Medical Information Processing

Mitarbeiter: Jörn Ostermann, Bodo Rosenhahn, Jan Voges, Yeremia Gunawan Adhisantoso
Background

At Institut für Informationsverarbeitung (TNT) we develop methods for processing and analyzing DNA sequencing data. The development of high-throughput sequencing technologies has the potential to enable the use of such genomic sequencing data as a daily practice in various areas. However, the IT costs associated with storing, transferring and processing large amounts of genomic sequencing data now significantly exceed the costs of performing the actual sequencing. Our work aims at democratizing genomic sequencing data access, for example to enable its broad use in personalized medicine.

Goal

Compression of Sequencing Data

In DNA sequencing, a nucleotide sequence to be read out is first fragmented. The fragments are first multiplied and then read out by a sequencing machine. All known sequencing technologies are generally defective. For this reason, a quality value is assigned to nucleotide. The read-out fragments are called reads and are stored together with the quality values in FASTQ files. Further processing steps are the alignment of the reads with the aim of reconstructing the underlying DNA sequence and the identification of structural variants of the sequenced material.

In our work we are especially concerned with compression methods for aligned reads and transparent lossy compression of quality values.

MPEG-G

The MPEG-G standard series is the first ISO/IEC project for the storage and transmission of sequencing data. Large parts of our work have been incorporated into MPEG-G.

Approach

Sequence alignment, lossy compression, machine learning, entropy coding methods

References

[1] Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jörn Ostermann, Claudio Alberti, Marco Mattavelli, S Cenk Sahinalp. Comparison of high-throughput sequencing data compression tools. Nature Methods 13(12), pp. 1005–1008, 2016.

[2] Jan Voges, Jörn Ostermann, Mikel Hernaez. CALQ: compression of quality values of aligned sequencing data. Bioinformatics 34(10), pp. 1650–1658, 2018

[3] Claudio Alberti, Noah Daniels, Mikel Hernaez, Jan Voges, Rachel L Goldfeder, Ana A Hernandez-Lopez, Marco Mattavelli, Bonnie Berger. An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. 2016 Data Compression Conference (DCC), pp. 221–230, Snowbird, UT (US), 2016.

[4] Claudio Alberti, Tom Paridaens, Jan Voges, Daniel Naro, Junaid J. Ahmad, Massimo Ravasi, Daniele Renzi, Giorgio Zoia, Idoia Ochoa, Marco Mattavelli, Jaime Delgado, Mikel Hernaez. An introduction to MPEG-G, the new ISO standard for genomic information representation. bioRxiv preprint, 2018.

