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Items: 1 to 50 of 114

1.

Stippling of 2D Scalar Fields.

Gortler J, Spicker M, Schulz C, Weiskopf D, Deussen O.

IEEE Trans Vis Comput Graph. 2019 Jun;25(6):2193-2204. doi: 10.1109/TVCG.2019.2903945. Epub 2019 Mar 15.

PMID:
30892212
2.

Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles.

Tian Y, Babor M, Lane J, Seumois G, Liang S, Goonawardhana NDS, De Silva AD, Phillips EJ, Mallal SA, da Silva Antunes R, Grifoni A, Vijayanand P, Weiskopf D, Peters B, Sette A.

J Clin Invest. 2019 Mar 18;130:1727-1741. doi: 10.1172/JCI123726. eCollection 2019 Mar 18.

3.

A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis.

Tian Y, da Silva Antunes R, Sidney J, Lindestam Arlehamn CS, Grifoni A, Dhanda SK, Paul S, Peters B, Weiskopf D, Sette A.

Front Immunol. 2018 Nov 29;9:2778. doi: 10.3389/fimmu.2018.02778. eCollection 2018. Review.

4.

Cutting Edge: Transcriptional Profiling Reveals Multifunctional and Cytotoxic Antiviral Responses of Zika Virus-Specific CD8+ T Cells.

Grifoni A, Costa-Ramos P, Pham J, Tian Y, Rosales SL, Seumois G, Sidney J, de Silva AD, Premkumar L, Collins MH, Stone M, Norris PJ, Romero CME, Durbin A, Ricciardi MJ, Ledgerwood JE, de Silva AM, Busch M, Peters B, Vijayanand P, Harris E, Falconar AK, Kallas E, Weiskopf D, Sette A.

J Immunol. 2018 Dec 15;201(12):3487-3491. doi: 10.4049/jimmunol.1801090. Epub 2018 Nov 9.

5.

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA.

Moore E, Grifoni A, Weiskopf D, Schulten V, Arlehamn CSL, Angelo M, Pham J, Leary S, Sidney J, Broide D, Frazier A, Phillips E, Mallal S, Mack SJ, Sette A.

Hum Immunol. 2018 Dec;79(12):821-822. doi: 10.1016/j.humimm.2018.09.008. Epub 2018 Sep 29.

PMID:
30278218
6.

Image-Based Aspect Ratio Selection.

Wang Y, Wang Z, Fu CW, Schmauder H, Deussen O, Weiskopf D.

IEEE Trans Vis Comput Graph. 2018 Aug 20. doi: 10.1109/TVCG.2018.2865266. [Epub ahead of print]

PMID:
30137008
7.

Development of a novel clustering tool for linear peptide sequences.

Dhanda SK, Vaughan K, Schulten V, Grifoni A, Weiskopf D, Sidney J, Peters B, Sette A.

Immunology. 2018 Nov;155(3):331-345. doi: 10.1111/imm.12984. Epub 2018 Aug 6.

8.

Predicting HLA CD4 Immunogenicity in Human Populations.

Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A.

Front Immunol. 2018 Jun 14;9:1369. doi: 10.3389/fimmu.2018.01369. eCollection 2018.

9.

Interactive Molecular Graphics for Augmented Reality Using HoloLens.

Müller C, Krone M, Huber M, Biener V, Herr D, Koch S, Reina G, Weiskopf D, Ertl T.

J Integr Bioinform. 2018 Jun 13;15(2). pii: /j/jib.2018.15.issue-2/jib-2018-0005/jib-2018-0005.xml. doi: 10.1515/jib-2018-0005.

10.

DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.

Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y.

Cytometry A. 2018 Jun;93(6):597-610. doi: 10.1002/cyto.a.23371. Epub 2018 Apr 17.

11.

Correction: Definition of Human Epitopes Recognized in Tetanus Toxoid and Development of an Assay Strategy to Detect Ex Vivo Tetanus CD4+ T Cell Responses.

da Silva Antunes R, Paul S, Sidney J, Weiskopf D, Dan JM, Phillips E, Mallal S, Crotty S, Sette A, Lindestam Arlehamn CS.

