Cited by 63Artificial Immune Systems ApplicationsT-cell and B-cell Immunologyvaccines and immunoinformatics approaches

The DOI matches its Crossref record; 418 of the 418 references it cites were found in a registry or an index.

Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires

Open access
Brown, Alex J., Snapkov, Igor, Akbar, Rahmad, Pavlović, Milena, Miho, Enkelejda, Sandve, Geir K., Greiff, Victor·2019·Molecular Systems Design & Engineering

Abstract

The adaptive immune system is a natural diagnostic sensor and therapeutic.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1039/c9me00071b

Cites

418 of 418 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 69

  1. National Research Council Committee on Theoretical Foundations for Decision Making in Engineering Design, Theoretical foundations for decision making in engineering design , National Academy Press , 2001
  2. A. K. Abbas and A.Lichtman , Cellular and Molecular Immunology , Saunders , 5th edn, 2005
  3. Heather, 2018, Briefings Bioinf., 19, 554
  4. Trepel, 1974, J. Mol. Med., 52, 511
  5. W. Zhang , L.Wang , K.Liu , X.Wei , K.Yang , W.Du and S.Wang , bioRxiv
  6. Sethna, 2017, Proc. Natl. Acad. Sci. U. S. A., 201700241
  7. R. Arora , H. M.Burke and R.Arnaout , 2018 , bioRxiv, 483131
  8. K. Grigaityte , J. A.Carter , S. J.Goldfless , E. W.Jeffery , R. J.Hause , Y.Jiang , D.Koppstein , A. W.Briggs , G. M.Church , F.Vigneault and G. S.Atwal , 2017 , bioRxiv, 213462
  9. Palme, 2015, Bioinformatics, btv176
  10. H. F. Moffett , C. K.Harms , K. S.Fitzpatrick , M. R.Tooley , J.Boonyaratankornkit and J. J.Taylor , 2019 , bioRxiv, 541979
  11. G. Altan-Bonnet , T.Mora and A. M.Walczak , 2019 , arXiv [q-bio.QM]
  12. J. H. Holland , Machine learning, an artificial intelligence approach , 1986 , vol. 2 , pp. 593–623
  13. S. Gielis , P.Moris , N.De Neuter , W.Bittremieux , B.Ogunjimi , K.Laukens and P.Meysman , 2018 , bioRxiv, 373472
  14. E. Jokinen , M.Heinonen , J.Huuhtanen and S.Mustjoki , bioRxiv
  15. N. Thakkar and C.Bailey-Kellogg , 2019 , bioRxiv, 526467
  16. S. Shalev-Shwartz , O.Shamir and S.Shammah , 2017 , arXiv [cs.LG]
  17. J. W. Sidhom , H. B.Larman , D. M.Pardoll and A. S.Baras , bioRxiv
  18. Thomas, 2014, Bioinformatics, 30, 3181, 10.1093/bioinformatics/btu523 · DOI
  19. R. Arora , J.Kaplinsky , A.Li and R.Arnaout , 2019 , bioRxiv, 519108
  20. J.-W. Sidhom , H.Benjamin Larman , D. M.Pardoll and A. S.Baras , 2018 , bioRxiv, 464107
  21. R. Shokri and V.Shmatikov , in Proceedings of the 22Nd ACM SIGSAC Conference on Computer and Communications Security , ACM , New York, NY, USA , 2015 , pp. 1310–1321
  22. D. Kotzias , M.Denil , N.de Freitas and P.Smyth , in Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining , ACM , 2015 , pp. 597–606
  23. I. Goodfellow , Y.Bengio and A.Courville , Deep Learning , MIT Press , 2016
  24. Lanchantin, 2017, Pac. Symp. Biocomput., 22, 254
  25. K. B. Hoehn , J. A.Vander Heiden , J. Q.Zhou , G.Lunter , O. G.Pybus and S.Kleinstein , 2019 , bioRxiv, 558825
  26. L. D. Goldstein , Y. J. J.Chen , J.Wu , S.Chaudhuri and Y. C.Hsiao , bioRxiv
  27. A. W. Briggs , S. J.Goldfless , S.Timberlake , B. J.Belmont , C. R.Clouser , D.Koppstein , D.Sok , J. V. A.Heiden , M. V.Tamminen , S. H.Kleinstein , D. R.Burton , G. M.Church and F.Vigneault , 2017 , bioRxiv, 134841
  28. Cao, 2017, Science, 357, 661, 10.1126/science.aam8940 · DOI · Paper page
  29. F. Broere , S. G.Apasov , M. V.Sitkovsky and W.van Eden , in Principles of Immunopharmacology: 3rd revised and extended edition , ed. F. P. Nijkamp and M. J. Parnham , Birkhäuser Basel, Basel , 2011 , pp. 15–27
  30. S. Mangul , I.Mandric , H. T.Yang , N.Strauli , D.Montoya , J.Rotman , W.Van Der Wey , J. R.Ronas , B.Statz , A.Zelikovsky , R.Spreafico , S.Shifman , N.Zaitlen , M.Rossetti , K.Mark Ansel and E.Eskin , 2018 , bioRxiv, 089235
  31. P. Ramos-López , J.Irizarry , I.Pino and S.Blackshaw , in Epitope Mapping Protocols , ed. J. Rockberg and J. Nilvebrant , Springer New York , New York, NY , 2018 , pp. 223–229
  32. Legutki, 2013, Proc. Natl. Acad. Sci. U. S. A., 201309390
  33. M. AlQuraishi , 2018 , bioRxiv, 265231
