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
Thin Nguyen
3Deakin University, Geelong, Australia
Buu Truong
4University of South Australia, Mawson Lakes, Australia
Nikos Karaiskos
5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
Mehmet Eren Ahsen
6Icahn School of Medicine at Mount Sinai, New York City, NY, USA
7University of Illinois, Urbana-Champaign, Champaign, IL, USA
Xinyu Zhang
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
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
Ke Xu
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
Xiaoyu Liang
8Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
Ying Hu
9Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
Hoang VV Pham
4University of South Australia, Mawson Lakes, Australia
Li Xiaomei
4University of South Australia, Mawson Lakes, Australia
Thuc D Le
4University of South Australia, Mawson Lakes, Australia
Adi L Tarca
10Department of Obstetrics and Gynecology and Department of Computer Science, Wayne State University, Detroit, MI, USA
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
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
Nestoras Karathanasis
13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
Phillipe Loher
13Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
Yang Chen
14The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
Zhengqing Ouyang
15University of Massachusetts, Amherst, MA, USA
Disheng Mao
16University of Connecticut, Storrs, CT, USA
Yuping Zhang
16University of Connecticut, Storrs, CT, USA
Maryam Zand
17University of Texas at San Antonio, San Antonio, TX, USA
Jianhua Ruan
17University of Texas at San Antonio, San Antonio, TX, USA
Christoph Hafemeister
18New York Genome Center, New York City, NY, USA
Peng Qiu
19Georgia Institute of Technology, Atlanta, GA, USA
20Emory University, Atlanta, GA, USA
Duc Tran
21University of Nevada, Reno, NV, USA
Tin Nguyen
21University of Nevada, Reno, NV, USA
Attila Gabor
1Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
Thomas Yu
22Sage Bionetworks, Seattle, WA, USA
Justin Guinney
22Sage Bionetworks, Seattle, WA, USA
Enrico Glaab
23Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
Roland Krause
24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
Peter Banda
24Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
Gustavo Stolovitzky
25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
Nikolaus Rajewsky
5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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
Pablo Meyer
25International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
Published 24 September 2020. DOI: 10.26508/lsa.202000867
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
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
In this Issue
Volume 3, No. 11
November 2020
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