List of Publications

Recent papers
Link to Supp. Material from our papers

2014

1)  Sánchez-Castillo M., Ruau D., Wilkinson A.C., Ng F.S., Hannah R., Diamanti E., Lombard P., Wilson N.K., Göttgens B. (2014) “CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.”  Nucleic Acids Res.  PMID:25270877


2) Calero-Nieto F.J., Ng F.S., Wilson N.K., Hannah R., Moignard V., Leal-Cervantes A.I., Jimenez-Madrid I., Diamanti E., Wernisch L., Göttgens B. (2014) “Key regulators control distinct transcriptional programmes in blood progenitor and mast cells.”  EMBO J.  PMID:24760698


3) Wilkinson A.C., Kawata V.K., Schütte J., Gao X., Antoniou S., Baumann C., Woodhouse S., Hannah R., Tanaka Y., Swiers G., Moignard V., Fisher J., Hidetoshi S., Tijssen M.R., de Bruijn M.F., Liu P., Göttgens B. (2014) “Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification.”  Development.  PMID:25252941


4) Ng F.S., Schütte J., Ruau D., Diamanti E., Hannah R., Kinston S.J., Göttgens B. (2014) “Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.”  Nucleic Acids Res.  PMID:25428352


5) Ng F.S., Calero-Nieto F.J., Göttgens B. (2014) “Shared transcription factors contribute to distinct cell fates.”  Transcription.  PMID:25425188


6) Joshi A., Göttgens B. (2014) “Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms.”  Mol Biosyst.  PMID:25133983


7) Sive J.I., Göttgens B. (2014) “Transcriptional network control of normal and leukaemic haematopoiesis.”  Exp Cell Res.  PMID:25014893


8) Moignard V., Göttgens B. (2014) “Transcriptional mechanisms of cell fate decisions revealed by single cell expression profiling.”  Bioessays.  PMID:24470343


9) Pooley C., Ruau D., Lombard P., Göttgens B., Joshi A. (2014) “TRES predicts transcription control in embryonic stem cells.”  Bioinformatics.  PMID:24958811


10) Mahata B., Zhang X., Kolodziejczyk A.A., Proserpio V., Haim-Vilmovsky L., Taylor A.E., Hebenstreit D., Dingler F.A., Moignard V. Göttgens B., Arlt W., McKenzie A.N., Teichmann S.A. (2014) “Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.”  Cell Rep.  PMID:24813893


11) Sun D., Luo M., Jeong M., Rodriguez B., Xia Z., Hannah R., Wang H., Le T., Faull K.F., Chen R., Gu H., Bock C., Meissner A., Göttgens B., Darlington G.J., Li W., Goodell M.A. (2014) “Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal.”  Cell Stem Cell.  PMID:24792119


12) Dickel D.E., Zhu Y., Nord A.S., Wylie J.N., Akiyama J.A., Afzal V., Plajzer-Frick I., Kirkpatrick A., Göttgens B., Bruneau B.G., Visel A., Pennacchio L.A. (2014) “Function-based identification of mammalian enhancers using site-specific integration.“  Nat Methods.  PMID:24658141


13) Buettner F., Moignard V., Göttgens B., Theis F.J. (2014) “Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data.”  Bioinformatics.  PMID:24618470

2013

1)   Moignard V., Macaulay I.C., Swiers G., Buettner F., Schütte J., Calero-Nieto F.J., Kinston S., Joshi A., Hannah R., Theis F.J., Jacobsen S.E., de Bruijn M.F., Göttgens B. (2013) “Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis”  Nat Cell Biol.  PMID:23524953


2)  Khandanpour C., Phelan J.D., Vassen L., Schütte J., Chen R., Horman S.R., Gaudreau M.C., Krongold J., Zhu J., Paul W.E., Dührsen U., Göttgens B., Grimes H.L., Möröy T. (2013) “Growth factor independence 1 antagonizes a p53-induced DNA damage response pathway in lymphoblastic leukemia”  Cancer Cell  23(2):200-14


3)  Staber P.B., Zhang P., Ye M., Welner R.S., Nombela-Arrieta C., Bach C., Kerenyi M., Bartholdy B.A., Zhang H., Alberich-Jordà M., Lee S., Yang H., Ng F., Zhang J., Leddin M., Silberstein L.E., Hoefler G., Orkin S.H., Göttgens B., Rosenbauer F., Huang G., Tenen D.G. (2013) “Sustained PU.1 Levels Balance Cell-Cycle Regulators to Prevent Exhaustion of Adult Hematopoietic Stem Cells”  Mol Cell 49(5):934-46


