Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq
Reinius, Björn, Mold, Jeff E, Ramsköld, Daniel, Deng, Qiaolin, Johnsson, Per, Michaëlsson, Jakob, Frisén, Jonas, Sandberg, Rickard·2016·Nature Genetics
DOI 10.1038/ng.3678
Cited by (157)
Items 101–157 of 157
- Assessment of cancer embryonic antigen (CEA) biomarker in women with breast cancer diseaseZahraa Mohammed AL-Nafakh, Arshad Noori Al-Dujaili, Ammar R. M. Rudha · 2020 · AIP conference proceedings
- Quality assessment of single-cell RNA sequencing data by coverage skewness analysisImad Abugessaisa, Shuhei Noguchi, Mélissa Cardon, Akira Hasegawa, Kazuhide Watanabe, Masataka Takahashi, Harukazu Suzuki, Shintaro Katayama, Juha Kere, Takeya Kasukawa · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational ratesNatali Papanicolaou, Antonio Lentini, Sebastian Wettersten, Michael Hagemann-Jensen, Annika Krüger, Jilin Zhang, Christos Coucoravas, Ioannis Petrosian, Xian Xin, Ilhan Ceyhan et al. · 2025 · Nature Communications
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seqVeronika Petrova, Muqing Niu, Thomas Vierbuchen, Emily S. W. Wong · 2025 · PLoS Computational Biology
- Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pre-gastrulation embryosC H Naik, Kishore Hari, Deepshikha Chandel, S Mandal, Mohit Kumar Jolly, Srimonta Gayen · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcriptionDig Bijay Mahat, Nathaniel D. Tippens, Jorge Diego Martin-Rufino, Sean K. Waterton, Jiayu Fu, Sarah E. Blatt, Phillip A. Sharp · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Multi-layered dosage compensation of the avian Z chromosomeNatali Papanicolaou, Antonio Lentini, Sebastian Wettersten, Michael Hagemann-Jensen, Annika Krüger, Jilin Zhang, Christos Coucoravas, Ioannis Petrosian, Xian Xin, Ilhan Ceyhan et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- 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
- CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variantsKazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Darvish Shafighi, Szymon M. Kiełbasa, Hugo W van Kessel, Ruben A. L. de Groen, Joost S.P. Vermaat, Julieta Sepúlveda-Yáñez, Marcelo A. Navarrete, Hendrik Veelken et al. · 2024 · Genome biology
- Starvation and Climate Change—How to Constrain Cancer Cell Epigenetic Diversity and Adaptability to Enhance Treatment EfficacyChristopher J. Gregg · 2021 · Frontiers in Ecology and Evolution
- Expression reduction of biallelically transcribed X-linked genes during the human female preimplantation developmentBjörn Reinius, Rickard Sandberg · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Structural diversity and evolutionary constraints of oxidative phosphorylationJosé Luis Cabrera-Alarcón, Marina Rosa-Moreno, Lucía Sánchez-García, Pablo Hernansanz‐Agustín, María Concepción Jiménez-Gómez, Fernando Martínez, Fátima Sánchez‐Cabo, José Antonio Enrı́quez · 2025 · Cell Genomics
- Rethinking disomy: Autosomal expression biasDusan Bogunovic · 2026 · The Journal of Experimental Medicine
- Single-cell variations in the expression of codominant alleles A and B on RBC of AB blood group individualsANJALI BAJPAI, Vidya S. Jonnalagadda, B. Sridevi, Pathma Muthukottiappan, Rachel A. Jesudasan · 2022 · Journal of Genetics
- Genomic Imprinting and Random Monoallelic ExpressionYaroslava Lobanova, Svetlana V. Zhenilo · 2024 · Biochemistry (Moscow)
- Advances in Single-Cell RNA Sequencing: Applications and Mechanistic Insights in Haematopoietic MalignanciesYixin Guo, Shuang Wang, Xinyue Huang, Yanhua Zheng, Fang Liu, Xiaoxue Wang · 2025 · Frontiers in Bioscience-Landmark
- Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasingJoanna Hård, Ezeddin Al Håkim, Marie Kindblom, Åsa K. Björklund, Ilke Demirci, Marta Paterlini, Pedro Réu, Bengt Sennblad, Erik Borgström, Patrik L. Ståhl et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA SequencingDonovan J. Anderson, Florian M. Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, Marshall S. Horwitz · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Diverse Patterns of Allele-Specific Expression in Healthy Human TissuesBlaise L. Mariner, Bryan Sands, Soo R. Yun, Tiffany Jones, Elizabeth M. Swisher, Mark A. McCormick, Alexander Mendenhall · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Single cell variations in expression of codominant alleles A and B on RBC of AB blood group individualsAnjali Bajpai, Vidya S. Jonnalagadda, B. Sridevi, Pathma Mutthukotti, Rachel A. Jesudasan · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Single cell transcriptomics2015 · Wiley eBooks
- Probabilistic cell lineage inference from mitochondrial mutationsS. Seidel, Joanna Hård, Pedro F. Ferreira, P. Berkes, K. Jahn, Carl-Johan Eriksson, Jeff E. Mold, J. Michaelsson, J. Kuipers, N. Beerenwinkel · 2026 · bioRxiv
- Endothelial Heterogeneity: A Role for Epigenetic Pathways in Constitutive Gene ExpressionLucy L Chen · 2019 · TSpace (University of Toronto)
- Single‐Cell TranscriptomicsSara Ballouz · 2020 · Wiley eBooks
- Single-Cell Rna-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X-Chromosome Dynamics During Early Postimplantation Mouse DevelopmentShangli Cheng, Yu Pei, Liqun He, Guangdun Peng, Björn Reinius, Patrick Tam, Naihe Jing, Qiaolin Deng · 2018 · SSRN Electronic Journal
