A citation-based method for searching scientific literature

Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S Egorov, Alexey N Davydov, Dmitriy M Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain, Anne Eugster, Karl Kashofer, Peter P Rainer, Samuel Darko, Amy Ransier, Daniel C Douek, David Klatzmann, Encarnita Mariotti-Ferrandiz. Nat Biotechnol 2021
Times Cited: 42







List of co-cited articles
441 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
40

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
28

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
26

IgBLAST: an immunoglobulin variable domain sequence analysis tool.
Jian Ye, Ning Ma, Thomas L Madden, James M Ostell. Nucleic Acids Res 2013
603
26

Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges.
Marco De Simone, Grazisa Rossetti, Massimiliano Pagani. Front Immunol 2018
88
23

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
21

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
21


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
19

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
19

High-throughput immune repertoire analysis with IGoR.
Quentin Marcou, Thierry Mora, Aleksandra M Walczak. Nat Commun 2018
102
16

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
16

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
16

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
14

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
14

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
14

The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.
Adrien Six, Maria Encarnita Mariotti-Ferrandiz, Wahiba Chaara, Susana Magadan, Hang-Phuong Pham, Marie-Paule Lefranc, Thierry Mora, Véronique Thomas-Vaslin, Aleksandra M Walczak, Pierre Boudinot. Front Immunol 2013
111
14


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
14

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
14

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


Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing.
Edward S Lee, Paul G Thomas, Jeff E Mold, Andrew J Yates. PLoS Comput Biol 2017
26
23

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
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

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
11

Genesis of the αβ T-cell receptor.
Thomas Dupic, Quentin Marcou, Aleksandra M Walczak, Thierry Mora. PLoS Comput Biol 2019
36
13

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
11

The many important facets of T-cell repertoire diversity.
Janko Nikolich-Zugich, Mark K Slifka, Ilhem Messaoudi. Nat Rev Immunol 2004
414
11

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
11

Clonal replacement of tumor-specific T cells following PD-1 blockade.
Kathryn E Yost, Ansuman T Satpathy, Daniel K Wells, Yanyan Qi, Chunlin Wang, Robin Kageyama, Katherine L McNamara, Jeffrey M Granja, Kavita Y Sarin, Ryanne A Brown,[...]. Nat Med 2019
538
11

The Future of Blood Testing Is the Immunome.
Ramy A Arnaout, Eline T Luning Prak, Nicholas Schwab, Florian Rubelt. Front Immunol 2021
15
33

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.
Felix Breden, Eline T Luning Prak, Bjoern Peters, Florian Rubelt, Chaim A Schramm, Christian E Busse, Jason A Vander Heiden, Scott Christley, Syed Ahmad Chan Bukhari, Adrian Thorogood,[...]. Front Immunol 2017
51
11

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
11

High-throughput sequencing of the zebrafish antibody repertoire.
Joshua A Weinstein, Ning Jiang, Richard A White, Daniel S Fisher, Stephen R Quake. Science 2009
301
11

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.
J Douglas Freeman, René L Warren, John R Webb, Brad H Nelson, Robert A Holt. Genome Res 2009
270
11


Rep-Seq: uncovering the immunological repertoire through next-generation sequencing.
Jennifer Benichou, Rotem Ben-Hamo, Yoram Louzoun, Sol Efroni. Immunology 2012
155
11

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.
Rahmad Akbar, Philippe A Robert, Milena Pavlović, Jeliazko R Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R Weber, Lonneke Scheffer, Enkelejda Miho, Ingrid Hobæk Haff,[...]. Cell Rep 2021
37
13

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.
Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D'Angelo, Branden Olson,[...]. Bioinformatics 2020
21
23

T cell receptor β repertoires as novel diagnostic markers for systemic lupus erythematosus and rheumatoid arthritis.
Xiao Liu, Wei Zhang, Ming Zhao, Longfei Fu, Limin Liu, Jinghua Wu, Shuangyan Luo, Longlong Wang, Zijun Wang, Liya Lin,[...]. Ann Rheum Dis 2019
44
11

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma.
Hanjie Li, Anne M van der Leun, Ido Yofe, Yaniv Lubling, Dikla Gelbard-Solodkin, Alexander C J van Akkooi, Marlous van den Braber, Elisa A Rozeman, John B A G Haanen, Christian U Blank,[...]. Cell 2019
410
11

Analysis of the B cell receptor repertoire in six immune-mediated diseases.
R J M Bashford-Rogers, L Bergamaschi, E F McKinney, D C Pombal, F Mescia, J C Lee, D C Thomas, S M Flint, P Kellam, D R W Jayne,[...]. Nature 2019
87
11

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
11

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
9

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
9

Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes.
Howard R Seay, Erik Yusko, Stephanie J Rothweiler, Lin Zhang, Amanda L Posgai, Martha Campbell-Thompson, Marissa Vignali, Ryan O Emerson, John S Kaddis, Dave Ko,[...]. JCI Insight 2016
67
9

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
9

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
9

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


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.