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Showing 157 to 166 of 166 entries
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Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression.

Bioinformatics (Oxford, England)

Li R, Tanigawa Y, Justesen JM, Taylor J, Hastie T, Tibshirani R, Rivas MA.
PMID: 33560296
Bioinformatics. 2021 Feb 09; doi: 10.1093/bioinformatics/btab095. Epub 2021 Feb 09.

MOTIVATION: The prediction performance of Cox proportional hazard model suffers when there are only few uncensored events in the training data.RESULTS: We propose a Sparse-Group regularized Cox regression method to improve the prediction performance of large-scale and high-dimensional survival...

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Li R, Tanigawa Y, Justesen JM, et al. Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab095.
Li, R., Tanigawa, Y., Justesen, J. M., Taylor, J., Hastie, T., Tibshirani, R., & Rivas, M. A. (2021). Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab095
Li, Ruilin, et al. "Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab095
Li R, Tanigawa Y, Justesen JM, Taylor J, Hastie T, Tibshirani R, Rivas MA. Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression. Bioinformatics. 2021 Feb 09; doi: 10.1093/bioinformatics/btab095. Epub 2021 Feb 09. PMID: 33560296; PMCID: PMC8652035.
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Discovery of a Novel Leaf Rust (.

Cells

Vendelbo NM, Mahmood K, Sarup P, Hovmøller MS, Justesen AF, Kristensen PS, Orabi J, Jahoor A.
PMID: 35011626
Cells. 2021 Dec 27;11(1). doi: 10.3390/cells11010064.

Leaf rust constitutes one of the most important foliar diseases in rye (

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Vendelbo NM, Mahmood K, Sarup P, et al. Discovery of a Novel Leaf Rust (. Cells. 2021;11(1)doi: 10.3390/cells11010064.
Vendelbo, N. M., Mahmood, K., Sarup, P., Hovmøller, M. S., Justesen, A. F., Kristensen, P. S., Orabi, J., & Jahoor, A. (2021). Discovery of a Novel Leaf Rust (. Cells, 11(1), . https://doi.org/10.3390/cells11010064
Vendelbo, Nikolaj Meisner, et al. "Discovery of a Novel Leaf Rust (." Cells vol. 11,1 (2021). doi: https://doi.org/10.3390/cells11010064
Vendelbo NM, Mahmood K, Sarup P, Hovmøller MS, Justesen AF, Kristensen PS, Orabi J, Jahoor A. Discovery of a Novel Leaf Rust (. Cells. 2021 Dec 27;11(1). doi: 10.3390/cells11010064. PMID: 35011626.
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Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS.

Proteomics

Khan A, Shin JY, So MK, Na JH, Justesen S, Ansari AA, Ko BJ, Ahn SM.
PMID: 34561969
Proteomics. 2022 Jan;22(1):e2100171. doi: 10.1002/pmic.202100171. Epub 2021 Oct 05.

Human leukocyte antigen (HLA) class I has more than 18,000 alleles, each of which binds to a set of unique peptides from the cellular degradome. Deciphering the interaction between antigenic peptides and HLA proteins is crucial for understanding immune...

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Khan A, Shin JY, So MK, et al. Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS. Proteomics. 2021;22(1):e2100171doi: 10.1002/pmic.202100171.
Khan, A., Shin, J. Y., So, M. K., Na, J. H., Justesen, S., Ansari, A. A., Ko, B. J., & Ahn, S. M. (2022). Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS. Proteomics, 22(1), e2100171. https://doi.org/10.1002/pmic.202100171
Khan, Amir, et al. "Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS." Proteomics vol. 22,1 (2022): e2100171. doi: https://doi.org/10.1002/pmic.202100171
Khan A, Shin JY, So MK, Na JH, Justesen S, Ansari AA, Ko BJ, Ahn SM. Characterization of HLA-A*33:03 epitopes via immunoprecipitation and LC-MS/MS. Proteomics. 2022 Jan;22(1):e2100171. doi: 10.1002/pmic.202100171. Epub 2021 Oct 05. PMID: 34561969.
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Commodity risk assessment of .