- scBASE: A Bayesian mixture model for the analysis of allelic expression in single cellsKwangbom Choi, Narayanan Raghupathy, Gary A. Churchill · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Introns Control Stochasticity in Metazoan Gene ExpressionBryan Sands, Soo R. Yun, Alexander Mendenhall · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Pseudoautosomal gene SHOX exhibits sex-biased random monoallelic expression and contributes to sex difference in heightAtsushi Hattori, Atsuhito Seki, Naoto Inaba, Kazuhiko Nakabayashi, Kazue Takeda, Kuniko Tatsusmi, Yasuhiro Naiki, Akie Nakamura, Keisuke Ishiwata, Kenji Matsumoto et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- FRET-FISH probes chromatin compaction at individual genomic loci in single cellsAna Mota, Erik Wernersson, Xiaoze Li-Wang, Katarina Gradin, Nicola Crosetto, Magda Bienko · 2021 · Research Square
- Faculty Opinions recommendation of Genomic encoding of transcriptional burst kinetics.Daniel Reines · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Faculty Opinions recommendation of Landscape of X chromosome inactivation across human tissues.Cheryl Shoubridge · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Single-cell transcriptomicsMichał Marczyk, Tomasz Kujawa, Anna Papież, Joanna Polańska · 2022 · Elsevier eBooks
- Additional file 5 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Additional file 3 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Additional file 2 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesisLyu, Jun, Chongyi Chen · 2023 · Figshare
- Additional file 4 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Additional file 6 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Additional file 1 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Additional file 2 of Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosisZhiyong Liu, Sun, Zhonghua, Hongyun Liu, Weipin Niu, Xin Wang, Na Liang, Xin Wang, Yanfei Wang, Yaxin Shi, Xu, Li et al. · 2021 · Figshare
- Genomic imprinting and random monoallelic expressionYaroslava Lobanova, Svetlana V. Zhenilo · 2024 · Biochemistry (Moscow)
- Dosage responses of aneuploid autosomal chromosomesNatali Papanicolaou, Sebastian Wettersten, Guilherme Augusto Maia, Antonio Lentini, Björn Reinius · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesisS. Raine Cedric, Louis Coussement, Tine Goovaerts, Femke De Graeve, Jeroen Galle, Wim Van Criekinge, Tim De Meyer · 2025 · GigaScience
- Additional file 3 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesisLyu, Jun, Chongyi Chen · 2023 · Figshare
- Additional file 1 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesisLyu, Jun, Chongyi Chen · 2023 · Figshare
- Additional file 3 of Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivationBonora, Giancarlo, Ramani, Vijay, Singh, Ritambhara, Fang, He, Dana L. Jackson, Sanjay R Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure et al. · 2021 · Figshare
- Additional file 1 of Single-nucleus transcriptomic analysis reveals the relationship between gene expression in oligodendrocyte lineage and major depressive disorderXie, Yinping, Chen, Lijuan, Wang, Leimin, Liu, Tongou, Zheng, Yage, Lujia Si, Hailong Ge, Hong Xu, Xiao, Ling, Wang, Gaohua · 2024 · Figshare
- Additional file 1 of Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivationBonora, Giancarlo, Ramani, Vijay, Singh, Ritambhara, Fang, He, Dana L. Jackson, Sanjay R Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure et al. · 2021 · Figshare
- Study of the C5-DNA methyltransferases and allele specific expression in the model diatom Phaeodactylum tricornutumAntoine Hoguin · 2019 · theses.fr (ABES)
- Étude de la composante génétique de l’efficience alimentaire (EA) chez des lignées de poules pondeuses divergentes pour l’EA en utilisant la technologie RNA-seqFrédéric Jehl · 2020
- Deciphering the immune heterosis mechanism against Mycobacterium tuberculosis infection in hybrid mice based on allele-specific expressionHaoqi Wang, Xianglong Shi, Jinxia Dai, Gang Cao, Xiaofeng Wu · 2026 · Animal Diseases
- Evolutionary origins and chromatin state shape X-chromosome upregulation pattern during eutherian and metatherian embryogenesisHemant Chandru Naik, Dr. Pavithra Narendran, Srimonta Gayen · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Next-generation sequencing in head and neck sarcoma: a single-centre institutional experience and review of the literatureYasmin Ghnatous, Deepti Sinha, Golnaz Sadeghian, Nicholas Kalavrezos · 2026 · British Journal of Oral and Maxillofacial Surgery
- Dissecting Allele‐Specific Expression ( ASE ) in Landrace × Meishan Cross Pig Fetal‐Placental Tissues: Distribution, Functional Split, and MechanismsJinbi Zhang, Shiyong Xu, Wangjun Wu, Lifan Zhang, Aiwen Jiang, Ming Shen, Jingli Tao, H Liu, Zengxiang Pan · 2026 · The FASEB Journal
- Escape from X-chromosome inactivation: from gene discovery to regulatory mechanismsCaterina Simoncini, Agnese Loda · 2026 · Biochemical Society Transactions
- Monoallelic Gene Expression: Stochastic or Clonal? From Detection to Mechanisms and Clinical SignificanceО. А. Земляная, V. V. Strelnikov, Dmitry V. Zaletaev, Marina V. Nemtsova · 2026 · International Journal of Molecular Sciences
- Autosomal random monoallelic expression in development and diseaseHarshada Jadhav, Srimonta Gayen · 2026 · Current Opinion in Genetics & Development
- Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo QuadrupletsRisa Karakida Kawaguchi, Sara Ballouz, Jesse A Gillis · 2026 · Zenodo (CERN European Organization for Nuclear Research)