PLoS One. 2018 Feb 20;13(2):e0193382. doi: 10.1371/journal.pone.0193382. eCollection 2018.

12.

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.

Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P.

Sci Immunol. 2018 Jan 19;3(19). pii: eaan8664. doi: 10.1126/sciimmunol.aan8664.

13.

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka.

Grifoni A, Weiskopf D, Lindestam Arlehamn CS, Angelo M, Leary S, Sidney J, Frazier A, Phillips E, Mallal S, Mack SJ, Tippalagama R, Goonewardana S, Premawansa S, Premawansa G, Wijewickrama A, De Silva AD, Sette A.

Hum Immunol. 2018 Feb;79(2):87-88. doi: 10.1016/j.humimm.2017.12.007. Epub 2017 Dec 28.

14.

Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL.

Ricciardi MJ, Magnani DM, Grifoni A, Kwon YC, Gutman MJ, Grubaugh ND, Gangavarapu K, Sharkey M, Silveira CGT, Bailey VK, Pedreño-Lopez N, Gonzalez-Nieto L, Maxwell HS, Domingues A, Martins MA, Pham J, Weiskopf D, Altman J, Kallas EG, Andersen KG, Stevenson M, Lichtenberger P, Choe H, Whitehead SS, Sette A, Watkins DI.

PLoS Negl Trop Dis. 2017 Dec 21;11(12):e0006000. doi: 10.1371/journal.pntd.0006000. eCollection 2017 Dec.

15.

Development of Envelope Protein Antigens To Serologically Differentiate Zika Virus Infection from Dengue Virus Infection.

Premkumar L, Collins M, Graham S, Liou GA, Lopez CA, Jadi R, Balmaseda A, Brackbill JA, Dietze R, Camacho E, De Silva AD, Giuberti C, Dos Reis HL, Singh T, Heimsath H, Weiskopf D, Sette A, Osorio JE, Permar SR, Miley MJ, Lazear HM, Harris E, de Silva AM.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01504-17. doi: 10.1128/JCM.01504-17. Print 2018 Mar.

16.

Cloth Animation Retrieval Using a Motion-Shape Signature.

Huber M, Eberhardt B, Weiskopf D.

IEEE Comput Graph Appl. 2017 Nov-Dec;37(6):52-64. doi: 10.1109/MCG.2017.4031068.

PMID:
29140782
17.

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA.

Tian Y, Babor M, Lane J, Schulten V, Patil VS, Seumois G, Rosales SL, Fu Z, Picarda G, Burel J, Zapardiel-Gonzalo J, Tennekoon RN, De Silva AD, Premawansa S, Premawansa G, Wijewickrama A, Greenbaum JA, Vijayanand P, Weiskopf D, Sette A, Peters B.

Nat Commun. 2017 Nov 13;8(1):1473. doi: 10.1038/s41467-017-01728-5.

18.

Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua.

Weiskopf D, Grifoni A, Arlehamn CSL, Angelo M, Leary S, Sidney J, Frazier A, Mack SJ, Phillips E, Mallal S, Cerpas C, Balmaseda A, Harris E, Sette A.

Hum Immunol. 2018 Jan;79(1):1-2. doi: 10.1016/j.humimm.2017.11.002. Epub 2017 Nov 7.

19.

Global Assessment of Dengue Virus-Specific CD4+ T Cell Responses in Dengue-Endemic Areas.

Grifoni A, Angelo MA, Lopez B, O'Rourke PH, Sidney J, Cerpas C, Balmaseda A, Silveira CGT, Maestri A, Costa PR, Durbin AP, Diehl SA, Phillips E, Mallal S, De Silva AD, Nchinda G, Nkenfou C, Collins MH, de Silva AM, Lim MQ, Macary PA, Tatullo F, Solomon T, Satchidanandam V, Desai A, Ravi V, Coloma J, Turtle L, Rivino L, Kallas EG, Peters B, Harris E, Sette A, Weiskopf D.

