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EMBL John Kendrew Award Lecture 2018
The document discusses various approaches to visualizing and interpreting transcriptomics and genomic data, highlighting the importance of hypothesis-driven and data-driven discovery. It emphasizes tools and methods developed by researchers, particularly in relation to The Cancer Genome Atlas and the Stratomex framework for patient stratifications. Additionally, it mentions collaborative contributions and the significance of open science in education and community building in biomedical informatics.
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EMBL John Kendrew Award Lecture 2018
- 1. Nils Gehlenborg, PhD Departmentof Biomedical Informatics Harvard Medical School @ngehlenborg
- 2. Nils Gehlenborg, PhD Departmentof Biomedical Informatics Harvard Medical School @ngehlenborg + = ?
- 3. My Time atEMBL-EBI
- 4. Visualization and Explorationof Transcriptomics Data
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- 29. ? Shoe salesperson -an expert to find the shoes you are looking for Display rack - a means to display the content of the shoe boxes
- 30.
- 31. Space Maps Multi-Resolution Glyphs Gehlenborg andBrazma, BMC Bioinformatics, 2009
- 32. Space Maps Real World Example lowhigh Human Gene Expression Map SNAP-25 Level 1 1 node Level 2 4 nodes Level 3 15 nodes Level 4 371 nodes Level 5 5,372 nodes Gehlenborg and Brazma, BMC Bioinformatics, 2009
- 33. Space Maps Arrangement of Glyphs GridProjection NeRV Knowledge-driven Data-driven Data-driven Gehlenborg and Brazma, BMC Bioinformatics, 2009
- 34. REX Topic Model Blei et al. (2003); Caldas, Gehlenborg et al. (2009) infer TopicModel comparison: list of gene sets w/ counts T T T GS GS GS GS comparison: C distribution over distributions over Caldas, Gehlenborg, et al., Bioinformatics, 2009 Retrieval of Relevant Experiments
- 35. REX Topic Model Blei et al. (2003); Caldas, Gehlenborg et al. (2009) infer TopicModel comparison: list of gene sets w/ counts T T T GS GS GS GS comparison: document: document: words C W W W W distribution over distributions over (for text documents) D “Car” driver engine driving tires mileage Caldas, Gehlenborg, et al., Bioinformatics, 2009 Retrieval of Relevant Experiments
- 36. REX Caldas, Gehlenborg, etal., Bioinformatics, 2009 Retrieval of Relevant Experiments
- 37. Moving on to HarvardMedical School
- 41. The Cancer GenomeAtlas 10,000+ patients 20+ tumor types
- 42. The Cancer GenomeAtlas 10,000+ patients 20+ tumor types
- 43. mRNA expression The CancerGenome Atlas 10,000+ patients 20+ tumor types
- 44. microRNA expression mRNA expression TheCancer Genome Atlas 10,000+ patients 20+ tumor types
- 45. microRNA expression protein expression mRNAexpression The Cancer Genome Atlas 10,000+ patients 20+ tumor types
- 46. microRNA expression protein expression mutationcalls mRNA expression The Cancer Genome Atlas 10,000+ patients 20+ tumor types
- 47. microRNA expression protein expression copynumber variants mutation calls mRNA expression The Cancer Genome Atlas 10,000+ patients 20+ tumor types
- 48. microRNA expression DNA methylation proteinexpression copy number variants mutation calls mRNA expression The Cancer Genome Atlas 10,000+ patients 20+ tumor types
- 49. microRNA expression DNA methylation proteinexpression copy number variants mutation calls clinical parameters mRNA expression The Cancer Genome Atlas 10,000+ patients 20+ tumor types
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- 52. C4C3C2C1 LONGER TYPICAL SHORTER patientsurvival time mRNA expression clustering Tumor Subtypes
- 53. C4C3C2C1 LONGER TYPICAL SHORTER WILDTYPEMUT patientsurvival time mutation status of gene Y mRNA expression clustering Tumor Subtypes
- 54. C4C3C2C1 WILDTYPEMUT mRNA expression clustering patientsurvival time mutation status of gene Y Tumor Subtypes LONGER TYPICAL SHORTER
- 55. C4C3C2C1 WILDTYPEMUT mRNA expression clustering patientsurvival time mutation status of gene Y Tumor Subtypes LONGER TYPICAL SHORTER
- 56. C4C3C2C1 WILDTYPEMUT mRNA expression clustering patientsurvival time mutation status of gene Y Tumor Subtypes LONGER TYPICAL SHORTER
- 57. C4C3C2C1 WILDTYPEMUT patient survival time mutationstatus of gene Y mRNA expression clustering Tumor Subtypes LONGER TYPICAL SHORTER
- 58.
