Skip to main content
Advertisement

Main menu

  • Home
  • Articles
    • Newest Articles
    • Current Issue
    • Methods & Resources
    • Archive
    • Subjects
  • Collections
  • Submit
    • Submit a Manuscript
    • Author Guidelines
    • License, Copyright, Fee
    • FAQ
    • Why submit
  • About
    • About Us
    • Editors & Staff
    • Board Members
    • Licensing and Reuse
    • Reviewer Guidelines
    • Privacy Policy
    • Advertise
    • Contact Us
    • LSA LLC
  • Alerts
  • Other Publications
    • EMBO Press
    • The EMBO Journal
    • EMBO reports
    • EMBO Molecular Medicine
    • Molecular Systems Biology
    • Rockefeller University Press
    • Journal of Cell Biology
    • Journal of Experimental Medicine
    • Journal of General Physiology
    • Cold Spring Harbor Laboratory Press
    • Genes & Development
    • Genome Research

User menu

  • My alerts

Search

  • Advanced search
Life Science Alliance
  • Other Publications
    • EMBO Press
    • The EMBO Journal
    • EMBO reports
    • EMBO Molecular Medicine
    • Molecular Systems Biology
    • Rockefeller University Press
    • Journal of Cell Biology
    • Journal of Experimental Medicine
    • Journal of General Physiology
    • Cold Spring Harbor Laboratory Press
    • Genes & Development
    • Genome Research
  • My alerts
Life Science Alliance

Advanced Search

  • Home
  • Articles
    • Newest Articles
    • Current Issue
    • Methods & Resources
    • Archive
    • Subjects
  • Collections
  • Submit
    • Submit a Manuscript
    • Author Guidelines
    • License, Copyright, Fee
    • FAQ
    • Why submit
  • About
    • About Us
    • Editors & Staff
    • Board Members
    • Licensing and Reuse
    • Reviewer Guidelines
    • Privacy Policy
    • Advertise
    • Contact Us
    • LSA LLC
  • Alerts
  • Follow lsa Template on Twitter
Research Article
Transparent Process
Open Access

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

View ORCID ProfileJovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, View ORCID ProfileChang Shu, View ORCID ProfileKe Xu, Xiaoyu Liang, View ORCID ProfileYing Hu, View ORCID ProfileHoang VV Pham, Li Xiaomei, View ORCID ProfileThuc D Le, View ORCID ProfileAdi L Tarca, Gaurav Bhatti, Roberto Romero, View ORCID ProfileNestoras Karathanasis, Phillipe Loher, View ORCID ProfileYang Chen, View ORCID ProfileZhengqing Ouyang, Disheng Mao, View ORCID ProfileYuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, View ORCID ProfileDuc Tran, View ORCID ProfileTin Nguyen, View ORCID ProfileAttila Gabor, Thomas Yu, Justin Guinney, View ORCID ProfileEnrico Glaab, View ORCID ProfileRoland Krause, View ORCID ProfilePeter Banda, DREAM SCTC Consortium, View ORCID ProfileGustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, View ORCID ProfilePablo Meyer  Correspondence email
Jovan Tanevski
1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
2Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jovan Tanevski
Thin Nguyen
3Deakin University, Geelong, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Buu Truong
4University of South Australia, Mawson Lakes, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nikos Karaiskos
5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mehmet Eren Ahsen
6Icahn School of Medicine at Mount Sinai, New York City, NY, USA
7University of Illinois, Urbana-Champaign, Champaign, IL, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xinyu Zhang
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chang Shu
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
27Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chang Shu
Ke Xu
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ke Xu
Xiaoyu Liang
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ying Hu
9Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ying Hu
Hoang VV Pham
4University of South Australia, Mawson Lakes, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hoang VV Pham
Li Xiaomei
4University of South Australia, Mawson Lakes, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thuc D Le
4University of South Australia, Mawson Lakes, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thuc D Le
Adi L Tarca
10Department of Obstetrics and Gynecology and Department of Computer Science, Wayne State University, Detroit, MI, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adi L Tarca
Gaurav Bhatti
11Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Insitutes of Health (NIH)/ Department of Health & Human Services (DHHS), Bethesda, MD, USA
12Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roberto Romero
11Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Insitutes of Health (NIH)/ Department of Health & Human Services (DHHS), Bethesda, MD, USA
12Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nestoras Karathanasis
13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nestoras Karathanasis
Phillipe Loher
13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yang Chen
14The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yang Chen
Zhengqing Ouyang
15University of Massachusetts, Amherst, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zhengqing Ouyang
Disheng Mao
16University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yuping Zhang
16University of Connecticut, Storrs, CT, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yuping Zhang
Maryam Zand
17University of Texas at San Antonio, San Antonio, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jianhua Ruan
17University of Texas at San Antonio, San Antonio, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christoph Hafemeister
18New York Genome Center, New York City, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peng Qiu
19Georgia Institute of Technology, Atlanta, GA, USA
20Emory University, Atlanta, GA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Duc Tran
21University of Nevada, Reno, NV, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Duc Tran
Tin Nguyen
21University of Nevada, Reno, NV, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tin Nguyen
Attila Gabor
1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Attila Gabor
Thomas Yu
22Sage Bionetworks, Seattle, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Justin Guinney
22Sage Bionetworks, Seattle, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Enrico Glaab
23Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Enrico Glaab
Roland Krause
24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Roland Krause
Peter Banda
24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Peter Banda
Gustavo Stolovitzky
25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gustavo Stolovitzky
Nikolaus Rajewsky
5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Julio Saez-Rodriguez
1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
26Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pablo Meyer
25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Pablo Meyer
  • For correspondence: pmeyerr@us.ibm.com
Published 24 September 2020. DOI: 10.26508/lsa.202000867
  • Article
  • Figures & Data
  • Info
  • Metrics
  • Reviewer Comments
  • PDF
Loading

