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ORCIDDmitry Chudakov
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Journal Articles
- 2024
[j10]Vadim K. Karnaukhov
, Dmitrii S. Shcherbinin, Anton O. Chugunov, Dmitriy M. Chudakov, Roman G. Efremov, Ivan V. Zvyagin, Mikhail Shugay:
Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen. Nat. Comput. Sci. 4(7): 510-521 (2024)- 2023
- [j9]Alexey N. Davydov, Dmitry Bolotin, Stanislav V. Poslavsky, Dmitry M. Chudakov:
Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'. Briefings Bioinform. 24(6) (2023) - 2020
- [j8]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:
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Nucleic Acids Res. 48(Database-Issue): D1057-D1062 (2020) - 2018
- [j7]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:
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res. 46(Database-Issue): D419-D427 (2018) - 2017
- [j6]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:
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput. Biol. 13(5) (2017) - [j5]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:
Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. PLoS Comput. Biol. 13(7) (2017) - 2016
- [j4]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:
Local fitness landscape of the green fluorescent protein. Nat. 533(7603): 397-401 (2016) - 2015
- [j3]Vadim Nazarov, Mikhail Pogorelyy, Ekaterina Komech, Ivan Zvyagin, Dmitry Bolotin, Mikhail Shugay, Dmitry Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov:
tcR: an R package for T cell receptor repertoire advanced data analysis. BMC Bioinform. 16: 175:1-175:5 (2015) - [j2]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:
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11(11) (2015) - 2010
- [j1]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:
The Structure of Ca2+ Sensor Case16 Reveals the Mechanism of Reaction to Low Ca2+ Concentrations. Sensors 10(9): 8143-8160 (2010)
Conference and Workshop Papers
- 2021
- [c1]Dmitry Chudakov, Sergey Alyamkin, Alexander Goncharenko, Andrey Denisov:
Iterative Adaptation to Quantization Noise. IWANN (1) 2021: 303-310
Coauthor Index
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