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1

EpiFactors: a comprehensive database of human epigenetic factors and complexes

Medvedeva, Yulia A., Lennartsson, Andreas, Ehsani, Rezvan, Kulakovskiy, Ivan V., Vorontsov, Ilya E., Panahandeh, Pouda, Khimulya, Grigory, Kasukawa, Takeya, Drabløs, Finn

Journal:

Year:

2015

Language:

english

File:

PDF, 659 KB

english, 2015

2

Jaccard index based similarity measure to compare transcription factor binding site models

Vorontsov, Ilya E, Kulakovskiy, Ivan V, Makeev, Vsevolod J

Journal:

Algorithms for Molecular Biology

Year:

2013

Language:

english

File:

PDF, 518 KB

english, 2013

3

High quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

Kasianov, Artem S., Klepikova, Anna V., Kulakovskiy, Ivan V., Gerasimov, Evgeny S., Fedotova, Anna V., Besedina, Elizaveta G., Kondrashov, Alexey S., Logacheva, Maria D., Penin, Aleksey A.

Journal:

The Plant Journal

Year:

2017

Language:

english

File:

PDF, 849 KB

english, 2017

4

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network

Gursky, Vitaly V., Kozlov, Konstantin N., Kulakovskiy, Ivan V., Zubair, Asif, Marjoram, Paul, Lawrie, David S., Nuzhdin, Sergey V., Samsonova, Maria G., Palsson, Arnar

Journal:

Year:

2017

Language:

english

File:

PDF, 8.21 MB

english, 2017

5

A promoter-level mammalian expression atlas

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, R

Journal:

Year:

2014

Language:

english

File:

PDF, 6.75 MB

english, 2014

6

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

Levitsky, Victor G, Kulakovskiy, Ivan V, Ershov, Nikita I, Oshchepkov, Dmitry, Makeev, Vsevolod J, Hodgman, T C, Merkulova, Tatyana I

Journal:

Year:

2014

Language:

english

File:

PDF, 2.31 MB

english, 2014

7

CpG traffic lights are markers of regulatory regions in human genome

Lioznova, Anna V., Khamis, Abdullah M., Artemov, Artem V., Besedina, Elizaveta, Ramensky, Vasily, Bajic, Vladimir B., Kulakovskiy, Ivan V., Medvedeva, Yulia A.

Journal:

Year:

2019

File:

PDF, 2.62 MB

2019

8

Brain-related genes are specifically enriched with long phase 1 introns

Baulin, Eugene F., Kulakovskiy, Ivan V., Roytberg, Mikhail A., Astakhova, Tatiana V., Rogozin, Igor B.

Journal:

Year:

2020

File:

PDF, 952 KB

2020

9

Analysis of functional importance of binding sites in theDrosophilagap gene network model

Konstantin Kozlov,Vitaly V Gursky,Ivan V Kulakovskiy,Arina Dymova…

Journal:

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

10

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Ambrosini, Giovanna, Vorontsov, Ilya, Penzar, Dmitry, Groux, Romain, Fornes, Oriol, Nikolaeva, Daria D., Ballester, Benoit, Grau, Jan, Grosse, Ivo, Makeev, Vsevolod, Kulakovskiy, Ivan, Bucher, Philipp

Journal:

Year:

2020

File:

PDF, 4.93 MB

2020

11

[Advances in Protein Chemistry and Structural Biology] Protein-Nucleic Acids Interactions Volume 91 || DNA Sequence Motif

Kulakovskiy, Ivan V.

Year:

2013

Language:

english

File:

PDF, 2.91 MB

english, 2013

12

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.

Journal:

Frontiers in Genetics

Year:

2019

File:

PDF, 2.43 MB

2019

13

Alternative Forms of Y-Box Binding Protein 1 and YB-1 mRNA

Lyabin, Dmitry N., Doronin, Alexander N., Eliseeva, Irina A., Guens, Gelena P., Kulakovskiy, Ivan V., Ovchinnikov, Lev P., Jan, Eric

Journal:

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

14

In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response

Eliseeva, Irina, Vorontsov, Ilya, Babeyev, Kirill, Buyanova, Sofya, Sysoeva, Maria, Kondrashov, Fyodor, Kulakovskiy, Ivan

Journal:

Year:

2013

Language:

english

File:

PDF, 621 KB

english, 2013

15

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity

Schwartz, Anton M., Demin, Denis E., Vorontsov, Ilya E., Kasyanov, Artem S., Putlyaeva, Lidia V., Tatosyan, Karina A., Kulakovskiy, Ivan V., Kuprash, Dmitry V.

Journal:

Year:

2016

Language:

english

File:

PDF, 521 KB

english, 2016

16

svist4get: a simple visualization tool for genomic tracks from sequencing experiments

Egorov, Artyom A., Sakharova, Ekaterina A., Anisimova, Aleksandra S., Dmitriev, Sergey E., Gladyshev, Vadim N., Kulakovskiy, Ivan V.