4)  Diffner E., Beck D., Gudgin E., Thoms J.A., Knezevic K., Pridans C., Foster S., Goode D., Lim W.K., Boelen L., Metzeler K.H., Micklem G., Bohlander S.K., Buske C., Burnett A., Ottersbach K., Vassiliou G.S., Olivier J., Wong J.W., Göttgens B., Huntly B.J., Pimanda J.E. (2013) “Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia”  Blood 121(12):2289-300


5)  Ferreira R., Spensberger D., Silber Y., Dimond A., Li J., Green A.R., Göttgens B. (2013) “Impaired In Vitro Erythropoiesis following Deletion of the Scl (Tal1) +40 Enhancer Is Largely Compensated for In Vivo despite a Significant Reduction in Expression.” Mol Cell Biol. 33(6):1254-66


6)  Oram S.H., Thoms J., Sive J.I., Calero-Nieto F.J., Kinston S.J., Schütte J., Knezevic K., Lock R.B., Pimanda J.E., Göttgens B. (2013) “Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia” Leukemia PMID:23302769


7)  Swiers G., Baumann C., O'Rourke J., Giannoulatou E., Taylor S., Joshi A., Moignard V., Pina C., Bee T., Kokkaliaris K.D., Yoshimoto M., Yoder M.C., Frampton J., Schroeder T., Enver T., Göttgens B., de Bruijn M.F. (2013) “Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level” Nat Commun. PMID:24326267


8)  Jeong M., Sun D., Luo M., Huang Y., Challen G.A., Rodriguez B., Zhang X., Chavez L., Wang H., Hannah R., Kim S.B., Yang L., Ko M., Chen R., Göttgens B., Lee J.S., Gunaratne P., Godley L.A., Darlington G.J., Rao A., Li W., Goodell M.A. (2013) “Large conserved domains of low DNA methylation maintained by Dnmt3a” Nat Genet. PMID:24270360


9)  Wilkinson A.C., Goode D.K., Cheng Y.H., Dickel D.E., Foster S., Sendall T., Tijssen M.R., Sanchez M.J., Pennacchio L.A., Kirkpatrick A.M., Göttgens B. (2013) “Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses” Biol Open. PMID:24244860


10)  Xiang P., Wei W., Lo C., Rosten P., Hou J., Hoodless P.A., Bilenky M., Bonifer C., Cockerill P.N., Kirkpatrick A., Göttgens B., Hirst M., Humphries K.R. (2013) “Delineating MEIS1 cis-regulatory elements active in hematopoietic cells” Leukemia PMID:24097337


11)  Ruau D., Ng F.S., Wilson N.K., Hannah R., Diamanti E., Lombard P., Woodhouse S., Göttgens B. (2013) “Building an ENCODE-style data compendium on a shoestring” Nat Methods. PMID:24076986


12)  Goldberg L., Tijssen M.R., Birger Y., Hannah R.L., Kinston S.J., Schütte J., Beck D., Knezevic K., Schiby G., Jacob-Hirsch J., Biran A., Kloog Y., Marcucci G., Bloomfield C.D., Aplan P.D., Pimanda J.E., Göttgens B., Izraeli S. (2013) “Genome-scale expression and transcription factor binding profiles reveal therapeutic targets in transgenic ERG myeloid leukemia” Blood PMID:23974202


13)  Beck D., Thoms J.A., Perera D., Schütte J., Unnikrishnan A., Knezevic K., Kinston S.J., Wilson N.K., O'Brien T.A., Göttgens B., Wong J.W., Pimanda J.E. (2013) “Genome-wide analysis of transcriptional regulators in human HSPCs reveals a densely interconnected network of coding and noncoding genes” Blood PMID:23974199


14)  Page M.E., Lombard P., Ng F., Göttgens B., Jensen K.B. (2013) “The epidermis comprises autonomous compartments maintained by distinct stem cell populations” Cell Stem Cell PMID:23954751


15)  Moignard V., Woodhouse S., Fisher J., Göttgens B. (2013) “Transcriptional hierarchies regulating early blood cell development” Blood Cells Mol Dis. PMID:23948234


