Publications by authors named "Sebastian Schmeier"

35Publications

Corrigendum to "Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes" [Mol. Phylogenet. Evolut. 133 (2019) 352-361].

Mol Phylogenet Evol 2020 06 28;147:106732. Epub 2020 Feb 28.

Institute of Natural and Mathematical Sciences, Massey University Auckland, Auckland 0632, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2020.106732DOI Listing
June 2020

Molecular subtyping improves prognostication of Stage 2 colorectal cancer.

BMC Cancer 2019 Nov 27;19(1):1155. Epub 2019 Nov 27.

Department of Surgery, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.

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http://dx.doi.org/10.1186/s12885-019-6327-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882162PMC
November 2019

Metagenomics and transcriptomics data from human colorectal cancer.

Sci Data 2019 07 5;6(1):116. Epub 2019 Jul 5.

Department of Surgery, University of Otago, Christchurch, New Zealand.

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http://dx.doi.org/10.1038/s41597-019-0117-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611873PMC
July 2019

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection.

BMC Genomics 2019 Jan 22;20(1):71. Epub 2019 Jan 22.

Massey University, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand.

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http://dx.doi.org/10.1186/s12864-019-5450-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341744PMC
January 2019

Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes.

Mol Phylogenet Evol 2019 04 30;133:352-361. Epub 2018 Dec 30.

Institute of Natural and Mathematical Sciences, Massey University Auckland, Auckland 0632, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2018.12.031DOI Listing
April 2019

An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.

Mol Biol Evol 2018 06;35(6):1451-1462

Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1093/molbev/msy046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967550PMC
June 2018

Genome-wide profiling of transcribed enhancers during macrophage activation.

Epigenetics Chromatin 2017 10 23;10(1):50. Epub 2017 Oct 23.

Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland, 0632, New Zealand.

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http://dx.doi.org/10.1186/s13072-017-0158-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654053PMC
October 2017

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.

Sci Rep 2017 09 14;7(1):11590. Epub 2017 Sep 14.

Department of Surgery, University of Otago, Christchurch, New Zealand.

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http://dx.doi.org/10.1038/s41598-017-11237-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599497PMC
September 2017

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

RNA Biol 2017 07 7;14(7):963-971. Epub 2017 Apr 7.

a King Abdullah University of Science and Technology (KAUST) , Computational Bioscience Research Center (CBRC) , Thuwal , Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1080/15476286.2017.1312243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546543PMC
July 2017

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions.

Nucleic Acids Res 2017 01 26;45(D1):D145-D150. Epub 2016 Oct 26.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkw1007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210517PMC
January 2017

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

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

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.

J Immunol 2015 Jun 8;194(12):6035-44. Epub 2015 May 8.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan; RIKEN Omics Science Center, Yokohama 230-0045, Japan;

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http://dx.doi.org/10.4049/jimmunol.1402521DOI Listing
June 2015

IL-4Rα-dependent alternative activation of macrophages is not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice.

PLoS One 2015 19;10(3):e0121070. Epub 2015 Mar 19.

International Centre for Genetic Engineering & Biotechnology (ICGEB), Cape Town component and Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology, University of Cape Town, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121070PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366092PMC
February 2016

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

Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model.

BMC Syst Biol 2012 Oct 26;6:135. Epub 2012 Oct 26.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/1752-0509-6-135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495646PMC
October 2012

Network analysis of microRNAs and their regulation in human ovarian cancer.

BMC Syst Biol 2011 Nov 3;5:183. Epub 2011 Nov 3.

Computational Bioscience Research Center (CBRC), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-5-183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219655PMC
November 2011

In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer.

BMC Syst Biol 2011 Sep 19;5:144. Epub 2011 Sep 19.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/1752-0509-5-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184078PMC
September 2011

Simplified method to predict mutual interactions of human transcription factors based on their primary structure.

PLoS One 2011 5;6(7):e21887. Epub 2011 Jul 5.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021887PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130058PMC
December 2011

dPORE-miRNA: polymorphic regulation of microRNA genes.

PLoS One 2011 Feb 4;6(2):e16657. Epub 2011 Feb 4.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016657PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033892PMC
February 2011

Text mining for systems modeling.

Methods Mol Biol 2011 ;696:305-18

Protagen AG, Dortmund, Germany.

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http://dx.doi.org/10.1007/978-1-60761-987-1_19DOI Listing
February 2011

TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins.

Nucleic Acids Res 2011 Jan 21;39(Database issue):D106-10. Epub 2010 Oct 21.

Computational Bioscience Research Center, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1093/nar/gkq945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013796PMC
January 2011

DDPC: Dragon Database of Genes associated with Prostate Cancer.

Nucleic Acids Res 2011 Jan 29;39(Database issue):D980-5. Epub 2010 Sep 29.

South African National Bioinformatics Institute, University of the Western Cape, Private Bag-X17, Modderdam Road, Bellville, Cape Town, South Africa.

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http://dx.doi.org/10.1093/nar/gkq849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013759PMC
January 2011

DDEC: Dragon database of genes implicated in esophageal cancer.

BMC Cancer 2009 Jul 6;9:219. Epub 2009 Jul 6.

South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.

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http://dx.doi.org/10.1186/1471-2407-9-219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711974PMC
July 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

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

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Database for exploration of functional context of genes implicated in ovarian cancer.

Nucleic Acids Res 2009 Jan 12;37(Database issue):D820-3. Epub 2008 Sep 12.

South African National Bioinformatics Institute, University of the Western Cape, Private Bag- X17, Modderdam Road, Bellville, Cape Town, South Africa.

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http://dx.doi.org/10.1093/nar/gkn593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686485PMC
January 2009

MACAT--microarray chromosome analysis tool.

Bioinformatics 2005 May 30;21(9):2112-3. Epub 2004 Nov 30.

Freie Universitaet Berlin, Bioinformatics programme and Max Planck Institute for Molecular Genetics, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bti183DOI Listing
May 2005

Finding kinetic parameters using text mining.

OMICS 2004 ;8(2):131-52

Humboldt-Universität zu Berlin, Department of Computer Science, Berlin, Germany.

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http://dx.doi.org/10.1089/1536231041388366DOI Listing
May 2005