Pluripotency, differentiation, and reprogramming

BMC Biology invites submissions to our Collection on Pluripotency, differentiation, and reprogramming. This Collection highlights the molecular and cellular mechanisms that establish, maintain, and relinquish pluripotency, drive differentiation in vivo and in vitro, and enable reprogramming, including natural reprogramming in vivo and experimentally induced reprogramming. We welcome work that links these processes to early embryonic organization and to applications in disease modelling, cell therapy, and regeneration. We particularly welcome studies on:

Molecular determinants of pluripotency, lineage commitment and differentiation : transcription factor and signaling networks; chromatin/epigenetic and 3D genome regulation; metabolic and post‑transcriptional (RNA‑based) control; and niche/mechanical cues shaping lineage priming, competence windows, fate restriction, and stochastic vs deterministic outcomes, as well as mechanisms governing terminal differentiation, functional maturation, and long-term maintenance of cell identity.
Reprogramming and developmental plasticity: identity flexibility in vivo (including adult tissue homeostasis and wound healing); dedifferentiation and fate switching; experimentally induced reprogramming (iPSC generation and direct lineage conversion); and mechanisms that stabilize, erase, or rewrite cell identity.
Spatial organization of cell identity during patterning and morphogenesis: how populations of cells coordinate fate allocation across space and time to generate reproducible tissue architecture, linking gradients/positional information, boundary formation, cell sorting, collective behaviors, and shape change to morphogenesis and early organogenesis.
Gene regulatory networks and systems control: GRN structure and dynamics; multi‑omic and computational reconstruction of developmental landscapes; network rewiring during pluripotency exit, differentiation, and reprogramming; quantitative or predictive models.

The Collection welcomes multidisciplinary studies across diverse model organisms and stem cell-based embryo models (such as blastoids and gastruloids) that advance understanding of these processes and support translational and disease‑relevant insights, including tissue engineering and regenerative medicine. Studies employing AI, machine learning, or computational modelling, broadly defined, will be considered if they are combined with complementary experimental analysis, offer significant insights into a biological process or are likely to be a useful resource to the field. For Methodology and Software manuscripts, authors should benchmark their approaches against existing methods to demonstrate an improvement over the current state of the art. Review articles are by invitation only. Authors are encouraged to send presubmission enquiries to bmcbiologyeditorial@biomedcentral.com.

This Collection supports and amplifies research related to SDG 3: Good Health and Well-Being.

All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.

Submit your manuscript to this collection through the participating journal.

Journal

BMC Biology

BMC Biology is a selective journal of the BMC series, publishing research and commissioned content across all areas of biology.

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Sekyu Choi PhD

Pohang University of Science and Technology, South Korea.

Dr Choi received his PhD in Biological Sciences from KAIST in 2014, followed by five years of postdoctoral training at Harvard University in the Department of Stem Cell and Regenerative Biology. In 2021, he was appointed as an Assistant Professor in Life Science at POSTECH. Dr Choi's research spans the fundamental processes of pluripotency, differentiation, and reprogramming, with a particular focus on understanding the molecular mechanisms that govern cell fate decisions in stem cells. His laboratory integrates cutting-edge approaches in genetics, cell biology, and animal models to investigate how stem cells and their niches control tissue regeneration. By elucidating the pathways that regulate pluripotent states and their transition toward differentiated lineages, his work aims to advance fundamental understanding of developmental biology and regenerative medicine. His expertise encompasses the dynamic regulation of transcriptional networks and epigenetic landscapes that underlie cell plasticity, as well as the environmental cues that direct lineage specification. This positions him as a leading contributor to the ongoing discourse on how cellular identity is established, maintained, and therapeutically manipulated. Website.
Ge Guo PhD

University of Exeter, United Kingdom.

