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Research Article
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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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  • ORCID record for Jovan Tanevski
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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  • ORCID record for Chang Shu
Ke Xu
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
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  • ORCID record for Ke Xu
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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  • ORCID record for Ying Hu
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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  • 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
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  • 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
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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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  • ORCID record for Nestoras Karathanasis
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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  • ORCID record for Yang Chen
Zhengqing Ouyang
15University of Massachusetts, Amherst, MA, USA
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  • ORCID record for Zhengqing Ouyang
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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  • ORCID record for Tin Nguyen
Attila Gabor
1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
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  • ORCID record for Attila Gabor
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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  • ORCID record for Pablo Meyer
  • 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

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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
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Volume 3, No. 11
November 2020
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