A citation-based method for searching scientific literature

Mikhail Shugay, Olga V Britanova, Ekaterina M Merzlyak, Maria A Turchaninova, Ilgar Z Mamedov, Timur R Tuganbaev, Dmitriy A Bolotin, Dmitry B Staroverov, Ekaterina V Putintseva, Karla Plevova, Carsten Linnemann, Dmitriy Shagin, Sarka Pospisilova, Sergey Lukyanov, Ton N Schumacher, Dmitriy M Chudakov. Nat Methods 2014
Times Cited: 264







List of co-cited articles
636 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


MiXCR: software for comprehensive adaptive immunity profiling.
Dmitriy A Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z Mamedov, Ekaterina V Putintseva, Dmitriy M Chudakov. Nat Methods 2015
728
45

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,[...]. PLoS Comput Biol 2015
289
25

High-quality full-length immunoglobulin profiling with unique molecular barcoding.
M A Turchaninova, A Davydov, O V Britanova, M Shugay, V Bikos, E S Egorov, V I Kirgizova, E M Merzlyak, D B Staroverov, D A Bolotin,[...]. Nat Protoc 2016
106
17

Identifying specificity groups in the T cell receptor repertoire.
Jacob Glanville, Huang Huang, Allison Nau, Olivia Hatton, Lisa E Wagar, Florian Rubelt, Xuhuai Ji, Arnold Han, Sheri M Krams, Christina Pettus,[...]. Nature 2017
453
17

Quantifiable predictive features define epitope-specific T cell receptor repertoires.
Pradyot Dash, Andrew J Fiore-Gartland, Tomer Hertz, George C Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E Bridie Clemens, Thi H O Nguyen, Katherine Kedzierska,[...]. Nature 2017
342
15

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.
Evgeny S Egorov, Ekaterina M Merzlyak, Andrew A Shelenkov, Olga V Britanova, George V Sharonov, Dmitriy B Staroverov, Dmitriy A Bolotin, Alexey N Davydov, Ekaterina Barsova, Yuriy B Lebedev,[...]. J Immunol 2015
60
23

Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling.
Ilgar Z Mamedov, Olga V Britanova, Ivan V Zvyagin, Maria A Turchaninova, Dmitriy A Bolotin, Ekaterina V Putintseva, Yuriy B Lebedev, Dmitriy M Chudakov. Front Immunol 2013
104
14

IgBLAST: an immunoglobulin variable domain sequence analysis tool.
Jian Ye, Ning Ma, Thomas L Madden, James M Ostell. Nucleic Acids Res 2013
603
11

Overview of methodologies for T-cell receptor repertoire analysis.
Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke. BMC Biotechnol 2017
136
11

Diversity and clonal selection in the human T-cell repertoire.
Qian Qi, Yi Liu, Yong Cheng, Jacob Glanville, David Zhang, Ji-Yeun Lee, Richard A Olshen, Cornelia M Weyand, Scott D Boyd, Jörg J Goronzy. Proc Natl Acad Sci U S A 2014
388
11

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Mikhail Shugay, Dmitriy V Bagaev, Ivan V Zvyagin, Renske M Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina A Komech, Anastasiya L Sycheva, Anna E Koneva, Evgeniy S Egorov,[...]. Nucleic Acids Res 2018
178
10

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
10

Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification.
Ke-Yue Ma, Chenfeng He, Ben S Wendel, Chad M Williams, Jun Xiao, Hui Yang, Ning Jiang. Front Immunol 2018
29
31

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9


Statistical inference of the generation probability of T-cell receptors from sequence repertoires.
Anand Murugan, Thierry Mora, Aleksandra M Walczak, Curtis G Callan. Proc Natl Acad Sci U S A 2012
154
8

Hydrophobic CDR3 residues promote the development of self-reactive T cells.
Brian D Stadinski, Karthik Shekhar, Iria Gómez-Touriño, Jonathan Jung, Katsuhiro Sasaki, Andrew K Sewell, Mark Peakman, Arup K Chakraborty, Eric S Huseby. Nat Immunol 2016
86
9


Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins.
Mikhail V Pogorelyy, Anastasia A Minervina, Maximilian Puelma Touzel, Anastasiia L Sycheva, Ekaterina A Komech, Elena I Kovalenko, Galina G Karganova, Evgeniy S Egorov, Alexander Yu Komkov, Dmitriy M Chudakov,[...]. Proc Natl Acad Sci U S A 2018
50
16

Counting absolute numbers of molecules using unique molecular identifiers.
Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Martin Bonke, Martin Enge, Sten Linnarsson, Jussi Taipale. Nat Methods 2011
569
8


Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T Reddy. Trends Immunol 2015
105
8

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
8

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire.
Ryan O Emerson, William S DeWitt, Marissa Vignali, Jenna Gravley, Joyce K Hu, Edward J Osborne, Cindy Desmarais, Mark Klinger, Christopher S Carlson, John A Hansen,[...]. Nat Genet 2017
215
8

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases.
Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S Egorov, Alexey N Davydov, Dmitriy M Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain,[...]. Nat Biotechnol 2021
42
19

Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells.
Harlan S Robins, Paulo V Campregher, Santosh K Srivastava, Abigail Wacher, Cameron J Turtle, Orsalem Kahsai, Stanley R Riddell, Edus H Warren, Christopher S Carlson. Blood 2009
762
7