Dr Ge Guo is a stem cell biologist who obtained her PhD from the University of Cambridge. During her doctoral studies, she developed an approach for recessive genetic screening using mouse embryonic stem cells. In 2006, she joined Professor Austin Smith’s laboratory and was awarded an MRC Stem Cell Career Development Fellowship to investigate novel regulators of mouse pluripotency. Her research later focused on the differences between mouse and human pluripotent stem cell states, leading to pioneering work in the establishment and characterization of human naïve pluripotent stem cells. In 2020, she joined the Living Systems Institute at the University of Exeter as a Principal Investigator. Her recent work uncovered the trophectoderm differentiation potential of human naïve pluripotent stem cells, contributing to the establishment of the human blastocyst model, the blastoid. Her current research focuses on the regulatory mechanisms underlying pluripotency and cell fate specification during early embryonic development. Website.
Sarah Hainer PhD

University of Pittsburgh, United States.

Sarah Hainer is an Associate Professor in the Department of Biological Sciences, a member of the UPMC Hillman Cancer Center, and co-leader of the Center for Transcriptional Medicine. Work in the Hainer lab focuses on how cell fate specification is mediated at the interface of transcription and chromatin dynamics, which are fundamental mechanisms that shape all aspects of biology including disease states. Website.
Masaki Kinoshita PhD

University of Nottingham, United Kingdom.

Masaki Kinoshita is an Assistant Professor in Stem Cell Biology at the University of Nottingham. He completed his PhD in Medical Sciences at Kyoto University (Japan) and subsequently conducted postdoctoral research at the RIKEN Center for Developmental Biology (Japan) and the University of Cambridge (UK). His research focuses on early mammalian embryonic development, with a particular interest in how pluripotent cells emerge, mature, and diminish, and how these cells can be captured and maintained as stem cells in the dish. By working across mouse, livestock, and human systems, his research aims to advance understanding of the fundamental mechanisms of pluripotency in both in vivo and in vitro. Website.
Stanley Strawbridge PhD

University of Sheffield, United Kingdom.

Stanley Strawbridge is a stem cell and developmental biologist with a dual background in biochemistry and applied mathematics. His research examines how stem cells transition between distinct cell states, how pluripotency is established and remodelled, and how signalling interactions guide cellular behaviour during early embryonic development. To investigate these processes, he combines experimental embryology with advanced imaging, sequencing, mathematical modelling, and machine learning. Stanley trained at the Cambridge Stem Cell Institute, where he completed his PhD in stem cell biology with Austin Smith. He subsequently carried out postdoctoral research in developmental biology with Jennifer Nichols and in super-resolution microscopy with Srinjan Basu as a Henry Wellcome Fellow. During this period, he also collaborated closely with mathematical biologist Alexander Fletcher on the development of computational tools and theoretical models for analysing embryonic systems. He is currently a Physics of Life and Quantitative Biology Fellow in the Centre for Stem Cell Biology at the University of Sheffield. His group develops experimental and computational approaches to study early human development, stem-cell-based embryo models, and implantation, with the aim of identifying mechanisms that underlie developmental failure and infertility. Website.
Chengchen Zhao PhD

Westlake University, China.

Dr Chengchen Zhao is a Research Associate Professor at Westlake University. He received his PhD from Tongji University in 2018, followed by postdoctoral training with Prof Yong Zhang from 2018 to 2021. After joining the Laboratory of Cell Fate Control led by Prof Duanqing Pei at Westlake University, his group aims to integrate bioinformatics, systems biology, and computational modeling to investigate how transcriptional and epigenomic programs govern cell fate determination during early embryogenesis, somatic cell reprogramming, and stem cell differentiation. His research focuses on establishing stem cell and developmental systems, including mouse engineered cell-fate regulators, porcine iPSCs and blastoids, and on developing computational and epigenetic modeling approaches, including CStreet and MethylTransition, to study cell fate regulation. Website.
Fan Zhou PhD

Tsinghua University, China.

Fan Zhou is a Principal Investigator at the School of Life Sciences, Tsinghua University. He is also an investigator at the Tsinghua-Peking Center for Life Sciences and the State Key Laboratory of Membrane Biology, China. He serves on the committee of the Reproductive Biology Branch of the Chinese Zoological Society and as a Youth Editorial Board member of Cell Regeneration. Dr Zhou received his PhD from the Academy of Military Medical Sciences in 2016 and completed his postdoctoral training at Peking University (2016–2020). He joined Tsinghua University as faculty and established his independent laboratory in 2020. His research group integrates functional assays, multi omics mining, and genetic manipulation to investigate cell fate regulation and peri implantation embryo development in mammals. Website.