26 Works

SparkEC: speeding up alignment-based DNA error correction tools

Roberto R. Expósito, Marco Martínez-Sánchez & Juan Touriño
Abstract Background In recent years, huge improvements have been made in the context of sequencing genomic data under what is called Next Generation Sequencing (NGS). However, the DNA reads generated by current NGS platforms are not free of errors, which can affect the quality of downstream analysis. Although error correction can be performed as a preprocessing step to overcome this issue, it usually requires long computational times to analyze those large datasets generated nowadays through...

Additional file 2 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 2.

Additional file 1 of SparkEC: speeding up alignment-based DNA error correction tools

Roberto R. Expósito, Marco Martínez-Sánchez & Juan Touriño
Additional file 1. Document including background information, additional figures related to the main text and a detailed user’s guide for SparkEC.

SparkEC: speeding up alignment-based DNA error correction tools

Roberto R. Expósito, Marco Martínez-Sánchez & Juan Touriño
Abstract Background In recent years, huge improvements have been made in the context of sequencing genomic data under what is called Next Generation Sequencing (NGS). However, the DNA reads generated by current NGS platforms are not free of errors, which can affect the quality of downstream analysis. Although error correction can be performed as a preprocessing step to overcome this issue, it usually requires long computational times to analyze those large datasets generated nowadays through...

Additional file 10 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 10.

Additional file 4 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 4.

Additional file 7 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 7.

Additional file 9 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 9.

Additional file 9 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 9.

Additional file 1 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 1.

Additional file 3 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 3.

Additional file 3 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 3.

Additional file 4 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 4.

Additional file 5 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 5.

Additional file 5 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 5.

Additional file 6 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 6.

Additional file 6 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 6.

Additional file 8 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 8.

Additional file 2 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 2.

Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Abstract Background The IMI-APPROACH cohort is an exploratory, 5-centre, 2-year prospective follow-up study of knee osteoarthritis (OA). Aim was to describe baseline multi-tissue semiquantitative MRI evaluation of index knees and to describe change for different MRI features based on number of subregion-approaches and change in maximum grades over a 24-month period. Methods MRIs were acquired using 1.5 T or 3 T MRI systems and assessed using the semi-quantitative MRI OA Knee Scoring (MOAKS) system. MRIs...

Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Abstract Background The IMI-APPROACH cohort is an exploratory, 5-centre, 2-year prospective follow-up study of knee osteoarthritis (OA). Aim was to describe baseline multi-tissue semiquantitative MRI evaluation of index knees and to describe change for different MRI features based on number of subregion-approaches and change in maximum grades over a 24-month period. Methods MRIs were acquired using 1.5 T or 3 T MRI systems and assessed using the semi-quantitative MRI OA Knee Scoring (MOAKS) system. MRIs...

Additional file 1 of SparkEC: speeding up alignment-based DNA error correction tools

Roberto R. Expósito, Marco Martínez-Sánchez & Juan Touriño
Additional file 1. Document including background information, additional figures related to the main text and a detailed user’s guide for SparkEC.

Additional file 10 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 10.

Additional file 1 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 1.

Additional file 7 of Structural tissue damage and 24-month progression of semi-quantitative MRI biomarkers of knee osteoarthritis in the IMI-APPROACH cohort

Frank W. Roemer, Mylène Jansen, Anne C. A. Marijnissen, Ali Guermazi, Rafael Heiss, Susanne Maschek, Agnes Lalande, Francisco J. Blanco, Francis Berenbaum, Lotte A. van de Stadt, Margreet Kloppenburg, Ida K. Haugen, Christoph H. Ladel, Jaume Bacardit, Anna Wisser, Felix Eckstein, Floris P. J. G. Lafeber, Harrie H. Weinans & Wolfgang Wirth
Additional file 7.

Registration Year

  • 2022
    26

Resource Types

  • Text
    22
  • Collection
    4

Affiliations

  • University of A Coruña
    26
  • Universitätsklinikum Erlangen
    22
  • Hôpital Saint-Antoine
    22
  • Newcastle University
    22
  • Diakonhjemmet Hospital
    22
  • Servier (France)
    22
  • Chondrometrics (Germany)
    22
  • Paracelsus Medical University
    22
  • Complexo Hospitalario Universitario A Coruña
    22
  • Utrecht University
    22