16)  Wyspia¿ska B.S., Bannister A.J., Barbieri I., Nangalia J., Godfrey A., Calero-Nieto F.J., Robson S., Rioja I., Li J., Wiese M., Cannizzaro E., Dawson M.A., Huntly B., Prinjha R.K., Green A.R., Göttgens B., Kouzarides T. (2013) “BET protein inhibition shows efficacy against JAK2V617F-driven neoplasms” Leukemia PMID:23929215


17)  Magnúsdóttir E., Dietmann S., Murakami K., Günesdogan U., Tang F., Bao S., Diamanti E., Lao K., Göttgens B., Azim Surani M. (2013) “A tripartite transcription factor network regulates primordial germ cell specification in mice” Nat Cell Biol. PMID:23851488


18)  Bonzanni N., Garg A., Feenstra K.A., Schütte J., Kinston S., Miranda-Saavedra D., Heringa J., Xenarios I., Göttgens B. (2013) “Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model” Bioinformatics PMID:23813012


19)  Calero-Nieto F.J., Joshi A., Bonadies N., Kinston S., Chan W.I., Gudgin E., Pridans C., Landry J.R., Kikuchi J., Huntly B.J., Göttgens B. (2013) “HOX-mediated LMO2 expression in embryonic mesoderm is recapitulated in acute leukaemias” Oncogene PMID:23708655

20)  Wilkinson A.C., Göttgens B. (2013) “Transcriptional regulation of haematopoietic stem cells” Adv Exp Med Biol. PMID:23696358

2012

1)   Lichtinger M., Ingram R., Hannah R., Müller D., Clarke D., Assi S.A., Lie-A-Ling M., Noailles L., Vijayabaskar M.S., Wu M., Tenen D.G., Westhead D.R., Kouskoff V., Lacaud G., Göttgens B., Bonifer C. (2012) “RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis” EMBO J  31(22):4318-33


2)  Fitch S.R., Kimber G.M., Wilson N.K., Parker A., Mirshekar-Syahkal B., Göttgens B., Medvinsky A., Dzierzak E., Ottersbach K. (2012) “Signaling from the Sympathetic Nervous System Regulates Hematopoietic Stem Cell Emergence during Embryogenesis” Cell Stem Cell 11(4):554-66


3)  Martello G., Sugimoto T., Diamanti E., Joshi A., Hannah R., Ohtsuka S., Göttgens B., Niwa H., Smith A. (2012) “Esrrb is a pivotal target of the gsk3/tcf3 axis regulating embryonic stem cell self-renewal” Cell Stem Cell 11(4):491-504


4)  Dawson M.A., Foster S.D., Bannister A.J., Robson S.C., Hannah R., Wang X., Xhemalce B., Wood .AD., Green A.R., Göttgens B., Kouzarides T. (2012) “Three Distinct Patterns of Histone H3Y41 Phosphorylation Mark Active Genes” Cell Rep 2(3):470-7


5)  Nürnberg S.T., Rendon A., Smethurst P.A., Paul D.S., Voss K., Thon J.N., Lloyd-Jones H., Sambrook J.G., Tijssen M.R., Italiano J.E. Jr., Deloukas P., Göttgens B., Soranzo N., Ouwehand W.H. (2012) “A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site” Blood 120(24):4859-68


6)  Dumon S., Walton D.S., Volpe G., Wilson N., Dassé E., Pozzo W.D., Landry J.R., Turner B., O'Neill L.P., Göttgens B., Frampton J. (2012) “Itga2b regulation at the onset of definitive hematopoiesis and commitment to differentiation” PLoS One 7(8):e43300


7)  Khandanpour C., Krongold J., Schütte J., Bouwman F., Vassen L., Gaudreau M.C., Chen R., Calero-Nieto F.J., Diamanti E., Hannah R., Meyer S.E., Grimes H.L., van der Reijden B.A., Jansen J.H., Patel C.V., Peeters J.K., Löwenberg B., Dührsen U., Göttgens B., Möröy T. (2012) “The human GFI136N variant induces epigenetic changes at the Hoxa9 locus and accelerates K-RAS driven myeloproliferative disorder in mice” Blood 120(19):4006-17


8)  Zohren F., Souroullas G.P., Luo M., Gerdemann U., Imperato M.R., Wilson N.K., Göttgens B., Lukov G.L., Goodell M.A. (2012) “The transcription factor Lyl-1 regulates lymphoid specification and the maintenance of early T lineage progenitors” Nat Immunol. 13(8):761-9


