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Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Zong Miao, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
doi: https://doi.org/10.1101/786285
Marcus Alvarez
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Elior Rahmani
2Computer Science Department in the School of Engineering, UCLA, Los Angeles, CA, USA
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Brandon Jew
3Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
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Kristina M. Garske
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Zong Miao
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
3Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
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Jihane N. Benhammou
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
5Vache and Tamar Manoukian Division of Digestive Diseases, UCLA, Los Angeles, CA, USA
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Chun Jimmie Ye
4Institute for Human Genetics, Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, USA
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Joseph R. Pisegna
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
5Vache and Tamar Manoukian Division of Digestive Diseases, UCLA, Los Angeles, CA, USA
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Kirsi H. Pietiläinen
6Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, Helsinki, Finland
7Obesity Center, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
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Eran Halperin
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
2Computer Science Department in the School of Engineering, UCLA, Los Angeles, CA, USA
3Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
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Päivi Pajukanta
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
3Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
8Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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  • For correspondence: ppajukanta@mednet.ucla.edu
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Article Information

doi 
https://doi.org/10.1101/786285
History 
  • October 2, 2019.

Article Versions

  • Version 1 (September 30, 2019 - 10:26).
  • You are viewing Version 2, the most recent version of this article.
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.

Author Information

  1. Marcus Alvarez1,*,
  2. Elior Rahmani2,*,
  3. Brandon Jew3,
  4. Kristina M. Garske1,
  5. Zong Miao1,3,
  6. Jihane N. Benhammou1,5,
  7. Chun Jimmie Ye4,
  8. Joseph R. Pisegna1,5,
  9. Kirsi H. Pietiläinen6,7,
  10. Eran Halperin1,2,3 and
  11. Päivi Pajukanta1,3,8,**
  1. 1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
  2. 2Computer Science Department in the School of Engineering, UCLA, Los Angeles, CA, USA
  3. 3Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
  4. 4Institute for Human Genetics, Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, USA
  5. 5Vache and Tamar Manoukian Division of Digestive Diseases, UCLA, Los Angeles, CA, USA
  6. 6Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, Helsinki, Finland
  7. 7Obesity Center, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
  8. 8Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
  1. ↵**Corresponding author: Päivi Pajukanta, MD, PhD, Professor, Vice Chair, Department of Human Genetics, Director of Cardiometabolic Genomics, Institute for Precision Health, David Geffen School of Medicine at UCLA, Gonda Center, Room 6335B, 695 Charles E. Young Drive South, Los Angeles, California 90095-7088, USA Email: ppajukanta{at}mednet.ucla.edu
  1. ↵* Equal first authorship

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Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Zong Miao, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
bioRxiv 786285; doi: https://doi.org/10.1101/786285
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Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Zong Miao, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
bioRxiv 786285; doi: https://doi.org/10.1101/786285

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