Quantitative assessment of single-cell RNA-sequencing methods

Wu, Angela R, Neff, Norma F, Kalisky, Tomer, Dalerba, Piero, Treutlein, Barbara, Rothenberg, Michael E, Mburu, Francis M, Mantalas, Gary L +3 more·2014·Nature Methods

Cited by (709)

Items 301–400 of 709

  1. Toxic effects of metal copper stress on immunity, metabolism and pathologic changes in Chinese mitten crab (Eriocheir japonica sinensis)
    Dan Tang, Ruobing Liu, Xueling Shi, Chenchen Shen, Yuze Bai, Boping Tang, Zhengfei Wang · 2021 · Ecotoxicology
  2. Applying gene regulatory network logic to the evolution of social behavior
    Nicole M. Baran, Patrick T. McGrath, Jeffrey Todd Streelman · 2017 · Proceedings of the National Academy of Sciences
  3. BCseq: accurate single cell RNA-seq quantification with bias correction
    Liang Chen, Sika Zheng · 2018 · Nucleic Acids Research
  4. Comparative RNAseq Analysis of the Insect-Pathogenic Fungus Metarhizium anisopliae Reveals Specific Transcriptome Signatures of Filamentous and Yeast-Like Development
    Natasha Sant′Anna Iwanicki, Ítalo Delalibera, Jørgen Eilenberg, Henrik H. De Fine Licht · 2020 · G3 Genes Genomes Genetics
  5. Single-Cell Analysis Using Machine Learning Techniques and Its Application to Medical Research
    Ken Asada, Ken Takasawa, Hidenori Machino, Satoshi Takahashi, Norio Shinkai, Amina Bolatkan, Kazuma Kobayashi, Masaaki Komatsu, Syuzo Kaneko, Koji Okamoto et al. · 2021 · Biomedicines
  6. Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint
    Sören Müller, Aaron A. Diaz · 2017 · Frontiers in Genetics
  7. netSmooth: Network-smoothing based imputation for single cell RNA-seq
    Jonathan Ronen, Altuna Akalin · 2018 · F1000Research
  8. Implications of Epigenetic Variability within a Cell Population for “Cell Type” Classification
    Inna Tabansky, Joel N. H. Stern, Donald W. Pfaff · 2015 · Frontiers in Behavioral Neuroscience
  9. Single cell sequencing approaches for complex biological systems
    Timour Baslan, James B Hicks · 2014 · Current Opinion in Genetics & Development
  10. Digital Encoding of Cellular mRNAs Enabling Precise and Absolute Gene Expression Measurement by Single-Molecule Counting
    Glenn K. Fu, Julie Wilhelmy, David Stern, H. Christina Fan, Stephen P. A. Fodor · 2014 · Analytical Chemistry
  11. Enhanced Neuronal Regeneration in the CAST/Ei Mouse Strain Is Linked to Expression of Differentiation Markers after Injury
    Véronique Lisi, Bhagat Singh, Michel Giroux, Elmer Guzman, Michio W. Painter, Yung‐Chih Cheng, Eric A. Huebner, Giovanni Coppola, Michael Costigan, Clifford J. Woolf et al. · 2017 · Cell Reports
  12. Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
    Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret E. Staton · 2017 · BMC Genomics
  13. The Listeria monocytogenes Bile Stimulon under Acidic Conditions Is Characterized by Strain-Specific Patterns and the Upregulation of Motility, Cell Wall Modification Functions, and the PrfA Regulon
    Verónica Guariglia-Oropeza, Renato Hohl Orsi, Claudia Guldimann, Martin Wiedmann, Kathryn J. Boor · 2018 · Frontiers in Microbiology
  14. Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species
    Tuan Viet Nguyen, Hyungtaek Jung, Guiomar Rotllant, David A. Hurwood, Peter Barclay Mather, Tomer Ventura · 2018 · Hydrobiologia
  15. Single-cell DNA and RNA sequencing of circulating tumor cells
    Masato Kojima, Takanori Harada, Takahiro Fukazawa, Sho Kurihara, Isamu Saeki, Shinya Takahashi, Eiso Hiyama · 2021 · Scientific Reports
  16. Cellular Deconstruction: Finding Meaning in Individual Cell Variation
    James H. Eberwine, Junhyong Kim · 2015 · Trends in Cell Biology
  17. Microfluidics: A new tool for microbial single cell analyses in human microbiome studies
    Yuguang Liu, Marina R. S. Walther-Antonio · 2017 · Biomicrofluidics
  18. A contamination focused approach for optimizing the single-cell RNA-seq experiment
    Deronisha Arceneaux, Zhengyi Chen, Alan J. Simmons, Cody N. Heiser, Austin N. Southard-Smith, Michael J. Brenan, Yilin Yang, Bob Chen, Yanwen Xu, Eun-Young K. Choi et al. · 2023 · iScience
  19. Cell Size Contributes to Single-Cell Proteome Variation
    Michael Charles Lanz, Lucas Fuentes Valenzuela, Joshua Eric Elias, Jan Marcel Skotheim · 2023 · Journal of Proteome Research
  20. Isotachophoresis for fractionation and recovery of cytoplasmic RNA and nucleus from single cells
    Kentaro Kuriyama, Hirofumi Shintaku, Juan Gabriel Santiago · 2015 · Electrophoresis
  21. A guide to visualizing the spatial epigenome with super‐resolution microscopy
    Jianquan Xu, Yang Liu · 2019 · FEBS Journal
  22. The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance
    Song, Wei, Sharan, Roded, Ovcharenko, Ivan · 2019 · Genome Biology
  23. New approach in SARS-CoV-2 surveillance using biosensor technology: a review