Front Immunol. 2017 Oct 13;8:1309. doi: 10.3389/fimmu.2017.01309. eCollection 2017.

20.

Prior Dengue Virus Exposure Shapes T Cell Immunity to Zika Virus in Humans.

Grifoni A, Pham J, Sidney J, O'Rourke PH, Paul S, Peters B, Martini SR, de Silva AD, Ricciardi MJ, Magnani DM, Silveira CGT, Maestri A, Costa PR, de-Oliveira-Pinto LM, de Azeredo EL, Damasco PV, Phillips E, Mallal S, de Silva AM, Collins M, Durbin A, Diehl SA, Cerpas C, Balmaseda A, Kuan G, Coloma J, Harris E, Crowe JE Jr, Stone M, Norris PJ, Busch M, Vivanco-Cid H, Cox J, Graham BS, Ledgerwood JE, Turtle L, Solomon T, Kallas EG, Watkins DI, Weiskopf D, Sette A.

J Virol. 2017 Nov 30;91(24). pii: e01469-17. doi: 10.1128/JVI.01469-17. Print 2017 Dec 15.

21.

Erratum: T cells from patients with Parkinson's disease recognize α-synuclein peptides.

Sulzer D, Alcalay RN, Garretti F, Cote L, Kanter E, Agin-Liebes J, Liong C, McMurtrey C, Hildebrand WH, Mao X, Dawson VL, Dawson TM, Oseroff C, Pham J, Sidney J, Dillon MB, Carpenter C, Weiskopf D, Phillips E, Mallal S, Peters B, Frazier A, Arlehamn CSL, Sette A.

Nature. 2017 Sep 13;549(7671):292. doi: 10.1038/nature23896.

PMID:
28905919
22.

Nonlinear Dot Plots.

Rodrigues N, Weiskopf D.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):616-625. doi: 10.1109/TVCG.2017.2744018. Epub 2017 Aug 29.

PMID:
28866514
23.

Bubble Treemaps for Uncertainty Visualization.

Gortler J, Schulz C, Weiskopf D, Deussen O.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):719-728. doi: 10.1109/TVCG.2017.2743959. Epub 2017 Aug 29.

PMID:
28866506
24.

Erratum for Verma et al., "Cytomegalovirus-Specific CD4 T Cells Are Cytolytic and Mediate Vaccine Protection".

Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA.

J Virol. 2017 Aug 10;91(17). pii: e00959-17. doi: 10.1128/JVI.00959-17. Print 2017 Sep 1. No abstract available.

25.

T cells from patients with Parkinson's disease recognize α-synuclein peptides.

Sulzer D, Alcalay RN, Garretti F, Cote L, Kanter E, Agin-Liebes J, Liong C, McMurtrey C, Hildebrand WH, Mao X, Dawson VL, Dawson TM, Oseroff C, Pham J, Sidney J, Dillon MB, Carpenter C, Weiskopf D, Phillips E, Mallal S, Peters B, Frazier A, Lindestam Arlehamn CS, Sette A.

Nature. 2017 Jun 29;546(7660):656-661. doi: 10.1038/nature22815. Epub 2017 Jun 21. Erratum in: Nature. 2017 Sep 13;549(7671):292.

26.

Indexed-Points Parallel Coordinates Visualization of Multivariate Correlations.

Zhou L, Weiskopf D.

IEEE Trans Vis Comput Graph. 2018 Jun;24(6):1997-2010. doi: 10.1109/TVCG.2017.2698041. Epub 2017 Apr 25.

PMID:
28459690
27.

Word-Sized Graphics for Scientific Texts.

Beck F, Weiskopf D.

IEEE Trans Vis Comput Graph. 2017 Jun;23(6):1576-1587. doi: 10.1109/TVCG.2017.2674958. Epub 2017 Feb 24.

PMID:
28252406
28.

Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2Δ30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain.