PD-1 blockade induces responses by inhibiting adaptive immune resistance.
Paul C Tumeh, Christina L Harview, Jennifer H Yearley, I Peter Shintaku, Emma J M Taylor, Lidia Robert, Bartosz Chmielowski, Marko Spasic, Gina Henry, Voicu Ciobanu,[...]. Nature 2014
7

Sequence analysis of T-cell repertoires in health and disease.
Daniel J Woodsworth, Mauro Castellarin, Robert A Holt. Genome Med 2013
119
7

Detecting T cell receptors involved in immune responses from single repertoire snapshots.
Mikhail V Pogorelyy, Anastasia A Minervina, Mikhail Shugay, Dmitriy M Chudakov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak. PLoS Biol 2019
52
13

Antigen receptor repertoire profiling from RNA-seq data.
Dmitriy A Bolotin, Stanislav Poslavsky, Alexey N Davydov, Felix E Frenkel, Lorenzo Fanchi, Olga I Zolotareva, Saskia Hemmers, Ekaterina V Putintseva, Anna S Obraztsova, Mikhail Shugay,[...]. Nat Biotechnol 2017
138
7

tcR: an R package for T cell receptor repertoire advanced data analysis.
Vadim I Nazarov, Mikhail V Pogorelyy, Ekaterina A Komech, Ivan V Zvyagin, Dmitry A Bolotin, Mikhail Shugay, Dmitry M Chudakov, Yury B Lebedev, Ilgar Z Mamedov. BMC Bioinformatics 2015
156
7

TCR Repertoire as a Novel Indicator for Immune Monitoring and Prognosis Assessment of Patients With Cervical Cancer.
Jin-Huan Cui, Kai-Rong Lin, Song-Hua Yuan, Ya-Bin Jin, Xiang-Ping Chen, Xi-Kang Su, Jun Jiang, Ying-Ming Pan, Shao-Long Mao, Xiao-Fan Mao,[...]. Front Immunol 2018
70
10

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.
René L Warren, J Douglas Freeman, Thomas Zeng, Gina Choe, Sarah Munro, Richard Moore, John R Webb, Robert A Holt. Genome Res 2011
240
6

Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing.
Ivan V Zvyagin, Mikhail V Pogorelyy, Marina E Ivanova, Ekaterina A Komech, Mikhail Shugay, Dmitry A Bolotin, Andrey A Shelenkov, Alexey A Kurnosov, Dmitriy B Staroverov, Dmitriy M Chudakov,[...]. Proc Natl Acad Sci U S A 2014
79
7

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 A Komech, Vadim I Nazarov, Olga V Britanova, Dmitriy M Chudakov, Ilgar Z Mamedov, Yury B Lebedev,[...]. PLoS Comput Biol 2017
51
11

Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach.
Daniel J Laydon, Charles R M Bangham, Becca Asquith. Philos Trans R Soc Lond B Biol Sci 2015
99
6

T cell fate and clonality inference from single-cell transcriptomes.
Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann. Nat Methods 2016
266
6

Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.
Tarik A Khan, Simon Friedensohn, Arthur R Gorter de Vries, Jakub Straszewski, Hans-Joachim Ruscheweyh, Sai T Reddy. Sci Adv 2016
74
8

Genesis of the αβ T-cell receptor.
Thomas Dupic, Quentin Marcou, Aleksandra M Walczak, Thierry Mora. PLoS Comput Biol 2019
36
16

Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity.
William S DeWitt, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen, Philip Bradley. Elife 2018
66
9

Using synthetic templates to design an unbiased multiplex PCR assay.
Christopher S Carlson, Ryan O Emerson, Anna M Sherwood, Cindy Desmarais, Moon-Wook Chung, Joseph M Parsons, Michelle S Steen, Marissa A LaMadrid-Herrmannsfeldt, David W Williamson, Robert J Livingston,[...]. Nat Commun 2013
356
6


Systematic Comparative Evaluation of Methods for Investigating the TCRβ Repertoire.
Xiao Liu, Wei Zhang, Xiaojing Zeng, Ruifang Zhang, Yuanping Du, Xueyu Hong, Hongzhi Cao, Zheng Su, Changxi Wang, Jinghua Wu,[...]. PLoS One 2016
27
22

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.
Chunlin Wang, Catherine M Sanders, Qunying Yang, Harry W Schroeder, Elijah Wang, Farbod Babrzadeh, Baback Gharizadeh, Richard M Myers, James R Hudson, Ronald W Davis,[...]. Proc Natl Acad Sci U S A 2010
202
6

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.
Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg,[...]. Nat Immunol 2017
86
6

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.
Enkelejda Miho, Alexander Yermanos, Cédric R Weber, Christoph T Berger, Sai T Reddy, Victor Greiff. Front Immunol 2018
87
6

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,[...]. Nucleic Acids Res 2020
117
6

SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors.
Alina S Shomuradova, Murad S Vagida, Savely A Sheetikov, Ksenia V Zornikova, Dmitry Kiryukhin, Aleksei Titov, Iuliia O Peshkova, Alexandra Khmelevskaya, Dmitry V Dianov, Maria Malasheva,[...]. Immunity 2020
101
6

Low-Avidity CD4+ T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19.
Petra Bacher, Elisa Rosati, Daniela Esser, Gabriela Rios Martini, Carina Saggau, Esther Schiminsky, Justina Dargvainiene, Ina Schröder, Imke Wieters, Yascha Khodamoradi,[...]. Immunity 2020
147
6


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.