EFSA journal. European Food Safety Authority

, Bragard C, Dehnen-Schmutz K, Di Serio F, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, van der Werf W, Civera AV, Yuen J, Zappalà L, Battisti A, Mas H, Rigling D, Mosbach-Schulz O, Gonthier P.
PMID: 33519991
EFSA J. 2021 Jan 21;19(1):e06353. doi: 10.2903/j.efsa.2021.6353. eCollection 2021 Jan.

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. This Scientific Opinion covers the...

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, Bragard C, Dehnen-Schmutz K, et al. Commodity risk assessment of . EFSA J. 2021;19(1):e06353doi: 10.2903/j.efsa.2021.6353.
, Bragard, C., Dehnen-Schmutz, K., Di Serio, F., Jacques, M. A., Jaques Miret, J. A., Justesen, A. F., MacLeod, A., Magnusson, C. S., Milonas, P., Navas-Cortes, J. A., Parnell, S., Potting, R., Reignault, P. L., Thulke, H. H., van der Werf, W., Civera, A. V., Yuen, J., Zappalà, L., Battisti, A., Mas, H., Rigling, D., Mosbach-Schulz, O., & Gonthier, P. (2021). Commodity risk assessment of . EFSA journal. European Food Safety Authority, 19(1), e06353. https://doi.org/10.2903/j.efsa.2021.6353
, et al. "Commodity risk assessment of ." EFSA journal. European Food Safety Authority vol. 19,1 (2021): e06353. doi: https://doi.org/10.2903/j.efsa.2021.6353
, Bragard C, Dehnen-Schmutz K, Di Serio F, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, van der Werf W, Civera AV, Yuen J, Zappalà L, Battisti A, Mas H, Rigling D, Mosbach-Schulz O, Gonthier P. Commodity risk assessment of . EFSA J. 2021 Jan 21;19(1):e06353. doi: 10.2903/j.efsa.2021.6353. eCollection 2021 Jan. PMID: 33519991; PMCID: PMC7818635.
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Commodity risk assessment of .

EFSA journal. European Food Safety Authority

, Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach-Schulz O, de la Peña E, Milonas P.
PMID: 33613739
EFSA J. 2021 Feb 13;19(2):e06396. doi: 10.2903/j.efsa.2021.6396. eCollection 2021 Feb.

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'.

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, Bragard C, Dehnen-Schmutz K, et al. Commodity risk assessment of . EFSA J. 2021;19(2):e06396doi: 10.2903/j.efsa.2021.6396.
, Bragard, C., Dehnen-Schmutz, K., Di Serio, F., Gonthier, P., Jacques, M. A., Jaques Miret, J. A., Justesen, A. F., MacLeod, A., Magnusson, C. S., Navas-Cortes, J. A., Parnell, S., Potting, R., Reignault, P. L., Thulke, H. H., Van der Werf, W., Civera, A. V., Yuen, J., Zappalà, L., Lucchi, A., Loomans, A., Mosbach-Schulz, O., de la Peña, E., & Milonas, P. (2021). Commodity risk assessment of . EFSA journal. European Food Safety Authority, 19(2), e06396. https://doi.org/10.2903/j.efsa.2021.6396
, et al. "Commodity risk assessment of ." EFSA journal. European Food Safety Authority vol. 19,2 (2021): e06396. doi: https://doi.org/10.2903/j.efsa.2021.6396
, Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach-Schulz O, de la Peña E, Milonas P. Commodity risk assessment of . EFSA J. 2021 Feb 13;19(2):e06396. doi: 10.2903/j.efsa.2021.6396. eCollection 2021 Feb. PMID: 33613739; PMCID: PMC7881711.
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Pest categorisation of .

EFSA journal. European Food Safety Authority

, Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Malumphy C, Czwienczek E, Kertesz V, Maiorano A, MacLeod A.
PMID: 34194574
EFSA J. 2021 Jun 25;19(6):e06664. doi: 10.2903/j.efsa.2021.6664. eCollection 2021 Jun.

