Piotr Jaroslaw Chmura

Search results

• 2024

  Finding Ophthalmic Risk and Evaluating the Value of Eye exams and their predictive Reliability (FOREVER)—A cohort study in a Danish high street optician setting: Design and methodology

  Freiberg, J., Rovelt, J., Gazzard, G., Cour, M. L., Kolko, M., Torp‐Pedersen, C., Benn, M., Brunak, S., Cour, M. L., Tolstrup, J., Toft‐Petersen, A. P., Burgdorf, K. S., Banasik, K., Chmura, P. J., Freiberg, J., Rovelt, J., Thornit, D. N., Foster, P., Gazzard, G., Crabb, D. P. & 4 others, Viswanathan, A., Barman, S., Owen, C. G. & Rudnicka, A. R., 2024, In: Acta Ophthalmologica. 102, 1, p. 80-90 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  2 Citations (Scopus)

• Multi-omics analysis reveals drivers of loss of β-cell function after newly diagnosed autoimmune type 1 diabetes: An INNODIA multicenter study

  the INNODIA investigators, 2024, In: Diabetes/Metabolism Research and Reviews. 40, 5, 15 p., e3833.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• 2023

  A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories

  Placido, D., Yuan, B., Hjaltelin, J. X., Zheng, C., Haue, A. D., Chmura, P. J., Yuan, C., Kim, J., Umeton, R., Antell, G., Chowdhury, A., Franz, A., Brais, L., Andrews, E., Marks, D. S., Regev, A., Ayandeh, S., Brophy, M. T., Do, N. V., Kraft, P. & 5 others, Wolpin, B. M., Rosenthal, M. H., Fillmore, N. R., Brunak, S. & Sander, C., 2023, In: Nature Medicine. 29, p. 1113-1122

  Research output: Contribution to journal › Journal article › Research › peer-review

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  97 Citations (Scopus)

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• DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

  Banasik, K., Møller, P. L., Techlo, T. R., Holm, P. C., Walters, G. B., Ingason, A., Rosengren, A., Rohde, P. D., Kogelman, L. J. A., Westergaard, D., Siggaard, T., Chmura, P. J., Chalmer, M. A., Magnússon, Ó., Þórisson, G., Stefánsson, H., Guðbjartsson, D. F., Stefánsson, K., Olesen, J., Winther, S. & 5 others, Bøttcher, M., Brunak, S., Werge, T., Nyegaard, M. & Hansen, T. F., 2023, In: BMC Genomic Data. 24, 1, 4 p., 30.

  Research output: Contribution to journal › Comment/debate › Research › peer-review

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  2 Citations (Scopus)

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• Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models: [with Author Correction]

  Allesøe, R. L., Lundgaard, A. T., Hernández Medina, R., Aguayo-Orozco, A., Johansen, J., Nissen, J. N., Brorsson, C., Mazzoni, G., Niu, L., Biel, J. H., Brasas, V., Webel, H., Benros, M. E., Pedersen, A. G., Chmura, P. J., Jacobsen, U. P., Mari, A., Koivula, R., Mahajan, A., Vinuela, A. & 31 others, Tajes, J. F., Sharma, S., Haid, M., Hong, M-G., Musholt, P. B., De Masi, F., Vogt, J., Pedersen, H. K., Gudmundsdottir, V., Jones, A., Kennedy, G., Bell, J., Thomas, E. L., Frost, G., Thomsen, H., Hansen, E., Hansen, T. H., Vestergaard, H., Muilwijk, M., Blom, M. T., 't Hart, L. M., Pattou, F., Raverdy, V., Brage, S., Ridderstråle, M., Pedersen, O., Hansen, T., Banasik, K., Rasmussen, S., Brunak, S. & IMI-DIRECT consortium, 2023, In: Nature Biotechnology. 41, 3, p. 399–408 18 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  40 Citations (Scopus)

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• Gene expression signature predicts rate of type 1 diabetes progression

  Suomi, T., Starskaia, I., Kalim, U. U., Rasool, O., Jaakkola, M. K., Grönroos, T., Välikangas, T., Brorsson, C., Mazzoni, G., Bruggraber, S., Overbergh, L., Dunger, D., Peakman, M., Chmura, P., Brunak, S., Schulte, A. M., Mathieu, C., Knip, M., Lahesmaa, R., Elo, L. L. & 4 others, Pociot, F., Johannesen, J., Rossing, P. & INNODIA consortium, 2023, In: EBioMedicine. 92, 18 p., 104625.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  9 Citations (Scopus)

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• Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory

  Moulder, R., Välikangas, T., Hirvonen, M. K., Suomi, T., Brorsson, C. A., Lietzén, N., Bruggraber, S. F. A., Overbergh, L., Dunger, D. B., Peakman, M., Chmura, P. J., Brunak, S., Schulte, A. M., Mathieu, C., Knip, M., Elo, L. L., Lahesmaa, R. & on behalf of the INNODIA consortium, 2023, In: Diabetologia. 66, p. 1983-1996

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  7 Citations (Scopus)

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• 2022

  Classification of Left and Right Coronary Arteries in Coronary Angiographies Using Deep Learning

  Eschen, C. K., Banasik, K., Christensen, A. H., Chmura, P. J., Pedersen, F., Køber, L., Engstrøm, T., Dahl, A. B., Brunak, S. & Bundgaard, H., 2022, In: Electronics (Switzerland). 11, 13, 9 p., 2087.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  4 Citations (Scopus)

