Publications by authors named "Ulf Schaefer"

25Publications

Identification and typing of Yersinia enterocolitica and Yersinia pseudotuberculosis isolated from human clinical specimens in England between 2004 and 2018.

J Med Microbiol 2019 Apr 19;68(4):538-548. Epub 2019 Mar 19.

National Infection Services, Public Health England, 61 Colindale Avenue, London NW9 5HT, UK.

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http://dx.doi.org/10.1099/jmm.0.000943DOI Listing
April 2019

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.

J Clin Microbiol 2017 02 14;55(2):616-623. Epub 2016 Dec 14.

Gastrointestinal Bacteria Reference Unit and Bioinformatics Unit, National Infection Service, Public Health England, London, United Kingdom

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http://dx.doi.org/10.1128/JCM.01790-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5277532PMC
February 2017

MOST: a modified MLST typing tool based on short read sequencing.

PeerJ 2016 17;4:e2308. Epub 2016 Aug 17.

Infectious Disease Informatics Unit, Public Health England , London , United Kingdom.

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http://dx.doi.org/10.7717/peerj.2308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991843PMC
September 2016

Identification of Salmonella for public health surveillance using whole genome sequencing.

PeerJ 2016 5;4:e1752. Epub 2016 Apr 5.

Gastrointestinal Bacterial Reference Unit, Public Health England, London, United Kingdom; Gastrointestinal Infections, NIHR Health Protection Research Unit in Gastrointestinal Infections, London, United Kingdom.

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http://dx.doi.org/10.7717/peerj.1752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824889PMC
April 2016

An outbreak of high-level azithromycin resistant Neisseria gonorrhoeae in England.

Sex Transm Infect 2016 08 24;92(5):365-7. Epub 2015 Nov 24.

Sexually Transmitted Bacteria Reference Unit, Microbiology Services, Public Health England, London, UK.

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http://dx.doi.org/10.1136/sextrans-2015-052312DOI Listing
August 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

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.

Nucleic Acids Res 2013 Jan 21;41(Database issue):D195-202. Epub 2012 Nov 21.

Laboratory of Bioinformatics and Systems Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, GSP-1, Russia.

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http://dx.doi.org/10.1093/nar/gks1089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531053PMC
January 2013

Mutations and binding sites of human transcription factors.

Front Genet 2012 1;3:100. Epub 2012 Jun 1.

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

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http://dx.doi.org/10.3389/fgene.2012.00100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365286PMC
October 2012

DESTAF: a database of text-mined associations for reproductive toxins potentially affecting human fertility.

Reprod Toxicol 2012 Jan 17;33(1):99-105. Epub 2011 Dec 17.

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

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http://dx.doi.org/10.1016/j.reprotox.2011.12.007DOI Listing
January 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

HCVpro: hepatitis C virus protein interaction database.

Infect Genet Evol 2011 Dec 9;11(8):1971-7. Epub 2011 Sep 9.

South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville 7535, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.meegid.2011.09.001DOI Listing
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

High sensitivity TSS prediction: estimates of locations where TSS cannot occur.

PLoS One 2010 Nov 15;5(11):e13934. Epub 2010 Nov 15.

Computational Bioscience Research Center (CBRC), 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.0013934PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981523PMC
November 2010

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

DDESC: Dragon database for exploration of sodium channels in human.

BMC Genomics 2008 Dec 20;9:622. Epub 2008 Dec 20.

South African National Bioinformatics Institute, University of the Western Cape, Private Bag- X17, Modderdam Road, Bellville, Cape Town 7535, South Africa.

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http://dx.doi.org/10.1186/1471-2164-9-622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631582PMC
December 2008

Genome-wide analysis of cancer/testis gene expression.

Proc Natl Acad Sci U S A 2008 Dec 16;105(51):20422-7. Epub 2008 Dec 16.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, SPH2, 4th Floor, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.0810777105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603434PMC
December 2008

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