9)  Lancrin C., Mazan M., Stefanska M., Patel R., Lichtinger M., Costa G., Vargel O., Wilson N.K., Möröy T., Bonifer C., Göttgens B., Kouskoff V., Lacaud G. (2012) “GFI1 and GFI1B control the loss of endothelial identity of hemogenic endothelium during hematopoietic commitment” Blood 120(2):314-22


10)  Wareing S., Mazan A., Pearson S., Göttgens B., Lacaud G., Kouskoff V. (2012) “The Flk1-Cre-mediated deletion of ETV2 defines its narrow temporal requirement during embryonic hematopoietic development ” Stem Cells 30(7):1521-31


11)  Tanaka Y., Joshi A., Wilson N.K., Kinston S., Nishikawa S., Göttgens B. (2012) “The transcriptional programme controlled by Runx1 during early embryonic blood development” Dev Biol. 366(2):404-19


12)  Mutasa-Göttgens E.S., Joshi A., Holmes H.F., Hedden P., Göttgens B. (2012) “A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses” BMC Genomics 13:99


13)  Spensberger D., Kotsopoulou E., Ferreira R., Broccardo C., Scott L.M., Fourouclas N., Ottersbach K., Green A.R., Göttgens B. (2012) “Deletion of the Scl +19 enhancer increases the blood stem cell compartment without affecting the formation of mature blood lineages” Exp Hematol. 40(7):588-598.el


14)  Follows G.A., Ferreira R., Janes M.E., Spensberger D., Cambuli F., Chaney A.F., Kinston S.J., Landry J.R., Green A.R., Göttgens B. (2012) “Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain” PLos One 7(3):e31484


15)  Dryden N.H., Sperone A., Martin-Almedina S., Hannah R.L., Birdsey G.M., Khan S.T., Layhadi J.A., Mason J.C., Haskard D.O., Göttgens B., Randi A.M. (2012) “The transcription factor Erg controls endothelial cell quiescence by repressing activity of nuclear factor (NF)-¿B p65 ” J Biol Chem. 287(15):12331-42


16)  Schütte J., Moignard V., Göttgens B. (2012) “Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development” Wiley Interdiscip Rev Syst Biol Med. 4(3):285-95


17)  Joshi A., Hannah R., Diamanti E., Göttgens B. (2012) “Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.” Exp Hematol. S0301-472X(12)00590-5

2011

1)  Dawson M.A., Bannister A.J., Saunders L., Wahab O.A., Liu F., Nimer S.D., Levine R.L., Göttgens B., Kouzarides T., Green A.R. (2011) “Nuclear JAK2”  Blood 118(26):6987-8


2)   Smith A.M., Calero-Nieto F.J., Schütte J., Kinston S., Timms R.T., Wilson N.K., Hannah R.L., Landry J.R., Göttgens B. (2011) “Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation” Mol Cell Biol. 32(4):763-73


3)   Birdsey G.M., Dryden N.H., Shah A.V., Hannah R., Hall M.D., Haskard D.O., Parsons M., Mason J.C., Zvelebil M., Göttgens B., Ridley A.J., Randi A.M. (2011) “The transcription factor Erg regulates expression of histone deacetylase 6 and multiple pathways involved in endothelial cell migration and angiogenesis” Blood 119(3):894-90


4)   Chan W.I., Hannah R.L., Dawson M.A., Pridans C., Foster D., Joshi A., Göttgens B., Van Deursen J.M., Huntly B.J. (2011) “The transcriptional coactivator Cbp regulates self-renewal and differentiation in adult hematopoietic stem cells” Mol Cell Biol. 31(24):5046-60


5)   Davison L.J., Wallace C., Cooper J.D., Cope N.F., Wilson N.K., Smyth D.J., Howson J.M., Saleh N., Al-Jeffery A., Angus K.L., Stevens H.E., Nutland S., Duley S., Coulson R.M., Walker N.M., Burren O.S., Rice C.M., Cambien .F, Zeller T., Munzel T., Lackner K., Blankenberg S.; Cardiogenics Consortium, Fraser P., Gottgens B., Todd J.A., Attwood T., Belz S., Braund P., Cambien F., Cooper J., Crisp-Hihn A., Diemert P., Deloukas P., Foad N., Erdmann J., Goodall A.H., Gracey J., Gray E., Gwilliams R., Heimerl S., Hengstenberg C., Jolley J., Krishnan U., Lloyd-Jones H., Lugauer I., Lundmark P., Maouche S., Moore J.S., Muir D., Murray E., Nelson C.P., Neudert J., Niblett D., O'Leary K., Ouwehand W.H., Pollard H., Rankin A., Rice C.M., Sager H., Samani N.J., Sambrook J., Schmitz G., Scholz M., Schroeder L., Schunkert H., Syvannen A.C., Tennstedt S., Wallace C. (2011) “Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene” Hum Mol Genet. 21(2):322-33