Article Information

vol. 3 no. 11 e202000867
DOI 
https://doi.org/10.26508/lsa.202000867
PubMed 
32972997

Published By 
Life Science Alliance
Online ISSN 
2575-1077
History 
  • Received July 31, 2020
  • Revision received August 26, 2020
  • Accepted August 31, 2020
  • Published online September 24, 2020.

Copyright & Usage 
© 2020 Tanevski et al. This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).

Author Information

  1. Jovan Tanevski1,2,*,
  2. Thin Nguyen3,*,
  3. Buu Truong4,*,
  4. Nikos Karaiskos5,
  5. Mehmet Eren Ahsen6,7,
  6. Xinyu Zhang8,
  7. Chang Shu8,27,
  8. Ke Xu8,
  9. Xiaoyu Liang8,
  10. Ying Hu9,
  11. Hoang VV Pham4,
  12. Li Xiaomei4,
  13. Thuc D Le4,
  14. Adi L Tarca10,
  15. Gaurav Bhatti11,12,
  16. Roberto Romero11,12,
  17. Nestoras Karathanasis13,
  18. Phillipe Loher13,
  19. Yang Chen14,
  20. Zhengqing Ouyang15,
  21. Disheng Mao16,
  22. Yuping Zhang16,
  23. Maryam Zand17,
  24. Jianhua Ruan17,
  25. Christoph Hafemeister18,
  26. Peng Qiu19,20,
  27. Duc Tran21,
  28. Tin Nguyen21,
  29. Attila Gabor1,
  30. Thomas Yu22,
  31. Justin Guinney22,
  32. Enrico Glaab23,
  33. Roland Krause24,
  34. Peter Banda24,
  35. DREAM SCTC Consortium‡,
  36. Gustavo Stolovitzky25,
  37. Nikolaus Rajewsky5,†,
  38. Julio Saez-Rodriguez1,26,† and
  39. Pablo Meyer25⇑
  1. 1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
  2. 2Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
  3. 3Deakin University, Geelong, Australia
  4. 4University of South Australia, Mawson Lakes, Australia
  5. 5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
  6. 6Icahn School of Medicine at Mount Sinai, New York City, NY, USA
  7. 7University of Illinois, Urbana-Champaign, Champaign, IL, USA
  8. 8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
  9. 9Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
  10. 10Department of Obstetrics and Gynecology and Department of Computer Science, Wayne State University, Detroit, MI, USA
  11. 11Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Insitutes of Health (NIH)/ Department of Health & Human Services (DHHS), Bethesda, MD, USA
  12. 12Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
  13. 13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
  14. 14The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  15. 15University of Massachusetts, Amherst, MA, USA
  16. 16University of Connecticut, Storrs, CT, USA
  17. 17University of Texas at San Antonio, San Antonio, TX, USA
  18. 18New York Genome Center, New York City, NY, USA
  19. 19Georgia Institute of Technology, Atlanta, GA, USA
  20. 20Emory University, Atlanta, GA, USA
  21. 21University of Nevada, Reno, NV, USA
  22. 22Sage Bionetworks, Seattle, WA, USA
  23. 23Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
  24. 24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
  25. 25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
  26. 26Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
  27. 27Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
  1. Correspondence: pmeyerr{at}us.ibm.com
  1. ↵* Jovan Tanevski, Thin Nguyen, and Buu Truong contributed equally to this work

