Abdelbaki A., McCarthy A., Karsa A., Muresan L., Elder K., Papathanasiou A., Snell P., Christie L., Wilding M., Steventon B.J. and Niakan K.K. (2025) Live imaging human embryos reveals mitotic errors and lineage restriction prior to implantation. bioRxiv https://doi.org/10.1101/2024.09.26.614906. Manuscript accepted Nature Biotechnology. https://doi.org/10.1038/s41587-025-02851-1
Menchero S., Barrington C., Alanis-Lobato G., Varsally W., Niakan K.K. and Turner J.M.A. (2025) Marsupial single-cell transcriptomics provides an atlas of developmental heterochrony. bioRxiv doi: https://doi.org/10.1101/2024.05.26.595746. Manuscript accepted Developmental Cell. doi: 10.1016/j.devcel.2025.06.037
Ziojla N.M., Guerra M.C., Socha M., Zizewska D., Blaszczk K., Urbaniak E., Henry S. and Niakan K.K., Warmflash A. and Borowiak M. (2025) ETVs dictate hPSC fate by tuning biophysical properties. Manuscript accepted Nature Communications. 16(1):1999. doi: 10.1038/s41467-025-56591-6.
Jonlin E.C., Fujita M., Isasi R., Kato K., Munsie M., Muto K., Niakan K., Saha K., Sugarman J., Turner L. and Hyun I.(2025) What Does ‘Scientific Rationale’ Mean for the Review of Human Pluripotent Stem Cell, Embryo, and Related Research? Stem Cell Reports. 17:102479. doi: 10.1016/j.stemcr.2025.102479. PMID: 40280137.
Simon C.S., McCarthy A., Woods L., Staneva D., Huang Q., Linneberg-Agerholm M., Faulkner A., Papathanasiou A., Elder K., Snell P., Christie L., Garcia P., Shaikly V., Taranissi M., Choudhary M., Herbert M., Brickman J.M. and Niakan K.K. (2025) Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst. Nature Communications. 10.1038/s41467-025-61830-x.
Simon C.S.+, Garg V., Kuo Y.Y., Niakan K.K., and Hadjantonakis A.K.+ (2025) ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation in early mouse development. Development. 152 (6):dev204278 https://doi.org/10.1242/dev.204278.
Brumm A.S., McCarthy A., Gerri C., Fallesen T., Woods L., McMahon R., Papathanasiou T., Elder K., Snell P., Christie L., Garcia P., Shaikly V., Taranissi M., Serhal P., Odia R.A., Vasilic M., Osnato A., Rugg-Gunn P.J., Vallier L., Hill C.S. and Niakan K.K. (2025) NODAL signalling does not maintain the pluripotent epiblast in pre-implantation human development. Developmental Cell. S1534-5807(24)00639-7. DOI: 10.1016/j.devcel.2024.10.020
Lea G., Doria-Borrell P., Ferrero-Micó A., Varma A., Simon C., Anderson H., Biggins L., De Clercq K., Andrews S., Niakan K.K., Gahurova L., McGovern N., Pérez-García V. and Hanna C.W. (2025) Determinants of DNA methylation patterning in human placental development and trophoblast stem cell models. Cell Stem Cell. S1934-5909(24)00447-8. DOI: 10.1016/j.stem.2024.12.007
Balestrini P.A., Abdelbaki A., McCarthy A., Devito L., Senner C.E., Chen A.E., Munusamy P., Blakeley P., Elder K., Snell P., Christie L., Serhal P., Odia R.A., Sangrithi M., Niakan K.K.+ and Fogarty N.M.E.+ (2024) Transcription factor-based transdifferentiation of human embryonic to trophoblast stem cells. Development. 151 (17):dev202778. DOI: 10.1242/dev.202778 (+Co-corresponding)
Iyer D.P., van der Weijden V.A, Khoei H.H., McCarthy A., Rayon T., Simon C.S., Dunkel I., Wamaitha S.E., Elder K., Snell P., Christie L., Schulz E.G., Niakan K.K., Rivron N. and Bulut-Karlioglu A. (2024) Delay of human early development via in vitro diapause. Cell. 187(23):6566-6583.e22. DOI: 10.1016/j.cell.2024.08.048