6)   Pimanda J.E., Göttgens B. (2011) “Gene regulatory networks governing haematopoietic stem cell development and identity” Int J Dev Biol. 54(6-7):1201-11


7)  Tijssen M.R., Cvejic A., Joshi A., Hannah R.L., Ferreira R., Forrai A., Bellissimo D.C., Oram S.H., Smethurst P.A., Wilson N.K., Wang X., Ottersbach K., Stemple D.L., Green A.R., Ouwehand W.H., Gottgens B. (2011) “Genome-Wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators” Dev Cell 20(5):597-609


8)    Griffiths D.S., Li J., Dawson M.A., Trotter M., Cheng Y.-H., Smith A.M., Mansfield W., Liu P., Kouzarides T., Nichols J., Bannister A.J., Green A.R., Gottgens B. (2011) “LIF independent JAK signalling to chromatin in embryonic stem cells uncovered from an adult stem cell disease” Nature Cell Biology 13: 13-21


9)  Bonadies N., Foster S.D., Chan W.-I., Kvinlaug B.T., Spensberger D., Dawson M.A., Spooncer E., Whetton A.D., Bannister A.J., Huntly B.J., Gottgens B. (2011). “Genome-wide Analysis of Transcriptional Reprogramming in Mouse Models of Acute Myeloid LeukaemiaPLoS One 6(1): e16330


10)  Hannah R., Joshi A., Wilson N.K., Kinston S., Gottgens B. (2011) “A Compendium of Genome-wide Haematopoietic Transcription Factor Maps supports the Identification of Gene Regulatory Control Mechanisms” Exp Hematology 39(5): 531-541


11)  Joshi A., Gottgens B. (2011) “Maximum Parsimony Analysis of Gene Expression Profiles Permits the Reconstruction of Developmental Cell Lineage Trees” Dev Biol 353(2): 440-447


12)  Thoms J., Birger Y., Foster S.D., Knezevic K., Kirshenbaum Y., Chandrakanthan V., Spensberger D., Wong J., Oram S.H., Kinston S., Groner Y., Lock R., Mackenzie K., Gottgens B.*, Izraeli S.*, Pimanda J.E.* (2011) “ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer” Blood 117(26):7079-89
* joint senior authors


13)  Knezevic K., Bee T., Wilson N., Janes M.E., Kinston S., Polderdijk S., Kolb-Kokocinski A., Ottersbach K., Pencovich N., Groner Y., de Bruijn M.F.T., Gottgens B., Pimanda J.E. (2011) “A Runx1-Smad6 rheostat controls Runx1 activity during embryonic hematopoiesis” Mol Cell Biol 31(14):2817-26


14)  Paul D.S., Nisbet J.P., Yang T.-P., Meacham S., Rendon A., Hautaviita K., Tallila J., White J., Tijssen M.R., Sivapalaratnam S., Basart H., Trip M.D., Cardiogenics Consortium, MuTHER Consortium, Gottgens B., Soranzo N., Ouwehand W.H., P. Deloukas (2011) “Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits” PLoS Genetics 7(6): e1002139


15)  Leddin M., Perrod C., Hoogenkamp M., Ghani S., Assi S., Heinz S., Wilson N., Follows G., Schoenheit J., Vockentanz L., Mosamam A., Chen W., Tenen D.G., Westhead D.R., Gottgens B., Bonifer C., Rosenbauer F. (2011). “Two distinct auto-regulatory loops operate at the Pu.1 locus in B cells and myeloid cells” Blood 117: 2827-2838


