Publications by authors named "Alistair R R Forrest"

100Publications

Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs.

Cell Rep 2020 Oct;33(4):108307

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2020.108307DOI Listing
October 2020

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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

Human genetics and genomics meetings going virtual: practical lessons learned from two international meetings in early 2020.

Hum Genomics 2020 07 8;14(1):27. Epub 2020 Jul 8.

Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD 4878, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40246-020-00275-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341463PMC
July 2020

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.

Genome Biol 2020 06 2;21(1):130. Epub 2020 Jun 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, 6009, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-020-02048-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265231PMC
June 2020

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes.

Sci Rep 2020 Jan 28;10(1):1286. Epub 2020 Jan 28.

Systems Biology and Health Data Analytics Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-58107-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6987109PMC
January 2020

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

BMC Genomics 2019 Sep 18;20(1):718. Epub 2019 Sep 18.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-6063-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751898PMC
September 2019

Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics.

Mol Cancer Ther 2019 12 29;18(12):2480-2489. Epub 2019 Aug 29.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1535-7163.MCT-19-0273DOI Listing
December 2019

scMatch: a single-cell gene expression profile annotation tool using reference datasets.

Bioinformatics 2019 11;35(22):4688-4695

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853649PMC
November 2019

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

BMC Genomics 2018 01 11;19(1):39. Epub 2018 Jan 11.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-017-4291-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763542PMC
January 2018

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

Cerebellum 2018 Jun;17(3):308-325

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12311-017-0912-3DOI Listing
June 2018

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

EBioMedicine 2017 Oct 12;24:257-266. Epub 2017 Sep 12.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ebiom.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5652006PMC
October 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Bioinformatics 2016 09 9;32(18):2858-60. Epub 2016 Jun 9.

Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018375PMC
September 2016

Transcription Factor NKX6.3 Sheds Light on Gastric Cancer Progression.

EBioMedicine 2016 Jul 16;9:9-10. Epub 2016 Jun 16.

Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ebiom.2016.06.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972556PMC
July 2016

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Nucleic Acids Res 2016 Apr 21;44(7):3233-52. Epub 2016 Mar 21.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838384PMC
April 2016

Reinforcing the association between distal 1q CNVs and structural brain disorder: A case of a complex 1q43-q44 CNV and a review of the literature.

Am J Med Genet B Neuropsychiatr Genet 2016 Apr 7;171B(3):458-67. Epub 2016 Feb 7.

The Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajmg.b.32427DOI Listing
April 2016

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

PLoS Biol 2015 Dec 18;13(12):e1002315. Epub 2015 Dec 18.

The Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.1002315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4686125PMC
December 2015

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.

Front Genet 2015 18;6:331. Epub 2015 Nov 18.

RIKEN Center for Life Science Technologies Yokohama, Japan ; Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan ; QEII Medical Centre and Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia Nedlands, WA, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2015.00331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650373PMC
December 2015

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Cancer Res 2016 Jan 9;76(2):216-26. Epub 2015 Nov 9.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-15-0484DOI Listing
January 2016

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.

View Article

Download full-text PDF

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

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Nucleic Acids Res 2015 Aug 27;43(14):6969-82. Epub 2015 Jun 27.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Riken Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538831PMC
August 2015

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

Nucleic Acids Res 2015 Aug 27;43(14):6787-98. Epub 2015 Jun 27.

Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkv608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538815PMC
August 2015

Retinoic acid potentiates inflammatory cytokines in human mast cells: identification of mast cells as prominent constituents of the skin retinoid network.

Mol Cell Endocrinol 2015 May 25;406:49-59. Epub 2015 Feb 25.

Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Berlin, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mce.2015.02.019DOI Listing
May 2015

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

J Leukoc Biol 2015 May 25;97(5):985-995. Epub 2015 Feb 25.

*The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1189/jlb.6TA1014-477RRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398258PMC
May 2015

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

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.

Nucleic Acids Res 2015 Apr 4;43(8):e51. Epub 2015 Feb 4.

Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Høyteknologisenteret, Thormøhlensgate 55, N-5008 Bergen, Norway

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417143PMC
April 2015

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Nat Commun 2015 Jan 14;6:6066. Epub 2015 Jan 14.

1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Ecology and Evolutionary Biology, Yale University, Prospect Street 165, OML Room 327, New Haven, Connecticut 06520-8106, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms7066DOI Listing
January 2015

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.

Nucleic Acids Res 2014 Aug 10;42(14):8905-13. Epub 2014 Jul 10.

RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama 230-0045, Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132712PMC
August 2014

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.

Sci Rep 2014 Jun 24;4:5228. Epub 2014 Jun 24.

1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep05228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067614PMC
June 2014

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

BMC Genomics 2014 Apr 25;15:269. Epub 2014 Apr 25.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-15-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029093PMC
April 2014

Deep sequencing blood transcriptomes.

Blood 2014 Apr;123(17):2595-6

RIKEN CENTRE FOR LIFE SCIENCE TECHNOLOGY.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2014-03-563452DOI Listing
April 2014

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

Nat Biotechnol 2014 Mar;32(3):217-9

1] RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan. [2] RIKEN Omics Science Center (OSC), Yokohama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.2840DOI Listing
March 2014

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

Bioinformatics 2014 04 27;30(8):1183-1184. Epub 2014 Mar 27.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan and RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu125DOI Listing
April 2014

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Proc Natl Acad Sci U S A 2014 Apr 27;111(14):5289-94. Epub 2014 Mar 27.

Departments of Experimental Immunology and Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1312717110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986152PMC
April 2014

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

Mol Genet Metab 2014 May 16;112(1):73-83. Epub 2013 Dec 16.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; The University of Queensland Northside Clinical School, Prince Charles Hospital, Chermside 4032, Australia. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymgme.2013.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019825PMC
May 2014

The evolution of human cells in terms of protein innovation.

Mol Biol Evol 2014 Jun 1;31(6):1364-74. Epub 2014 Apr 1.

Department of Computer Science, University of Bristol, Bristol, United KingdomMedical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/mst139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032124PMC
June 2014

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

Blood 2014 Apr 26;123(17):e46-57. Epub 2014 Mar 26.

Department of Bioscience and Nutrition, Center for Biosciences, NOVUM, Karolinska Institutet, Stockholm, Sweden;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood-2013-02-483537DOI Listing
April 2014

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

View Article

Download full-text PDF

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

Effects of cytosine methylation on transcription factor binding sites.

BMC Genomics 2014 Mar 26;15:119. Epub 2014 Mar 26.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-15-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986887PMC
March 2014

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

Nature 2012 Nov 14;491(7424):454-7. Epub 2012 Oct 14.

Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature11508DOI Listing
November 2012

CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells.

Stem Cells 2011 Aug;29(8):1196-205

RIKEN Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/stem.673DOI Listing
August 2011

Whole genome transcriptome analysis.

RNA Biol 2009 Apr-Jun;6(2):107-12

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4161/rna.6.2.7931DOI Listing
February 2010

Annotating non-coding transcription using functional genomics strategies.

Brief Funct Genomic Proteomic 2009 Nov;8(6):437-43

Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045 Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elp041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762128PMC
November 2009