Kruger R.E., Frum T., Brumm S., Hickey S.L., Niakan K.K., Aziz F., Shammami M.A., Roberts J.G. and Ralston A. (2024) Smad4 is essential for epiblast scaling and morphogenesis after implantation, but nonessential prior to implantation in the mouse. Development. 151(11):dev202377. DOI: 10.1242/dev.202377
Rivron N.C., Martinez-Arias A., Sermon K., Mummery C., Schöler H.R., Wells J., Nichols J., Hadjantonakis A.K., Lancaster M.A., Moris N., Fu J., Sturmey R.G., Niakan K., Rossant J. and Kato K. (2023) Changing the public perception of human embryology. Nature Cell Biology. 25(12): 1717-1719. DOI: 10.1038/s41556-023-01289-4
Foreman A.L., Liddell K., Franklin S., Jackson E., Rozeik C. and Niakan K.K. (2023) Human embryo models: the importance of national policy and governance review. Current Opinion in Genetics and Development. 82: 102103. DOI: 10.1016/j.gde.2023.102103
Alanis-Lobato G., Bartlett T.E., Huang Q., Simon C., McCarthy A., Elder K., Snell P., Christie L. and Niakan K.K. (2023) MICA: A multi-omics method to predict gene regulatory networks in early human embryos. Life Science Alliance. 7(1):e202302415. DOI: 10.26508/lsa.202302415
ReginM., Essahib W., Demtschenko A., Dewandre D., David L., Gerri C., Niakan K.K., Verheyen G., Tournaye H., Sterckx J., Sermon K. and Van de Velde H. (2023) Lineage segregation in human pre-implantation embryos is specified by YAP1 and TEAD1. Human Reproduction. 38(8): 1484-1498. DOI: 10.1093/humrep/dead107
Gerri C., McCarthy A., Scott G.M., Regis M., Stamatiadis P., Brumm S., Simon C.S., Lee J., Montesinos C., Hassitt C., Hockenhull S., Hampshire D., Elder K., Snell P., Christie L., Fouladi-Nashta A.A., Van de Velde H. and Niakan K.K. (2023) A conserved role of the Hippo signalling pathway in initiation of the first lineage specification event across mammals. Development. 150(8):dev201112. DOI: 10.1242/dev.201112
Barry D.J., Gerri C., Bell, D.M., D’Antuono, R. and Niakan K.K. (2022) GIANI: open-source software for automated analysis of 3D microscopy images. Journal of Cell Science. 135(10). DOI: 10.1101/2020.10.15.340810
Lea R.A., McCarthy A., Boeing S., Fallesen T., Elder K., Snell P., Christie L., Adkins S., Shaikly V. and Niakan K.K. (2021) KLF17 promotes human naïve pluripotency but is not required for its establishment. Development, 148(22):dev199378. DOI: 10.1242/dev.199378
Alanis-Lobato G., Zohren J., McCarthy A., Fogarty N.M.E., Kubikova N., Hardman E., Greco M., Wells D., Turner J.M.A. and Niakan K.K. (2021) Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos. PNAS, 118(22):e2004832117. DOI: 10.1073/pnas.2004832117
Osnato A., Brown S., Krueger C., Andrews S., Collier A.J., Nakanoh S., Londono M.Q., Wesley B.T., Muraro D., Brumm A.S., Niakan K.K., Vallier L., Ortmann D. and Rugg-Gunn P.J. (2021) TGFb signalling is required to maintain pluripotency of naïve human pluripotent stem cells. eLIFE. 10:e67259. DOI: 10.7554/eLife.67259
Haniffa M., Taylor D., Linnarsson S., Aronow B.J., Bader G.D., Camara P.G., Camp G., Chédotal A., Copp A., Etchevers H.C., Giacobini P., Göttgens B., Guo G., Hupalowska A., James K., Kirby E., Kriegstein A., Lundeberg J., Marioni J., Meyer K.B., Niakan K.K., Nilsson M., OlabiB., Pe’er D., Regev A., Rozenblatt-Rosen O., Rood J., Satija R., Teichmann S.A., Treutlein B., Vento-Tormo R., Webb S. and the Human Cell Atlas Developmental Biological Network. (2021) Human Developmental Cell Atlas: milestones achieved and the roadmap ahead. Nature, 597:196-205. DOI: 10.1038/s41586-021-03620-1
