Publications by authors named "Jordan A Ramilowski"

18Publications

Predicting cell-to-cell communication networks using NATMI.

Nat Commun 2020 10 6;11(1):5011. Epub 2020 Oct 6.

Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia.

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http://dx.doi.org/10.1038/s41467-020-18873-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7538930PMC
October 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Authors:
Jordan A Ramilowski Chi Wai Yip Saumya Agrawal Jen-Chien Chang Yari Ciani Ivan V Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher JF Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J Makeev Luigi Marchionni Yulia A Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J C Parr Owen J L Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A M Semple Youtaro Shibayama Divya M Sivaraman Takahiro Suzuki Suzannah C Szumowski Michihira Tagami Martin S Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E Vorontsov Chinatsu Yamamoto Robert S Young J Kenneth Baillie Alistair R R Forrest Roderic Guigó Michael M Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki Ken Yagi Michiel J L de Hoon Jay W Shin Piero Carninci

Genome Res 2020 07 27;30(7):1060-1072. Epub 2020 Jul 27.

RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.254219.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864PMC
July 2020

A draft network of ligand-receptor-mediated multicellular signalling in human.

Nat Commun 2015 Jul 22;6:7866. Epub 2015 Jul 22.

1] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan [2] Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6008, Australia.

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http://dx.doi.org/10.1038/ncomms8866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525178PMC
July 2015

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

J Allergy Clin Immunol 2015 Sep 9;136(3):638-48. Epub 2015 Apr 9.

Department of Biosciences and Nutrition and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm, Sweden; Omics Science Center,§ RIKEN Yokohama Institute, Yokohama, Japan; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.

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https://linkinghub.elsevier.com/retrieve/pii/S00916749150032
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http://dx.doi.org/10.1016/j.jaci.2015.02.026DOI Listing
September 2015

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.

Plant Cell Physiol 2013 May 14;54(5):697-710. Epub 2013 Apr 14.

RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045 Japan.

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https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/
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http://dx.doi.org/10.1093/pcp/pct057DOI Listing
May 2013

Fixed node diffusion Monte Carlo using a genetic algorithm: a study of the CO-(4)He(N) complex, N = 1…10.

Phys Chem Chem Phys 2012 Jun 26;14(22):8123-36. Epub 2012 Apr 26.

Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.

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http://dx.doi.org/10.1039/c2cp40541eDOI Listing
June 2012

Planar to linear structural transition in small boron-carbon mixed clusters: C(x)B(5-x)- (x = 1-5).

J Am Chem Soc 2010 Oct;132(40):14104-12

Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1021/ja103846qDOI Listing
October 2010

Computation of nodal surfaces in fixed-node diffusion Monte Carlo calculations using a genetic algorithm.

Phys Chem Chem Phys 2010 Oct 18;12(39):12450-6. Epub 2010 Aug 18.

Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.

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http://dx.doi.org/10.1039/c0cp00373eDOI Listing
October 2010

Fractal Weyl law behavior in an open Hamiltonian system.

Phys Rev E Stat Nonlin Soft Matter Phys 2009 Nov 30;80(5 Pt 2):055201. Epub 2009 Nov 30.

Departamento de Química, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

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https://link.aps.org/doi/10.1103/PhysRevE.80.055201
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http://dx.doi.org/10.1103/PhysRevE.80.055201DOI Listing
November 2009

Chaos in the classical mechanics of bound and quasi-bound HX-4He complexes with X = F, Cl, Br, CN.

Phys Chem Chem Phys 2009 Oct 30;11(37):8203-13. Epub 2009 Jun 30.

Grupo de Sistemas Complejos, Departamento de Física y Mecánica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain.

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http://dx.doi.org/10.1039/b902486gDOI Listing
October 2009

Rotational structure of small 4He clusters seeded with HF, HCl, and HBr molecules.

J Phys Chem A 2007 Dec 11;111(49):12275-88. Epub 2007 Oct 11.

Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300.

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http://dx.doi.org/10.1021/jp0746143DOI Listing
December 2007

Quantum solvation dynamics of HCN in a helium-4 droplet.

J Chem Phys 2006 Jul;125(1):014312

Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.

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http://aip.scitation.org/doi/10.1063/1.2213253
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http://dx.doi.org/10.1063/1.2213253DOI Listing
July 2006