Decoding the regulatory network of early blood development from single-cell gene expression measurements
Moignard, Victoria, Woodhouse, Steven, Haghverdi, Laleh, Lilly, Andrew J, Tanaka, Yosuke, Wilkinson, Adam C, Buettner, Florian, Macaulay, Iain C, Jawaid, Wajid, Diamanti, Evangelia, Nishikawa, Shin-Ichi, Piterman, Nir, Kouskoff, Valerie, Theis, Fabian J, Fisher, Jasmin, Göttgens, Berthold·2015·Nature Biotechnology
DOI 10.1038/nbt.3154
Cited by (384)
Items 201–300 of 384
- A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivityMuhammad Yassin, Nasma Aqaqe, Abed Alkader Yassin, Peter van Galen, Eitan Kugler, B Bernstein, Maya Koren‐Michowitz, Jonathan Canaani, Arnon Nagler, Eric R. Lechman et al. · 2019 · Leukemia
- Data integration in logic-based models of biological mechanismsBenjamin A. Hall, Anna Niarakis · 2021 · Current Opinion in Systems Biology
- scSGL: kernelized signed graph learning for single-cell gene regulatory network inferenceAbdullah Karaaslanli, Satabdi Saha, Selin Aviyente, Tapabrata Maiti · 2022 · Bioinformatics
- Normal vs. Malignant hematopoiesis: the complexity of acute leukemia through systems biologyJennifer Enciso, Luis Mendoza, Rosana Pelayo · 2015 · Frontiers in Genetics
- Ancestral developmental potentials in early bony fish contributed to vertebrate water-to-land transitionBi, Xu-Peng, 深圳华大基因,广东 深圳518083,中国, BGI-Shenzhen, Shenzhen, Guangdong 518083, China, Zhang, Guo-Jie, 中国科学院动物进化与遗传前沿交叉卓越创新中心,云南 昆明 650223,中国, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室,云南 昆明 650223,中国, Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China, Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark · 2021 · Zoological Research
- Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy DataAlireza Karbalayghareh, Ulisses Braga-Neto, Edward R. Dougherty · 2017 · IEEE Transactions on Computational Biology and Bioinformatics
- wpLogicNet: logic gate and structure inference in gene regulatory networksSeyed Amir Malekpour, Maryam Shahdoust, Rosa Aghdam, Mehdi Sadeghi · 2023 · Bioinformatics
- Reverse-engineering of gene networks for regulating early blood development from single-cell measurementsJiangyong Wei, Xiaohua Tony Hu, Xiufen Zou, Tianhai Tian · 2017 · BMC Medical Genomics
- Dimensionality reduction for single cell RNA sequencing data using constrained robust non-negative matrix factorizationShuqin Zhang, Yang Liu, Jinwen Yang, Zhixiang Lin, Michael K. Ng · 2020 · NAR Genomics and Bioinformatics
- Chasing Mavericks: The quest for defining developmental waves of hematopoiesisTaylor Cool, E. Camilla Forsberg · 2019 · Current topics in developmental biology/Current Topics in Developmental Biology
- Model-based branching point detection in single-cell data by K-branches clusteringNikolaos‐Kosmas Chlis, Florian Wolf, Fabian Joachim Theis · 2017 · Bioinformatics
- Forecasting cellular states: from descriptive to predictive biology via single-cell multiomicsGenevieve Stein-O’Brien, Michaela C. Ainslie, Elana Judith Fertig · 2021 · Current Opinion in Systems Biology
- Computational systems‐biology approaches for modeling gene networks driving epithelial–mesenchymal transitionsAtaur Katebi, Daniel Ramirez, Mingyang Lu · 2021 · Computational and Systems Oncology
- A descriptive marker gene approach to single-cell pseudotime inferenceKieran R Campbell, Christopher Yau · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Revealing lineage-related signals in single-cell gene expression using random matrix theoryMor Nitzan, Michael P. Brenner · 2021 · Proceedings of the National Academy of Sciences
- A computational strategy for predicting lineage specifiers in stem cell subpopulationsSatoshi Okawa, Antonio del Sol · 2015 · Stem Cell Research
- Identification via Numerical Computation of Transcriptional Determinants of a Cell Phenotype Decision MakingMarilisa Cortesi, Alice Pasini, Simone Furini, Emanuele� Giordano · 2019 · Frontiers in Genetics
- Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex DiseaseAida Moreno‐Moral, Francesco Pesce, Jacques V. Behmoaras, Enrico G. Petretto · 2016 · Methods in molecular biology
- Current Scenario on Application of Computational Tools in Biological SystemsHemant J. Purohit, Hitesh Tikariha, Vipin Chandra Kalia · 2018 · Springer eBooks
- TCM visualizes trajectories and cell populations from single cell dataWuming Gong, Il‐Youp Kwak, Naoko Koyano‐Nakagawa, Wei Pan, Daniel J. Garry · 2018 · Nature Communications
- Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seqShujing Lai, Lifeng Ma, E Weigao, Fang Ye, Haide Chen, Xiaoping Han, Guoji Guo · 2020 · Cell Regeneration
- Localized immune surveillance of primary melanoma in the skin deciphered through executable modelingRowan S. M. Howell, James Davies, Matthew A. Clarke, Anna Appios, Inês Mesquita, Yashoda Jayal, Benjamin Ringham-Terry, Isabel Boned del Río, Jasmin Fisher, Clare L. Bennett · 2023 · Science Advances
- $\ell_1$ -Penalized censored Gaussian graphical modelLuigi Augugliaro, Antonino Abbruzzo, Veronica Vinciotti · 2018 · Biostatistics
- An Early Stage Researcher's Primer on Systems Medicine TerminologyMassimiliano Zanin, Nadim A.A. Aitya, José Basílio, Jan Baumbach, Arriel Benis, Chandan Kumar Behera, Magda Bucholc, Filippo Castiglione, Ioanna Chouvarda, Blandine Comte et al. · 2021 · Network and Systems Medicine
- scTFBridge: a disentangled deep generative model informed by TF-motif binding for gene regulation inference in single-cell multi-omicsFeng‐ao Wang, Chenxin Yi, Jiajun Chen, Ruikun He, Junwei Liu, Yixue Li · 2025 · Nature Communications
- Inferring structural and dynamical properties of gene networks from data with deep learningFeng Chen, Chunhe Li · 2022 · NAR Genomics and Bioinformatics
- A Darwinian and Physical Look at Stem Cell Biology Helps Understanding the Role of Stochasticity in DevelopmentJean‐Pascal Capp, B. Laforge · 2020 · Frontiers in Cell and Developmental Biology
- Bringing LTL Model Checking to BiologistsZara Ahmed, David Benqué, Sergey Berezin, Anna Caroline E. Dahl, Jasmin Fisher, Benjamin A. Hall, Samin S. Ishtiaq, Jay Nanavati, Nir Piterman, Maik Riechert et al. · 2017 · Lecture notes in computer science
- Temporal Logic Based Synthesis of Experimentally Constrained Interaction NetworksJudah Goldfeder, Hillel Kugler · 2019 · Lecture notes in computer science
- FASTGenomics: An analytical ecosystem for single-cell RNA sequencing dataClaus Jürgen Scholz, Paweł Biernat, Matthias Becker, Kevin E. Bassler, Patrick S. Günther, Jenny Balfer, Henning Dickten, Lars Flöer, Kathrin Heikamp, Philipp Angerer et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring projectMaxime Dubart, Pascal Alonso, Didac Barroso‐Bergadà, Nathalie Becker, Kévin Béthune, David Andrew Bohan, Christophe Boury, Marine C. Cambon, Elsa Canard, Émilie Chancerel et al. · 2021 · Advances in ecological research/Advances in Ecological Research
- Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiationVladimir Espinosa Angarica, Antonio del Sol · 2016 · BioEssays
- Illuminating stem cell transcription factor dynamics: long-term single-cell imaging of fluorescent protein fusionsMartin Etzrodt, Timm Schroeder · 2017 · Current Opinion in Cell Biology
- Statistical Network Inference for Time-Varying Molecular Data with Dynamic Bayesian NetworksFrank Dondelinger, Sach Mukherjee · 2018 · Methods in molecular biology
- Diffusion Mapping of Eosinophil‐Activation StateJustyna Piasecka, Catherine A. Thornton, Paul C. T. Rees, Huw D. Summers · 2019 · Cytometry Part A