Bower O.J., McCarthy A., Lea R.A., Alanis-Lobato G., Zohren J., Gerri C., Turner J.M.A. and Niakan K.K. (2021) Generating CRISPR-Cas9-mediated null mutations and screening targeting efficiency in human pluripotent stem cells. Current Protocols, 1:e232. DOI: 10.1002/cpz1.232
Clark A.T., Brivanlou, A., Fu J., Kato K., Mathews D., Niakan K.K., Rivron N., Saitou M., Surani A., Tang F. and Rossant J. (2021) Human embryo research, stem cell-derived embryo models and in vitro gametogenesis: Considerations leading to the revised ISSCR guidelines. Stem Cell Reports 16(6):1416-1424. DOI: 10.1016/j.stemcr.2021.05.008
Lovell-Badge R., Anthony E., Barker, R., Bubela, T., Carpenter, A., Charo, A., Clark, A., Clayton, E., Cong Y., Daley, G., Fu J., Fujita M., Greenfield A., Goldman S., Hill L., Hyun I., Isasi R., Khan J., Kato K., Kim J.-S., Kimmelman J., Knoblich J., Mathews D., Montserrat N., Mosher J., Munsie M., Nakauchi H., Naldini L., Naughton G., Niakan K.K., Pedersen R., Riveron N., Rooke H., Rossant J., Round J., Saitou M., Sipp D., Steffann J. Sugarman J., Surani A., Takahashi J., Tang F., Turner L., Zettler P. and Zhai X. (2021) ISSCR Guidelines for Stem Cell Research and Clinical Translation: The 2021 update. Stem Cell Reports 16(6):1398-1408. DOI: 10.1016/j.stemcr.2021.05.012
Ruis P., Van Ly D., Borel V., Kafer G., McCarthy A., Howell S., Blassberg R., Snijders A., Briscoe J., Niakan K.K., Marzec P., Cesare A. and Boulton S. (2021) TRF2-independent chromosome end protection in pluripotent cells and early development. Nature, 589:103-109. DOI: 10.1038/s41586-020-2960-y
Gerri C., McCarthy A., Alanis-Lobato G., Demtschenko A., Bruneau A., Loubersac S., Fogarty N.M.E., Hampshire D., Elder K., Snell P., Christie L., David L., Van de Velde H., Fouladi-Nashta A.A. and Niakan K.K. (2020) A conserved molecular cascade initiates trophectoderm differentiation in human, bovine and mouse embryos prior to blastocyst formation. Nature, 587: 443-447. DOI: 10.1038/s41586-020-2759-x
Gerri C., Manchero S., Mahadevaiah, S.K., Turner J.M.A. and Niakan K.K. (2020) Human embryogenesis: a comparative perspective. Annual Review of Cell and Developmental Biology, 36: 411-440. DOI: 10.1146/annurev-cellbio-022020-024900
Wamaitha S.E., Grybel K.J., Alanis-Lobato G., Gerri C., Ogushi S., Mahadevaiah S.K., Healy L., Lea, R.A., Molina-Arcas M., Elder K., Snell P., Christie L., Downward J., Turner J.M.A and Niakan K.K. (2020) IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche. Nature Communications, 11: 764. DOI: 10.1038/s41467-020-14629-x
ElInati E., Zielinska A., McCarthy A., Kubikova N., Mahadevaiah S.K., Sangrithi M.N., Maciulyte V., Wells D., Niakan K.K., Schuh M. and Turner J.M.A. (2020) The BCL-2 pathway preserves genome integrity by eliminating recombination-defective oocytes. Nature Communications, 11: 2598. DOI: 10.1038/s41467-020-16441-z
Lea R. and Niakan K.K. (2019) Human germline genome editing. Invited review Nature Cell Biology, 21: 1479-1489. DOI: 10.1038/s41556-019-0424-0
Noli L., Khorsandi S.E., Pyle A., Giritharan G., Fogarty N., Capalbo A., Devito L., Jovanovic V.M., Khurana P., Rosa H., Kolundzic N., Cvoro A., Niakan K.K., Malik A., Foulk R., Heaton N., Ardawi M.S., Chinnery P.F., Ogilvie C., Khalaf Y. and Ilic D. (2019) Effects of Thyroid Hormone on Mitochondria and Metabolism of Human Preimplantation Embryos. Stem Cells. 38(3):369-381. DOI: 10.1002/stem.3129
