Carrie A Davis

Carrie A Davis

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Carrie A Davis

Carrie A Davis

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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.

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

Effect of fentanyl on the induction dose and minimum infusion rate of propofol preventing movement in dogs.

Vet Anaesth Analg 2017 Jul 11;44(4):727-737. Epub 2017 Jan 11.

Department of Large Animal Clinical Sciences, University of Tennessee, Knoxville, TN, USA.

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http://dx.doi.org/10.1016/j.vaa.2016.11.002DOI Listing
July 2017

Erratum to: A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 09 30;17(1):203. Epub 2016 Sep 30.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-1060-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045616PMC
September 2016

Gene-specific patterns of expression variation across organs and species.

Genome Biol 2016 07 8;17(1):151. Epub 2016 Jul 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s13059-016-1008-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937605PMC
July 2016

Erratum to: A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 May 23;17(1):107. Epub 2016 May 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-0986-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877800PMC
May 2016

A benchmark for RNA-seq quantification pipelines.

Genome Biol 2016 Apr 23;17:74. Epub 2016 Apr 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-0940-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842274PMC
April 2016

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling.

Cell 2014 Apr;157(2):382-394

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.01.066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001090PMC
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

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

STAR: ultrafast universal RNA-seq aligner.

Bioinformatics 2013 Jan 25;29(1):15-21. Epub 2012 Oct 25.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905PMC
January 2013

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Synthetic spike-in standards for RNA-seq experiments.

Genome Res 2011 Sep 4;21(9):1543-51. Epub 2011 Aug 4.

Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1101/gr.121095.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166838PMC
September 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
Publisher Site
http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica.

Eukaryot Cell 2007 Jun 27;6(6):940-8. Epub 2007 Apr 27.

Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.

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http://ec.asm.org/lookup/doi/10.1128/EC.00059-07
Publisher Site
http://dx.doi.org/10.1128/EC.00059-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951529PMC
June 2007

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome.

Nucleic Acids Res 2004 11;32(14):4281-96. Epub 2004 Aug 11.

Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkh768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514388PMC
August 2004