Dmitry Chudakov

According to our database, Dmitry Chudakov authored at least 11 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen.

Vadim K. Karnaukhov, Dmitrii S. Shcherbinin, Anton O. Chugunov, Dmitriy M. Chudakov, Roman G. Efremov, Ivan V. Zvyagin, Mikhail Shugay

Nat. Comput. Sci., July, 2024

2023

Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'.

Alexey N. Davydov, Dmitry Bolotin, Stanislav V. Poslavsky, Dmitry M. Chudakov

Briefings Bioinform., September, 2023

2021

Iterative Adaptation to Quantization Noise.

Dmitry Chudakov, Sergey Alyamkin, Alexander Goncharenko, Andrey Denisov

Proceedings of the Advances in Computational Intelligence, 2021

2020

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.

Dmitry V. Bagaev, Renske M. A. Vroomans, Jerome Samir, Ulrik Stervbo, Cristina Rius, Garry Dolton, Alexander Greenshields-Watson, Meriem Attaf, Evgeny S. Egorov, Ivan V. Zvyagin, Nina Babel, David K. Cole, Andrew J. Godkin, Andrew K. Sewell, Can Kesmir, Dmitry M. Chudakov, Fabio Luciani, Mikhail Shugay

Nucleic Acids Res., 2020

2018

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.

Mikhail Shugay, Dmitriy V. Bagaev, Ivan V. Zvyagin, Renske M. A. Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina Komech, Anastasiya L. Sycheva, Anna E. Koneva, Evgeniy S. Egorov, Alexey V. Eliseev, Ewald van Dyk, Pradyot Dash, Meriem Attaf, Cristina Rius, Kristin Ladell, James E. McLaren, Katherine K. Matthews, E. Bridie Clemens, Daniel C. Douek, Fabio Luciani, Debbie van Baarle, Katherine Kedzierska, Can Kesmir, Paul G. Thomas, David A. Price, Andrew K. Sewell, Dmitry M. Chudakov

Nucleic Acids Res., 2018

2017

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.

Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey A. Lukyanov, Dmitry M. Chudakov

PLoS Comput. Biol., 2017

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires.

Mikhail V. Pogorelyy, Yuval Elhanati, Quentin Marcou, Anastasiia L. Sycheva, Ekaterina Komech, Vadim I. Nazarov, Olga V. Britanova, Dmitry M. Chudakov, Ilgar Z. Mamedov, Yuri B. Lebedev, Thierry Mora, Aleksandra M. Walczak

PLoS Comput. Biol., 2017

2016

Local fitness landscape of the green fluorescent protein.

Karen S. Sarkisyan, Dmitry Bolotin, Margarita V. Meer, Dinara R. Usmanova, Alexander S. Mishin, George V. Sharonov, Dmitry N. Ivankov, Nina G. Bozhanova, Mikhail S. Baranov, Onuralp Soylemez, Natalya S. Bogatyreva, Peter K. Vlasov, Evgeny S. Egorov, Maria D. Logacheva, Alexey S. Kondrashov, Dmitry M. Chudakov, Ekaterina V. Putintseva, Ilgar Z. Mamedov, Dan S. Tawfik, Konstantin A. Lukyanov, Fyodor A. Kondrashov

Nat., 2016

2015

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitry M. Chudakov

PLoS Comput. Biol., 2015

tcR: an R package for T cell receptor repertoire advanced data analysis.

Vadim Nazarov, Mikhail Pogorelyy, Ekaterina Komech, Ivan Zvyagin, Dmitry Bolotin, Mikhail Shugay, Dmitry Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov

BMC Bioinform., 2015

2010

The Structure of Ca²⁺ Sensor Case16 Reveals the Mechanism of Reaction to Low Ca²⁺ Concentrations.

Lukas Leder, Wilhelm Stark, Felix Freuler, May Marsh, Marco Meyerhofer, Thomas Stettler, Lorenz M. Mayr, Olga V. Britanova, Lydia A. Strukova, Dmitry M. Chudakov, Ekaterina A. Souslova

Sensors, 2010