Hirota T., Blakeley P., Sangrithi M.N., Mahadevaiah S.K., Encheva V., Snijders A.P., ElInati E., Ojarikre O.A., de Rooij D.G., Niakan K.K. and Turner J.M.A. (2018) SETDB1 links the meiotic DNA damage response to sex chromosome silencing in mice. Developmental Cell, 47: 645-659. DOI: 10.1016/j.devcel.2018.10.004
Wamaitha S.E. and Niakan K.K. (2018) Human pregastrulation development. Current Topics in Developmental Biology, 128:295-338. DOI: 10.1016/bs.ctdb.2017.11.004
Gialitakis M., Tolaini M., Li Y., Pardo M., Yu L., Toribio A., Choudhary J.S., Niakan K., Papayannopoulos, V. and Stockinger, B. (2017) Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development. Stem Cell Reports, 9(5):1377-1386. DOI: 10.1016/j.stemcr.2017.09.025
Fogarty, N.M.E., McCarthy, A., Snijders, K.E., Powell, B.E., Kubikova, N., Blakeley, P., Lea, R., Elder, K., Wamaitha, S.E., Kim, D., Maciulyte, V., Kleinjung, J., Kim, J.-S., Wells, D., Vallier, L., Bertero, A., Turner, J.M.A. and Niakan K.K. (2017) Genome editing reveals a role for OCT4 in human embryogenesis. Nature, 550(7674): 67-73. DOI: 10.1038/nature24033
Tomaz, R.A., Harman, J.L., Karimlou, D. Weavers, L., Fritsch, L., Bou-Kheir, T., Del Valle, I., Niakan, K.K., Ait-Si-Ali, S., Jorgensen, H.F. and Azuara, V. (2017) Jmjd2c/Kdm4c facilitates epiblast multi-lineage priming at the onset of mouse embryonic stem cell differentiation. Development, 144(4): 567-579.
Hyslop L.A., Blakeley P., Craven L., Richardson J., Fogarty N.M., Fragouli E., Lamb M., Wamaitha S.E., Prathalingam N., Zhang Q., O’Keefe H., Takeda Y., Arizzi L., Alfarawati S., Tuppen H.A., Irving L., Kalleas D., Choudhary M., Wells D., Murdoch A.P., Turnbull D.M., Niakan K.K. and Herbert M. (2016) Towards clinical application of pronuclear transfer to prevent mitochondrial DNA disease. Nature, 534(7607): 383-386. DOI: 10.1038/nature18303
Shahbazi M.N., Jedrusik A., Vuoristo S., Recher G., Hupalowska A., Bolton V., Fogarty N.M., Campbell A., Devito L.G., Ilic D., Khalaf Y., Niakan K.K., Fishel S. and Zernicka-Goetz M. (2016) Self-organization of the human embryo in the absence of maternal tissues. Nature Cell Biology, 18(6):700-708. DOI: 10.1038/ncb3347
Blakeley P., Fogarty N.M., Del Valle I., Wamaitha S.E., Hu T.X., Elder K., Snell P., Christie L., Robson P. and Niakan K.K. (2015) Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Development, 142(20): 3151-3165. DOI: 10.1242/dev.123547
Wamaitha S.E., del Valle I., Cho L.T., Wei Y., Fogarty N.M.E., Blakeley P., Sherwood R.I., Ji H. and Niakan K.K. (2015) Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells. Genes and Development, 29(12): 1239-1255. DOI: 10.1101/gad.257071.114
Mulvey C.M., Schröter C., Gatto L., Dikicioglu D., Fidaner I.B., Christoforou A., Deery M.J., Cho L.T., Niakan K.K., Martinez-Arias A. and Lilley K.S. (2015) Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells. Stem Cells, 10.1002/stem.2067. DOI: 10.1002/stem.2067
Niakan K.K.+ and Eggan K.+ (2013) Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse. Developmental Biology, 375: 54-64. DOI: 10.1016/j.ydbio.2012.12.008 (+Co-corresponding authors)
Niakan K.K.+, Schrode, N., Cho, L.T. and Hadjantonakis A.K.+ (2013) Isolation of (eXtra-embryonic ENdoderm) XEN cells from mouse embryos and by conversion of ES cells. Nature Protocols, 8: 1028-41. DOI: 10.1038/nprot.2013.049 (+Co-corresponding authors)
