Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling

por Rakhmanov, Sergei V, Makeev, Vsevolod J
Publicado 2007

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

por Vorontsov, Ilya E, Kulakovskiy, Ivan V, Makeev, Vsevolod J
Publicado 2013

Preservation of methylated CpG dinucleotides in human CpG islands

por Panchin, Alexander Y., Makeev, Vsevolod J., Medvedeva, Yulia A.
Publicado 2016

Positional weight matrices have sufficient prediction power for analysis of noncoding variants

por Boytsov, Alexandr, Abramov, Sergey, Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Publicado 2022

A model of evolution with constant selective pressure for regulatory DNA sites

por Enikeeva, Farida N, Kotelnikova, Ekaterina A, Gelfand, Mikhail S, Makeev, Vsevolod J
Publicado 2007

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

por Boeva, Valentina, Clément, Julien, Régnier, Mireille, Roytberg, Mikhail A, Makeev, Vsevolod J
Publicado 2007

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

por Nikulova, Anna A., Favorov, Alexander V., Sutormin, Roman A., Makeev, Vsevolod J., Mironov, Andrey A.
Publicado 2012

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

por Favorov, Alexander, Mularoni, Loris, Cope, Leslie M., Medvedeva, Yulia, Mironov, Andrey A., Makeev, Vsevolod J., Wheelan, Sarah J.
Publicado 2012

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

por Logacheva, Maria D, Kasianov, Artem S, Vinogradov, Dmitriy V, Samigullin, Tagir H, Gelfand, Mikhail S, Makeev, Vsevolod J, Penin, Aleksey A
Publicado 2011

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

por Kulakovskiy, Ivan V., Medvedeva, Yulia A., Schaefer, Ulf, Kasianov, Artem S., Vorontsov, Ilya E., Bajic, Vladimir B., Makeev, Vsevolod J.
Publicado 2013

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

por Papatsenko, Dmitri, Darr, Henia, Kulakovskiy, Ivan V., Waghray, Avinash, Makeev, Vsevolod J., MacArthur, Ben D., Lemischka, Ihor R.
Publicado 2015

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

por Levitsky, Victor G, Kulakovskiy, Ivan V, Ershov, Nikita I, Oshchepkov, Dmitry Yu, Makeev, Vsevolod J, Hodgman, T C, Merkulova, Tatyana I
Publicado 2014

Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains

por Zakharevich, Natalia V., Averina, Olga V., Klimina, Ksenia M., Kudryavtseva, Anna V., Kasianov, Artem S., Makeev, Vsevolod J., Danilenko, Valery N.
Publicado 2014

Negative selection maintains transcription factor binding motifs in human cancer

por Vorontsov, Ilya E., Khimulya, Grigory, Lukianova, Elena N., Nikolaeva, Daria D., Eliseeva, Irina A., Kulakovskiy, Ivan V., Makeev, Vsevolod J.
Publicado 2016

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

por Vorontsov, Ilya E., Fedorova, Alla D., Yevshin, Ivan S., Sharipov, Ruslan N., Kolpakov, Fedor A., Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Publicado 2018

GTRD: an integrated view of transcription regulation

por Kolmykov, Semyon, Yevshin, Ivan, Kulyashov, Mikhail, Sharipov, Ruslan, Kondrakhin, Yury, Makeev, Vsevolod J, Kulakovskiy, Ivan V, Kel, Alexander, Kolpakov, Fedor
Publicado 2020

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

por Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Publicado 2019

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

por Medvedeva, Yulia A, Fridman, Marina V, Oparina, Nina J, Malko, Dmitry B, Ermakova, Ekaterina O, Kulakovskiy, Ivan V, Heinzel, Andreas, Makeev, Vsevolod J
Publicado 2010

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance

por Odintsova, Tatyana I., Slezina, Marina P., Istomina, Ekaterina A., Korostyleva, Tatyana V., Kasianov, Artem S., Kovtun, Alexey S., Makeev, Vsevolod J., Shcherbakova, Larisa A., Kudryavtsev, Alexander M.
Publicado 2019

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

por 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
Publicado 2020