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Stem cell bioinformatics group publications

2018

Tosti L, Ashmore J, Tan BSiang Nich, Carbone B, Mistri TK, Wilson V, Tomlinson SR, Kaji K.  2018.  Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo.Genome Res. 28(4):592-605.
Dewari PSingh, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner M-C, Plumb C, Kalantzaki M et al..  2018.  An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein.Elife. 7

2017

McGarvey AC, Rybtsov S, Souilhol C, Tamagno S, Rice R, Hills D, Godwin D, Rice D, Tomlinson SR, Medvinsky A.  2017.  A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation.J Exp Med. 214(12):3731-3751.

2015

Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME, De Sousa PA.  2015.  Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State.PLoS One. 10(7):e0131102.
Mistri TKumar, Devasia AGeorge, Chu LThean, Ng WPing, Halbritter F, Colby D, Martynoga B, Tomlinson SR, Chambers I, Robson P et al..  2015.  Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells.EMBO Rep.

2014

Halbritter F, Kousa AI, Tomlinson SR.  2014.  GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments.Nucleic Acids Res. 42(Database issue):D851-8.
Masaki T, McGlinchey A, Cholewa-Waclaw J, Qu J, Tomlinson SR, Rambukkana A.  2014.  Innate immune response precedes Mycobacterium leprae-induced reprogramming of adult Schwann cells.Cell Reprogram. 16(1):9-17.

2013

O'Malley J, Skylaki S, Iwabuchi KA, Chantzoura E, Ruetz T, Johnsson A, Tomlinson SR, Linnarsson S, Kaji K.  2013.  High-resolution analysis with novel cell-surface markers identifies routes to iPS cells.Nature. 499(7456):88-91.
Meek S, Wei J, Sutherland L, Nilges B, Buehr M, Tomlinson SR, Thomson AJ, Burdon T.  2013.  Tuning of β-catenin activity is required to stabilize self-renewal of rat embryonic stem cells.Stem Cells. 31(10):2104-15.
Farley A, Morris LX, Vroegindeweij E, Depreter MGL, Vaidya HJayesh, Stenhouse FH, Tomlinson SR, Anderson RA, Cupedo T, Cornelissen JJ et al..  2013.  Dynamics of thymus organogenesis and colonization in early human development.Development. 140(9):2015-26.
Gagliardi A, Mullin NP, Tan ZYing, Colby D, Kousa AI, Halbritter F, Weiss JT, Felker A, Bezstarosti K, Favaro R et al..  2013.  A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal.EMBO J. 32(16):2231-47.
Karwacki-Neisius V, Göke J, Osorno R, Halbritter F, Ng JHui, Weiße AY, Wong F, Gagliardi A, Mullin NP, Festuccia N et al..  2013.  Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog.Cell Stem Cell. 12(5):531-45.

2012

Halbritter F, Vaidya HJayesh, Tomlinson SR.  2012.  GeneProf: analysis of high-throughput sequencing experiments.Nat Methods. 9(1):7-8.
Skylaki S, Tomlinson SR.  2012.  Recurrent transcriptional clusters in the genome of mouse pluripotent stem cells.Nucleic Acids Res. 40(19):e153.
Festuccia N, Osorno R, Halbritter F, Karwacki-Neisius V, Navarro P, Colby D, Wong F, Yates A, Tomlinson SR, Chambers I.  2012.  Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells.Cell Stem Cell. 11(4):477-90.

2010

Lee E-K, Jin Y-W, Park JHyun, Yoo YMi, Hong SMi, Amir R, Yan Z, Kwon E, Elfick A, Tomlinson SR et al..  2010.  Cultured cambial meristematic cells as a source of plant natural products.Nat Biotechnol. 28(11):1213-7.

2009

Hall J, Guo G, Wray J, Eyres I, Nichols J, Grotewold L, Morfopoulou S, Humphreys P, Mansfield W, Walker R et al..  2009.  Oct4 and LIF/Stat3 additively induce Krüppel factors to sustain embryonic stem cell self-renewal.Cell Stem Cell. 5(6):597-609.
Chambers I, Tomlinson SR.  2009.  The transcriptional foundation of pluripotency.Development. 136(14):2311-22.

2008

Depreter MGL, Blair NF, Gaskell TL, Nowell CS, Davern K, Pagliocca A, Stenhouse FH, Farley A, Fraser A, Vrana J et al..  2008.  Identification of Plet-1 as a specific marker of early thymic epithelial progenitor cells.Proc Natl Acad Sci U S A. 105(3):961-6.

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