  34. Greenspan, 1992, Bull. Inst. Pasteur, 90, 267
  35. Flower, 2007, Methods Mol. Biol., 409, v
  36. Frank, 2002, Methods, 267, 13
  37. A. Kramer and J.Schneider-Mergener , in Combinatorial Peptide Library Protocols , ed. S. Cabilly , Humana Press , 1998 , vol. 87 , pp. 25–39
  38. Y. EL-Manzalawy , D.Dobbs and V. G.Honavar , in Prediction of Protein Secondary Structure , ed. Y. Zhou , A. Kloczkowski , E. Faraggi and Y. Yang , Springer New York , New York, NY , 2017 , pp. 255–264
  39. Trolle, 2015, Bioinformatics, btv123
  40. Sela-Culang, 2014, Bioinformatics, btu790
  41. J. M. S. van der Schoot , F. L.Fennemann , M.Valente , Y.Dolen , I. M.Hagemans , A. M. D.Becker , C. M.Le Gall , D.van Dalen , A.Cevirgel , J. A. C.van Bruggen , M.Engelfriet , M. F.Fransen , T.Caval , A. E. H.Bentlage , M.Nederend , J. H. W.Leusen , A. J. R.Heck , G.Vidarsson , C. G.Figdor , M.Verdoes and F. A.Scheeren , 2019 , bioRxiv, 551382
  42. Williams, 2018, Methods, 462, 65
  43. Li, 2013, Front. Immunol., 4, 206
  44. A. C. R. Martin , in Antibody Engineering , ed. R. Kontermann and S. Dübel , Springer Berlin Heidelberg , Berlin, Heidelberg , 2010 , pp. 33–51
  45. Krawczyk, 2019, mAbs, 10.1080/19420862.2019.1633884 · DOI · Paper page
  46. D. M. Mason , S.Friedensohn , C. R.Weber and C.Jordi , bioRxiv
  47. S. Pittala and C.Bailey-Kellogg , 2019 , bioRxiv, 511360
  48. M. Hebditch and J.Warwicker , 2019 , bioRxiv, 625830
  49. S. Biswas , G.Kuznetsov , P. J.Ogden and N. J.Conway , bioRxiv
  50. M. Simonovsky and N.Komodakis , in Artificial Neural Networks and Machine Learning – ICANN 2018 , Springer International Publishing , 2018 , pp. 412–422
  51. Y. Li , O.Vinyals , C.Dyer , R.Pascanu and P.Battaglia , 2018 , arXiv [cs.LG]
  52. D. C. Elton , Z.Boukouvalas , M. D.Fuge and P. W.Chung , 2019 , arXiv [cs.LG]
  53. Z. Wang , Y.Li , B.Hou , M. I.Pronobis , Y.Wang , M.Wang , G.Cheng , Z.Zhang , W.Weng , Y.Wang , Y.Tang , X.Xu , R.Pan , F.Lin , N.Wang , Z.Chen , S.Wang , L. Z.Ma , Y.Li , D.Huang , L.Jiang , Z.Wang , W.Zeng , Y.Zhang , X.Du , Y.Lin , Z.Li , Q.Xia , J.Geng , H.Dai , C.Wang , Y.Yu , X.Zhao , Z.Yuan , J.Yan , B.Ren , Q.Nie , X.Zhang , K.Wang , F.Chen , Q.Zhang , Y.Zhu , K. D.Poss , S.Tao and X.Meng , 2019 , bioRxiv, 553339
  54. Marrack, 2017, eLife, 6, e30918, 10.7554/eLife.30918 · DOI
  55. F. Rosenblatt , Two theorems of statistical separability in the perceptron , Cornell Aeronautical Laboratory, Inc. , 1958
  56. T. Bepler and B.Berger , 2019 , arXiv [cs.LG]
  57. A. Rives , S.Goyal , J.Meier , D.Guo , M.Ott and C. L.Zitnick , bioRxiv
  58. T. L. Fine , Feedforward Neural Network Methodology , Springer-Verlag , Berlin, Heidelberg , 1st edn., 1999
  59. Y. LeCun , P.Haffner , L.Bottou and Y.Bengio , in Shape, Contour and Grouping in Computer Vision , ed. D. A. Forsyth , J. L. Mundy , V. di Gesú and R. Cipolla , Springer Berlin Heidelberg , Berlin, Heidelberg , 1999 , pp. 319–345
  60. C. Wang , C.Xu , X.Yao and D.Tao , 2018 , arXiv [cs.LG]
  61. K. Simonyan and A.Zisserman , 2014 , arXiv [cs.CV]
  62. C. Szegedy , W.Liu , Y.Jia , P.Sermanet , S.Reed , D.Anguelov , D.Erhan , V.Vanhoucke and A.Rabinovich , in Proceedings of the IEEE conference on computer vision and pattern recognition , 2015 , pp. 1–9
  63. J. Ba and R.Caruana , in Advances in Neural Information Processing Systems 27 , ed. Z. Ghahramani , M. Welling , C. Cortes , N. D. Lawrence and K. Q. Weinberger , Curran Associates, Inc. , 2014 , pp. 2654–2662
  64. K. He , X.Zhang , S.Ren and J.Sun , in Proceedings of the IEEE conference on computer vision and pattern recognition , 2016 , pp. 770–778
  65. D. P. Kingma , 2013 , arXiv [cs.LG]
  66. I. J. Goodfellow , J.Pouget-Abadie , M.Mirza , B.Xu , D.Warde-Farley , S.Ozair , A.Courville and Y.Bengio , 2014 , arXiv [stat.ML]
  67. M. Sundararajan , A.Taly and Q.Yan , in Proceedings of the 34th International Conference on Machine Learning - Volume 70 , JMLR.org, Sydney, NSW, Australia , 2017 , pp. 3319–3328
  68. M. Ribeiro , S.Singh and C.Guestrin , in Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations , 2016
  69. A. Holzinger , M.Plass , K.Holzinger , G. C.Crisan , C.-M.Pintea and V.Palade , 2017 , arXiv [cs.AI]