16)  Heuser M., Yun H., Berg T., Yung E., Argiropoulos B., Kuchenbauer F., Park G., Hamwi I.,  Palmqvist L., Lai C., Leung M., Lin G., Chaturvedi A., Kumar Thakur B., Iwasaki M., Bilenky M., Thiessen N., Robertson G.,  Hirst M., Kent D., Wilson N.K., Gottgens B., Eaves C., Cleary M.L., Marra M., Ganser A., Humphries R.K. (2011) “Cell of origin in AML: Susceptibility to MN1-induced transformation is regulated by the MEIS1/AbdB-like HOX protein complex” Cancer Cell 20(1):39-52


17)  Levantini E., Lee S., Radomska H.S., Hetherington C.J., Alberich-Jorda M., Amabile G., Zhang P., Gonzalez D., Zhang J., Basseres D.S., Wilson N.K., Koschmieder S., Huang G., Zhang D., Ebralidze A.K., Bonifer C., Okuno Y., Gottgens B., Tenen D.G. (2011) “RUNX1 regulates human CD34 gene expression in long-term hematopoietic stem cells by mediating interaction of a proximal and a distal downstream regulatory element” EMBO J in press


18)  Wilson N.K., Calero-Nieto F.J., Ferreira R., Gottgens B. (2011). “Transcriptional regulation of haematopoietic transcription factors” Stem Cell Research & Therapy 2:6


19)  Wilson N.K., Tijssen M.R., Gottgens B. (2011). “Deciphering transcriptional control mechanisms in haematopoiesis – the impact of high-throughput sequencing technologies” Exp Hematology in press

2010

1Wilson N.K., Foster S.D., Wang X., Knezevic K., Schütte J., Kaimakis P., Chilarska P., Kinston S., Ouwehand W.H., Dzierzak E., Pimanda J.E., de Bruijn M.F., Gottgens B. (2010) “Combinatorial Transcriptional Control in Blood Stem/Progenitor Cells: Genome-wide Analysis of 10 major Transcriptional Regulators” Cell Stem Cell 7(4):532-544

2) Wilson N.K., Timms R.T., Kinston S.J., Cheng Y., Oram S.H., Landry J.R., Mullender J., Ottersbach K., & Gottgens B. (2010) “Gfi1 expression is controlled by five distinct regulatory regions spread over 100kb with Scl/Tal1, Gata2, PU.1, Erg, Meis1 and Runx1 acting as upstream regulators in early haematopoietic cells” Mol Cell Biol 30(15): 3853-3863

3) Vezzoli A., Bonadies N., Allen M.D., Freund S.M.V., Santiveri C.M., Kvinlaug B., Huntly B.J.P., Gottgens B., Bycroft M. (2010) “Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1” Nature Structural & Molecular Biology 17(5):617-619

4) Narula J., Smith A.M., Gottgens B., Igoshin O.A. (2010) “Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate” PLoS Computational Biology 6;6(5):e1000771

5) Oram S.H., Thoms J.A.I., Pridans C., Janes M.E., Kinston S.J., Anand S., Josette-Renee Landry J.-R., Lock R.B., Jayaraman P.-S., Huntly B.J., Pimanda J.E., Gottgens B. (2010) “A previously unrecognised promoter of LMO2 forms part of a transcriptional regulatory circuit mediating LMO2 expression in a subset of T-Acute Lymphoblastic Leukemia patients” Oncogene 29: 5796–5808

6) Gottgens B., Ferreira R., Sanchez M.J., Ishibashi S., Li J., Spensberger D., Lefevre P., Ottersbach K., Chapman M., Kinston S., Knezevic K., Hoogenkamp M., Follows G.A., Bonifer C.,  Amaya E., Green A.R. (2010) “Cis-regulatory remodeling of the Scl locus during vertebrate evolutionMol Cell Biol 30(24): 5741-5751

7Li P., Burke S., Wang J., Chen X., Ortiz M., Lee S., Lu D., Campos L., Goulding D., Ng B.L., Dougan G., Huntly B.J., Gottgens B., Jenkins N.A., Copeland N.G., Colucci F., Liu P. (2010) “Reprogramming of T Cells to Natural Killer-like Cells upon Bcl11b Deletion” Science 329(5987): 85-89

8) Calero-Nieto F. Wood A., Wilson N.K., Kinston S., Landry J.-R., Gottgens B., (2010) “Transcriptional regulation of Elf-1: Locus-wide analysis reveals 4 distinct promoters, a tissue specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation” Nucleic Acids Res. 38(19):6363-6374

9) Ottersbach K., Smith A., Wood A., Göttgens B. (2010). “Ontogeny of Haematopoiesis: Recent Advances and Open Questions” British Journal of Haematology 148(3):343-355

