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

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

doi:10.26508/lsa.202000867

Research Article

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

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Thin Nguyen

3Deakin University, Geelong, Australia

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Buu Truong

4University of South Australia, Mawson Lakes, Australia

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Nikos Karaiskos

5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany

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Mehmet Eren Ahsen

6Icahn School of Medicine at Mount Sinai, New York City, NY, USA

7University of Illinois, Urbana-Champaign, Champaign, IL, USA

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Xinyu Zhang

8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA

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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

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Ke Xu

8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA

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Xiaoyu Liang

8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA

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Ying Hu

9Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA

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Hoang VV Pham

4University of South Australia, Mawson Lakes, Australia

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Li Xiaomei

4University of South Australia, Mawson Lakes, Australia

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Thuc D Le

4University of South Australia, Mawson Lakes, Australia

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Adi L Tarca

10Department of Obstetrics and Gynecology and Department of Computer Science, Wayne State University, Detroit, MI, USA

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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

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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

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Nestoras Karathanasis

13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA

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Phillipe Loher

13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA

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Yang Chen

14The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA

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Zhengqing Ouyang

15University of Massachusetts, Amherst, MA, USA

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Disheng Mao

16University of Connecticut, Storrs, CT, USA

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Yuping Zhang

16University of Connecticut, Storrs, CT, USA

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Maryam Zand

17University of Texas at San Antonio, San Antonio, TX, USA

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Jianhua Ruan

17University of Texas at San Antonio, San Antonio, TX, USA

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Christoph Hafemeister

18New York Genome Center, New York City, NY, USA

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Peng Qiu

19Georgia Institute of Technology, Atlanta, GA, USA

20Emory University, Atlanta, GA, USA

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Duc Tran

21University of Nevada, Reno, NV, USA

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Tin Nguyen

21University of Nevada, Reno, NV, USA

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Attila Gabor

1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany

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Thomas Yu

22Sage Bionetworks, Seattle, WA, USA

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Justin Guinney

22Sage Bionetworks, Seattle, WA, USA

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Enrico Glaab

23Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg

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Roland Krause

24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg

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Peter Banda

24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg

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Gustavo Stolovitzky

25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA

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Nikolaus Rajewsky

5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany

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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

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Pablo Meyer

25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA

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For correspondence: pmeyerr@us.ibm.com

Published 24 September 2020. DOI: 10.26508/lsa.202000867

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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