Archive Page: Vallier Group | Pancreatic genetics

Archive Page: Vallier Group | Pancreatic genetics

Vallier Group

The Vallier research team was based jointly at the Wellcome Sanger Institute and the Wellcome - MRC Cambridge Stem Cell Institute until 2019, when the team became fully based at the Stem Cell Institute. To find out more about the team's ongoing work, please visit: This page is maintained as a historical record of the team's work while at the Sanger Institute, and is no longer being updated.
Vallier GroupSanger Institute, Genome Research Limited
Vallier Group

Our Research and Approach


Vallier, Ludovic
Dr Ludovic Vallier
Group Leader

Ludovic Vallier is jointly based at the Cambridge Stem Cell Institute and the Wellcome Sanger Institute. His laboratory studies the basic mechanisms controlling differentiation of human pluripotent cells into pancreas, lung, gut and liver cells. His overall objective is not only to investigate molecular mechanisms of differentiation but also to generate cell types for clinical studies and for cell based therapy.

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  • Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

    Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ et al.

    Nature communications 2020;11;1;810

  • HNF4A Haploinsufficiency in MODY1 Abrogates Liver and Pancreas Differentiation from Patient-Derived Induced Pluripotent Stem Cells.

    Ng NHJ, Jasmen JB, Lim CS, Lau HH, Krishnan VG et al.

    iScience 2019;16;192-205

  • A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells.

    Hurrell T, Segeritz CP, Vallier L, Lilley KS and Cromarty AD

    Scientific reports 2019;9;1;3270

  • Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

    Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S et al.

    Genome biology 2019;20;1;30

  • GATA6 Cooperates with EOMES/SMAD2/3 to Deploy the Gene Regulatory Network Governing Human Definitive Endoderm and Pancreas Formation.

    Chia CY, Madrigal P, Denil SLIJ, Martinez I, Garcia-Bernardo J et al.

    Stem cell reports 2019;12;1;57-70

  • Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics.

    Yiangou L, Grandy RA, Morell CM, Tomaz RA, Osnato A et al.

    Stem cell reports 2019;12;1;165-179

  • Conditional Gene Knockout in Human Cells with Inducible CRISPR/Cas9.

    Snijders KE, Cooper JD, Vallier L and Bertero A

    Methods in molecular biology (Clifton, N.J.) 2019;1961;185-209

  • Derivation of Intestinal Organoids from Human Induced Pluripotent Stem Cells for Use as an Infection System.

    Forbester JL, Hannan N, Vallier L and Dougan G

    Methods in molecular biology (Clifton, N.J.) 2019;1576;157-169

  • Genome-Wide Epigenetic and Transcriptomic Characterization of Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids.

    Kraiczy J, Ross ADB, Forbester JL, Dougan G, Vallier L and Zilbauer M

    Cellular and molecular gastroenterology and hepatology 2019;7;2;285-288

  • hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α1-antitrypsin deficiency.

    Segeritz CP, Rashid ST, de Brito MC, Serra MP, Ordonez A et al.

    Journal of hepatology 2018;69;4;851-860

  • Human Pluripotent Stem Cell-Derived Endoderm for Modeling Development and Clinical Applications.

    Yiangou L, Ross ADB, Goh KJ and Vallier L

    Cell stem cell 2018;22;4;485-499

  • Advances in the generation of bioengineered bile ducts.

    Justin AW, Saeb-Parsy K, Markaki AE, Vallier L and Sampaziotis F

    Biochimica et biophysica acta. Molecular basis of disease 2018;1864;4 Pt B;1532-1538

  • The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency.

    Bertero A, Brown S, Madrigal P, Osnato A, Ortmann D et al.

    Nature 2018;555;7695;256-259

  • Conditional Manipulation of Gene Function in Human Cells with Optimized Inducible shRNA.

    Bertero A, Yiangou L, Brown S, Ortmann D, Pawlowski M and Vallier L

    Current protocols in stem cell biology 2018;44;5C.4.1-5C.4.48

  • Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

    Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A et al.

    Nature cell biology 2018;20;2;127-134

  • Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos.

    Jennings RE, Berry AA, Gerrard DT, Wearne SJ, Strutt J et al.

    Stem cell reports 2017;9;5;1387-1394

  • Genome editing reveals a role for OCT4 in human embryogenesis.

    Fogarty NME, McCarthy A, Snijders KE, Powell BE, Kubikova N et al.

    Nature 2017;550;7674;67-73

  • Variability of human pluripotent stem cell lines.

    Ortmann D and Vallier L

    Current opinion in genetics & development 2017;46;179-185

  • Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids.

    Sampaziotis F, Justin AW, Tysoe OC, Sawiak S, Godfrey EM et al.

