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Items: 1 to 50 of 71

1.

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

Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y; FANTOM Consortium, Aitken S, Semple CA.

Open Biol. 2018 Aug;8(8). pii: 180011. doi: 10.1098/rsob.180011.

2.

Characterization of the human RFX transcription factor family by regulatory and target gene analysis.

Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P.

BMC Genomics. 2018 Mar 6;19(1):181. doi: 10.1186/s12864-018-4564-6.

3.

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

Zhang P, Dimont E, Ha T, Swanson DJ, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E; FANTOM Consortium, Carninci P, Hayashizaki Y, Forrest ARR, Hide W, Goldowitz D.

BMC Genomics. 2018 Jan 11;19(1):39. doi: 10.1186/s12864-017-4291-4.

4.

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

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.

Cerebellum. 2018 Jun;17(3):308-325. doi: 10.1007/s12311-017-0912-3.

PMID:
29307116
5.

Long-Term Improvement in Aortic Pulse Wave Velocity After Weight Loss Can Be Predicted by White Adipose Tissue Factors.

Bäckdahl J, Andersson DP, Eriksson-Hogling D, Caidahl K, Thorell A, Mileti E, Daub CO, Arner P, Rydén M.

Am J Hypertens. 2018 Mar 10;31(4):450-457. doi: 10.1093/ajh/hpx201.

PMID:
29177471
6.

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.

Yu NY, Bieder A, Raman A, Mileti E, Katayama S, Einarsdottir E, Fredholm BB, Falk A, Tapia-Páez I, Daub CO, Kere J.

Sci Rep. 2017 Sep 13;7(1):11458. doi: 10.1038/s41598-017-11574-6.

7.

FANTOM5 CAGE profiles of human and mouse samples.

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.

Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.

8.

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

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.

Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

9.

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

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.

Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.

PMID:
28241135
10.

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

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; FANTOM Consortium, Rydén M, Laurencikiene J, Arner P, Arner E.

Diabetes. 2017 Jan;66(1):218-230. doi: 10.2337/db16-0631. Epub 2016 Nov 1.

11.

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

Rydén M, Hrydziuszko O, Mileti E, Raman A, Bornholdt J, Boyd M, Toft E, Qvist V, Näslund E, Thorell A, Andersson DP, Dahlman I, Gao H, Sandelin A, Daub CO, Arner P.

Cell Rep. 2016 Aug 30;16(9):2317-26. doi: 10.1016/j.celrep.2016.07.070. Epub 2016 Aug 18.

12.

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

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.

J Cell Sci. 2016 Jul 1;129(13):2573-85. doi: 10.1242/jcs.186767. Epub 2016 May 19.

13.

A predictive computational framework for direct reprogramming between human cell types.

Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J.

Nat Genet. 2016 Mar;48(3):331-5. doi: 10.1038/ng.3487. Epub 2016 Jan 18.

PMID:
26780608
14.

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.

Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO; FANTOM consortium, Okada-Hatakeyama M, Mar JC.

PLoS One. 2015 Dec 14;10(12):e0144176. doi: 10.1371/journal.pone.0144176. eCollection 2015.

15.

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

Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, 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.

Cell Rep. 2015 Nov 17;13(7):1493-1504. doi: 10.1016/j.celrep.2015.10.002. Epub 2015 Nov 5.

16.

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

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.

Sci Rep. 2015 Jul 16;5:11999. doi: 10.1038/srep11999.

17.

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR; Fantom Consortium, Hayashizaki Y, Uhlén M, Daub CO.

Nucleic Acids Res. 2015 Aug 18;43(14):6787-98. doi: 10.1093/nar/gkv608. Epub 2015 Jun 27.

18.

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

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.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004217. doi: 10.1371/journal.pcbi.1004217. eCollection 2015 Apr. Erratum in: PLoS Comput Biol. 2017 Feb 10;13(2):e1005279.

19.

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.

Persson H, Kwon AT, Ramilowski JA, Silberberg G, Söderhäll C, Orsmark-Pietras C, Nordlund B, Konradsen JR, de Hoon MJ, Melén E, Hayashizaki Y, Hedlin G, Kere J, Daub CO.

J Allergy Clin Immunol. 2015 Sep;136(3):638-48. doi: 10.1016/j.jaci.2015.02.026. Epub 2015 Apr 9.

20.

Gateways to the FANTOM5 promoter level mammalian expression atlas.

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.

Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6.

21.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

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, Hara M, 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, 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 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.

Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.

22.

System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions.

Sakata K, Ohyanagi H, Sato S, Nobori H, Hayashi A, Ishii H, Daub CO, Kawai J, Suzuki H, Saito T.

Sci Rep. 2015 Feb 6;5:8283. doi: 10.1038/srep08283.

23.

Telomerase reverse transcriptase regulates microRNAs.

Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, Kasim V, Simon C, Daub CO, Carninci P, Hayashizaki Y, Masutomi K.

Int J Mol Sci. 2015 Jan 6;16(1):1192-208. doi: 10.3390/ijms16011192.

24.

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

Gao H, Mejhert N, Fretz JA, Arner E, Lorente-Cebrián S, Ehrlund A, Dahlman-Wright K, Gong X, Strömblad S, Douagi I, Laurencikiene J, Dahlman I, Daub CO, Rydén M, Horowitz MC, Arner P.

Cell Metab. 2014 Jun 3;19(6):981-92. doi: 10.1016/j.cmet.2014.03.032. Epub 2014 May 22.

25.

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y; FANTOM Consortium, Bertin N, Forrest AR.

Nat Biotechnol. 2014 Mar;32(3):217-9. doi: 10.1038/nbt.2840. No abstract available.