  39 Downloads (Pure)

• Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data

  Thorsen-Meyer, H-C., Placido, D., Kaas-Hansen, B. S., Nielsen, A. P., Lange, T., Nielsen, A. B., Toft, P., Schierbeck, J., Strøm, T., Chmura, P. J., Heimann, M., Belling, K., Perner, A. & Brunak, S., 2022, In: npj Digital Medicine. 5, 10 p., 142.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  15 Citations (Scopus)

  49 Downloads (Pure)

• INNODIA Master Protocol for the evaluation of investigational medicinal products in children, adolescents and adults with newly diagnosed type 1 diabetes

  Dunger, D. B., Bruggraber, S. F. A., Mander, A. P., Marcovecchio, M. L., Tree, T., Chmura, P. J., Knip, M., Schulte, A. M., Mathieu, C. & INNODIA consortium, 2022, In: Trials. 23, 1, 9 p., 414.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  18 Citations (Scopus)

  14 Downloads (Pure)
• 2021

  biotoolsSchema: a formalized schema for bioinformatics software description

  Ison, J., Ienasescu, H., Rydza, E., Chmura, P., Rapacki, K., Gaignard, A., Schwämmle, V., Van Helden, J., Kalaš, M. & Ménager, H., 2021, In: GigaScience. 10, 1, 19 p., giaa157.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  6 Citations (Scopus)

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• Study protocol Minimum effective low dose: Anti-human thymocyte globulin (MELD-ATG): Phase II, dose ranging, efficacy study of antithymocyte globulin (ATG) within 6 weeks of diagnosis of type 1 diabetes

  Wilhelm-Benartzi, C. S., Miller, S. E., Bruggraber, S., Picton, D., Wilson, M., Gatley, K., Chhabra, A., Marcovecchio, M. L., Hendriks, A. E. J., Morobé, H., Chmura, P. J., Bond, S., Aschemeier-Fuchs, B., Knip, M., Tree, T., Overbergh, L., Pall, J., Arnaud, O., Haller, M. J., Nitsche, A. & 4 others, Schulte, A. M., Mathieu, C., Mander, A. & Dunger, D., 2021, In: BMJ Open. 11, 12, 24 p., e053669.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  6 Citations (Scopus)

  14 Downloads (Pure)
• 2020

  Community curation of bioinformatics software and data resources

  Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T., Lamprecht, A. L., Palmblad, M., Kalaš, M., Chmura, P., Hancock, J. M., Schwämmle, V. & Ienasescu, H. I., 2020, In: Briefings in Bioinformatics. 21, 5, p. 1697-1705 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  10 Citations (Scopus)

  15 Downloads (Pure)

• Dynamic and explainable machine learning prediction of mortality in patients in the intensive care unit: a retrospective study of high-frequency data in electronic patient records

  Thorsen-Meyer, H-C., Nielsen, A. B., Nielsen, A. P., Kaas-Hansen, B. S., Toft, P., Schierbeck, J., Strøm, T., Chmura, P. J., Heimann, M., Dybdahl, L., Spangsege, L., Hulsen, P., Belling, K., Brunak, S. & Perner, A., 2020, In: The Lancet Digital Health. 2, 4, p. e179–91 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  192 Citations (Scopus)

  90 Downloads (Pure)

• High-throughput sequencing of circulating plasma microRNAs in newly diagnosed type 1 diabetes identifies four different patient clusters

  Sebastiani, G., Grieco, G. E., Fignani, D., Chmura, P. J., Brorsson, C. A., Bruggraber, S., Pugliese, A., Evans-Molina, C., Knip, M., Peakman, M., Schulte, A. M., Brunak, S., Dunger, D. B., Mathieu, C. & Dotta, F., 2020, In: Diabetologia. 63, Suppl. 1, p. S160 1 p.

  Research output: Contribution to journal › Conference abstract in journal › Research

• JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

  Friedrichs, M., Shoshi, A., Chmura, P. J., Ison, J., Schwammle, V., Schreiber, F., Hofestadt, R. & Sommer, B., 2020, In: Journal of integrative bioinformatics. 16, 8 p., 20190059.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  3 Citations (Scopus)

  35 Downloads (Pure)

• Supercomputing and Secure Cloud Infrastructures in Biology and Medicine

  Jespersgaard, C., Syed, A., Chmura, P. & Longreen, P., 2020, In: Annual Review of Biomedical Data Science. 3, p. 391-410 20 p.

  Research output: Contribution to journal › Review › Research › peer-review
  2 Citations (Scopus)
• 2019

  Survival prediction in intensive-care units based on aggregation of long-term disease history and acute physiology: a retrospective study of the Danish National Patient Registry and electronic patient records

  Nielsen, A. B., Thorsen-Meyer, H. C., Belling, K., Nielsen, A. P., Thomas, C. E., Chmura, P. J., Lademann, M., Moseley, P. L., Heimann, M., Dybdahl, L., Spangsege, L., Hulsen, P., Perner, A. & Brunak, S., 2019, In: The Lancet Digital Health. 1, 2, p. e78-e89 12 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  74 Citations (Scopus)

  266 Downloads (Pure)

• The bio.tools registry of software tools and data resources for the life sciences

  Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Ménager, H., Kalaš, M., Schwämmle, V., Grüning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Vařeková, R. S., Raček, T., Vondrášek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R. & 16 others, Nyrönen, T., Valencia, A., Capella, S., Gelpí, J., Zambelli, F., Savakis, B., Leskošek, B., Rapacki, K., Blanchet, C., Jimenez, R., Oliveira, A., Vriend, G., Collin, O., van Helden, J., Løngreen, P. & Brunak, S., 2019, In: Genome Biology. 20, 1, 4 p., 164.

  Research output: Contribution to journal › Letter › Research › peer-review

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  39 Citations (Scopus)

  158 Downloads (Pure)