    Nature medicine 2017;23;8;954-963

  • Inducible and Deterministic Forward Programming of Human Pluripotent Stem Cells into Neurons, Skeletal Myocytes, and Oligodendrocytes.

    Pawlowski M, Ortmann D, Bertero A, Tavares JM, Pedersen RA et al.

    Stem cell reports 2017;8;4;803-812

  • Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells.

    Sampaziotis F, de Brito MC, Geti I, Bertero A, Hannan NR and Vallier L

    Nature protocols 2017;12;4;814-827

  • Optimized inducible shRNA and CRISPR/Cas9 platforms for in vitro studies of human development using hPSCs.

    Bertero A, Pawlowski M, Ortmann D, Snijders K, Yiangou L et al.

    Development (Cambridge, England) 2016;143;23;4405-4418

  • The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages.

    Zhu L, Gomez-Duran A, Saretzki G, Jin S, Tilgner K et al.

    The Journal of cell biology 2016;215;2;187-202

  • The role of hepatocyte nuclear factor 1β in disease and development.

    El-Khairi R and Vallier L

    Diabetes, obesity & metabolism 2016;18 Suppl 1;23-32

  • Interleukin-13 Activates Distinct Cellular Pathways Leading to Ductular Reaction, Steatosis, and Fibrosis.

    Gieseck RL, Ramalingam TR, Hart KM, Vannella KM, Cantu DA et al.

    Immunity 2016;45;1;145-58

  • Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.

    Rouhani FJ, Nik-Zainal S, Wuster A, Li Y, Conte N et al.

    PLoS genetics 2016;12;4;e1005932

  • Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D.

    Pauklin S, Madrigal P, Bertero A and Vallier L

    Genes & development 2016;30;4;421-33

  • Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells.

    Butcher LM, Ito M, Brimpari M, Morris TJ, Soares FAC et al.

    Nature communications 2016;7;10458

  • Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations.

    Iovino M, Agathou S, González-Rueda A, Del Castillo Velasco-Herrera M, Borroni B et al.

    Brain : a journal of neurology 2015;138;Pt 11;3345-59

  • Putting induced pluripotent stem cells to the test.

    Vallier L

    Nature biotechnology 2015;33;11;1145-6

  • Successful Generation of Human Induced Pluripotent Stem Cell Lines from Blood Samples Held at Room Temperature for up to 48 hr.

    Agu CA, Soares FA, Alderton A, Patel M, Ansari R et al.

    Stem cell reports 2015;5;4;660-71

  • Cell Cycle Rules Pluripotency.

    Vallier L

    Cell stem cell 2015;17;2;131-2

  • Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation.

    Sampaziotis F, de Brito MC, Madrigal P, Bertero A, Saeb-Parsy K et al.

    Nature biotechnology 2015;33;8;845-852

  • Generation of Distal Airway Epithelium from Multipotent Human Foregut Stem Cells.

    Hannan NR, Sampaziotis F, Segeritz CP, Hanley NA and Vallier L

    Stem cells and development 2015;24;14;1680-90

  • Potential of human induced pluripotent stem cells in studies of liver disease.

    Sampaziotis F, Segeritz CP and Vallier L

    Hepatology (Baltimore, Md.) 2015;62;1;303-11

  • TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

    Cebola I, Rodríguez-Seguí SA, Cho CH, Bessa J, Rovira M et al.

    Nature cell biology 2015;17;5;615-626

  • Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.

    Bertero A, Madrigal P, Galli A, Hubner NC, Moreno I et al.

    Genes & development 2015;29;7;702-17

  • Phenotypic and functional analyses show stem cell-derived hepatocyte-like cells better mimic fetal rather than adult hepatocytes.

    Baxter M, Withey S, Harrison S, Segeritz CP, Zhang F et al.

    Journal of hepatology 2015;62;3;581-9

  • Fucci2a mouse upgrades live cell cycle imaging.

    Bertero A and Vallier L

    Cell cycle (Georgetown, Tex.) 2015;14;7;948-9

  • International coordination of large-scale human induced pluripotent stem cell initiatives: Wellcome Trust and ISSCR workshops white paper.

    Soares FA, Sheldon M, Rao M, Mummery C and Vallier L

    Stem cell reports 2014;3;6;931-9

  • Human stem cells for craniomaxillofacial reconstruction.

    Jalali M, Kirkpatrick WN, Cameron MG, Pauklin S and Vallier L

    Stem cells and development 2014;23;13;1437-51

  • Genetic background drives transcriptional variation in human induced pluripotent stem cells.

    Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L and Gaffney D

    PLoS genetics 2014;10;6;e1004432

  • Investigating the feasibility of scale up and automation of human induced pluripotent stem cells cultured in aggregates in feeder free conditions.

