Publications by authors named "Yulia A Medvedeva"

28Publications

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.

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

Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction.

Int J Mol Sci 2020 Jan 28;21(3). Epub 2020 Jan 28.

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia.

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http://dx.doi.org/10.3390/ijms21030830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7037363PMC
January 2020

CpG traffic lights are markers of regulatory regions in human genome.

BMC Genomics 2019 Feb 1;20(1):102. Epub 2019 Feb 1.

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.

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http://dx.doi.org/10.1186/s12864-018-5387-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359853PMC
February 2019

DNA sequence features in the establishing of H3K27ac.

F1000Res 2018 8;7:165. Epub 2018 Feb 8.

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russian Federation.

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http://dx.doi.org/10.12688/f1000research.13441.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989146PMC
August 2019

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.

Brief Bioinform 2019 03;20(2):551-564

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation.

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http://dx.doi.org/10.1093/bib/bby032DOI Listing
March 2019

A novel method for improved accuracy of transcription factor binding site prediction.

Nucleic Acids Res 2018 07;46(12):e72

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

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http://dx.doi.org/10.1093/nar/gky237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037060PMC
July 2018

Peripubertal serum dioxin concentrations and subsequent sperm methylome profiles of young Russian adults.

Reprod Toxicol 2018 06 14;78:40-49. Epub 2018 Mar 14.

Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina St., 119991, Moscow, Russia; Chapaevsk Medical Association, 3a Meditsinskaya st., 446100, Chapaevsk, Samara region, Russia; A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.reprotox.2018.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6130911PMC
June 2018

Purine-rich low complexity regions are potential RNA binding hubs in the human genome.

F1000Res 2018 17;7:76. Epub 2018 Jan 17.

Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation.

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http://dx.doi.org/10.12688/f1000research.13522.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518440PMC
September 2019

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions.

Mol Biol Evol 2017 09;34(9):2203-2213

Department of Vertebrate Genomics and Epigenomics, Institute of Bioengineering, Research Center of Biotechnology RAS, Moscow, Russia.

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http://dx.doi.org/10.1093/molbev/msx156DOI Listing
September 2017

Preservation of methylated CpG dinucleotides in human CpG islands.

Biol Direct 2016 Mar 22;11(1):11. Epub 2016 Mar 22.

Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, GSP-1, 119991, Russia.

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http://dx.doi.org/10.1186/s13062-016-0113-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804638PMC
March 2016

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.

Nucleic Acids Res 2016 Jan 19;44(D1):D116-25. Epub 2015 Nov 19.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia Moscow Institute of Physics and Technology, 141700, Institutskiy per. 9, Dolgoprudny, Moscow Region, Russia

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http://dx.doi.org/10.1093/nar/gkv1249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702883PMC
January 2016

EpiFactors: a comprehensive database of human epigenetic factors and complexes.

Database (Oxford) 2015 7;2015:bav067. Epub 2015 Jul 7.

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway,

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http://dx.doi.org/10.1093/database/bav067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494013PMC
March 2016

Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera.

Sci Rep 2015 Jun 15;5:11136. Epub 2015 Jun 15.

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.

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http://dx.doi.org/10.1038/srep11136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466890PMC
June 2015

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.

PLoS One 2014 2;9(10):e109443. Epub 2014 Oct 2.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109443PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183604PMC
December 2015

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

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.

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

Heavy-light chain interrelations of MS-associated immunoglobulins probed by deep sequencing and rational variation.

Mol Immunol 2014 Dec 16;62(2):305-14. Epub 2014 Feb 16.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.molimm.2014.01.013DOI Listing
December 2014

Regional differences in gene expression and promoter usage in aged human brains.

Neurobiol Aging 2013 Jul 19;34(7):1825-36. Epub 2013 Feb 19.

Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.neurobiolaging.2013.01.005DOI Listing
July 2013

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

Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets.

J Biomol Struct Dyn 2013 18;31(1):115-24. Epub 2012 Jul 18.

Vavilov Institute of General Genetics, 3 Gubkina str. , Moscow, GSP-1, 119991, Russia.

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http://dx.doi.org/10.1080/07391102.2012.691368DOI Listing
October 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

Intergenic, gene terminal, and intragenic CpG islands in the human genome.

BMC Genomics 2010 Jan 19;11:48. Epub 2010 Jan 19.

Research Institute for Genetics and Selection of Industrial Microorganisms, Genetika, 1st Dorozhny proezd, 1, Moscow, 117545, Russia.

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http://dx.doi.org/10.1186/1471-2164-11-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817693PMC
January 2010