Ivan V Kulakovskiy

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 33

Top Topics

Binding Protein

Transcription Factor

Acute Heart Failure

Top Venues

International journal of molecular sciences

Nucleic acids research

bioRxiv : the preprint server for biology

This page only lists publications with an associated author ORCID identifier.

Publications

Abdul Muntakim Rafi, Daria S Nogina, Dmitry Penzar, Do Hoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Random Promoter Dream Challenge Consortium, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V Kulakovskiy, Pablo Meyer, Carl G de Boer
Evaluation and optimization of sequence-based gene regulatory deep learning models. bioRxiv : the preprint server for biology (2024)
Abdul Muntakim Rafi, Daria S Nogina, Dmitry Penzar, Do Hoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, null null, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V Kulakovskiy, Pablo Meyer, Carl G de Boer
Evaluation and optimization of sequence-based gene regulatory deep learning models. bioRxiv : the preprint server for biology (2024)
Irina A Eliseeva, Andrey I Buyan, Egor A Smolin, Karina S Kaliadzenka, Sergey Popov, Ivan V Kulakovskiy, Dmitry N Lyabin
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. International journal of molecular sciences 25 (3) (2024)
Irina A Eliseeva, Andrey I Buyan, Egor A Smolin, Karina S Kaliadzenka, Sergey Popov, Ivan V Kulakovskiy, Dmitry N Lyabin
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. International journal of molecular sciences 25 (3) (2024)
Abdul Muntakim Rafi, Daria S Nogina, Dmitry Penzar, Do Hoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, null null, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V Kulakovskiy, Pablo Meyer, Carl G de Boer
Evaluation and optimization of sequence-based gene regulatory deep learning models. bioRxiv : the preprint server for biology (2024)
Irina A Eliseeva, Andrey I Buyan, Egor A Smolin, Karina S Kaliadzenka, Sergey Popov, Ivan V Kulakovskiy, Dmitry N Lyabin
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. International journal of molecular sciences 25 (3) (2024)
Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A Ramilowski, Andrey I Sigorskikh, Lisa J Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M Hoffman, Chikashi C Terao, Ivan V Kulakovskiy, Takeya Kasukawa, Jay W Shin, Piero Carninci, Michiel J L de Hoon
Annotation of nuclear lncRNAs based on chromatin interactions. PloS one 19 (5) (2024)
Irina A Eliseeva, Andrey I Buyan, Egor A Smolin, Karina S Kaliadzenka, Sergey Popov, Ivan V Kulakovskiy, Dmitry N Lyabin
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. International journal of molecular sciences 25 (3) (2024)
Matvei Khoroshkin, Andrey I Buyan, Martin Dodel, Albertas Navickas, Johnny Yu, Fathima Trejo, Anthony Doty, Rithvik Baratam, Shaopu Zhou, Sean B Lee, Tanvi Joshi, Kristle Garcia, Benedict Choi, Sohit Miglani, Vishvak Subramanyam, Hailey Modi, Christopher Carpenter, Daniel Markett, M Ryan Corces, Faraz K Mardakheh, Ivan V Kulakovskiy, Hani Goodarzi
Systematic identification of post-transcriptional regulatory modules. Nature communications 15 (1) (2024)
Abdul Muntakim Rafi, Daria S Nogina, Dmitry Penzar, Do Hoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, null null, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V Kulakovskiy, Pablo Meyer, Carl G de Boer
Evaluation and optimization of sequence-based gene regulatory deep learning models. bioRxiv : the preprint server for biology (2024)
Irina A Eliseeva, Andrey I Buyan, Egor A Smolin, Karina S Kaliadzenka, Sergey Popov, Ivan V Kulakovskiy, Dmitry N Lyabin
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. International journal of molecular sciences 25 (3) (2024)
Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A Ramilowski, Andrey I Sigorskikh, Lisa J Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M Hoffman, Chikashi C Terao, Ivan V Kulakovskiy, Takeya Kasukawa, Jay W Shin, Piero Carninci, Michiel J L de Hoon
Annotation of nuclear lncRNAs based on chromatin interactions. PloS one 19 (5) (2024)
Ruslan M Deviatiiarov, Anna Gams, Ivan V Kulakovskiy, Andrey I Buyan, Georgy Meshcheryakov, Roman Syunyaev, Ramesh Singh, Palak Shah, Tatiana V Tatarinova, Oleg A Gusev, Igor R Efimov
An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure. Nature cardiovascular research 2 (1) (2023)
Maksim Erokhin, J Lesley Brown, Dmitry Lomaev, Nadezhda E Vorobyeva, Liangliang Zhang, Lika V Fab, Marina Yu Mazina, Ivan V Kulakovskiy, Rustam H Ziganshin, Paul Schedl, Pavel G Georgiev, Ming-An Sun, Judith A Kassis, Darya Chetverina
Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila. Nucleic acids research (2023)
Aleksandra S Anisimova, Natalia M Kolyupanova, Nadezhda E Makarova, Artyom A Egorov, Ivan V Kulakovskiy, Sergey E Dmitriev
Human Tissues Exhibit Diverse Composition of Translation Machinery. International journal of molecular sciences 24 (9) (2023)
