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ORCIDVsevolod J. Makeev
Person information
- affiliation: Vavilov Institute of General Genetics (VIGG), Department of Computational Systems Biology
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2020 – today
- 2022
[j21]Alexandr Boytsov
, Sergey Abramov, Ariuna Z. Aiusheeva, Alexandra M. Kasianova, Eugene Baulin, Ivan A. Kuznetsov, Yurii S. Aulchenko, Semyon Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov, Ilya E. Vorontsov, Vsevolod J. Makeev, Ivan V. Kulakovskiy:
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. Nucleic Acids Res. 50(W1): 51-56 (2022)- 2021
- [j20]Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49(Database-Issue): D104-D111 (2021)
2010 – 2019
- 2018
- [j19]Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Ruslan N. Sharipov, Alla D. Fedorova, Eugene I. Rumynskiy, Yulia A. Medvedeva, Arturo Magana-Mora, Vladimir B. Bajic, Dmitri A. Papatsenko, Fedor A. Kolpakov, Vsevolod J. Makeev:
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 46(Database-Issue): D252-D259 (2018) - 2016
- [j18]Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev:
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res. 44(Database-Issue): 116-125 (2016) - 2015
- [c5]Ilya E. Vorontsov, Ivan V. Kulakovskiy, Grigory Khimulya, Daria D. Nikolaeva, Vsevolod J. Makeev:
PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation. BIOINFORMATICS 2015: 102-108 - 2014
- [j17]The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), 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. M. 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 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 Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. 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, Fumi 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 Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine 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, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, 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, Hironori 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, Takaaki 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 Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, 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:
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2013
- [j16]Ilya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod J. Makeev:
Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol. Biol. 8: 23 (2013) - [j15]Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry Yu. Oshchepkov, Leonid Bryzgalov, Ilya E. Vorontsov, Vsevolod J. Makeev:
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites. J. Bioinform. Comput. Biol. 11(1) (2013) - [j14]Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev:
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 41(Database-Issue): 195-202 (2013) - [c4]Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod J. Makeev:
Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices. BIOINFORMATICS 2013: 146-150 - 2012
- [j13]Alexander V. Favorov, Loris Mularoni, Leslie M. Cope, Yulia A. Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan:
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package. PLoS Comput. Biol. 8(5) (2012) - [c3]Anna A. Nilulova, Alexander V. Favorov, Vsevolod J. Makeev, Andrey A. Mironov:
A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure. BIOINFORMATICS 2012: 34-41 - 2011
- [j12]Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalia G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod J. Makeev:
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinform. 27(19): 2621-2624 (2011) - 2010
- [j11]Ivan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod J. Makeev:
Deep and wide digging for binding motifs in ChIP-Seq data. Bioinform. 26(20): 2622-2623 (2010) - [j10]Sergei Rahmanov, Ivan V. Kulakovskiy, Leonid Uroshlev, Vsevolod J. Makeev:
Empirical Potentials for ion Binding in proteins. J. Bioinform. Comput. Biol. 8(3): 427-435 (2010)
2000 – 2009
- 2009
- [j9]Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev:
Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinform. 25(18): 2318-2325 (2009) - 2007
- [j8]Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A. Roytberg, Vsevolod J. Makeev:
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol. 2 (2007) - 2006
- [j7]Valentina Boeva, Mireille Régnier, Dmitri A. Papatsenko, Vsevolod J. Makeev:
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinform. 22(6): 676-684 (2006) - 2005
- [j6]Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod J. Makeev:
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinform. 21(10): 2240-2245 (2005) - 2003
- [j5]Mathias Vandenbogaert, Vsevolod J. Makeev:
Analysis of bacterial RM-Systems through genome-scale analysis and related taxonomic issues. Silico Biol. 3(1-2): 127-143 (2003) - [j4]Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova:
The channel in transporters is formed by residues that are rare in transmembrane helices. Silico Biol. 3(1-2): 197-204 (2003) - 2001
- [j3]Vasily Ramensky, Vsevolod J. Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan:
Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software. Bioinform. 17(11): 1065-1066 (2001) - 2000
- [j2]Vasily Ramensky, Vsevolod J. Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan:
DNA Segmentation Through the Bayesian Approach. J. Comput. Biol. 7(1-2): 215-231 (2000) - [c2]Mireille Régnier, Alexandre Lifanov, Vsevolod J. Makeev:
Three Variations on Word Counting. German Conference on Bioinformatics 2000: 75-82 - [c1]Vsevolod J. Makeev, Vasily Ramensky, Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan:
Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. JOBIM 2000: 57-73
1990 – 1999
- 1996
- [j1]Vsevolod J. Makeev, Vladimir G. Tumanyan:
Search of periodicities in primary structure of biopolymers: a general Fourier approach. Comput. Appl. Biosci. 12(1): 49-54 (1996)
Coauthor Index
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