  • Conference Contributions
    • Idoia Ochoa, Hongyi Li, Florian Baumgarte, Charles Hergenrother, Jan Voges, Mikel Hernaez
      AliCo: a new efficient representation for SAM files
      2019 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), pp. 93-102, Snowbird, UT (US), March 2019
    • Tom Paridaens, Jan Voges, Mikel Hernaez, Jan Fostier, Jörn Ostermann
      GABAC: an arithmetic coding solution for genomic data
      27th Conference on Intelligent Systems for Molecular Biology (ISMB) and 18th European Conference on Computational Biology (ECCB) 2019, International Society for Computational Biology (ISCB), Vol. 8, p. 1463 (poster), Basel (CH), July 2019
    • Jan Voges
      Optimization Strategy for MPEG-G Compliant Entropy Encoding
      Contributions 5th ITG/VDE Summer School Video Compression and Processing (SVCP), University of Konstanz, pp. 228-255, Konstanz (DE), June 2019, edited by Dietmar Saupe, André Kaup, Jens-Rainer Ohm
    • Brian E Bliss, Joshua M Allen, Saurabh Baheti, Matthew A Bockol, Shubham Chandak, Jaime Delgado, Jan Fostier, Josep L Gelpi, Steven N Hart, Mikel Hernaez Arrazola, Matthew E Hudson, Michael T Kalmbach, Eric W Klee, Liudmila S Mainzer, Fabian Müntefering, Daniel Naro, Idoia Ochoa-Alvarez, Jörn Ostermann, Tom Paridaens, Christian A Ross, Jan Voges, Eric D Wieben, Mingyu Yang, Tsachy Weissman, Mathieu Wiepert
      Genie: an MPEG-G conformant software to compress genomic data
      International Conference for High Performance Computing, Networking, Storage and Analysis (SC19), p. (poster), Denver, CO (US), November 2019
    • Jan Voges, Ali Fotouhi, Jörn Ostermann, M. Oguzhan Külekci
      A Two-Level Scheme for Quality Score Compression
      Proceedings of the 10th International Conference on Bioinformatics and Computational Biology (BICOB 2018), International Society for Computers and their Applications (ISCA), pp. 161-167, Las Vegas, NV (US), March 2018, edited by Hisham Al-Mubaid, Qin Ding, Oliver Eulenstein
    • Ana A Hernandez-Lopez, Jan Voges, Claudio Alberti, Marco Mattavelli, Jörn Ostermann
      Lossy Compression of Quality Scores in Differential Gene Expression: A First Assessment and Impact Analysis
      2018 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), pp. 167-176, Snowbird, UT (US), March 2018
    • Jan Voges
      MPEG-G: The Standard for Genomic Information Representation
      Proceedings of the 4th Summer School on Video Compression and Processing (SVCP) 2018, Leibniz Universität Hannover, Institut für Informationsverarbeitung, pp. 7-8, Hannover (DE), July 2018, edited by Jan Voges
    • Ana A Hernandez-Lopez, Jan Voges, Claudio Alberti, Marco Mattavelli, Jörn Ostermann
      Differential Gene Expression with Lossy Compression of Quality Scores in RNA-Seq Data
      2017 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), p. 444 (poster), Snowbird, UT (US), April 2017
    • Jan Voges, Jörn Ostermann, Mikel Hernaez
      CALQ: compression of quality values of aligned sequencing data
      Joint 25th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology (ECCB) 2017, International Society for Computational Biology (ISCB), Vol. 6, p. 1382 (poster), Prague (CZ), August 2017
    • Jan Voges, Jörn Ostermann
      MPEG-G: The Emerging Standard for Genomic Data
      Poster abstracts of the 25th German Conference on Bioinformatics, PeerJ, Vol. 5, p. 2 (poster), Tübingen (DE), September 2017
    • Claudio Alberti, Noah Daniels, Mikel Hernaez, Jan Voges, Rachel L Goldfeder, Ana A Hernandez-Lopez, Marco Mattavelli, Bonnie Berger
      An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values
      2016 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), pp. 221-230, Snowbird, UT (US), April 2016
    • Jan Voges, Marco Munderloh, Jörn Ostermann
      Predictive Coding of Aligned Next-Generation Sequencing Data
      2016 Data Compression Conference (DCC), IEEE Computer Society Conference Publishing Services (CPS), pp. 241-250, Snowbird, UT (US), April 2016
    • Erik Soltow, Bodo Rosenhahn
      Automatic Pose Estimation Using Contour Information from X-Ray Images
      Image and Video Technology – PSIVT 2015 Workshops, Springer International Publishing, March 2016, edited by Fay Huang and Akihiro Sugimoto
    • Erik Soltow, Christof Hurschler, Bodo Rosenhahn
      Geometric bone models for marker-less RSA in total knee arthroplasty: a proof of concept
      4th International RSA Meeting, May 2015
    • Oliver Müller, Sabine Donner, Tobias Klinder, Ivonne Bartsch, Alexander Krüger, Alexander Heisterkamp, Bodo Rosenhahn