PMID:
24727769
26.

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

Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, Lassmann T, Daub CO, Forrest AR, Lennartsson A, Ekwall K; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e46-57. doi: 10.1182/blood-2013-02-483537. Epub 2014 Mar 26.

27.

A promoter-level mammalian expression atlas.

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, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, 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, Ha TJ, 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, 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 JF, 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, de Lima Morais 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, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya 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 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, Sugiyama T, 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 de Wetering 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, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

28.

An atlas of active enhancers across human cell types and tissues.

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.

Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787.

29.

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F; FANTOM consortium.

BMC Genomics. 2014 Mar 26;15:120. doi: 10.1186/1471-2164-15-120.

30.

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements.

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S.

Front Cell Neurosci. 2014 Feb 18;8:41. doi: 10.3389/fncel.2014.00041. eCollection 2014.

31.

Additive effects of microRNAs and transcription factors on CCL2 production in human white adipose tissue.

Kulyté A, Belarbi Y, Lorente-Cebrián S, Bambace C, Arner E, Daub CO, Hedén P, Rydén M, Mejhert N, Arner P.

Diabetes. 2014 Apr;63(4):1248-58. doi: 10.2337/db13-0702. Epub 2013 Dec 30.

32.

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

Sompallae R, Hofmann O, Maher CA, Gedye C, Behren A, Vitezic M, Daub CO, Devalle S, Caballero OL, Carninci P, Hayashizaki Y, Lawlor ER, Cebon J, Hide W.

Front Genet. 2013 Oct 29;4:209. doi: 10.3389/fgene.2013.00209. eCollection 2013.

33.

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.

Ramilowski JA, Sawai S, Seki H, Mochida K, Yoshida T, Sakurai T, Muranaka T, Saito K, Daub CO.

Plant Cell Physiol. 2013 May;54(5):697-710. doi: 10.1093/pcp/pct057. Epub 2013 Apr 14.

PMID:
23589666
34.

Regional differences in gene expression and promoter usage in aged human brains.

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.

Neurobiol Aging. 2013 Jul;34(7):1825-36. doi: 10.1016/j.neurobiolaging.2013.01.005. Epub 2013 Feb 19.

35.

Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins.

Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T, Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I.

Biol Psychiatry. 2013 Mar 15;73(6):583-90. doi: 10.1016/j.biopsych.2012.08.012. Epub 2012 Oct 1.

PMID:
23036959
36.

Adipose tissue microRNAs as regulators of CCL2 production in human obesity.

Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P.

Diabetes. 2012 Aug;61(8):1986-93. doi: 10.2337/db11-1508. Epub 2012 Jun 11.

37.

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, 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.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. doi: 10.1073/pnas.1110156109. Epub 2012 Mar 26.

38.

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes.

Kato L, Begum NA, Burroughs AM, Doi T, Kawai J, Daub CO, Kawaguchi T, Matsuda F, Hayashizaki Y, Honjo T.

Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2479-84. doi: 10.1073/pnas.1120791109. Epub 2012 Jan 30.

39.

Promoter architecture of mouse olfactory receptor genes.

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.

Genome Res. 2012 Mar;22(3):486-97. doi: 10.1101/gr.126201.111. Epub 2011 Dec 22.

40.

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.

Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y.

Nucleic Acids Res. 2012 Feb;40(4):1424-37. doi: 10.1093/nar/gkr903. Epub 2011 Nov 3.

41.

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.

Franzén O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki Y, Aslund L, Andersson B, Daub CO.

PLoS Negl Trop Dis. 2011 Aug;5(8):e1283. doi: 10.1371/journal.pntd.0001283. Epub 2011 Aug 30.

42.

Unamplified cap analysis of gene expression on a single-molecule sequencer.

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.

Genome Res. 2011 Jul;21(7):1150-9. doi: 10.1101/gr.115469.110. Epub 2011 May 19.

43.

Optimization of turn-back primers in isothermal amplification.

Kimura Y, de Hoon MJ, Aoki S, Ishizu Y, Kawai Y, Kogo Y, Daub CO, Lezhava A, Arner E, Hayashizaki Y.

Nucleic Acids Res. 2011 May;39(9):e59. doi: 10.1093/nar/gkr041. Epub 2011 Feb 9.

44.

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO.

RNA Biol. 2011 Jan-Feb;8(1):158-77. Epub 2011 Jan 1.

45.

SAMStat: monitoring biases in next generation sequencing data.

Lassmann T, Hayashizaki Y, Daub CO.

Bioinformatics. 2011 Jan 1;27(1):130-1. doi: 10.1093/bioinformatics/btq614. Epub 2010 Nov 18.

46.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.

Nucleic Acids Res. 2011 Jan;39(Database issue):D856-60. doi: 10.1093/nar/gkq1112. Epub 2010 Nov 12.

47.

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

Vitezic M, Lassmann T, Forrest AR, Suzuki M, Tomaru Y, Kawai J, Carninci P, Suzuki H, Hayashizaki Y, Daub CO.

Nucleic Acids Res. 2010 Dec;38(22):8141-8. doi: 10.1093/nar/gkq729. Epub 2010 Aug 19.

48.

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO.

Genome Res. 2010 Oct;20(10):1398-410. doi: 10.1101/gr.106054.110. Epub 2010 Aug 18.

49.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.

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.

Nat Methods. 2010 Jul;7(7):528-34. doi: 10.1038/nmeth.1470. Epub 2010 Jun 13.

50.

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

Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO.

BMC Genomics. 2010 Apr 21;11:257. doi: 10.1186/1471-2164-11-257.

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