The EFSA Panel on Plant Health performed a pest categorisation of the citrus pulp borer,

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, Bragard C, Dehnen-Schmutz K, et al. Pest categorisation of . EFSA J. 2021;19(6):e06664doi: 10.2903/j.efsa.2021.6664.
, Bragard, C., Dehnen-Schmutz, K., Di Serio, F., Gonthier, P., Jacques, M. A., Jaques Miret, J. A., Justesen, A. F., Magnusson, C. S., Milonas, P., Navas-Cortes, J. A., Parnell, S., Potting, R., Reignault, P. L., Thulke, H. H., Van der Werf, W., Vicent Civera, A., Yuen, J., Zappalà, L., Malumphy, C., Czwienczek, E., Kertesz, V., Maiorano, A., & MacLeod, A. (2021). Pest categorisation of . EFSA journal. European Food Safety Authority, 19(6), e06664. https://doi.org/10.2903/j.efsa.2021.6664
, et al. "Pest categorisation of ." EFSA journal. European Food Safety Authority vol. 19,6 (2021): e06664. doi: https://doi.org/10.2903/j.efsa.2021.6664
, Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Malumphy C, Czwienczek E, Kertesz V, Maiorano A, MacLeod A. Pest categorisation of . EFSA J. 2021 Jun 25;19(6):e06664. doi: 10.2903/j.efsa.2021.6664. eCollection 2021 Jun. PMID: 34194574; PMCID: PMC8229750.
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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Nature biotechnology

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A.
PMID: 34663921
Nat Biotechnol. 2021 Oct 18; doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18.

Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to...

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Ouspenskaia T, Law T, Clauser KR, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2021;doi: 10.1038/s41587-021-01021-3.
Ouspenskaia, T., Law, T., Clauser, K. R., Klaeger, S., Sarkizova, S., Aguet, F., Li, B., Christian, E., Knisbacher, B. A., Le, P. M., Hartigan, C. R., Keshishian, H., Apffel, A., Oliveira, G., Zhang, W., Chen, S., Chow, Y. T., Ji, Z., Jungreis, I., Shukla, S. A., Justesen, S., Bachireddy, P., Kellis, M., Getz, G., Hacohen, N., Keskin, D. B., Carr, S. A., Wu, C. J., & Regev, A. (2021). Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature biotechnology, . https://doi.org/10.1038/s41587-021-01021-3
Ouspenskaia, Tamara, et al. "Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer." Nature biotechnology vol. (2021). doi: https://doi.org/10.1038/s41587-021-01021-3
Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2021 Oct 18; doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18. PMID: 34663921.
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Pest categorisation of .

EFSA journal. European Food Safety Authority

, Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, Sven Magnusson C, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Stefani E, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Gregoire JC, Malumphy C, Antonatos S, Kertesz V, Maiorano A, Papachristos D, MacLeod A.
PMID: 35035580
EFSA J. 2022 Jan 11;20(1):e07024. doi: 10.2903/j.efsa.2022.7024. eCollection 2022 Jan.

The EFSA Panel on Plant Health performed a pest categorisation of

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, Bragard C, Baptista P, et al. Pest categorisation of . EFSA J. 2022;20(1):e07024doi: 10.2903/j.efsa.2022.7024.
, Bragard, C., Baptista, P., Chatzivassiliou, E., Di Serio, F., Gonthier, P., Jaques Miret, J. A., Justesen, A. F., Sven Magnusson, C., Milonas, P., Navas-Cortes, J. A., Parnell, S., Potting, R., Reignault, P. L., Stefani, E., Thulke, H. H., Van der Werf, W., Civera, A. V., Yuen, J., Zappalà, L., Gregoire, J. C., Malumphy, C., Antonatos, S., Kertesz, V., Maiorano, A., Papachristos, D., & MacLeod, A. (2022). Pest categorisation of . EFSA journal. European Food Safety Authority, 20(1), e07024. https://doi.org/10.2903/j.efsa.2022.7024
, et al. "Pest categorisation of ." EFSA journal. European Food Safety Authority vol. 20,1 (2022): e07024. doi: https://doi.org/10.2903/j.efsa.2022.7024
, Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, Sven Magnusson C, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Stefani E, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Gregoire JC, Malumphy C, Antonatos S, Kertesz V, Maiorano A, Papachristos D, MacLeod A. Pest categorisation of . EFSA J. 2022 Jan 11;20(1):e07024. doi: 10.2903/j.efsa.2022.7024. eCollection 2022 Jan. PMID: 35035580; PMCID: PMC8749475.
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A vaccine targeting mutant IDH1 in newly diagnosed glioma.