    Soares FA, Chandra A, Thomas RJ, Pedersen RA, Vallier L and Williams DJ

    Journal of biotechnology 2014;173;53-8

  • Heps with pep: direct reprogramming into human hepatocytes.

    Vallier L

    Cell stem cell 2014;14;3;267-9

  • Maturation of induced pluripotent stem cell derived hepatocytes by 3D-culture.

    Gieseck RL, Hannan NR, Bort R, Hanley NA, Drake RA et al.

    PloS one 2014;9;1;e86372

  • Survival and differentiation of adenovirus-generated induced pluripotent stem cells transplanted into the rat striatum.

    Fink KD, Rossignol J, Lu M, Lévêque X, Hulse TD et al.

    Cell transplantation 2014;23;11;1407-23

  • The cell-cycle state of stem cells determines cell fate propensity.

    Pauklin S and Vallier L

    Cell 2013;155;1;135-47

  • Human pluripotent stem cells for modelling human liver diseases and cell therapy.

    Dianat N, Steichen C, Vallier L, Weber A and Dubart-Kupperschmitt A

    Current gene therapy 2013;13;2;120-32

  • Multiple roles of Activin/Nodal, bone morphogenetic protein, fibroblast growth factor and Wnt/β-catenin signalling in the anterior neural patterning of adherent human embryonic stem cell cultures.

    Lupo G, Novorol C, Smith JR, Vallier L, Miranda E et al.

    Open biology 2013;3;4;120167

  • Production of hepatocyte-like cells from human pluripotent stem cells.

    Hannan NR, Segeritz CP, Touboul T and Vallier L

    Nature protocols 2013;8;2;430-7

  • A practical and efficient cellular substrate for the generation of induced pluripotent stem cells from adults: blood-derived endothelial progenitor cells.

    Geti I, Ormiston ML, Rouhani F, Toshner M, Movassagh M et al.

    Stem cells translational medicine 2012;1;12;855-65

  • Status of genomic imprinting in epigenetically distinct pluripotent stem cells.

    Sun B, Ito M, Mendjan S, Ito Y, Brons IG et al.

    Stem cells (Dayton, Ohio) 2012;30;2;161-8

  • Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells.

    Evans AL, Faial T, Gilchrist MJ, Down T, Vallier L et al.

    PloS one 2012;7;3;e33346

  • Pancreatic transcription factors containing protein transduction domains drive mouse embryonic stem cells towards endocrine pancreas.

    Lima MJ, Docherty HM, Chen Y, Vallier L and Docherty K

    PloS one 2012;7;5;e36481

  • Mouse pluripotent stem cells at a glance.

    Pauklin S, Pedersen RA and Vallier L

    Journal of cell science 2011;124;Pt 22;3727-32

  • Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells.

    Yusa K, Rashid ST, Strick-Marchand H, Varela I, Liu PQ et al.

    Nature 2011;478;7369;391-4

  • Activin/Nodal signaling controls divergent transcriptional networks in human embryonic stem cells and in endoderm progenitors.

    Brown S, Teo A, Pauklin S, Hannan N, Cho CH et al.

    Stem cells (Dayton, Ohio) 2011;29;8;1176-85

  • Pluripotency factors regulate definitive endoderm specification through eomesodermin.

    Teo AK, Arnold SJ, Trotter MW, Brown S, Ang LT et al.

    Genes & development 2011;25;3;238-50

  • The serpinopathies studying serpin polymerization in vivo.

    Irving JA, Ekeowa UI, Belorgey D, Haq I, Gooptu B et al.

    Methods in enzymology 2011;501;421-66

  • Activin/nodal signaling and pluripotency.

    Chng Z, Vallier L and Pedersen R

    Vitamins and hormones 2011;85;39-58

  • Serum-free and feeder-free culture conditions for human embryonic stem cells.

    Vallier L

    Methods in molecular biology (Clifton, N.J.) 2011;690;57-66

  • A factor(s) secreted from MIN-6 beta-cells stimulates differentiation of definitive endoderm enriched embryonic stem cells towards a pancreatic lineage.

    Uroić DS, Baudouin G, Ferguson LA, Docherty HM, Vallier L and Docherty K

    Molecular and cellular endocrinology 2010;328;1-2;80-6

  • Modeling inherited metabolic disorders of the liver using human induced pluripotent stem cells.

    Rashid ST, Corbineau S, Hannan N, Marciniak SJ, Miranda E et al.

    The Journal of clinical investigation 2010;120;9;3127-36

  • Emerging use of stem cells in regenerative medicine.

