A citation-based method for searching scientific literature

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, 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, Dmitriy M Chudakov. Nucleic Acids Res 2018
Times Cited: 178







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



Times Cited
  Times     Co-cited
Similarity


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
44

McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences.
Nili Tickotsky, Tal Sagiv, Jaime Prilusky, Eric Shifrut, Nir Friedman. Bioinformatics 2017
126
38

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
36

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
28

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
26

Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening.
Huang Huang, Chunlin Wang, Florian Rubelt, Thomas J Scriba, Mark M Davis. Nat Biotechnol 2020
103
20

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
18

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
34

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
17

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
16

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
14

The Immune Epitope Database (IEDB): 2018 update.
Randi Vita, Swapnil Mahajan, James A Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R Cantrell, Daniel K Wheeler, Alessandro Sette, Bjoern Peters. Nucleic Acids Res 2019
634
13

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
12

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
12

The molecular basis for public T-cell responses?
Vanessa Venturi, David A Price, Daniel C Douek, Miles P Davenport. Nat Rev Immunol 2008
241
11

High-throughput immune repertoire analysis with IGoR.
Quentin Marcou, Thierry Mora, Aleksandra M Walczak. Nat Commun 2018
102
11

High-resolution repertoire analysis reveals a major bystander activation of Tfh and Tfr cells.
Paul-Gydeon Ritvo, Ahmed Saadawi, Pierre Barennes, Valentin Quiniou, Wahiba Chaara, Karim El Soufi, Benjamin Bonnet, Adrien Six, Mikhail Shugay, Encarnita Mariotti-Ferrandiz,[...]. Proc Natl Acad Sci U S A 2018
41
26

NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.
Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters, Morten Nielsen. J Immunol 2017
652
11

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs.
Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M Walczak, Thierry Mora. Bioinformatics 2019
71
15

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates.
Yannick Simoni, Etienne Becht, Michael Fehlings, Chiew Yee Loh, Si-Lin Koo, Karen Wei Weng Teng, Joe Poh Sheng Yeong, Rahul Nahar, Tong Zhang, Hassen Kared,[...]. Nature 2018
597
11

Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers.
Hongyi Zhang, Longchao Liu, Jian Zhang, Jiahui Chen, Jianfeng Ye, Sachet Shukla, Jian Qiao, Xiaowei Zhan, Hao Chen, Catherine J Wu,[...]. Clin Cancer Res 2020
48
22

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
10

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.
Elham Azizi, Ambrose J Carr, George Plitas, Andrew E Cornish, Catherine Konopacki, Sandhya Prabhakaran, Juozas Nainys, Kenmin Wu, Vaidotas Kiseliovas, Manu Setty,[...]. Cell 2018
775
10

Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling.
Olga V Britanova, Ekaterina V Putintseva, Mikhail Shugay, Ekaterina M Merzlyak, Maria A Turchaninova, Dmitriy B Staroverov, Dmitriy A Bolotin, Sergey Lukyanov, Ekaterina A Bogdanova, Ilgar Z Mamedov,[...]. J Immunol 2014
239
10

Towards error-free profiling of immune repertoires.
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,[...]. Nat Methods 2014
264
9

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
10

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire.
John F Beausang, Amanda J Wheeler, Natalie H Chan, Violet R Hanft, Frederick M Dirbas, Stefanie S Jeffrey, Stephen R Quake. Proc Natl Acad Sci U S A 2017
36
25

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity.
Asaf Madi, Eric Shifrut, Shlomit Reich-Zeliger, Hilah Gal, Katharine Best, Wilfred Ndifon, Benjamin Chain, Irun R Cohen, Nir Friedman. Genome Res 2014
112
9

Why must T cells be cross-reactive?
Andrew K Sewell. Nat Rev Immunol 2012
278
9

Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs.
Ido Springer, Hanan Besser, Nili Tickotsky-Moskovitz, Shirit Dvorkin, Yoram Louzoun. Front Immunol 2020
35
25