Maksim Erokhin, J Lesley Brown, Dmitry Lomaev, Nadezhda E Vorobyeva, Liangliang Zhang, Lika V Fab, Marina Yu Mazina, Ivan V Kulakovskiy, Rustam H Ziganshin, Paul Schedl, Pavel G Georgiev, Ming-An Sun, Judith A Kassis, Darya Chetverina
Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila. Nucleic acids research (2023)
Aleksandra S Anisimova, Natalia M Kolyupanova, Nadezhda E Makarova, Artyom A Egorov, Ivan V Kulakovskiy, Sergey E Dmitriev
Human Tissues Exhibit Diverse Composition of Translation Machinery. International journal of molecular sciences 24 (9) (2023)
Ilya E Vorontsov, Irina A Eliseeva, Arsenii Zinkevich, Mikhail Nikonov, Sergey Abramov, Alexandr Boytsov, Vasily Kamenets, Alexandra Kasianova, Semyon Kolmykov, Ivan S Yevshin, Alexander Favorov, Yulia A Medvedeva, Arttu Jolma, Fedor Kolpakov, Vsevolod J Makeev, Ivan V Kulakovskiy
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors. Nucleic acids research (2023)
Aksinya N Uvarova, Ekaterina M Stasevich, Alina S Ustiugova, Nikita A Mitkin, Elina A Zheremyan, Savely A Sheetikov, Ksenia V Zornikova, Apollinariya V Bogolyubova, Mikhail A Rubtsov, Ivan V Kulakovskiy, Dmitry V Kuprash, Kirill V Korneev, Anton M Schwartz
rs71327024 Associated with COVID-19 Hospitalization Reduces CXCR6 Promoter Activity in Human CD4 + T Cells via Disruption of c-Myb Binding. International journal of molecular sciences 24 (18) (2023)
Alexandr Boytsov, Sergey Abramov, Vsevolod J Makeev, Ivan V Kulakovskiy
Positional weight matrices have sufficient prediction power for analysis of noncoding variants. F1000Research 11 (2022)
Alexandr Boytsov, Sergey Abramov, Vsevolod J Makeev, Ivan V Kulakovskiy
Positional weight matrices have sufficient prediction power for analysis of noncoding variants. F1000Research 11 (2022)
Daria Marakulina, Ilya E Vorontsov, Ivan V Kulakovskiy, Andreas Lennartsson, Finn Drabløs, Yulia A Medvedeva
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. Nucleic acids research (2022)
Victoria V Smirnova, Ekaterina D Shestakova, Daria S Nogina, Polina A Mishchenko, Tatiana A Prikazchikova, Tatiana A Prikazchikova, Ivan V Kulakovskiy, Ilya M Terenin, Ilya M Terenin
Ribosomal leaky scanning through a translated uORF requires eIF4G2. Nucleic acids research 50 (2) (2022)
Alexandr Boytsov, Sergey Abramov, Ariuna Z Aiusheeva, Alexandra M Kasianova, Eugene F Baulin, Ivan A Kuznetsov, Yurii S Aulchenko, Semyon K Kolmykov, Ivan Yevshin, Fedor 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 research (2022)
Alexandr Boytsov, Sergey Abramov, Vsevolod J Makeev, Ivan V Kulakovskiy
Positional weight matrices have sufficient prediction power for analysis of noncoding variants. F1000Research 11 (2022)
Sergey Abramov, Alexandr Boytsov, Daria Bykova, Dmitry D Penzar, Ivan Yevshin, Semyon K Kolmykov, Marina V Fridman, Alexander V Favorov, Ilya E Vorontsov, Eugene F Baulin, Fedor Kolpakov, Vsevolod J Makeev, Ivan V Kulakovskiy
Landscape of allele-specific transcription factor binding in the human genome. Nature communications 12 (1) (2021)
Anna A Shalybkova, Darya S Mikhailova, Ivan V Kulakovskiy, Liliia I Fakhranurova, Eugene F Baulin
Annotation of the local context of the RNA secondary structure improves the classification and prediction of A-minors. RNA (New York, N.Y.) (2021)
Alexander Tomashevsky, Ekaterina Kulakovskaya, Ludmila Trilisenko, Ivan V Kulakovskiy, Tatiana Kulakovskaya, Alexey Fedorov, Mikhail Eldarov
VTC4 Polyphosphate Polymerase Knockout Increases Stress Resistance of Saccharomyces cerevisiae Cells. Biology 10 (6) (2021)
Aleksandra S Anisimova, Mark B Meerson, Maxim V Gerashchenko, Ivan V Kulakovskiy, Sergey E Dmitriev, Vadim N Gladyshev
Multifaceted deregulation of gene expression and protein synthesis with age. Proceedings of the National Academy of Sciences of the United States of America 117 (27) (2020)
Artyom A Egorov, Ekaterina A Sakharova, Aleksandra S Anisimova, Sergey E Dmitriev, Vadim N Gladyshev, Ivan V Kulakovskiy
svist4get: a simple visualization tool for genomic tracks from sequencing experiments. BMC bioinformatics 20 (1) (2019)
Dustin Shigaki, Orit Adato, Aashish N Adhikari, Shengcheng Dong, Alex Hawkins-Hooker, Fumitaka Inoue, Tamar Juven-Gershon, Henry Kenlay, Beth Martin, Ayoti Patra, Dmitry D Penzar, Max Schubach, Chenling Xiong, Zhongxia Yan, Alan P Boyle, Anat Kreimer, Ivan V Kulakovskiy, John Reid, Ron Unger, Nir Yosef, Jay Shendure, Nadav Ahituv, Martin Kircher, Michael A Beer
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. Human mutation 40 (9) (2019)
Ludmila Trilisenko, Anton N Zvonarev, Airat Valiakhmetov, Alexey A Penin, Irina A Eliseeva, Vladimir Ostroumov, Ivan V Kulakovskiy, Tatiana Kulakovskaya
The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae. Cells 8 (5) (2019)
Ilya E Vorontsov, Alla D Fedorova, Ivan S Yevshin, Ruslan N Sharipov, Fedor A Kolpakov, Vsevolod J Makeev, Ivan V Kulakovskiy
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. BMC research notes 11 (1) (2018)