Publications by authors named "Hiroshi Akashi"

23Publications

Characterization of G protein-coupled estrogen receptors in Japanese medaka, Oryzias latipes.

Authors:
Kaori Miyaoku Yukiko Ogino Anke Lange Ayaka Ono Tohru Kobayashi Masaru Ihara Hiroaki Tanaka Kenji Toyota Hiroshi Akashi Genki Yamagishi Tomomi Sato Charles R Tyler Taisen Iguchi Shinichi Miyagawa

J Appl Toxicol 2020 Dec 17. Epub 2020 Dec 17.

Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan.

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December 2020

Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution.

Authors:
Masayuki Horie Hiroshi Akashi Masakado Kawata Keizo Tomonaga

Virus Genes 2020 Nov 7. Epub 2020 Nov 7.

Department of Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.

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November 2020

Physiological responses of ionotropic histamine receptors, PxHCLA and PxHCLB, to neurotransmitter candidates in a butterfly, .

Authors:
Hiroshi D Akashi Pei-Ju Chen Tokiho Akiyama Yohey Terai Motohiro Wakakuwa Yasunori Takayama Makoto Tominaga Kentaro Arikawa

J Exp Biol 2018 10 29;221(Pt 21). Epub 2018 Oct 29.

Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan

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October 2018

Factors affecting interspecific differences in genetic divergence among populations of lizards in Cuba.

Authors:
Antonio Cádiz Nobuaki Nagata Luis M Díaz Yukari Suzuki-Ohno Lázaro M Echenique-Díaz Hiroshi D Akashi Takashi Makino Masakado Kawata

Zoological Lett 2018 9;4:21. Epub 2018 Aug 9.

1Graduate School of Life Sciences, Tohoku University, Sendai, Japan.

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August 2018

Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards.

Authors:
Hiroshi D Akashi Shigeru Saito Antonio Cádiz Díaz Takashi Makino Makoto Tominaga Masakado Kawata

Mol Ecol 2018 05 23;27(9):2234-2242. Epub 2018 Apr 23.

Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.

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May 2018

Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations.

Authors:
Tomotaka Matsumoto Hiroshi Akashi

G3 (Bethesda) 2018 05 4;8(5):1755-1769. Epub 2018 May 4.

Division of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan

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May 2018

Red-shift of spectral sensitivity due to screening pigment migration in the eyes of a moth, .

Authors:
Aya Satoh Finlay J Stewart Hisaharu Koshitaka Hiroshi D Akashi Primož Pirih Yasushi Sato Kentaro Arikawa

Zoological Lett 2017 30;3:14. Epub 2017 Aug 30.

Laboratory of Neuroethology, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, 240-0193 Japan.

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August 2017

HSF1 and HSF3 cooperatively regulate the heat shock response in lizards.

Authors:
Ryosuke Takii Mitsuaki Fujimoto Yuki Matsuura Fangxu Wu Namiko Oshibe Eiichi Takaki Arpit Katiyar Hiroshi Akashi Takashi Makino Masakado Kawata Akira Nakai

PLoS One 2017 7;12(7):e0180776. Epub 2017 Jul 7.

Departments of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Minami-Kogushi, Ube, Japan.

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October 2017

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards.

Authors:
Hiroshi D Akashi Antonio Cádiz Díaz Shuji Shigenobu Takashi Makino Masakado Kawata

Mol Ecol 2016 05 14;25(10):2273-85. Epub 2016 May 14.

Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan.

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May 2016

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

Authors:
Tomotaka Matsumoto Anoop John Pablo Baeza-Centurion Boyang Li Hiroshi Akashi

Mol Biol Evol 2016 06 12;33(6):1580-9. Epub 2016 Feb 12.

Division of Evolutionary Genetics, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata, Mishima, Shizuoka, Japan

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June 2016

Assembly constraints drive co-evolution among ribosomal constituents.

Authors:
Saurav Mallik Hiroshi Akashi Sudip Kundu

Nucleic Acids Res 2015 Jun 8;43(11):5352-63. Epub 2015 May 8.

Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase II), University of Calcutta, Kolkata 700009, West Bengal, India

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June 2015

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.

Authors:
Tomotaka Matsumoto Hiroshi Akashi Ziheng Yang

Genetics 2015 Jul 6;200(3):873-90. Epub 2015 May 6.

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom

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July 2015

Weak selection and protein evolution.

Authors:
Hiroshi Akashi Naoki Osada Tomoko Ohta

Genetics 2012 Sep;192(1):15-31

Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

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September 2012

Comprehensive primer design for analysis of population genetics in non-sequenced organisms.

Authors:
Ayumi Tezuka Noe Matsushima Yoriko Nemoto Hiroshi D Akashi Masakado Kawata Takashi Makino

PLoS One 2012 24;7(2):e32314. Epub 2012 Feb 24.

Department of Ecology and Evolutionary Biology, Graduate School of Science, Tohoku University, Sendai, Japan.

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July 2012

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

Authors:
Naoki Osada Hiroshi Akashi

Mol Biol Evol 2012 Jan 1;29(1):337-46. Epub 2011 Sep 1.

Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Japan.

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January 2012

Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?

Authors:
Douglas W Raiford Esley M Heizer Robert V Miller Hiroshi Akashi Michael L Raymer Dan E Krane

J Mol Evol 2008 Dec;67(6):621-30

Department of Computer Science and Engineering, Southern Methodist University, P.O. Box 750122, Dallas, TX 75275, USA.

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December 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup.

Authors:
Hiroshi Akashi Piyush Goel Anoop John

PLoS One 2007 Oct 24;2(10):e1065. Epub 2007 Oct 24.

Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, State College, Pennsylvania, United States of America.

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October 2007

Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome.

Authors:
Wen-Ya Ko Shengfu Piao Hiroshi Akashi

Genetics 2006 Sep 17;174(1):349-62. Epub 2006 Mar 17.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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September 2006

Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence.

Authors:
Hiroshi Akashi Wen-Ya Ko Shengfu Piao Anoop John Piyush Goel Chiao-Feng Lin Alexa P Vitins

Genetics 2006 Mar 30;172(3):1711-26. Epub 2005 Dec 30.

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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March 2006

Molecular phylogeny of the Drosophila melanogaster species subgroup.

Authors:
Wen-Ya Ko Ryan M David Hiroshi Akashi

J Mol Evol 2003 Nov;57(5):562-73

Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.

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November 2003

Translational selection and yeast proteome evolution.

Authors:
Hiroshi Akashi

Genetics 2003 Aug;164(4):1291-303

Institute of Molecular Evolutionary Genetics and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.

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August 2003

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis.

Authors:
Hiroshi Akashi Takashi Gojobori

Proc Natl Acad Sci U S A 2002 Mar;99(6):3695-700

Institute of Molecular Evolutionary Genetics and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.

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March 2002