      Compensating motion artifacts of 3D in vivo SD-OCT scans
      Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 7510, pp. 198--205, October 2012, edited by Nicholas Ayache, Hervé Delingette, Polina Golland, Kensaku Mori
    • Stojan Maleschlijski, Laura Leal-Taixé, Sebastian Weiße, Alessio Di Fino, Nicholas Aldred, A. S. Clare, G. Hernán Sendra, Bodo Rosenhahn, Axel Rosenhahn
      A stereoscopic approach for three dimensional tracking of marine biofouling microorganisms
      Microscopic Image Analysis with Applications in Biology (MIAAB). Heidelberg, Germany, September 2011
    • Oliver Müller, Sabine Donner, Tobias Klinder, Ralf Dragon, Ivonne Bartsch, Frank Witte, Alexander Krüger, Alexander Heisterkamp, Bodo Rosenhahn
      Model Based 3D Segmentation and OCT Image Undistortion of Percutaneous Implants
      Medical Image Computing and Computer-Assisted Intervention – MICCAI 2011 14th International Conference, Lecture Notes in Computer Science (LNCS), Springer Berlin / Heidelberg, Vol. 6893, pp. 454-462, September 2011, edited by Fichtinger, Gabor and Martel, Anne and Peters, Terry
    • Arne Ehlers, Florian Baumann, Ralf Spindler, Birgit Glasmacher, Bodo Rosenhahn
      PCA Enhanced Training Data for Adaboost
      Computer Analysis of Images and Patterns - 14th International Conference, CAIP 2011, Seville, Spain, August 29-31, 2011, Proceedings, Part I, Springer, Vol. 6854, pp. 410-419, August 2011
    • Laura Leal-Taixé, Matthias Heydt, Sebastian Weiße, Axel Rosenhahn, Bodo Rosenhahn
      Classification of swimming microorganisms motion patterns in 4D digital in-line holography data
      32nd Annual Symposium of the German Association for Pattern Recognition (DAGM), Springer, Vol. 6376, pp. 283-292, 2010
    • Tobias Klinder, Cristian Lorenz, Jörn Ostermann
      Free-Breathing Intra- and Intersubject Respiratory Motion Capturing, Modeling, and Prediction
      SPIE 2009, SPIE Medical Imaging, Orlando, Florida, USA , February 2009
    • Matthias Ehm, Tobias Klinder, Reinhard Kneser, Cristian Lorenz
      Automated Vertebra Identification in CT images
      SPIE 2009, SPIE Medical Imaging, Orlando, Florida, USA , February 2009
    • Laura Leal-Taixé, Ahmet U. Coskun, Bodo Rosenhahn, Dana H. Brooks
      Automatic segmentation of arteries in multi-stain histology images
      World Congress on Medical Physics and Biomedical Engineering, Munich (Germany), September 7th-12th, 2009
    • Laura Leal-Taixé, Matthias Heydt, Axel Rosenhahn, Bodo Rosenhahn
      Automatic tracking of swimming microorganisms in 4D digital in-line holography data
      IEEE Workshop on Motion and Video Computing (WMVC), Snowbird, Utah, USA., December 2009
    • Tobias Klinder, Cristian Lorenz, Jens von Berg, Steffen Renisch, Thomas Blaffert, Jörn Ostermann
      4DCT Image-Based Lung Motion Field Extraction and Analysis
      SPIE 2008, SPIE Medical Imaging, San Diego, California, USA , February 2008
    • Thomas Blaffert, Hans Barschdorff, Jens von Berg, Sebastian Dries, Astrid Franz, Tobias Klinder, Cristian Lorenz, Steffen Renisch, Rafael Wiemker
      Lung Lobe Modeling and Segmentation with Individualized Surface Meshes
      SPIE 2008, SPIE Medical Imaging, San Diego, California, USA, February 2008
    • Torbjörn Vik, Sven Kabus, Jens von Berg, Konstantin Ens, Sebastian Dries, Tobias Klinder, Cristian Lorenz
      Validation and Comparison of Registration Methods for Free-Breathing 4D Lung-CT
      SPIE 2008, SPIE Medical Imaging, San Diego, California, USA , February 2008
    • Tobias Klinder, Cristian Lorenz, Jörn Ostermann
      Respiratory Motion Modeling and Estimation
      The First Annual Workshop on Pulmonary Image Analysis, MICCAI 2008, Medical Image Computing and Computer Assisted Intervention, New York, USA, September 2008
    • Jalda Dworzak, Hans Lamecker, Jens von Berg, Tobias Klinder, Cristian Lorenz, Dagmar Kainmüller, Heiko Seim, Hans-Christian Hege, Stefan Zachow
      Towards Model-based 3-D Reconstruction of the Human Rib Cage from Radiographs
      CURAC 2008, Computer- und Roboterassistierte Chirurgie e.V., September 2008
    • Udo van Stevendaal, Tobias Klinder, Cristian Lorenz, Thomas Köhler
      Breathing-Motion Correction for Helical CT
      IEEE NSS/MIC, IEEE Nuclear Science Symposium and Medical Imaging Conference, Dresden, Germany, October 2008
    • Astrid Franz, Robin Wolz, Tobias Klinder, Cristian Lorenz, Hans Barschdorf, Thomas Blaffert, Sebastian Dries, Steffen Renisch
      Simultaneous Model-Based Segmentation of Multiple Objects