    Teo AK and Vallier L

    The Biochemical journal 2010;428;1;11-23

  • Generation of functional hepatocytes from human embryonic stem cells under chemically defined conditions that recapitulate liver development.

    Touboul T, Hannan NR, Corbineau S, Martinez A, Martinet C et al.

    Hepatology (Baltimore, Md.) 2010;51;5;1754-65

  • Nuclear transfer-derived epiblast stem cells are transcriptionally and epigenetically distinguishable from their fertilized-derived counterparts.

    Maruotti J, Dai XP, Brochard V, Jouneau L, Liu J et al.

    Stem cells (Dayton, Ohio) 2010;28;4;743-52

  • SIP1 mediates cell-fate decisions between neuroectoderm and mesendoderm in human pluripotent stem cells.

    Chng Z, Teo A, Pedersen RA and Vallier L

    Cell stem cell 2010;6;1;59-70

  • Induced pluripotent stem cells--alchemist's tale or clinical reality?

    Rashid ST and Vallier L

    Expert reviews in molecular medicine 2010;12;25

  • Signaling pathways controlling pluripotency and early cell fate decisions of human induced pluripotent stem cells.

    Vallier L, Touboul T, Brown S, Cho C, Bilican B et al.

    Stem cells (Dayton, Ohio) 2009;27;11;2655-66

  • Senescence impairs successful reprogramming to pluripotent stem cells.

    Banito A, Rashid ST, Acosta JC, Li S, Pereira CF et al.

    Genes & development 2009;23;18;2134-9

  • Activin/Nodal signalling maintains pluripotency by controlling Nanog expression.

    Vallier L, Mendjan S, Brown S, Chng Z, Teo A et al.

    Development (Cambridge, England) 2009;136;8;1339-49

  • Biphasic induction of Pdx1 in mouse and human embryonic stem cells can mimic development of pancreatic beta-cells.

    Bernardo AS, Cho CH, Mason S, Docherty HM, Pedersen RA et al.

    Stem cells (Dayton, Ohio) 2009;27;2;341-51

  • Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways.

    Vallier L, Touboul T, Chng Z, Brimpari M, Hannan N et al.

    PloS one 2009;4;6;e6082

  • Differentiation of human embryonic stem cells in adherent and in chemically defined culture conditions.

    Vallier L and Pedersen R

    Current protocols in stem cell biology 2008;Chapter 1;Unit 1D.4.1-1D.4.7

  • Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm.

    Smith JR, Vallier L, Lupo G, Alexander M, Harris WA and Pedersen RA

    Developmental biology 2008;313;1;107-17

  • Embryonic stem cell therapy for diabetes mellitus.

    Docherty K, Bernardo AS and Vallier L

    Seminars in cell & developmental biology 2007;18;6;827-38

  • Pleiotrophin enhances clonal growth and long-term expansion of human embryonic stem cells.

    Soh BS, Song CM, Vallier L, Li P, Choong C et al.

    Stem cells (Dayton, Ohio) 2007;25;12;3029-37

  • Derivation of pluripotent epiblast stem cells from mammalian embryos.

    Brons IG, Smithers LE, Trotter MW, Rugg-Gunn P, Sun B et al.

    Nature 2007;448;7150;191-5

  • Conditional gene expression in human embryonic stem cells.

    Vallier L, Alexander M and Pedersen R

    Stem cells (Dayton, Ohio) 2007;25;6;1490-7

  • Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique.

    Follows GA, Janes ME, Vallier L, Green AR and Gottgens B

    Nucleic acids research 2007;35;8;e56

  • HOXB4 overexpression promotes hematopoietic development by human embryonic stem cells.

    Bowles KM, Vallier L, Smith JR, Alexander MR and Pedersen RA

    Stem cells (Dayton, Ohio) 2006;24;5;1359-69

  • Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells.

    Vallier L, Alexander M and Pedersen RA

    Journal of cell science 2005;118;Pt 19;4495-509

  • Human embryonic stem cells: an in vitro model to study mechanisms controlling pluripotency in early mammalian development.

    Vallier L and Pedersen RA

    Stem cell reviews 2005;1;2;119-30

  • Nodal inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway.

    Vallier L, Reynolds D and Pedersen RA

    Developmental biology 2004;275;2;403-21

  • Navigating the pathway from embryonic stem cells to beta cells.

    Stoffel M, Vallier L and Pedersen RA

    Seminars in cell & developmental biology 2004;15;3;327-36

  • Enhancing and diminishing gene function in human embryonic stem cells.

    Vallier L, Rugg-Gunn PJ, Bouhon IA, Andersson FK, Sadler AJ and Pedersen RA

    Stem cells (Dayton, Ohio) 2004;22;1;2-11