Nature

Platten M, Bunse L, Wick A, Bunse T, Le Cornet L, Harting I, Sahm F, Sanghvi K, Tan CL, Poschke I, Green E, Justesen S, Behrens GA, Breckwoldt MO, Freitag A, Rother LM, Schmitt A, Schnell O, Hense J, Misch M, Krex D, Stevanovic S, Tabatabai G, Steinbach JP, Bendszus M, von Deimling A, Schmitt M, Wick W.
PMID: 33762734
Nature. 2021 Apr;592(7854):463-468. doi: 10.1038/s41586-021-03363-z. Epub 2021 Mar 24.

Mutated isocitrate dehydrogenase 1 (IDH1) defines a molecularly distinct subtype of diffuse glioma

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Platten M, Bunse L, Wick A, et al. A vaccine targeting mutant IDH1 in newly diagnosed glioma. Nature. 2021;592(7854):463-468doi: 10.1038/s41586-021-03363-z.
Platten, M., Bunse, L., Wick, A., Bunse, T., Le Cornet, L., Harting, I., Sahm, F., Sanghvi, K., Tan, C. L., Poschke, I., Green, E., Justesen, S., Behrens, G. A., Breckwoldt, M. O., Freitag, A., Rother, L. M., Schmitt, A., Schnell, O., Hense, J., Misch, M., Krex, D., Stevanovic, S., Tabatabai, G., Steinbach, J. P., Bendszus, M., von Deimling, A., Schmitt, M., & Wick, W. (2021). A vaccine targeting mutant IDH1 in newly diagnosed glioma. Nature, 592(7854), 463-468. https://doi.org/10.1038/s41586-021-03363-z
Platten, Michael, et al. "A vaccine targeting mutant IDH1 in newly diagnosed glioma." Nature vol. 592,7854 (2021): 463-468. doi: https://doi.org/10.1038/s41586-021-03363-z
Platten M, Bunse L, Wick A, Bunse T, Le Cornet L, Harting I, Sahm F, Sanghvi K, Tan CL, Poschke I, Green E, Justesen S, Behrens GA, Breckwoldt MO, Freitag A, Rother LM, Schmitt A, Schnell O, Hense J, Misch M, Krex D, Stevanovic S, Tabatabai G, Steinbach JP, Bendszus M, von Deimling A, Schmitt M, Wick W. A vaccine targeting mutant IDH1 in newly diagnosed glioma. Nature. 2021 Apr;592(7854):463-468. doi: 10.1038/s41586-021-03363-z. Epub 2021 Mar 24. PMID: 33762734; PMCID: PMC8046668.
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Pest categorisation of .

EFSA journal. European Food Safety Authority

, Bragard C, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Gregoire JC, Malumphy C, Campese C, Czwienczek E, Kertesz V, Maiorano A, MacLeod A.
PMID: 34429782
EFSA J. 2021 Aug 18;19(8):e06801. doi: 10.2903/j.efsa.2021.6801. eCollection 2021 Aug.

The EFSA Panel on Plant Health performed a pest categorisation of

Cite
, Bragard C, Di Serio F, et al. Pest categorisation of . EFSA J. 2021;19(8):e06801doi: 10.2903/j.efsa.2021.6801.
, Bragard, C., Di Serio, F., Gonthier, P., Jaques Miret, J. A., Justesen, A. F., Magnusson, C. S., Milonas, P., Navas-Cortes, J. A., Parnell, S., Potting, R., Reignault, P. L., Thulke, H. H., Van der Werf, W., Civera, A. V., Yuen, J., Zappalà, L., Gregoire, J. C., Malumphy, C., Campese, C., Czwienczek, E., Kertesz, V., Maiorano, A., & MacLeod, A. (2021). Pest categorisation of . EFSA journal. European Food Safety Authority, 19(8), e06801. https://doi.org/10.2903/j.efsa.2021.6801
, et al. "Pest categorisation of ." EFSA journal. European Food Safety Authority vol. 19,8 (2021): e06801. doi: https://doi.org/10.2903/j.efsa.2021.6801
, Bragard C, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Gregoire JC, Malumphy C, Campese C, Czwienczek E, Kertesz V, Maiorano A, MacLeod A. Pest categorisation of . EFSA J. 2021 Aug 18;19(8):e06801. doi: 10.2903/j.efsa.2021.6801. eCollection 2021 Aug. PMID: 34429782; PMCID: PMC8371560.
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