      BVM 2008, Bildverarbeitung für die Medizin, Berlin, Germany, April 2008
    • Tobias Klinder, Robin Wolz, Cristian Lorenz, Astrid Franz, Jörn Ostermann
      Spine Segmentation Using Articulated Shape Models
      MICCAI 2008, Medical Image Computing and Computer Assisted Intervention, Springer, New York, USA, September 2008
    • Tobias Klinder, Cristian Lorenz, Jens von Berg, Sebastian Dries, Thomas Bülow, Jörn Ostermann
      Automated Model-Based Rib Cage Segmentation and Labeling in CT images
      MICCAI 2007, Medical Image Computing and Computer Assisted Intervention, Springer, Brisbane, Australia, October 2007
    • Tobias Klinder, Cristian Lorenz, Jens von Berg
      Geometrical Rib-Cage Modeling, Detection, and Segmentation
      CARS 2007, Computer Assisted Radiology and Surgery, Berlin, Germany, June 2007
  • Journals
    • Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
      GABAC: an arithmetic coding solution for genomic data
      Bioinformatics, Oxford University Press, Vol. 36, No. 7, pp. 2275-2277, December 2019, edited by John Hancock
    • Jan Voges, Jörn Ostermann, Mikel Hernaez
      CALQ: compression of quality values of aligned sequencing data
      Bioinformatics, Oxford University Press, Vol. 34, No. 10, pp. 1650-1658, May 2018, edited by Bonnie Berger
    • Jan Voges, Ali Fotouhi, Jörn Ostermann, M. Oguzhan Külekci
      A Two-level Scheme for Quality Score Compression
      Journal of Computational Biology, Mary Ann Liebert, Inc., Vol. 25, No. 10, October 2018
    • Claudio Alberti, Tom Paridaens, Jan Voges, Daniel Naro, Junaid J. Ahmad, Massimo Ravasi, Daniele Renzi, Giorgio Zoia, Idoia Ochoa, Marco Mattavelli, Jaime Delgado, Mikel Hernaez
      An introduction to MPEG-G, the new ISO standard for genomic information representation
      bioRxiv, Cold Spring Harbor Laboratory, September 2018
    • Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jörn Ostermann, Claudio Alberti, Marco Mattavelli, S Cenk Sahinalp
      Comparison of high-throughput sequencing data compression tools
      Nature Methods, Nature Publishing Group, Vol. 13, No. 12, pp. 1005-1008, October 2016
    • Sabine Donner, Oliver Müller, Frank Witte, Ivonne Bartsch, Elmar Willbold, Tammo Ripken, Alexander Heisterkamp, Bodo Rosenhahn, Alexander Krüger
      In situ optical coherence tomography of percutaneous implant-tissue interfaces in a murine model
      Biomedical Engineering/Biomedizinische Technik, De Gruyter, pp. 1-9, Karlsruhe, May 2013, edited by Dössel, Olaf
    • S. Maleschlijski, G. H. Sendra, A. Di Fino, L. Leal-Taixé, I. Thome, A. Terfort, N. Aldred, M. Grunze, A. S. Clare, B. Rosenhahn, A. Rosenhahn
      Three dimensional tracking of exploratory behavior of barnacle cyprids using stereoscopy
      Biointerphases. Journal for the Quantitative Biological Interface Data., Springer, August 2012
    • Ralf Spindler, Bodo Rosenhahn, Nicola Hofmann, Birgit Glasmacher
      Video analysis of osmotic cell response during cryopreservation
      Cryobiology, Elsevier, February 2012
    • Tobias Klinder, Jörn Ostermann, Matthias Ehm, Astrid Franz, Reinhard Kneser, Cristian Lorenz
      Automated Model-Based Vertebra Detection, Identification, and Segmentation in CT Images
      Medical Image Analysis, Elsevier, Vol. 13, pp. 471-482, 2009
  • Book Chapters
    • Laura Leal-Taixé, Matthias Heydt, Axel Rosenhahn, Bodo Rosenhahn
      Understanding what we cannot see: automatic analysis of 4D digital in-line holographic microscopy data
      Video Processing and Computational Video, Springer, July 2011, edited by D. Cremers, M.A. Magnor, M.R. Oswald, L. Zelnik-Manor
  • Standardisation Contributions
    • Jan Voges, Christian Rohlfing, Viktor Tunev, Yeremia Gunawan, Jörn Ostermann
      Method for the coding of genomic variants
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M52489, Brussels (BE), January 2020
    • Jan Voges, Giorgio Zoia
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M52977, Alpbach (AT) [Online], April 2020
    • Jan Voges, Fabian Müntefering, Yeremia Gunawan Adhisantoso, Junaid Ahmad, Shubham Chandak, Liudmila S Mainzer, Mikel Hernaez, Idoia Ochoa, Jörn Ostermann
      Draft Description of the MPEG-G Reference Encoder Software
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M52978, Alpbach (AT) [Online], April 2020
    • Yeremia Gunawan Adhisantoso, Viktor Tunev, Jan Voges, Christian Rohlfing
      MPEG-G Part 6 CE3 Results Leibniz University Hannover, RWTH Aachen University
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M53496, Alpbach (AT) [Online], April 2020
