Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

Geoffrey Schiebinger; Jian Shu; Marcin Tabaka; Brian Cleary; Vidya Subramanian; Aryeh Solomon; Siyan Liu; Stacie Lin; Peter Berube; Lia Lee; Jenny Chen; Justin Brumbaugh; Philippe Rigollet; Konrad Hochedlinger; Rudolf Jaenisch; Aviv Regev; Eric S. Lander

doi:10.1101/191056

New Results

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, Eric S. Lander

doi: https://doi.org/10.1101/191056

Geoffrey Schiebinger

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

11MIT Center for Statistics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Jian Shu

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Marcin Tabaka

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Brian Cleary

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

3Computational and Systems Biology Program, MIT, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Vidya Subramanian

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Aryeh Solomon

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Siyan Liu

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

15Biochemistry Program, Wellesley College, Wellesley, 02481, MA, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Stacie Lin

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

6Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Peter Berube

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Lia Lee

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Jenny Chen

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

4Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139 USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Justin Brumbaugh

5Cancer Center, Massachusetts General Hospital, Boston, MA 02114 USA

7Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA

8Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

9Harvard Stem Cell Institute, Cambridge, MA 02138, USA

10Harvard Medical School, Boston, MA 02115, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Philippe Rigollet

11MIT Center for Statistics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

12Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Konrad Hochedlinger

7Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA

8Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

9Harvard Stem Cell Institute, Cambridge, MA 02138, USA

13Howard Hughes Medical Institute, Chevy Chase, MD, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Rudolf Jaenisch

2Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

3Computational and Systems Biology Program, MIT, Cambridge, MA 02142, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Aviv Regev

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

6Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

13Howard Hughes Medical Institute, Chevy Chase, MD, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Eric S. Lander

1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

6Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

14Department of Systems Biology Harvard Medical School, Boston, MA 02125, USA

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Abstract
Full Text
Info/History
Metrics
Supplementary material
Preview PDF

Article usage

Article usage: January 2018 to March 2023

	Abstract	Full	Pdf
Jan 2018	913	0	513
Feb 2018	606	0	329
Mar 2018	675	0	434
Apr 2018	512	0	298
May 2018	585	0	289
Jun 2018	769	0	290
Jul 2018	565	0	252
Aug 2018	441	0	219
Sep 2018	504	0	233
Oct 2018	480	0	259
Nov 2018	532	0	278
Dec 2018	406	0	243
Jan 2019	658	0	366
Feb 2019	888	0	547
Mar 2019	577	10	308
Apr 2019	378	38	217
May 2019	283	53	163
Jun 2019	256	46	148
Jul 2019	256	56	142
Aug 2019	240	61	146
Oct 2019	261	60	158
Nov 2019	216	55	156
Dec 2019	169	48	93
Jan 2020	195	53	100
Feb 2020	180	50	81
Mar 2020	150	47	62
May 2020	180	60	93
Jun 2020	119	38	55
Jul 2020	96	48	55
Aug 2020	101	31	39
Sep 2020	123	21	37
Oct 2020	125	25	68
Nov 2020	123	55	54
Dec 2020	161	24	42
Jan 2021	104	53	60
Feb 2021	108	46	43
Mar 2021	143	41	58
Apr 2021	112	39	47
May 2021	133	28	51
Jun 2021	109	25	59
Jul 2021	105	39	49
Aug 2021	137	29	55
Sep 2021	90	18	58
Oct 2021	145	25	68
Nov 2021	91	13	59
Dec 2021	117	9	33
Jan 2022	159	10	76
Feb 2022	86	8	18
Mar 2022	77	9	38
Apr 2022	100	23	25
May 2022	85	24	36
Jun 2022	104	20	38
Jul 2022	84	9	14
Aug 2022	108	19	32
Sep 2022	121	16	51
Oct 2022	135	13	39
Nov 2022	144	15	34
Dec 2022	67	16	32
Jan 2023	99	18	27
Feb 2023	70	18	18
Mar 2023	71	11	25