Linking T-cell receptor sequence to functional phenotype at the single-cell level.
Arnold Han, Jacob Glanville, Leo Hansmann, Mark M Davis. Nat Biotechnol 2014
335
9

Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires.
Sofie Gielis, Pieter Moris, Wout Bittremieux, Nicolas De Neuter, Benson Ogunjimi, Kris Laukens, Pieter Meysman. Front Immunol 2019
32
28

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab.
Nadeem Riaz, Jonathan J Havel, Vladimir Makarov, Alexis Desrichard, Walter J Urba, Jennifer S Sims, F Stephen Hodi, Salvador Martín-Algarra, Rajarsi Mandal, William H Sharfman,[...]. Cell 2017
927
8


Determinants of public T cell responses.
Hanjie Li, Congting Ye, Guoli Ji, Jiahuai Han. Cell Res 2012
77
10

The many important facets of T-cell repertoire diversity.
Janko Nikolich-Zugich, Mark K Slifka, Ilhem Messaoudi. Nat Rev Immunol 2004
414
8

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
8

Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing.
Mark Klinger, Francois Pepin, Jen Wilkins, Thomas Asbury, Tobias Wittkop, Jianbiao Zheng, Martin Moorhead, Malek Faham. PLoS One 2015
63
12

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians.
Olga V Britanova, Mikhail Shugay, Ekaterina M Merzlyak, Dmitriy B Staroverov, Ekaterina V Putintseva, Maria A Turchaninova, Ilgar Z Mamedov, Mikhail V Pogorelyy, Dmitriy A Bolotin, Mark Izraelson,[...]. J Immunol 2016
74
10

High-throughput determination of the antigen specificities of T cell receptors in single cells.
Shu-Qi Zhang, Ke-Yue Ma, Alexandra A Schonnesen, Mingliang Zhang, Chenfeng He, Eric Sun, Chad M Williams, Weiping Jia, Ning Jiang. Nat Biotechnol 2018
82
9

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.
Asaf Madi, Asaf Poran, Eric Shifrut, Shlomit Reich-Zeliger, Erez Greenstein, Irena Zaretsky, Tomer Arnon, Francois Van Laethem, Alfred Singer, Jinghua Lu,[...]. Elife 2017
76
10

PIRD: Pan Immune Repertoire Database.
Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang, Wensi Du, Shiyu Wang, Nannan Guo, Chuanchuan Ma, Lihua Luo,[...]. Bioinformatics 2020
24
33

Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges.
Marco De Simone, Grazisa Rossetti, Massimiliano Pagani. Front Immunol 2018
88
9

Peripheral T cell expansion predicts tumour infiltration and clinical response.
Thomas D Wu, Shravan Madireddi, Patricia E de Almeida, Romain Banchereau, Ying-Jiun J Chen, Avantika S Chitre, Eugene Y Chiang, Hina Iftikhar, William E O'Gorman, Amelia Au-Yeung,[...]. Nature 2020
232
8

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Brian D Corrie, Nishanth Marthandan, Bojan Zimonja, Jerome Jaglale, Yang Zhou, Emily Barr, Nicole Knoetze, Frances M W Breden, Scott Christley, Jamie K Scott,[...]. Immunol Rev 2018
53
13

High-throughput pairing of T cell receptor α and β sequences.
Bryan Howie, Anna M Sherwood, Ashley D Berkebile, Jan Berka, Ryan O Emerson, David W Williamson, Ilan Kirsch, Marissa Vignali, Mark J Rieder, Christopher S Carlson,[...]. Sci Transl Med 2015
142
7

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang,[...]. Cell 2017
942
7

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.
Scott Christley, Walter Scarborough, Eddie Salinas, William H Rounds, Inimary T Toby, John M Fonner, Mikhail K Levin, Min Kim, Stephen A Mock, Christopher Jordan,[...]. Front Immunol 2018
36
19

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
10

Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination.
Vanessa Venturi, Katherine Kedzierska, David A Price, Peter C Doherty, Daniel C Douek, Stephen J Turner, Miles P Davenport. Proc Natl Acad Sci U S A 2006
115
7


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.