A citation-based method for searching scientific literature

Emmi Jokinen, Jani Huuhtanen, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki. PLoS Comput Biol 2021
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


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
271
75

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
371
62

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
90
37

DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires.
John-William Sidhom, H Benjamin Larman, Drew M Pardoll, Alexander S Baras. Nat Commun 2021
17
37

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
56
37

Predicting antigen specificity of single T cells based on TCR CDR3 regions.
David S Fischer, Yihan Wu, Benjamin Schubert, Fabian J Theis. Mol Syst Biol 2020
17
37

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
705
37

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
21
25

Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity.
Jason A Carter, Jonathan B Preall, Kristina Grigaityte, Stephen J Goldfless, Eric Jeffery, Adrian W Briggs, Francois Vigneault, Gurinder S Atwal. Front Immunol 2019
22
25


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
161
25

Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction.
Paul L Klarenbeek, Marieke E Doorenspleet, Rebecca E E Esveldt, Barbera D C van Schaik, Neubury Lardy, Antoine H C van Kampen, Paul P Tak, Robert M Plenge, Frank Baas, Paul I W de Bakker,[...]. PLoS One 2015
18
25

T cell antigen receptor recognition of antigen-presenting molecules.
Jamie Rossjohn, Stephanie Gras, John J Miles, Stephen J Turner, Dale I Godfrey, James McCluskey. Annu Rev Immunol 2015
360
25

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
20
25

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
138
25

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.
William D Chronister, Austin Crinklaw, Swapnil Mahajan, Randi Vita, Zeynep Koşaloğlu-Yalçın, Zhen Yan, Jason A Greenbaum, Leon E Jessen, Morten Nielsen, Scott Christley,[...]. Front Immunol 2021
7
28

Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.
Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman. Brief Bioinform 2021
7
28

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition.
Nicolas De Neuter, Wout Bittremieux, Charlie Beirnaert, Bart Cuypers, Aida Mrzic, Pieter Moris, Arvid Suls, Viggo Van Tendeloo, Benson Ogunjimi, Kris Laukens,[...]. Immunogenetics 2018
20
25

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
26
25

Do HLA genes play a prominent role in determining T cell receptor V alpha segment usage in humans?
B Gulwani-Akolkar, B Shi, P N Akolkar, K Ito, W B Bias, J Silver. J Immunol 1995
27
12

Understanding the drivers of MHC restriction of T cell receptors.
Nicole L La Gruta, Stephanie Gras, Stephen R Daley, Paul G Thomas, Jamie Rossjohn. Nat Rev Immunol 2018
81
12

The molecular basis of TCR germline bias for MHC is surprisingly simple.
K Christopher Garcia, Jarrett J Adams, Dan Feng, Lauren K Ely. Nat Immunol 2009
163
12

Epstein-Barr Virus Epitope-Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires.
Anna Gil, Larisa Kamga, Ramakanth Chirravuri-Venkata, Nuray Aslan, Fransenio Clark, Dario Ghersi, Katherine Luzuriaga, Liisa K Selin. mBio 2020
8
12

T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.
Jarrett J Adams, Samanthi Narayanan, Baoyu Liu, Michael E Birnbaum, Andrew C Kruse, Natalie A Bowerman, Wei Chen, Aron M Levin, Janet M Connolly, Cheng Zhu,[...]. Immunity 2011
165
12

T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus.
Amandine Bovay, Vincent Zoete, Garry Dolton, Anna M Bulek, David K Cole, Pierre J Rizkallah, Anna Fuller, Konrad Beck, Olivier Michielin, Daniel E Speiser,[...]. Eur J Immunol 2018
17
12

How T cells 'see' antigen.
Michelle Krogsgaard, Mark M Davis. Nat Immunol 2005
161
12

Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide.
Christopher G Kanakry, David G Coffey, Andrea M H Towlerton, Ante Vulic, Barry E Storer, Jeffrey Chou, Cecilia C S Yeung, Christopher D Gocke, Harlan S Robins, Paul V O'Donnell,[...]. JCI Insight 2016
72
12


SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction.
Yao Tong, Jiayin Wang, Tian Zheng, Xuanping Zhang, Xiao Xiao, Xiaoyan Zhu, Xin Lai, Xiang Liu. Comput Biol Chem 2020
6
16


Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor.
David K Cole, Fang Yuan, Pierre J Rizkallah, John J Miles, Emma Gostick, David A Price, George F Gao, Bent K Jakobsen, Andrew K Sewell. J Biol Chem 2009
109
12

Genetic variation in MHC proteins is associated with T cell receptor expression biases.
Eilon Sharon, Leah V Sibener, Alexis Battle, Hunter B Fraser, K Christopher Garcia, Jonathan K Pritchard. Nat Genet 2016
67
12

Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides.
Florian Madura, Pierre J Rizkallah, Christopher J Holland, Anna Fuller, Anna Bulek, Andrew J Godkin, Andrea J Schauenburg, David K Cole, Andrew K Sewell. Eur J Immunol 2015
43
12

CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection.
Larisa Kamga, Anna Gil, Inyoung Song, Robin Brody, Dario Ghersi, Nuray Aslan, Lawrence J Stern, Liisa K Selin, Katherine Luzuriaga. PLoS Pathog 2019
8
12


Immunoglobulins or Antibodies: IMGT® Bridging Genes, Structures and Functions.
Marie-Paule Lefranc, Gérard Lefranc. Biomedicines 2020
10
12

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
Leming Shi, Laura H Reid, Wendell D Jones, Richard Shippy, Janet A Warrington, Shawn C Baker, Patrick J Collins, Francoise de Longueville, Ernest S Kawasaki, Kathleen Y Lee,[...]. Nat Biotechnol 2006
12

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
308
12

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.
Jacob Glanville, Wenwu Zhai, Jan Berka, Dilduz Telman, Gabriella Huerta, Gautam R Mehta, Irene Ni, Li Mei, Purnima D Sundar, Giles M R Day,[...]. Proc Natl Acad Sci U S A 2009
300
12

An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors.
Yong-Chen Lu, Zhili Zheng, Paul F Robbins, Eric Tran, Todd D Prickett, Jared J Gartner, Yong F Li, Satyajit Ray, Zulmarie Franco, Valery Bliskovsky,[...]. Mol Ther 2018
45
12

Analyzing Immunoglobulin Repertoires.
Neha Chaudhary, Duane R Wesemann. Front Immunol 2018
35
12

Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery.
Shin-Heng Chiou, Diane Tseng, Alexandre Reuben, Vamsee Mallajosyula, Irene S Molina, Stephanie Conley, Julie Wilhelmy, Alana M McSween, Xinbo Yang, Daisuke Nishimiya,[...]. Immunity 2021
8
12

A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies.
Eve Richardson, Jacob D Galson, Paul Kellam, Dominic F Kelly, Sarah E Smith, Anne Palser, Simon Watson, Charlotte M Deane. MAbs 2021
5
20

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
22
12

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
90
12

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire.
Brandon J DeKosky, Gregory C Ippolito, Ryan P Deschner, Jason J Lavinder, Yariv Wine, Brandon M Rawlings, Navin Varadarajan, Claudia Giesecke, Thomas Dörner, Sarah F Andrews,[...]. Nat Biotechnol 2013
289
12

The promise and challenge of high-throughput sequencing of the antibody repertoire.
George Georgiou, Gregory C Ippolito, John Beausang, Christian E Busse, Hedda Wardemann, Stephen R Quake. Nat Biotechnol 2014
386
12

The Transcription Factor T-bet Resolves Memory B Cell Subsets with Distinct Tissue Distributions and Antibody Specificities in Mice and Humans.
John L Johnson, Rebecca L Rosenthal, James J Knox, Arpita Myles, Martin S Naradikian, Joanna Madej, Mariya Kostiv, Aaron M Rosenfeld, Wenzhao Meng, Shannon R Christensen,[...]. Immunity 2020
46
12

Measuring T cell receptor and T cell gene expression diversity in antigen-responsive human CD4+ T cells.
Anne Eugster, Annett Lindner, Anne-Kristin Heninger, Carmen Wilhelm, Sevina Dietz, Mara Catani, Anette-G Ziegler, Ezio Bonifacio. J Immunol Methods 2013
23
12



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.