- Empirical Bayes Meets Information Theoretical Network Reconstruction from Single Cell DataThalia E. Chan, Ananth V. Pallaseni, Ann C. Babtie, Kirsten R. McEwen, Michael P.H. Stumpf · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- BoNesis: a Python-Based Declarative Environment for the Verification, Reprogramming, and Synthesis of Most Permissive Boolean NetworksStéphanie Chevalier, Déborah Boyenval, Gustavo Magaña López, Théo Roncalli, Athénaïs Vaginay, Loïc Paulevé · 2024 · Lecture notes in computer science
- scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-MeansXiaolin Wang, Hongli Gao, Ren Qi, Ruiqing Zheng, Xin Gao, Bin Yu · 2022 · IEEE Transactions on Computational Biology and Bioinformatics
- Inference on autoregulation in gene expression with variance-to-mean ratioYue Wang, Siqi He · 2023 · Journal of Mathematical Biology
- A logic-incorporated gene regulatory network deciphers principles in cell fate decisionsGang Xue, Xiaoyi Zhang, Wanqi Li, Lu Zhang, Zongxu Zhang, Xiaolin Zhou, Di Zhang, Lei Zhang, Zhiyuan Li · 2023 · eLife
- A framework for scRNA-seq data clustering based on multi-view feature integrationFeng Li, Yang Liu, Jin‐Xing Liu, Daohui Ge, Junliang Shang · 2023 · Biomedical Signal Processing and Control
- Defining the Emerging Blood System During Development at Single-Cell ResolutionGöran Karlsson, Mikael N.E. Sommarin, Charlotta Böiers · 2021 · Frontiers in Cell and Developmental Biology
- BioCyBig: A Cyberphysical System for Integrative Microfluidics-Driven Analysis of Genomic Association StudiesMohamed Ibrahim, Krishnendu Chakrabarty, Jun Zeng · 2016 · IEEE Transactions on Big Data
- Analysis on gene modular network reveals morphogen-directed development robustness in DrosophilaShuo Zhang, Juan Zhao, Xiangdong Lv, Jialin Fan, Yi Lu, Tao Zeng, Hailong Wu, Luonan Chen, Yun Zhao · 2020 · Cell Discovery
- scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing dataXiao Kun Zheng, Yuan Huang, Xiufen Zou · 2020 · PLoS Computational Biology
- Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility countsVasilis Ntranos, Govinda M. Kamath, Jesse M. Zhang, Lior S. Pachter, David N. C. Tse · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- HIPSD&R-seq enables scalable genomic copy number and transcriptome profilingJan Otoničar, Olga Lazareva, Jan‐Philipp Mallm, Milena Simovic-Lorenz, George Philippos, Pooja Sant, Urja Parekh, Linda Hammann, Albert Li, Umut Yildiz et al. · 2024 · Genome biology
- When blood development meets single-cell transcriptomicsJie R Zhou, Bing Liu, Yu Lan · 2019 · Blood Science
- Mechanistic models of blood cell fate decisions in the era of single-cell dataIngmar Glauche, Carsten Marr · 2021 · Current Opinion in Systems Biology
- Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon AgingLéonard Hérault, Mathilde Poplineau, Élisabeth Rémy, Estelle Duprez · 2022 · Cells
- Revisiting regulatory coherence: accounting for temporal bias in plant gene co‐expression analysesHaoran Cai, David L. Des Marais · 2023 · New Phytologist
- Application of Single Cell Sequencing in CancerLan Yu, Hua Zhao, Meng Li, Cuilian Zhang · 2018 · Advances in experimental medicine and biology
- GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolutionMagdalena E Strauß, Paul Kirk, John E. Reid, Lorenz Wernisch · 2019 · Bioinformatics
- Approaches for Benchmarking Single-Cell Gene Regulatory Network MethodsKaramveer Karamveer, Yasin Uzun · 2024 · Bioinformatics and Biology Insights
- Quantitative analysis of high‐throughput biological dataHsueh‐Fen Juan, Hsuan‐Cheng Huang · 2023 · Wiley Interdisciplinary Reviews Computational Molecular Science
- Towards precise reconstruction of gene regulatory networks by data integrationZhi‐Ping Liu · 2018 · Quantitative Biology
- Revealing routes of cellular differentiation by single-cell RNA-seqDominic Grün · 2018 · Current Opinion in Systems Biology