    • Jan Voges, Mikel Hernaez, Idoia Ochoa
      Results of Core Experiment 3
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M53713, Alpbach (AT) [Online], April 2020
    • Jan Voges
      MPEG-G Part 6 CE3 Cross-Check of UIUC/University of Navarra Results
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M53789, Alpbach (AT) [Online], April 2020
    • Jan Voges, Idoia Ochoa, Mikel Hernaez, Fabian Müntefering, Giorgio Zoia
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M45266, Marrakesh (MA), January 2019
    • Paolo Ribeca, Jan Voges, Tom Paridaens, Mikel Hernaez, Idoia Ochoa, Claudio Alberti, Marco Mattavelli, Giuseppe Codispoti, Jaime Delgado, Daniel Naro
      Thoughts on future standardization activities in the area of genomic information representation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M45267, Marrakesh (MA), January 2019
    • Jan Voges, Tom Paridaens, Daniel Naro, Dmitry Repchevski, Jaime Delgado, Mikel Hernaez
      Study on ISO/IEC 23092-2
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M45294, Marrakesh (MA), January 2019
    • Daniel Naro, Jan Voges, Tom Paridaens, Dmitry Repchevski, Jaime Delgado, Paolo Ribeca, Idoia Ochoa, Mikel Hernaez
      Comments on ISO/IEC DIS 23092-1 and ISO/IEC DIS 23092-2
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M45601, Marrakesh (MA), January 2019
    • Massimo Ravasi, Daniel Naro, Junaid Ahmad, Jan Voges
      Current status of MPEG-G reference software implementation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M46068, Marrakesh (MA), January 2019
    • Jan Voges, Idoia Ochoa, Mikel Hernaez, James Bonfield
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M46660, Geneva (CH), March 2019
    • Massimo Ravasi, Daniel Naro, Junaid Ahmad, Jan Voges, Tom Paridaens
      Current status of MPEG-G reference software implementation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M47166, Geneva (CH), March 2019
    • Jan Voges, Idoia Ochoa, Mikel Hernaez, Giorgio Zoia, Marco Mattavelli
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M48100, Gothenburg (SE), July 2019
    • Dunling Li, Claudio Alberti, Jaime Delgado, Jan Voges, Itaru Kaneko, Marco Mattavelli, Patrick Cheung, Paolo Ribeca
      MPEG-G Best Practices Deployment Guide
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M50913, Geneva (CH), October 2019
    • Christian Rohlfing, Viktor Tunev, Jan Voges
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M51192, Geneva (CH), October 2019
    • Jan Voges
      Study on White paper on the objectives and benefits of the MPEG-G standard (Draft 1)
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M41956, Gwangju (KR), January 2018
    • Massimo Ravasi, Daniel Naro, Junaid Ahmad, Jan Voges
      Current status of MPEG-G reference software implementation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M42083, Gwangju (KR), January 2018
    • Jan Voges
      Study of ISO/IEC 23092-2
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M42305, San Diego, CA (US), April 2018
    • Jan Voges
      Quality value coding and functional equivalence of genomic analysis pipelines
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M42306, San Diego, CA (US), April 2018
    • Jan Voges
      Study of ISO/IEC CD 23092-3
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M42919, Ljubljana (SI), July 2018
    • Jan Voges, Idoia Ochoa, Mikel Hernaez
      Update to the genomic information database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M42920, Ljubljana (SI), July 2018
    • Jan Voges, Idoia Ochoa, Mikel Hernaez
      Proposed Updates to the MPEG-G Genomic Information Database
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M44035, Macao (MO), October 2018
    • Jan Voges, Shubham Chandak, Mikel Hernaez
      Study on ISO/IEC DIS 23092-2
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M44049, Macao (MO), October 2018
    • Jan Voges
      Core Experiment 2 summary
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39663, Geneva (CH), January 2017
    • Jan Voges, Mikel Hernaez
      Core Experiment 2 results LUH-Stanford/UIUC
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39664, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 1 results LUH
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39665, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 3 results LUH
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39666, Geneva (CH), January 2017
    • Jan Voges, Mikel Hernaez
      Core Experiment 2 on Genomic Information Representation results LUH/Stanford/UIUC