View Full Text

Funding

  • PROACTIVE 2017 “From Single-Cell to Multi-Cells Information Systems Analysis”

    C92F17003530005
    BD Camillo
  • National Institutes of Health

    U54CA21729
    J Ruan
  • Indian Council of Medical Research - Junior Research Fellowship

    S Ahmad
  • National Natural Science Foundation of China

    61702421 and 61772426
    X Wang
PreviousNext
Back to top
Download PDF
Email Article

Thank you for your interest in spreading the word on Life Science Alliance.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
(Your Name) has sent you a message from Life Science Alliance
(Your Name) thought you would like to see the Life Science Alliance web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Predicting cells position from single-cell transcriptomics
Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang VV Pham, Li Xiaomei, Thuc D Le, Adi L Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, DREAM SCTC Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer
Life Science Alliance Sep 2020, 3 (11) e202000867; DOI: 10.26508/lsa.202000867

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Share
Predicting cells position from single-cell transcriptomics
Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang VV Pham, Li Xiaomei, Thuc D Le, Adi L Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, DREAM SCTC Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer
Life Science Alliance Sep 2020, 3 (11) e202000867; DOI: 10.26508/lsa.202000867
Reddit logo Twitter logo Facebook logo Mendeley logo
  • Tweet Widget
  • Facebook Like
Issue Cover

In this Issue

Volume 3, No. 11
November 2020
  • Table of Contents
  • Cover (PDF)
  • About the Cover
  • Masthead (PDF)
Advertisement

Jump to section

  • Article
    • Abstract
    • Introduction
    • Results
    • Discussion
    • Materials and Methods
    • Acknowledgements
    • Footnotes
    • References
  • Figures & Data
  • Info
  • Metrics
  • Reviewer Comments
  • PDF

Subjects

  • Systems & Computational Biology

Related Articles

  • No related articles found.

Cited By...

  • Museum of Spatial Transcriptomics
  • Google Scholar

More in this TOC Section

  • miR-33b inhibition improves NAFLD/NASH
  • Regulation of survival of C. elegans by amphid neurons
  • Genome-wide modeling of fly metabolism
Show more Research Article

Similar Articles

EMBO Press LogoRockefeller University Press LogoCold Spring Harbor Logo

Content

  • Home
  • Newest Articles
  • Current Issue
  • Archive
  • Subject Collections

For Authors

  • Submit a Manuscript
  • Author Guidelines
  • License, copyright, Fee

Other Services

  • Alerts
  • Twitter
  • RSS Feeds

More Information

  • Editors & Staff
  • Reviewer Guidelines
  • Feedback
  • Licensing and Reuse
  • Privacy Policy

ISSN: 2575-1077
© 2023 Life Science Alliance LLC

Life Science Alliance is registered as a trademark in the U.S. Patent and Trade Mark Office and in the European Union Intellectual Property Office.