR 2020 22:1 6- View record in PubMed®
14	Grankvist R, Chireh A, Sandell M, Mukarram AK, Jaff N, Berggren I, Persson H, Linde C, Arnberg F, Lundberg J, Ugander M, La Manno G, Jonsson S, Daub CO, Holmin S. Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. Scientific reports 2020 10:1 8029- View record in PubMed®
15	Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Goldowitz D, FANTOM Consortium. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC genomics 2019 20:1 718- View record in PubMed®
16	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- View record in PubMed®
17	Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y, Aitken S, Semple CA, FANTOM Consortium. Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. Open biology 2018 8:8 View record in PubMed®
18	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, FANTOM consortium. Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection. Cerebellum (London, England) 2018 17:3 308-325 View record in PubMed®
19	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 View record in PubMed®
20	Alhendi AMN, Patrikakis M, Daub CO, Kawaji H, Itoh M, de Hoon M, Carninci P, Hayashizaki Y, Arner E, Khachigian LM. Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β. Scientific reports 2018 8:1 13164- View record in PubMed®
21	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, IIBDGC Consortium. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS computational biology 2018 14:3 e1005934- View record in PubMed®
22	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- View record in PubMed®
23	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- View record in PubMed®
24	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 View record in PubMed®
25	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, FANTOM Consortium. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature biotechnology 2017 35:9 872-878 View record in PubMed®
26	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- View record in PubMed®
27	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, FANTOM Consortium. Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. DIABETES 2017 66:1 218-230 View record in PubMed®
28	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, FANTOM consortium. Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes. EBioMedicine 2017 24: 257-266 View record in PubMed®
29	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, FANTOM Consortium. A predictive computational framework for direct reprogramming between human cell types. Nature genetics 2016 48:3 331-5 View record in PubMed®
30	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, FANTOM Consortium. DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C. JOURNAL OF CELL SCIENCE 2016 129:13 2573-85 View record in PubMed®
31	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 View record in PubMed®
32	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, FANTOM consortium. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PloS one 2015 10:12 e0144176- View record in PubMed®
33	Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y, Uhlén M, Daub CO, Fantom Consortium. 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 View record in PubMed®
34	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 View record in PubMed®
35	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, FANTOM consortium. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome biology 2015 16: 22- View record in PubMed®
36	Mina M, Magi S, Jurman G, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest ARR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Furlanello C, FANTOM Consortium. Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells. Scientific reports 2015 5: 11999- View record in PubMed®
37	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- View record in PubMed®
38	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 View record in PubMed®
39	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, FANTOM Consortium. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. SCIENCE 2015 347:6225 1010-4 View record in PubMed®
40	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, FANTOM Consortium. Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS computational biology 2015 11:4 e1004217- View record in PubMed®
41	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 View record in PubMed®
42	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 View record in PubMed®
43	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 View record in PubMed®
44	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, FANTOM Consortium, RIKEN PMI CLST DGT. A promoter-level mammalian expression atlas. NATURE 2014 507:7493 462-70 View record in PubMed®
45	Hurst LD, Sachenkova O, Daub C, Forrest AR, Huminiecki L, FANTOM consortium. 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- View record in PubMed®
46	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 2014 15: 120- View record in PubMed®
47	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 View record in PubMed®
48	Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, Lassmann T, Daub CO, Forrest AR, Lennartsson A, Ekwall K, FANTOM consortium. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood 2014 123:17 e46-57 View record in PubMed®
49	Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T. MOIRAI: a compact workflow system for CAGE analysis. BMC bioinformatics 2014 15: 144- View record in PubMed®
50	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- View record in PubMed®
51	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- View record in PubMed®
52	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 View record in PubMed®
53	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 View record in PubMed®
54	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 View record in PubMed®
55	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 View record in PubMed®
56	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 View record in PubMed®
57	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 View record in PubMed®
58	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 View record in PubMed®
59	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 View record in PubMed®
60	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 View record in PubMed®
61	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- View record in PubMed®
62	Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in next generation sequencing data. BIOINFORMATICS 2011 27:1 130-1 View record in PubMed®
63	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- View record in PubMed®
64	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 View record in PubMed®
65	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 View record in PubMed®
66	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 View record in PubMed®
67	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 View record in PubMed®
68	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 View record in PubMed®
69	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- View record in PubMed®
70	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 View record in PubMed®
71	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 View record in PubMed®
72	Arner E, Hayashizaki Y, Daub CO. NGSView: an extensible open source editor for next-generation sequencing data. BIOINFORMATICS 2010 26:1 125-6 View record in PubMed®
73	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- View record in PubMed®
74	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 View record in PubMed®
75	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- View record in PubMed®
76	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- View record in PubMed®
77	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 View record in PubMed®
78	Kawaji H, Hayashizaki Y, Daub CO. SDRF2GRAPH-a visualization tool of a spreadsheet-based description of experimental processes. BMC BIOINFORMATICS 2009 10: 133- View record in PubMed®
79	Lassmann T, Hayashizaki Y, Daub CO. TagDust-a program to eliminate artifacts from next generation sequencing data. BIOINFORMATICS 2009 25:21 2839-40 View record in PubMed®
80	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- View record in PubMed®
81	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 View record in PubMed®
82	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, FANTOM Consortium, Riken Omics Sci Ctr. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. NATURE GENETICS 2009 41:5 553-62 View record in PubMed®
83	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 View record in PubMed®
84	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- View record in PubMed®
85	Daub CO, Sonnhammer ELL. Employing conservation of co-expression to improve functional inference. BMC SYSTEMS BIOLOGY 2008 2: 81- View record in PubMed®
86	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- View record in PubMed®
87	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 View record in PubMed®
88	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 View record in PubMed®
89	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- View record in PubMed®
90	Daub CO, Kloska S, Selbig J. MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. BIOINFORMATICS 2003 19:17 2332-3 View record in PubMed®
91	Steuer R, Kurths J, Daub CO, Weise J, Selbig J. The mutual information: Detecting and evaluating dependencies between variables. BIOINFORMATICS 2002 18: S231-40 View record in PubMed®
92	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	Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y, Bertin N, Forrest ARR, FANTOM Consortium. Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. NATURE BIOTECHNOLOGY 2014 32:3 217-9 View record in PubMed®

Editorial

1	ANONYMOUS. Joint Formal Comment for PLGE and Commentary for G3. G3 (Bethesda, Md.) 2020 10:11 3881- View record in PubMed®
2	Stevens I, Mukarram AK, Hortenhuber M, Meehan TF, Rung J, Daub CO. Ten simple rules for annotating sequencing experiments. PLOS COMPUTATIONAL BIOLOGY 2020 16:10 e1008260- View record in PubMed®

Other

1	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, FANTOM Consortium. Relatively frequent switching of transcription start sites during cerebellar development (vol 18, 461, 2017). BMC GENOMICS 2018 19: 39- View record in PubMed®
2	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
3	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