- Single-cell eQTLGen Consortium: a personalized understanding of diseaseMonique G.P. van der Wijst, Dylan H. de Vries, Hilde E. Groot, Gosia Trynka, Chung-Chau Hon, Martijn C. Nawijn, Youssef Idaghdour, Pim van der Harst, Chun Ye, Joseph E. Powell et al. · 2019 · arXiv (Cornell University)
- A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translationErpai Luo, Lei Wei, Minsheng Hao, Xuegong Zhang, Qiao Liu · 2026 · Nature Communications
- Epigenomics of Pancreatic Cancer: A Critical Role for Epigenome-Wide StudiesRahul Raj Singh, Katie M. Reindl, Rick J. Jansen · 2019 · Epigenomes
- Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzerBenjamin A. Hall, Jasmin Fisher · 2020 · Current Protocols in Bioinformatics
- Leveraging developmental landscapes for model selection in Boolean gene regulatory networksAjay Subbaroyan, Priyotosh Sil, Olivier Martin, Areejit Samal · 2023 · Briefings in Bioinformatics
- Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologiesGuangdun Peng, Patrick Tam, Naihe Jing · 2017 · National Science Review
- From mathematical modeling and machine learning to clinical realityBen D. MacArthur, Patrick S. Stumpf, Richard O. C. Oreffo · 2020 · Elsevier eBooks
- A Robustness Analysis of Dynamic Boolean Models of Cellular CircuitsAriel Bruner, Roded Sharan · 2019 · Journal of Computational Biology
- Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanismsSeyed Amir Malekpour, Laleh Haghverdi, Mehdi Sadeghi · 2024 · Briefings in Bioinformatics
- Facilitate integrated analysis of single cell multiomic data by binarizing gene expression valuesRohan Misra, Alexander Ferrena, Deyou Zheng · 2025 · Nature Communications
- Regulatory Dynamics of Cell Differentiation Revealed by True Time Series From Multinucleate Single CellsAnna Pretschner, Sophie Pabel, Markus Haas, Monika Heiner, Wolfgang Marwan · 2021 · Frontiers in Genetics
- Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformationYongjie Xu, Zelin Zang, Bozhen Hu, Yue Yuan, Cheng Tan, Jun Xia, Stan Ziqing Li · 2024 · Briefings in Bioinformatics
- Advancing haematopoietic stem and progenitor cell biology through single‐cell profilingFiona Hamey, Sonia Nestorowa, Nicola K. Wilson, Berthold Göttgens · 2016 · FEBS Letters
- Single-Cell RNA-Seq Steps Up to the Growth PlateSamantha A. Morris · 2016 · Trends in biotechnology
- Vertical flow array chips reliably identify cell types from single-cell mRNA sequencing experimentsMasataka Shirai, Koji Arikawa, Kiyomi Taniguchi, Maiko Tanabe, Tomoyuki Sakai · 2016 · Scientific Reports
- Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding ChallengesSamarendra Das, Upendra Kumar Pradhan, Shesh Nath Rai · 2022 · Current Bioinformatics
- Program synthesis meets deep learning for decoding regulatory networksJasmin Fisher, Steven Woodhouse · 2017 · Current Opinion in Systems Biology
- Nabo – a framework to define leukemia-initiating cells and differentiation in single-cell RNA-sequencing dataParashar Dhapola, Mohamed Eldeeb, Amol Sanjay Ugale, Rasmus Olofzon, Eva Erlandsson, Shamit Soneji, David Bryder, Karlsson Göran · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Unlocking hematopoietic stem cell potential: integrative computational approaches for genomic and transcriptomic analysisPawan Kumar Raghav, Basudha Banerjee, Rajni Chadha · 2025 · Frontiers in Cell and Developmental Biology
- Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogrammingStéphanie Chevalier, Julia Becker, Yujuan Gui, Vincent Noël, Cui Su, Sascha Jung, Laurence Calzone, Andrei Y. Zinovyev, Antonio del Sol, Jun Pang et al. · 2025 · npj Systems Biology and Applications
- Identification of dynamic driver sets controlling phenotypical landscapesSilke D Werle, Nensi Ikonomi, Julian D. Schwab, Johann Michael Kraus, Felix M. Weidner, K. Lenhard Rudolph, Astrid S. Pfister, Rainer Schuler, Michael Kühl, Hans Armin Kestler · 2022 · Computational and Structural Biotechnology Journal