Journal:

BMC Bioinformatics

Year:

2019

File:

PDF, 1.70 MB

2019

17

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

Yulia A Medvedeva, Marina V Fridman, Nina J Oparina, Dmitry B Malko, Ekaterina O Ermakova, Ivan V Kulakovskiy, Andreas Heinzel, Vsevolod J Makeev

Journal:

Year:

2010

Language:

english

File:

PDF, 1.98 MB

english, 2010

18

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

Moskalev, Alexey А., Kudryavtseva, Anna V., Graphodatsky, Alexander S., Beklemisheva, Violetta R., Serdyukova, Natalya A., Krutovsky, Konstantin V., Sharov, Vadim V., Kulakovskiy, Ivan V., Lando, Andr

Journal:

BMC Evolutionary Biology

Year:

2017

Language:

english

File:

PDF, 476 KB

english, 2017

19

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Kulakovskiy, Ivan V, Vorontsov, Ilya E, Yevshin, Ivan S, Sharipov, Ruslan N, Fedorova, Alla D, Rumynskiy, Eugene I, Medvedeva, Yulia A, Magana-Mora, Arturo, Bajic, Vladimir B, Papatsenko, Dmitry A, Ko

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 751 KB

english, 2018

20

Functional annotation of human long noncoding RNAs via molecular phenotyping

Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, MickaÃ«l, Ooi, Jasmine Li Ching, Ouyang, John F., Parkinson, Nick, Petri, Andreas, Ro

Journal:

Genome Research

Year:

2020

File:

PDF, 8.73 MB

2020

21

EMPIRICAL POTENTIALS FOR ION BINDING IN PROTEINS

RAHMANOV, SERGEI, KULAKOVSKIY, IVAN, UROSHLEV, LEONID, MAKEEV, VSEVOLOD

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 445 KB

english, 2010

22

Multifaceted deregulation of gene expression and protein synthesis with age

Anisimova, Aleksandra S., Meerson, Mark B., Gerashchenko, Maxim V., Kulakovskiy, Ivan V., Dmitriev, Sergey E., Gladyshev, Vadim N.

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 2.49 MB

2020

23

svist4get: a simple visualization tool for genomic tracks from sequencing experiments

Egorov, Artyom A., Sakharova, Ekaterina A., Anisimova, Aleksandra S., Dmitriev, Sergey E., Gladyshev, Vadim N., Kulakovskiy, Ivan V.

Journal:

BMC Bioinformatics

Year:

2019

Language:

english

File:

PDF, 1.70 MB

english, 2019

24

Effects of cytosine methylation on transcription factor binding sites

Medvedeva, Yulia A, Khamis, Abdullah M, Kulakovskiy, Ivan V, Ba-Alawi, Wail, Bhuyan, Md Shariful I, Kawaji, Hideya, Lassmann, Timo, Harbers, Matthias, Forrest, Alistair RR, Bajic, Vladimir B

Journal:

Year:

2014

Language:

english

File:

PDF, 486 KB

english, 2014

25

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

KULAKOVSKIY, IVAN, LEVITSKY, VICTOR, OSHCHEPKOV, DMITRY, BRYZGALOV, LEONID, VORONTSOV, ILYA, MAKEEV, VSEVOLOD

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.62 MB

english, 2013

26

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila

Zolotarev, Nikolay, Fedotova, Anna, Kyrchanova, Olga, Bonchuk, Artem, Penin, Aleksey A., Lando, Andrey S., Eliseeva, Irina A., Kulakovskiy, Ivan V., Maksimenko, Oksana, Georgiev, Pavel

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 5.79 MB

english, 2016

27

Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression

Korneev, Kirill V., Sviriaeva, Ekaterina N., Mitkin, Nikita A., Gorbacheva, Alisa M., Uvarova, Aksinya N., Ustiugova, Alina S., Polanovsky, Oleg L., Kulakovskiy, Ivan V., Afanasyeva, Marina A., Schwar

Journal:

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease

Year:

2019

Language:

english

File:

PDF, 1.46 MB

english, 2019

28

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease

Sethi, Siddharth, Vorontsov, Ilya E., Kulakovskiy, Ivan V., Greenaway, Simon, Williams, John, Makeev, Vsevolod J., Brown, Steve D. M., Simon, Michelle M., Mallon, Ann-Marie

Journal:

Year:

2020

File:

PDF, 4.87 MB

2020

29

GTRD: an integrated view of transcription regulation

Kolmykov, Semyon, Yevshin, Ivan, Kulyashov, Mikhail, Sharipov, Ruslan, Kondrakhin, Yury, Makeev, Vsevolod J, Kulakovskiy, Ivan V, Kel, Alexander, Kolpakov, Fedor

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 2.72 MB

2020

30

Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression

Korneev, Kirill V., Sviriaeva, Ekaterina N., Mitkin, Nikita A., Gorbacheva, Alisa M., Uvarova, Aksinya N., Ustiugova, Alina S., Polanovsky, Oleg L., Kulakovskiy, Ivan V., Afanasyeva, Marina A., Schwar

Journal:

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease

Year:

2019

File:

PDF, 1.46 MB

2019

31

Sequence-based model of gap gene regulatory network

Kozlov, Konstantin, Gursky, Vitaly, Kulakovskiy, Ivan, Samsonova, Maria

Journal:

Year:

2014

Language:

english

File:

PDF, 3.80 MB

english, 2014

32

The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae

Trilisenko, Ludmila, Zvonarev, Anton, Valiakhmetov, Airat, Penin, Alexey A., Eliseeva, Irina A., Ostroumov, Vladimir, Kulakovskiy, Ivan V., Kulakovskaya, Tatiana

Journal:

Year:

2019

Language:

english

File:

PDF, 3.83 MB

english, 2019

33

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.

Journal:

Frontiers in Genetics

Year:

2019

Language:

english

File:

PDF, 2.43 MB

english, 2019

34

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data

Vorontsov, Ilya E., Fedorova, Alla D., Yevshin, Ivan S., Sharipov, Ruslan N., Kolpakov, Fedor A., Makeev, Vsevolod J., Kulakovskiy, Ivan V.

Journal:

BMC Research Notes

Year:

2018

Language:

english

File:

PDF, 778 KB

english, 2018

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