A citation-based method for searching scientific literature

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, I Z Mamedov, M Izraelson, M D Logacheva, O Kladova, K Plevova, S Pospisilova, D M Chudakov. Nat Protoc 2016
Times Cited: 106







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



Times Cited
  Times     Co-cited
Similarity


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
43

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
34

IgBLAST: an immunoglobulin variable domain sequence analysis tool.
Jian Ye, Ning Ma, Thomas L Madden, James M Ostell. Nucleic Acids Res 2013
603
30

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
416
24

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
29

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
Namita T Gupta, Jason A Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari, Steven H Kleinstein. Bioinformatics 2015
327
21

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
Jason A Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N H Stern, Kevin C O'Connor, David A Hafler, Francois Vigneault, Steven H Kleinstein. Bioinformatics 2014
224
17


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
305
16

Genetic measurement of memory B-cell recall using antibody repertoire sequencing.
Christopher Vollmers, Rene V Sit, Joshua A Weinstein, Cornelia L Dekker, Stephen R Quake. Proc Natl Acad Sci U S A 2013
165
16

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Martin M Corcoran, Ganesh E Phad, Néstor Vázquez Bernat, Christiane Stahl-Hennig, Noriyuki Sumida, Mats A A Persson, Marcel Martin, Gunilla B Karlsson Hedestam. Nat Commun 2016
103
15


High-resolution antibody dynamics of vaccine-induced immune responses.
Uri Laserson, Francois Vigneault, Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Jason A Vander Heiden, William Kelton, Sang Taek Jung, Yi Liu, Jonathan Laserson,[...]. Proc Natl Acad Sci U S A 2014
116
14

In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire.
Brandon J DeKosky, Takaaki Kojima, Alexa Rodin, Wissam Charab, Gregory C Ippolito, Andrew D Ellington, George Georgiou. Nat Med 2015
244
14


Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.
Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Steven H Kleinstein. Proc Natl Acad Sci U S A 2015
119
13

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
13

Lineage structure of the human antibody repertoire in response to influenza vaccination.
Ning Jiang, Jiankui He, Joshua A Weinstein, Lolita Penland, Sanae Sasaki, Xiao-Song He, Cornelia L Dekker, Nai-Ying Zheng, Min Huang, Meghan Sullivan,[...]. Sci Transl Med 2013
237
13

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
13

Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires.
Simon Friedensohn, Tarik A Khan, Sai T Reddy. Trends Biotechnol 2017
68
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
12

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.
Joel N H Stern, Gur Yaari, Jason A Vander Heiden, George Church, William F Donahue, Rogier Q Hintzen, Anita J Huttner, Jon D Laman, Rashed M Nagra, Alyssa Nylander,[...]. Sci Transl Med 2014
292
11

Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.
Scott D Boyd, Eleanor L Marshall, Jason D Merker, Jay M Maniar, Lyndon N Zhang, Bita Sahaf, Carol D Jones, Birgitte B Simen, Bozena Hanczaruk, Khoa D Nguyen,[...]. Sci Transl Med 2009
314
11

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
11

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
11

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T Reddy. Trends Immunol 2015
105
11

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
11

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
18

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis.
Xavier Brochet, Marie-Paule Lefranc, Véronique Giudicelli. Nucleic Acids Res 2008
824
11

An atlas of B-cell clonal distribution in the human body.
Wenzhao Meng, Bochao Zhang, Gregory W Schwartz, Aaron M Rosenfeld, Daqiu Ren, Joseph J C Thome, Dustin J Carpenter, Nobuhide Matsuoka, Harvey Lerner, Amy L Friedman,[...]. Nat Biotechnol 2017
88
12

Convergent antibody signatures in human dengue.
Poornima Parameswaran, Yi Liu, Krishna M Roskin, Katherine K L Jackson, Vaishali P Dixit, Ji-Yeun Lee, Karen L Artiles, Simona Zompi, Maria José Vargas, Birgitte B Simen,[...]. Cell Host Microbe 2013
180
10

Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes.
Christian E Busse, Irina Czogiel, Peter Braun, Peter F Arndt, Hedda Wardemann. Eur J Immunol 2014
88
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
10


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
10

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development.
Victor Greiff, Ulrike Menzel, Enkelejda Miho, Cédric Weber, René Riedel, Skylar Cook, Atijeh Valai, Telma Lopes, Andreas Radbruch, Thomas H Winkler,[...]. Cell Rep 2017
77
12

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
11

Commonality despite exceptional diversity in the baseline human antibody repertoire.
Bryan Briney, Anne Inderbitzin, Collin Joyce, Dennis R Burton. Nature 2019
216
10

Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Gur Yaari, Mohamed Uduman, Steven H Kleinstein. Nucleic Acids Res 2012
137
9

Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.
J J M van Dongen, A W Langerak, M Brüggemann, P A S Evans, M Hummel, F L Lavender, E Delabesse, F Davi, E Schuuring, R García-Sanz,[...]. Leukemia 2003
9

IMGT®, the international ImMunoGeneTics information system® 25 years on.
Marie-Paule Lefranc, Véronique Giudicelli, Patrice Duroux, Joumana Jabado-Michaloud, Géraldine Folch, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amélie Houles, Typhaine Paysan-Lafosse,[...]. Nucleic Acids Res 2015
313
9


High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment.
Aaron C Logan, Hong Gao, Chunlin Wang, Bita Sahaf, Carol D Jones, Eleanor L Marshall, Ismael Buño, Randall Armstrong, Andrew Z Fire, Kenneth I Weinberg,[...]. Proc Natl Acad Sci U S A 2011
131
9

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
9

Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations.
Rachael J M Bashford-Rogers, Anne L Palser, Brian J Huntly, Richard Rance, George S Vassiliou, George A Follows, Paul Kellam. Genome Res 2013
84
10

Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells.
Sai T Reddy, Xin Ge, Aleksandr E Miklos, Randall A Hughes, Seung Hyun Kang, Kam Hon Hoi, Constantine Chrysostomou, Scott P Hunicke-Smith, Brent L Iverson, Philip W Tucker,[...]. Nat Biotechnol 2010
205
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

Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods.
Rachael J M Bashford-Rogers, Anne L Palser, Saad F Idris, Lisa Carter, Michael Epstein, Robin E Callard, Daniel C Douek, George S Vassiliou, George A Follows, Mike Hubank,[...]. BMC Immunol 2014
35
25

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status.
Victor Greiff, Pooja Bhat, Skylar C Cook, Ulrike Menzel, Wenjing Kang, Sai T Reddy. Genome Med 2015
92
9

Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements.
Katherine J L Jackson, Yi Liu, Krishna M Roskin, Jacob Glanville, Ramona A Hoh, Katie Seo, Eleanor L Marshall, Thaddeus C Gurley, M Anthony Moody, Barton F Haynes,[...]. Cell Host Microbe 2014
167
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.