Grifoni A, Angelo M, Sidney J, Paul S, Peters B, de Silva AD, Phillips E, Mallal S, Diehl SA, Botten J, Boyson J, Kirkpatrick BD, Whitehead SS, Durbin AP, Sette A, Weiskopf D.

J Virol. 2017 Mar 29;91(8). pii: e02133-16. doi: 10.1128/JVI.02133-16. Print 2017 Apr 15.

29.

Definition of Human Epitopes Recognized in Tetanus Toxoid and Development of an Assay Strategy to Detect Ex Vivo Tetanus CD4+ T Cell Responses.

da Silva Antunes R, Paul S, Sidney J, Weiskopf D, Dan JM, Phillips E, Mallal S, Crotty S, Sette A, Lindestam Arlehamn CS.

PLoS One. 2017 Jan 12;12(1):e0169086. doi: 10.1371/journal.pone.0169086. eCollection 2017. Erratum in: PLoS One. 2018 Feb 20;13(2):e0193382.

30.

An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.

Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann RH, Sette A, Peters B.

J Immunol. 2017 Feb 15;198(4):1748-1758. doi: 10.4049/jimmunol.1601750. Epub 2017 Jan 9.

31.

Mapping the Human Memory B Cell and Serum Neutralizing Antibody Responses to Dengue Virus Serotype 4 Infection and Vaccination.

Nivarthi UK, Kose N, Sapparapu G, Widman D, Gallichotte E, Pfaff JM, Doranz BJ, Weiskopf D, Sette A, Durbin AP, Whitehead SS, Baric R, Crowe JE Jr, de Silva AM.

J Virol. 2017 Feb 14;91(5). pii: e02041-16. doi: 10.1128/JVI.02041-16. Print 2017 Mar 1.

32.

Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species.

Xu X, Vaughan K, Weiskopf D, Grifoni A, Diamond MS, Sette A, Peters B.

PLoS Curr. 2016 Nov 15;8. pii: ecurrents.outbreaks.9aa2e1fb61b0f632f58a098773008c4b. doi: 10.1371/currents.outbreaks.9aa2e1fb61b0f632f58a098773008c4b.

33.

Cytotoxic CD4 T Cells: Differentiation, Function, and Application to Dengue Virus Infection.

Tian Y, Sette A, Weiskopf D.

Front Immunol. 2016 Dec 7;7:531. doi: 10.3389/fimmu.2016.00531. eCollection 2016. Review.

34.

Human CD4+ T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity.

Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, Peters B, de Silva AD, Phillips E, Mallal S, Diehl SA, Kirkpatrick BD, Whitehead SS, Durbin AP, Sette A, Weiskopf D.

J Virol. 2017 Feb 14;91(5). pii: e02147-16. doi: 10.1128/JVI.02147-16. Print 2017 Mar 1.

35.

Probabilistic Graph Layout for Uncertain Network Visualization.

Schulz C, Nocaj A, Goertler J, Deussen O, Brandes U, Weiskopf D.

IEEE Trans Vis Comput Graph. 2017 Jan;23(1):531-540.

PMID:
27875169
36.

An Evaluation of Visual Search Support in Maps.

Netzel R, Hlawatsch M, Burch M, Balakrishnan S, Schmauder H, Weiskopf D.

IEEE Trans Vis Comput Graph. 2017 Jan;23(1):421-430.

PMID:
27875158
37.

Visual Analytics for Mobile Eye Tracking.

Kurzhals K, Hlawatsch M, Seeger C, Weiskopf D.

IEEE Trans Vis Comput Graph. 2017 Jan;23(1):301-310.

PMID:
27875146
38.

Visual Interaction with Dimensionality Reduction: A Structured Literature Analysis.

Sacha D, Zhang L, Sedlmair M, Lee JA, Peltonen J, Weiskopf D, North SC, Keim DA.

IEEE Trans Vis Comput Graph. 2017 Jan;23(1):241-250.

PMID:
27875141
39.

Protective Role of Cross-Reactive CD8 T Cells Against Dengue Virus Infection.