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40224, Hobart (AU), April 2017
    • Jan Voges, Claudio Alberti, Mikel Hernaez, Tom Paridaens, James Bonfield, Paolo Ribeca, Jaime Delgado
      Unified representation of sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40222, Hobart (AU), April 2017
    • Jan Voges
      Summary of Core Experiment 2 on Genomic Information Representation
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40223, Hobart (AU), April 2017
    • Claudio Alberti, Jan Voges, Giorgio Zioa
      Unified representation of genomic reads
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40277, Hobart (AU), April 2017
    • Jan Voges
      Core Experiment 5 on Genomic Information Representation results LUH
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40804, Turin (IT), July 2017
    • Jan Voges
      Proposed changes for ISO/IEC 23092-2 WD 2
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40860, Turin (IT), July 2017
    • Jan Voges
      A Rate-Distortion Analysis of Sequencing Quality Value Compression
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M40861, Turin (IT), July 2017
    • Claudio Alberti, Jan Voges
      Study on ISO/IEC 23092-2 WD 3
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M41393, Macao (CN), October 2017
    • Jan Voges
      Core Experiment 1 cross-check SFU
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39748, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 2 cross-check SFU
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39749, Geneva (CH), January 2017
    • Jan Voges
      Core Experiment 3 cross-check SFU
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M39750, Geneva (CH), January 2017
    • Jan Voges
      Reference-free Compression of Aligned Next-Generation Sequencing Data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37678, San Diego, CA (US), February 2016
    • Ibrahim Numanagic, Faraz Hach, James Bonfield, Claudio Alberti, Jan Voges
      Review of genomic information compression tools
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37766, San Diego, CA (US), February 2016
    • Claudio Alberti, Marco Mattavelli, Ana A. Hernandez-Lopez, Mikel Hernaez, Rachel G. Goldfeder, Noah Daniels, Jan Voges
      Proposal for the update to the database of genomic test data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37767, San Diego, CA (US), February 2016
    • Claudio Alberti, Marco Mattavelli, Ana A. Hernandez-Lopez, Noah Daniels, Mikel Hernaez, Idoia Ochoa, Jan Voges, Rachel Goldfeder, Daniel Greenfield
      Evaluation framework for lossy compression of genomic Quality Values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37768, San Diego, CA (US), February 2016
    • Jan Voges, Mikel Hernaez, Ana Angelica Hernandez-Lopez, Claudio Alberti, Marco Mattavelli, Al Wegener, Dan Greenfield, Noah Daniels, S Cenk Sahinalp, James Bonfield, Bonnie Berger
      Extensions and notes to the evaluation framework for lossy compression of genome sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38376, Geneva (CH), May 2016
    • Jan Voges, Mikel Hernaez, Idoia Ochoa, Ana Angelica Hernandez-Lopez, Claudio Alberti, Marco Mattavelli, Al Wegener, Dan Greenfield, Noah Daniels, S Cenk Sahinalp, James Bonfield, Bonnie Berger, Jörn Ostermann
      Benchmark framework for lossy compression of genome sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38916, Chengdu (CN), October 2016
    • Jan Voges, Mikel Hernaez, Jörn Ostermann
      Adaptive lossy compression of high-throughput sequencing quality values
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38917, Chengdu (CN), October 2016
    • Jan Voges, Marco Munderloh, Jörn Ostermann
      Reference-free compression of aligned high-throughput sequencing data
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M38918, Chengdu (CN), October 2016
    • Jan Voges, Marco Munderloh
      Approaches to SAM File Compression
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M36282, Warsaw (PL), June 2015
    • Jan Voges
      A Framework for the Evaluation of Genomic Information Compression
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37061, Geneva (CH), October 2015
    • Claudio Alberti, Marco Mattavelli, Ioannis Xenarios, Nicolas Guex, Heinz Stockinger, Thierry Schuepbach, Christian Iseli, Daniel Zerzion, Ivan Topolsky, Yann Thoma, Enrico Petraglio, Mikel Hernaez, Jan Voges
      A framework for the comparison of genomic information compression tools
      ISO/IEC JTC 1/SC 29/WG 11, Document Number M37151, Geneva (CH), October 2015