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Page 1
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. Andersson R, et al. Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787. Nature. 2014. PMID: 24670763 Free PMC article.
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Grapotte M, et al. Among authors: ramilowski ja. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7. Nat Commun. 2021. PMID: 34078885 Free PMC article.
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, … See abstract for full author list ➔ FANTOM Consortium and the RIKEN PMI and CLST (DGT), et al. Among authors: ramilowski ja. Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182. Nature. 2014. PMID: 24670764 Free PMC article.
Predicting cell-to-cell communication networks using NATMI.
Hou R, Denisenko E, Ong HT, Ramilowski JA, Forrest ARR. Hou R, et al. Among authors: ramilowski ja. Nat Commun. 2020 Oct 6;11(1):5011. doi: 10.1038/s41467-020-18873-z. Nat Commun. 2020. PMID: 33024107 Free PMC article.
Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers.
Jikuya R, Murakami K, Nishiyama A, Kato I, Furuya M, Nakabayashi J, Ramilowski JA, Hamanoue H, Maejima K, Fujita M, Mitome T, Ohtake S, Noguchi G, Kawaura S, Odaka H, Kawahara T, Komeya M, Shinoki R, Ueno D, Ito H, Ito Y, Muraoka K, Hayashi N, Kondo K, Nakaigawa N, Hatano K, Baba M, Suda T, Kodama T, Fujii S, Makiyama K, Yao M, Shuch BM, Schmidt LS, Linehan WM, Nakagawa H, Tamura T, Hasumi H. Jikuya R, et al. Among authors: ramilowski ja. iScience. 2022 May 25;25(6):104463. doi: 10.1016/j.isci.2022.104463. eCollection 2022 Jun 17. iScience. 2022. PMID: 35874919 Free PMC article.
Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.
Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Yip CW, et al. Among authors: ramilowski ja. Cell Rep. 2022 Dec 27;41(13):111893. doi: 10.1016/j.celrep.2022.111893. Cell Rep. 2022. PMID: 36577377 Free article.
Annotation of nuclear lncRNAs based on chromatin interactions.
Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, Ramilowski JA, Sigorskikh AI, Strug LJ, Yagi K, Yasuzawa K, Yip CW, Hon CC, Hoffman MM, Terao C, Kulakovskiy IV, Kasukawa T, Shin JW, Carninci P, de Hoon MJL. Agrawal S, et al. Among authors: ramilowski ja. PLoS One. 2024 May 6;19(5):e0295971. doi: 10.1371/journal.pone.0295971. eCollection 2024. PLoS One. 2024. PMID: 38709794 Free PMC article.
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Grapotte M, et al. Among authors: ramilowski ja. Nat Commun. 2022 Mar 1;13(1):1200. doi: 10.1038/s41467-022-28758-y. Nat Commun. 2022. PMID: 35232988 Free PMC article. No abstract available.
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman … See abstract for full author list ➔ Ramilowski JA, et al. Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27. Genome Res. 2020. PMID: 32718982 Free PMC article.
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia.
Hashimoto M, Saito Y, Nakagawa R, Ogahara I, Takagi S, Takata S, Amitani H, Endo M, Yuki H, Ramilowski JA, Severin J, Manabe RI, Watanabe T, Ozaki K, Kaneko A, Kajita H, Fujiki S, Sato K, Honma T, Uchida N, Fukami T, Okazaki Y, Ohara O, Shultz LD, Yamada M, Taniguchi S, Vyas P, de Hoon M, Momozawa Y, Ishikawa F. Hashimoto M, et al. Among authors: ramilowski ja. Nat Cancer. 2021 Mar;2(3):340-356. doi: 10.1038/s43018-021-00177-w. Epub 2021 Mar 18. Nat Cancer. 2021. PMID: 35121960
37 results