Elong Ngono A, Chen HW, Tang WW, Joo Y, King K, Weiskopf D, Sidney J, Sette A, Shresta S.

EBioMedicine. 2016 Nov;13:284-293. doi: 10.1016/j.ebiom.2016.10.006. Epub 2016 Oct 7.

40.

HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses.

Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S, Premawansa G, Wijewickrama A, Peters B, Sette A.

J Infect Dis. 2016 Oct 1;214(7):1117-24. doi: 10.1093/infdis/jiw309. Epub 2016 Jul 20.

41.

A Cytokine-Independent Approach To Identify Antigen-Specific Human Germinal Center T Follicular Helper Cells and Rare Antigen-Specific CD4+ T Cells in Blood.

Dan JM, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Havenar-Daughton C, Reiss SM, Brigger M, Bothwell M, Sette A, Crotty S.

J Immunol. 2016 Aug 1;197(3):983-93. doi: 10.4049/jimmunol.1600318. Epub 2016 Jun 24.

42.

Immunodominant Dengue Virus-Specific CD8+ T Cell Responses Are Associated with a Memory PD-1+ Phenotype.

de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E, Sette A, Weiskopf D.

J Virol. 2016 Apr 14;90(9):4771-4779. doi: 10.1128/JVI.02892-15. Print 2016 May.

43.

Visualizing Dynamic Hierarchies in Graph Sequences.

Vehlow C, Beck F, Weiskopf D.

IEEE Trans Vis Comput Graph. 2016 Oct;22(10):2343-2357. doi: 10.1109/TVCG.2015.2507595. Epub 2015 Dec 10.

PMID:
26685254
44.

Automatic Generation of Validated Specific Epitope Sets.

Carrasco Pro S, Sidney J, Paul S, Lindestam Arlehamn C, Weiskopf D, Peters B, Sette A.

J Immunol Res. 2015;2015:763461. doi: 10.1155/2015/763461. Epub 2015 Oct 19.

45.

Gaze Stripes: Image-Based Visualization of Eye Tracking Data.

Kurzhals K, Hlawatsch M, Heimerl F, Burch M, Ertl T, Weiskopf D.

IEEE Trans Vis Comput Graph. 2016 Jan;22(1):1005-14. doi: 10.1109/TVCG.2015.2468091.

PMID:
26529744
46.

Visual Analysis and Dissemination of Scientific Literature Collections with SurVis.

Beck F, Koch S, Weiskopf D.

IEEE Trans Vis Comput Graph. 2016 Jan;22(1):180-9. doi: 10.1109/TVCG.2015.2467757.

PMID:
26529698
47.

Cytomegalovirus-Specific CD4 T Cells Are Cytolytic and Mediate Vaccine Protection.

Verma S, Weiskopf D, Gupta A, McDonald B, Peters B, Sette A, Benedict CA.

J Virol. 2015 Oct 21;90(2):650-8. doi: 10.1128/JVI.02123-15. Print 2016 Jan 15. Erratum in: J Virol. 2017 Aug 10;91(17 ):.

48.

Highlights from the 5th Symposium on Biological Data Visualization: Part 2.

Aerts J, Marai GE, Nieselt K, Nielsen C, Streit M, Weiskopf D.

BMC Proc. 2015 Aug 13;9(Suppl 6 Proceedings of the 5th Symposium on Biological Data):S1. doi: 10.1186/1753-6561-9-S6-S1. eCollection 2015. No abstract available.

49.

Low-Pass Filtered Volumetric Shadows.

Ament M, Sadlo F, Dachsbacher C, Weiskopf D.

IEEE Trans Vis Comput Graph. 2014 Dec;20(12):2437-46. doi: 10.1109/TVCG.2014.2346333.

PMID:
26356957
50.

Comparative Eye Tracking Study on Node-Link Visualizations of Trajectories.

Netzel R, Burch M, Weiskopf D.

IEEE Trans Vis Comput Graph. 2014 Dec;20(12):2221-30. doi: 10.1109/TVCG.2014.2346420.

PMID:
26356936

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