- 59. StratomeX PROBLEM 1 Visualize overlapof patient sets across two or more stratifications.
- 60. StratomeX PROBLEM 1 Visualize overlapof patient sets across two or more stratifications. PROBLEM 2 Visualize characteristics of patient sets within a stratification of interest.
- 61. M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, PPark, N Gehlenborg , Nature Methods, 2014
- 62. StratomeX PROBLEM 1 Visualize overlapof patient sets across two or more stratifications. PROBLEM 2 Visualize characteristics of patient sets within a stratification of interest.
- 63. StratomeX PROBLEM 1 Visualize overlapof patient sets across two or more stratifications. PROBLEM 2 Visualize characteristics of patient sets within a stratification of interest. PROBLEM 3 Identify relevant stratifications, pathways, and clinical variables.
- 64. Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister,P Park, N Gehlenborg , Nature Methods (2014)
- 65. Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister,P Park, N Gehlenborg , Nature Methods (2014)
- 66. Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister,P Park, N Gehlenborg , Nature Methods (2014)
- 67. Is there amutation that overlaps with this mRNA cluster? Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, P Park, N Gehlenborg , Nature Methods (2014)
- 68. Is there amutation that overlaps with this mRNA cluster? Is there a mutually exclusive mutation? Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, P Park, N Gehlenborg , Nature Methods (2014)
- 69. Is there amutation that overlaps with this mRNA cluster? Is there a CNV that affects survival? Is there a mutually exclusive mutation? Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, P Park, N Gehlenborg , Nature Methods (2014)
- 70. Is there amutation that overlaps with this mRNA cluster? Is there a CNV that affects survival? Is there a pathway that is enriched in this cluster? Is there a mutually exclusive mutation? Query Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, P Park, N Gehlenborg , Nature Methods (2014)
- 71. Query Rank Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister,P Park, N Gehlenborg , Nature Methods (2014)
- 72. Query Rank Visualize Stratifications Clinical Params Pathways Guided Exploration M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister,P Park, N Gehlenborg , Nature Methods (2014)
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- 80. Genome Interaction Data PROBLEM1 Visualize a matrix of 3 million x 3 million cells across multiple scales
- 81. Genome Interaction Data PROBLEM1 Visualize a matrix of 3 million x 3 million cells across multiple scales PROBLEM 2 Support comparison of many different conditions
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- 95. Lekschas et al.,Transactions on Visualization and Computer Graphics, 2018
- 96. Lekschas et al.,Transactions on Visualization and Computer Graphics, 2018
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- 99. EDUCATION Nature Methods Pointsof View; courses and workshops
- 101. OPEN SCIENCE Preprints for4D Nucleome Consortium
- 102. OPEN SCIENCE Preprints for4D Nucleome Consortium
- 104. COMMUNITY BUILDING VIZBI, BioVis,and other meetings
- 105. A Tale ofGreat Perseverance
- 109.
- 110. EMBL Alumni Association KayNieselt Alvis Brazma Nicholas Luscombe Gos Micklem Lars Steinmetz Peter J Park Isaac Kohane Alexander Lex Marc Streit Hanspeter Pfister Peter Kerpedjiev Fritz Lekschas Sabrina Nusrat Jennifer Marx Scott Ouellette Chuck McCallum Theresa Harbig Danielle Nguyen Jake Conway Undina Gisladottir Maureen Ruby and Clara
- 111. EMBL Alumni Association KayNieselt Alvis Brazma Nicholas Luscombe Gos Micklem Lars Steinmetz Peter J Park Isaac Kohane Alexander Lex Marc Streit Hanspeter Pfister Peter Kerpedjiev Fritz Lekschas Sabrina Nusrat Jennifer Marx Scott Ouellette Chuck McCallum Theresa Harbig Danielle Nguyen Jake Conway Undina Gisladottir Maureen Ruby and Clara