Cho L.T., Wamaitha S.E., Sherwood R.I., Artus J, Pedersen R.A., Hadjantonakis A.K. and Niakan K.K. (2012) Conversion from mouse embryonic to extra-embryonic endoderm stem cells reveals distinct differentiation capacities of pluripotent stem cell states. Development, 139: 2866-77. DOI: 10.1242/dev.078519
Krueger C., King M.R., Krueger F., Branco M.R., Osborne C.S., Niakan K.K., Higgins M.J. and Reik W. (2012) Pairing of Homologous Regions in the Mouse Genome Is Associated with Transcription but not Imprinting Status. PLoS ONE, 7(7): e38983. DOI: 10.1371/journal.pone.0038983
Niakan K.K., Han, J., Pedersen, R.A., Simon C. and Riejo Pera R.A. (2012) Human pre-implantation embryo development. Development, 139(5): 829-41. DOI: 10.1242/dev.060426 (Primer)
Bernardo A.S., Faial T., Gardner L., Niakan K.K., Ortmann D., Senner C., Sharkey A., Hemberger M., Moffett A. and Pedersen R.A.P. (2011). BRACHYURY and CDX2 mediate BMP-induced differentiation of human and mouse pluripotent stem cells into embryonic and extraembryonic lineages. Cell Stem Cell, 9(2): 144-55. DOI: 10.1016/j.stem.2011.06.015
Niakan K.K., Ji H., Maehr R., Vokes S., Rodolfa K.T., Sherwood R.I., Dimos J., Chen A.E., Melton D.A., McMahon A.P. and Eggan K. (2010). Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes and Development 24(3): 312-26. DOI: 10.1101/gad.1833510
Chen A.E.+, Egli D.+, Niakan K.K., Deng J., Akutsu H., Yamaki M., Cowan C., Zhang K., Melton D.A. and Eggan K. (2009). Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation. Cell Stem Cell4:103-6. DOI: 10.1016/j.stem.2008.12.001 (+Equal authorship)
Dimos J.T.+, Rodolfa K.T.+, Niakan K.K., Weisenthal L.M., Mitsumoto H., Chung W., Croft G.F., Saphier G., Leibel R., Goland R., Wichterle H., Henderson C.E. and Eggan K. (2008). Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science 321(5893): 1218-21. DOI: 10.1126/science.1158799 (+Equal authorship)
Niakan K.K., Davis E.C., Clipsham R.C., Jiang M., Dehart D.B., Sulik K.K. and McCabe E.R.B. (2006). Novel role for the orphan nuclear receptor Dax1 in embryogenesis, different from steroidogenesis. Molecular Genetics and Metabolism 88(3): 261-71. DOI: 10.1016/j.ymgme.2005.12.010
Niakan K.K. and McCabe E.R.B. (2005). DAX1 origin, function, and novel role. Molecular Genetics and Metabolism 86(1-2): 70-83. DOI: 10.1016/j.ymgme.2005.07.019 (Review article)
Zhang Y.H., Huang B.L., Niakan K.K., McCabe L.L., McCabe E.R. and Dipple K.M. (2004). IL1RAPL1 is associated with mental retardation in patients with complex glycerol kinase deficiency who have deletions extending telomeric of DAX1. Human Mutation, 24(3): 273-8. DOI: 10.1002/humu.9269
Clipsham R.C., Niakan K.K. and McCabe E.R.B. (2004). Nr0b1 and its network partners are expressed early in murine embryos prior to steroidogenic axis organogenesis. Gene Expression Patterns, 4(1): 3-14. DOI: 10.1016/j.modgep.2003.08.004
Yu C.+, Niakan K.K.+, Matsushita M., Stamatoyannopoulos G., Orkin S.H. and Raskind W.H. (2002). X-linked thrombocytopenia with thalassemia due to a mutation in the amino-finger of GATA-1 affecting DNA-binding rather than FOG-1 interaction.Blood, 100(6): 2040-5. DOI: 10.1182/blood-2002-02-0387 (+Equal authorship)
Raskind W.H., Niakan K.K., Wolff J., Matsushita M., Vaughan T., Stamatoyannopoulos G., Watanabe C., Rios J. and Ochs H.D. (2000). Mapping of a syndrome of X-linked thrombocytopenia with Thalassemia to band Xp11-12: further evidence of genetic heterogeneity of X-linked thrombocytopenia. Blood,95(7): 2262-8. EID: 2-s2.0-0034177890
Niakan lab 