Cited by

Sorted by citations

See all 63

Metadata

Authors
Brown, A. J., Snapkov, I., Akbar, R., Pavlović, M., Miho, E., Sandve, G. K., & Greiff, V.
Affiliations
  • Department of Biomedical Research
  • University of Oslo (NO)
  • FHNW University of Applied Sciences and Arts Northwestern Switzerland (CH)
Corresponding author
  • Sandve, Geir K.
  • Greiff, Victor
Venue
Molecular Systems Design & Engineering
Published
2019
Volume
4
Issue
4
Pages
701-736
ISSN
2058-9689 (ISSN-L)
OpenAlex
W2926687552
Cited by
59
References
414
Citations by year
2026: 1 · 2025: 6 · 2024: 11 · 2023: 7 · 2022: 10 · 2021: 10 · 2020: 11 · 2019: 3
FWCI
2.99
Type
journal article
Language
en
Open access
Locations
  • Molecular Systems Design & Engineering (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • arXiv (Cornell University)
Funders
  • Stiftelsen Kristian Gerhard Jebsen
  • Leona M. and Harry B. Helmsley Charitable Trust (2019PG-T1D011)
  • Horizon 2020 (825821)
Topics
  • Physical Sciences › Computer Science › Artificial Intelligence › Artificial Immune Systems Applications
  • Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords
adaptive immunity, immune receptor repertoire, T cell receptor, B cell receptor

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review