Selected Publications 

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects.

de Soysa TY, Ranade SS, Okawa S, Ravichandran S, Huang Y, Salunga HT,
Schricker A, Del Sol A, Gifford CA*, Srivastava D*. Nature. 2019, Aug;572(7767):120-124. *co-corresponding authors 


 

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.

Stone NR*, Gifford CA*, Thomas R, Pratt KJB, Samse-Knapp K, Mohamed TMA,
Radzinsky EM, Schricker A, Ye L, Yu P, van Bemmel JG, Ivey KN, Pollard KS,
Srivastava D. Cell Stem Cell. 2019, Jul 3;25(1):87-102.e9. *co-first authors

 


Oligogenic inheritance of a human heart disease involving a genetic modifier.
Gifford CA, Ranade SS, Samarakoon R, Salunga HT, de Soysa TY, Huang Y, Zhou P,
Elfenbein A, Wyman SK, Bui YK, Cordes Metzler KR, Ursell P, Ivey KN, Srivastava
D. Science. 2019 May 31;364(6443):865-870. 

 

Genetic determinants and epigenetic effects of pioneer-factor occupancy.
Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement
K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke
A, Ziller MJ, Meissner A. Nat Genet. 2018 Feb;50(2):250-258. 

 

Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma.
Aguilar CA, Pop R, Shcherbina A, Watts A, Matheny RW Jr, Cacchiarelli D, Han
WM, Shin E, Nakhai SA, Jang YC, Carrigan CT, Gifford CA, Kottke MA, Cesana M, Lee
J, Urso ML, Meissner A. Stem Cell Reports. 2016 Nov 8;7(5):983-997.

 


A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells.
Tsankov AM, Akopian V, Pop R, Chetty S, Gifford CA, Daheron L, Tsankova NM,
Meissner A. Nat Biotechnol. 2015 Nov;33(11):1182-92. 

 


In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing.
Aguilar CA, Shcherbina A, Ricke DO, Pop R, Carrigan CT, Gifford CA, Urso ML,
Kottke MA, Meissner A. Sci Rep. 2015 Sep 18;5:13885. 


 

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.
Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R,
Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V,
Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.
Cell. 2015 Jul 16;162(2):412-424. 

 


Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.
Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford
CA
, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn
JL, Gnirke A, Meissner A. Nat Genet. 2015 May;47(5):469-78. 

 


Dissecting neural differentiation regulatory networks through epigenetic footprinting.
Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford
CA
, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR,
Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A.
Nature. 2015 Feb 19;518(7539):355-359. 

 


Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.
Gifford CA*, Ziller MJ*, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK,
Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim
J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES,
Bernstein BE, Meissner A. Cell. 2013 May 23;153(5):1149-63. *co-first authors

 

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BASE Initiative