Alexander V Favorov

Alexander V Favorov

UNVERIFIED PROFILE

Are you Alexander V Favorov?   Register this Author

Register author
Alexander V Favorov

Alexander V Favorov

Publications by authors named "Alexander V Favorov"

Are you Alexander V Favorov?   Register this Author

38Publications

1033Reads

41Profile Views

Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data.

Cancer Res 2019 Oct 23;79(19):5102-5112. Epub 2019 Jul 23.

Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-18-3882DOI Listing
October 2019

Allele-specific nonstationarity in evolution of influenza A virus surface proteins.

Proc Natl Acad Sci U S A 2019 Oct 2;116(42):21104-21112. Epub 2019 Oct 2.

Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Russia;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1904246116DOI Listing
October 2019

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

Trends Genet 2018 10 22;34(10):790-805. Epub 2018 Aug 22.

Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309559PMC
October 2018

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Bioinformatics 2017 Oct;33(20):3158-3165

Department of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860031PMC
October 2017

Genetic risk factors for myocardial infarction more clearly manifest for early age of first onset.

Mol Biol Rep 2017 Aug 6;44(4):315-321. Epub 2017 Jul 6.

Institute of Experimental Cardiology, Russian Cardiology Scientific and Production Center, Moscow, Russia.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s11033-017-4112-5
Publisher Site
http://dx.doi.org/10.1007/s11033-017-4112-5DOI Listing
August 2017

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:

View Article

Download full-text PDF

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

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.

Bioinformatics 2014 Oct 6;30(19):2757-63. Epub 2014 Jun 6.

Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205, USA, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia, Research Institute for Genetics and Selection of Industrial Microorganisms "GosNIIGenetika", Moscow 117545, Russia, Department of Statistics and Biostatistics, Rutgers University, NJ 08854, USA and Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173013PMC
October 2014

Weak negative and positive selection and the drift load at splice sites.

Genome Biol Evol 2014 May 14;6(6):1437-47. Epub 2014 May 14.

Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, RussiaLife Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evu100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079205PMC
May 2014

Comparative pharmacogenetics of multiple sclerosis: IFN-β versus glatiramer acetate.

Pharmacogenomics 2014 Apr;15(5):679-85

Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997, Moscow, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/pgs.14.26DOI Listing
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

View Article

Download full-text PDF

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

Hidden Markov models for evolution and comparative genomics analysis.

PLoS One 2013 7;8(6):e65012. Epub 2013 Jun 7.

A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065012PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676395PMC
January 2014

Identifying context-specific transcription factor targets from prior knowledge and gene expression data.

IEEE Trans Nanobioscience 2013 Sep 16;12(3):142-9. Epub 2013 May 16.

Department of Oncology, SKCCC, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/TNB.2013.2263390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759534PMC
September 2013

Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development.

Front Genet 2011 8;2:77. Epub 2011 Nov 8.

Division of Oncology Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University Baltimore, MD, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2011.00077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268630PMC
October 2012

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

Nucleic Acids Res 2012 Jul 15;40(12):e93. Epub 2012 Mar 15.

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73 Leninskie Gory, Moscow 119991, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gks235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384346PMC
July 2012

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Bioinformatics 2010 Nov 1;26(21):2792-3. Epub 2010 Sep 1.

Department of Oncology and Division of Oncology, Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btq503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025742PMC
November 2010

Motif discovery and motif finding from genome-mapped DNase footprint data.

Bioinformatics 2009 Sep 15;25(18):2318-25. Epub 2009 Jul 15.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp434DOI Listing
September 2009

Conserved and species-specific alternative splicing in mammalian genomes.

BMC Evol Biol 2007 Dec 22;7:249. Epub 2007 Dec 22.

Faculty of Bioengineering and Bioinformatics, M,V, Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow, 119992, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2148-7-249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231371PMC
December 2007

Three allele combinations associated with multiple sclerosis.

BMC Med Genet 2006 Jul 26;7:63. Epub 2006 Jul 26.

Department of Molecular Biology and Medical Biotechnology, Russian State Medical University, 15 3d Cherepkovskaya ul,, Moscow 121552, Russia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2350-7-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557481PMC
July 2006

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.

J Bioinform Comput Biol 2006 Apr;4(2):589-96

Institute for Problems of Information Transition RAS, Bolshoi Karetnyi per. 19, Moscow, 127994, Russia.

View Article

Download full-text PDF

Source
April 2006