10Pimanda J.E., Göttgens B. (2010). “Gene Regulatory Networks Governing Haematopoietic Stem Cell Development and Identity” Int. J. Dev. Biol. 54: 1201-1211

11) Garcia-Ortega A.M., Cañete A., Quintero C., Silberstein L., Piquer-Gil M., Alvarez-Dolado M., Dekel B., Gottgens B., Sanchez M.J. (2010) “Enhanced hemato-vascular contribution of SCL-3’Enh expressing fetal liver cells uncovers their potential to integrate in extra-medullary adult niches” Stem Cells 28(1):100-12

12)   Hirose K., Inukai T., Kikuchi J., Furukawa Y., Ikawa T., Kawamoto H., Oram S.H., Gottgens B., Kiyokawa N., Miyagawa Y., Okita H., Akahane K., Zhang X., Kuroda I., Honna H., Kagami K., Goi K., Kurosawa H., Look A.T., Matsui H., Inaba T., Sugita K. (2010) “Aberrant induction of LMO2 by the E2A-HLF chimeric transcription factor and its implication in leukemogenesis of B-precursor ALL with t(17;19)” Blood 116(6): 962-970

13)  Bachmann P.S., Piazza R.G., Janes M.E., Wong N.C., Davies C., Mogavero A., Bhadri V.A., Szymanska B., Geninson G., Magistroni V., Cazzaniga G., Biondi A., Miranda-Saavedra D., Gottgens B., Saffery R., Craig J.M., Marshall G.M., Gambacorti-Passerini C., Pimanda J.E., Richard B Lock R.B. (2010) “Epigenetic silencing of BIMI in glucocorticoid poor-responsive pediatric acute lymphoblastic leukemia, and its reversal by histone deacetylase inhibition” Blood 116(16):3013-302

2009

1) Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B*, Halfon MS*, Sinha S* "Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse" Dev Cell. 2009 Oct;17(4):568-79 * joint senior authors  PMID: 19853570

2) Dawson MA, Bannister AJ, Göttgens B, Foster SD, Bartke T, Green AR, Kouzarides T. "JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin" Nature. 2009 Oct 8;461(7265):819-22 PMID: 19783980

3) Garcia-Ortega AM, Cañete A, Quintero C, Silberstein L, Gil MP, Alvarez-Dolado M, Dekel B, Gottgens B, Sanchez MJ. "Enhanced Hemato-Vascular Contribution Of SCL-3'Enh Expressing Fetal Liver Cells Uncovers Their Potential To Integrate In Extra-Medullary Adult Niches" Stem Cells. 2009 Sep 25. [Epub ahead of print] PMID: 19785037

4) Wilson, NK et al (2009) The transcriptional programme controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic haematopoietic development.  Blood (2009) April 3. [Epub ahead of print]  PMID: 19346495

5) Foster SD, Oram SH, Wilson NK, Göttgens B. "From genes to cells to tissues-modelling the haematopoietic system" Mol Biosyst. 2009 Jul 14. [Epub ahead of print] PMID: 19763334

6) Wood AD, Chen E, Donaldson IJ, Hattangadi S, Burke KA, Dawson MA, Miranda-Saavedra D, Lodish HF, Green AR, Göttgens B. "ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling." Blood. 2009 Aug 27;114(9):1820-30 PMID: 19571317

7) Landry, JR et al (2009) Expression of the leukaemia oncogene Lmo2 is controlled by an array of tissue specific elements dispersed over 100kb and bound by Tal/Lmo2, Ets and Gata factors.  Blood. 2009 Jan 26. [Epub ahead of print]  PMID: 19171877

8) Bee T, Ashley EL, Bickley SR, Jarratt A, Li PS, Sloane-Stanley J, Göttgens B, de Bruijn MF. "The mouse Runx1 +23 hematopoietic stem cell enhancer confers hematopoietic specificity to both Runx1 promoters" Blood. 2009 May 21;113(21):5121-4. PMID: 19321859

9) Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium. "A HaemAtlas: characterizing gene expression in differentiated human blood cells" Blood. 2009 May 7;113(19):e1-9. PMID: 19228925

10) Miranda-Saavedra D, De S, Trotter MW, Teichmann SA, Gottgens B (2008) BloodExpress: a database of gene expression in mouse haematopoiesis.  Nucleic Acids Research Jan; 37 (Database issue): D873-9. PMID: 18987008