- Normalizing Input–Output Relationships of Cancer Networks for Reversion TherapyJae Il Joo, Hwa‐Jeong Park, Kwang‐Hyun Cho · 2023 · Advanced Science
- Multiscale computational and machine learning models for designing stem cell-based regenerative medicine therapiesShraddha Pandit, Tanya Jamal, Anamta Ali, Ramakrishnan Parthasarathi · 2024 · Elsevier eBooks
- Computing hematopoiesis plasticity in response to genetic mutations and environmental stimulationsYuchen Wen, Hang He, Yunxi Ma, Dengyi Bao, Lorie Chen Cai, Huaquan Wang, Yanmei Li, Baobing Zhao, Zhigang Cai · 2024 · Life Science Alliance
- Immunological face of megakaryocytesYueying Li, Kunying Chen, Qian‐Fei Wang · 2024 · Frontiers of Medicine
- Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cellsMirko Francesconi, Ben Lehner · 2015 · Molecular BioSystems
- Inference of genetic regulatory network for stem cell using single cells expression dataJiangyong Wei, Xiaohua Tony Hu, Xiufen Zou, Tianhai Tian · 2016 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate DecisionsThalia E. Chan, Michael P. H. Stumpf, Ann C. Babtie · 2019 · Methods in molecular biology
- Single-cell RNA-Seq: a next generation sequencing tool for a high-resolution view of the individual cellKevin B. Stevenson, Vladimir Nikolaevich Uversky · 2019 · Journal of Biomolecular Structure and Dynamics
- A non-linear reverse-engineering method for inferring genetic regulatory networksSiyuan Wu, Tiangang Cui, Xinan Zhang, Tianhai Tian · 2020 · PeerJ
- A framework for exhaustive modelling of genetic interaction patterns using Petri netsAnnika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra · 2019 · Bioinformatics
- Gene Regulatory Network Inference Using Time-Stamped Cross-Sectional Single Cell Expression DataNan Papili Gao, S. M. Minhaz Ud-Dean, Rudiyanto Gunawan · 2016 · IFAC-PapersOnLine
- Reconstructing Gene Regulatory Networks That Control Hematopoietic CommitmentFiona Hamey, Berthold Göttgens · 2019 · Methods in molecular biology
- FORKS: Finding Orderings Robustly using k-means and Steiner treesMayank Sharma, Huipeng Li, Debarka Sengupta, Shyam Prabhakar, Jayadeva · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Gene regulatory network inference from single-cell data using a self-consistent proteomic fieldUlysse Herbach · 2021 · arXiv (Cornell University)
- LogicSR: prior-guided symbolic regression for gene regulatory network inference from single-cell transcriptomics dataDezhen Zhang, Zhi‐Ping Liu, Rui Gao · 2025 · Briefings in Bioinformatics
- Transcriptomics at the Single Cell Level and Human Diseases: Opportunities and Challenges in Data Processing and AnalysisVinicius Maracaja‐Coutinho, Patrícia Severino · 2022 · Springer eBooks
- Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networksRyan H. Boe, Vinay Ayyappan, Lea Schuh, Arjun Raj · 2022 · Cell Systems
- Network Activity Evaluation Reveals Significant Gene Regulatory Architectures During SARS-CoV-2 Viral Infection From Dynamic scRNA-seq DataChuanyuan Wang, Zhi‐Ping Liu · 2024 · IEEE Journal of Biomedical and Health Informatics
- Automated Reasoning for the Synthesis and Analysis of Biological ProgramsSara-Jane Dunn, Boyan Yordanov · 2019 · Computational biology
- Integrated Pipelines for Inferring Gene Regulatory Networks from Single-Cell DataAimin Chen, Tianshou Zhou, Tianhai Tian · 2022 · Current Bioinformatics
- Bayesian Inference of Stochastic Dynamic Models Using Early-Rejection Methods Based on Sequential Stochastic SimulationsHu Zhang, Jingsong Chen, Tianhai Tian · 2020 · IEEE Transactions on Computational Biology and Bioinformatics
- A Logic-incorporated Gene Regulatory Network Deciphers Principles in Cell Fate DecisionsGang Xue, Xiaoyi Zhang, Wanqi Li, Lu Zhang, Zongxu Zhang, Xiaolin Zhou, Di Zhang, Lei Zhang, Zhiyuan Li · 2023 · bioRxiv (Cold Spring Harbor Laboratory)