A citation-based method for searching scientific literature

Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke. BMC Biotechnol 2017
Times Cited: 136







List of co-cited articles
906 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
28

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
22

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
18

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
17

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
15

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

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
14

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
14

Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges.
Marco De Simone, Grazisa Rossetti, Massimiliano Pagani. Front Immunol 2018
88
15

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
13

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
12

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
12

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
26

Sequence analysis of T-cell repertoires in health and disease.
Daniel J Woodsworth, Mauro Castellarin, Robert A Holt. Genome Med 2013
119
10


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
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
10

Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma.
Michael A Postow, Manuarii Manuel, Phillip Wong, Jianda Yuan, Zhiwan Dong, Cailian Liu, Solène Perez, Isabelle Tanneau, Marlène Noel, Anaïs Courtier,[...]. J Immunother Cancer 2015
144
10

Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma.
Sabrina A Hogan, Anaïs Courtier, Phil F Cheng, Nicoletta F Jaberg-Bentele, Simone M Goldinger, Manuarii Manuel, Solène Perez, Nadia Plantier, Jean-François Mouret, Thi Dan Linh Nguyen-Kim,[...]. Cancer Immunol Res 2019
69
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
10

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
10

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

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
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
12

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
9

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T Reddy. Trends Immunol 2015
105
9

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
9

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
9

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance.
Whijae Roh, Pei-Ling Chen, Alexandre Reuben, Christine N Spencer, Peter A Prieto, John P Miller, Vancheswaran Gopalakrishnan, Feng Wang, Zachary A Cooper, Sangeetha M Reddy,[...]. Sci Transl Med 2017
476
9

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
9

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
9

Improved survival with ipilimumab in patients with metastatic melanoma.
F Stephen Hodi, Steven J O'Day, David F McDermott, Robert W Weber, Jeffrey A Sosman, John B Haanen, Rene Gonzalez, Caroline Robert, Dirk Schadendorf, Jessica C Hassel,[...]. N Engl J Med 2010
8

How many TCR clonotypes does a body maintain?
Grant Lythe, Robin E Callard, Rollo L Hoare, Carmen Molina-París. J Theor Biol 2016
71
11

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


Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
8

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
8

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
683
8

Structural determinants of T-cell receptor bias in immunity.
Stephen J Turner, Peter C Doherty, James McCluskey, Jamie Rossjohn. Nat Rev Immunol 2006
274
8

PD-1 identifies the patient-specific CD8⁺ tumor-reactive repertoire infiltrating human tumors.
Alena Gros, Paul F Robbins, Xin Yao, Yong F Li, Simon Turcotte, Eric Tran, John R Wunderlich, Arnold Mixon, Shawn Farid, Mark E Dudley,[...]. J Clin Invest 2014
676
8

αβ T cell receptors as predictors of health and disease.
Meriem Attaf, Eric Huseby, Andrew K Sewell. Cell Mol Immunol 2015
80
10

IgBLAST: an immunoglobulin variable domain sequence analysis tool.
Jian Ye, Ning Ma, Thomas L Madden, James M Ostell. Nucleic Acids Res 2013
603
8

High-throughput identification of antigen-specific TCRs by TCR gene capture.
Carsten Linnemann, Bianca Heemskerk, Pia Kvistborg, Roelof J C Kluin, Dmitriy A Bolotin, Xiaojing Chen, Kaspar Bresser, Marja Nieuwland, Remko Schotte, Samira Michels,[...]. Nat Med 2013
128
7

High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities.
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain. Brief Bioinform 2018
62
11

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.
Dmitry A Bolotin, Ilgar Z Mamedov, Olga V Britanova, Ivan V Zvyagin, Dmitriy Shagin, Svetlana V Ustyugova, Maria A Turchaninova, Sergey Lukyanov, Yury B Lebedev, Dmitriy M Chudakov. Eur J Immunol 2012
125
7

T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma.
Alexander C Hopkins, Mark Yarchoan, Jennifer N Durham, Erik C Yusko, Julie A Rytlewski, Harlan S Robins, Daniel A Laheru, Dung T Le, Eric R Lutz, Elizabeth M Jaffee. JCI Insight 2018
135
7

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
7

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
7

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
7

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.
Peter Savas, Balaji Virassamy, Chengzhong Ye, Agus Salim, Christopher P Mintoff, Franco Caramia, Roberto Salgado, David J Byrne, Zhi L Teo, Sathana Dushyanthen,[...]. Nat Med 2018
440
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.