2008

1) Miranda-Saavedra D, Gottgens B (2008) Transcriptional regulatory networks in haematopoiesis.  Curr Opin Genet Dev 18(6): 530-5. PMID: 1838119

2) Pimanda JE, Chan WY, Wilson NK, Smith AM, Kinston S, Knezevic K, Janes ME, Landry JR, Kolb-Kokocinski A, Frampton J, Tannahill D, Ottersbach K, Follows GA, Lacaud G, Kouskoff V, Gottgens B. (2008) Endoglin expression in blood and endothelium is differentially regulated by modular assembly of the Ets/Gata hemangioblast code. Blood 112(12): 4512-22.  PMID: 18805961

3) Smith AM, Sanchez MJ, Follows GA, Kinston S, Donaldson IJ, Green AR, Göttgens B. (2008) A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity.  Genome Research 18(9):1422-32. Epub 2008 Aug 7. PMID: 18687876 

4) Landry JR, Kinston S, Knezevic K, de Bruijn MF, Wilson N, Nottingham WT, Peitz M, Edenhofer F, Pimanda JE, Ottersbach K, Gottgens B. (2008) Runx genes are direct targets of Scl/Tal1 in the yolk sac and fetal liver. Blood 111(6): 3005-14. PMID: 18184866

 2007

1) Pimanda JE, Ottersbach K, Knezevic K, Kinston S, Chan WY, Wilson NK, Landry JR, Wood AD, Kolb-Kokocinski A, Green AR, Tannahill D, Lacaud G, Kouskoff V, Göttgens B (2007) Gata2, Fli1, and Scl form a recursively wired gene-regulatory circuit during early hematopoietic development. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17692-7. Epub 2007 Oct 25. PMID: 17962413 [PubMed - in process]

2) Ogilvy S, Ferreira R, Piltz SG, Bowen JM, Göttgens B, Green AR. (2007) The SCL +40 enhancer targets the midbrain together with primitive and definitive hematopoiesis and is regulated by SCL and GATA proteins. Mol Cell Biol. 2007 Oct;27(20):7206-19. Epub 2007 Aug 20. PMID: 17709394 [PubMed - in process]

3) Soneji S, Huang S, Loose M, Donaldson IJ, Patient R, Göttgens B, Enver T, May G. (2007) Inference, validation, and dynamic modeling of transcription networks in multipotent hematopoietic cells. Ann N Y Acad Sci. 2007 Jun;1106:30-40. Epub 2007 Apr 18. Review. PMID: 17442775 [PubMed - indexed for MEDLINE]

4) Follows GA, Janes ME, Vallier L, Green AR, Gottgens B. (2007) Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique. Nucleic Acids Res. 2007;35(8):e56. Epub 2007 Mar 27. PMID: 17389645 [PubMed - indexed for MEDLINE]

5) Bradley CK, Takano EA, Göthert JR, Göttgens B, Green AR, Begley CG, van Eekelen JA. (2007) Temporal regulation of Cre-recombinase activity in Scl-positive neurons of the central nervous system. Genesis. 2007 Mar;45(3):145-51. PMID: 17330263 [PubMed - indexed for MEDLINE]

6) Pimanda JE, Donaldson IJ, de Bruijn MF, Kinston S, Knezevic K, Huckle L, Piltz S, Landry JR, Green AR, Tannahill D, Göttgens B. (2007) The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity.  Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):840-5. Epub 2007 Jan 9. PMID: 17213321 [PubMed - indexed for MEDLINE]

7) Donaldson IJ, Göttgens B. (2007) CoMoDis: composite motif discovery in mammalian genomes.Nucleic Acids Res. 2007;35(1):e1. Epub 2006 Nov 27.PMID: 17130158 [PubMed - indexed for MEDLINE]

8) Chan WY, Follows GA, Lacaud G, Pimanda JE, Landry JR, Kinston S, Knezevic K, Piltz S, Donaldson IJ, Gambardella L, Sablitzky F, Green AR, Kouskoff V, Göttgens B. (2007) The paralogous hematopoietic regulators Lyl1 and Scl are coregulated by Ets and GATA factors, but Lyl1 cannot rescue the early Scl-/- phenotype. Blood. 2007 Mar 1;109(5):1908-16. Epub 2006 Oct 19. PMID: 17053063 [PubMed - indexed for MEDLINE]

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