    Dina M. El‐Sherif, Mohamed Abouzid, Mohamed Saad Gaballah, Alhassan Ali Ahmed, Muhammad Adeel, Sheta M. Sheta · 2021 · Environmental Science and Pollution Research
  24. Microfluidics in systems biology — hype or truly useful?
    Yi Liu, Hang Lu · 2016 · Current Opinion in Biotechnology
  25. Singled out for sequencing
    Kelly Rae Chi · 2013 · Nature Methods
  26. Needs and opportunities in bio-design automation: four areas for focus
    Evan Appleton, Douglas Michael Densmore, Curtis K. Madsen, Nicholas Roehner · 2017 · Current Opinion in Chemical Biology
  27. Analysis of mRNA abundance for histone variants, histone- and DNA-modifiers in bovine in vivo and in vitro oocytes and embryos
    Jingyue Ellie Duan, Linkai Zhu, Hong Dong, Xinbao Zheng, Z. Jiang, J. Chen, Xiuchun Tian · 2019 · Scientific Reports
  28. Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function
    Franziska Paul, Ido Amit · 2014 · Current Opinion in Immunology
  29. Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data
    Anna Mantsoki, Guillaume Devailly, Anagha Joshi · 2016 · Computational Biology and Chemistry
  30. Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry
    Gordon T. Taylor, Elizabeth A. Suter, Zhuo Q. Li, Stephanie Chow, Dallyce Stinton, Tatiana Zaliznyak, Steven R. Beaupré · 2017 · Frontiers in Microbiology
  31. Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
    Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara · 2019 · PLoS Computational Biology
  32. Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH
    Danson Shek Chun Loi, Lei Yu, Angela Ruohao Wu · 2021 · PeerJ
  33. Gut Mucosal Microbiome Is Perturbed in Rheumatoid Arthritis Mice and Partly Restored after TDAG8 Deficiency or Suppression by Salicylanilide Derivative
    Ngọc Tuấn Nguyễn, Wei‐Hsin Sun, Tzu-Hsuan Chen, Po-Chun Tsai, Chihchen Chen, Shir‐Ly Huang · 2022 · International Journal of Molecular Sciences
  34. Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis
    Hiroko Matsunaga, Koji Arikawa, Miki Yamazaki, Ryota Wagatsuma, Keigo Ide, Ashok Zachariah Samuel, Kazuya Takamochi, Kenji Suzuki, Takuo Hayashi, Masahito Hosokawa et al. · 2022 · Scientific Reports
  35. CellCommuNet: an atlas of cell–cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states
    Qinfeng Ma, Qiang Li, Zheng Xiao, Jianbo Pan · 2023 · Nucleic Acids Research
  36. What has single‐cell RNA sequencing revealed about microglial neuroimmunology?
    Norwin Kubick, Patrick C. Henckell Flournoy, Pavel Klimovich, Gina Manda, Michel‐Edwar Mickael · 2020 · Immunity Inflammation and Disease
  37. RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability
    Alloza, Iraide, Goikuria, Haize, Idro, Juan Luis, Triviño, Juan Carlos, Fernández Velasco, José María, Elizagaray, Elena, García-Barcina, María, Montoya-Murillo, Genoveva, Sarasola, Esther, Vega Manrique, Reyes et al. · 2017 · Scientific Reports
  38. Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols
    Peter A. Combs, Michael B. Eisen · 2015 · PeerJ
  39. Analysis of Single-Cell RNA-seq Data by Clustering Approaches
    Xiaoshu Zhu, Hong‐Dong Li, Lilu Guo, Fang‐Xiang Wu, Jianxin Wang · 2018 · Current Bioinformatics
  40. The accuracy of absolute differential abundance analysis from relative count data
    Kimberly E. Roche, Sayan Mukherjee · 2022 · PLoS Computational Biology
  41. SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data
    Qiong Zhang, Wei Liu, Chunjie Liu, Sheng‐Yan Lin, An‐Yuan Guo · 2017 · Briefings in Bioinformatics
  42. Transcriptomic behavior of genes associated with chromosome 21 aneuploidies in early embryo development
    Imma Sanchez-Ribas, Patricia Díaz-Gimeno, Patricia Sebastián-León, Amparo Mercader, Alicia Quiñonero, A. Ballesteros, António Pellicer, Francisco Domı́nguez · 2019 · Fertility and Sterility
  43. Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication
    Sascha Young Kupke, Lam-Ha Ly, Stefan T. Börno, Alexander Ruff, Bernd Timmermann, Martin Vingron, Stefan A. Haas, Udo Reichl · 2020 · Viruses
  44. Deconvolution of heterogeneous tumor samples using partial reference signals
    Yufang Qin, Weiwei Zhang, Xiaoqiang Sun, Siwei Nan, Nana Wei, Hua‐Jun Wu, Xiaoqi Zheng · 2020 · PLoS Computational Biology
  45. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse
    Guangyao Tian, Mingqian Li, Guoyue Lv · 2022 · Frontiers in Immunology
  46. Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
    Daphne Ezer, Victoria Moignard, B. Göttgens, B. Adryan · 2016 · PLoS Comput. Biol.
  47. A diffusion-based microfluidic device for single-cell RNA-seq
    Mimosa Sarma, Jiyoung Lee, Sai Ma, Song Li, Chang Lu · 2019 · Lab on a Chip
  48. A Microfluidic System for One‐Chip Harvesting of Single‐Cell‐Laden Hydrogels in Culture Medium
    Lang Nan, Zhenyu Yang, Hao Lyu, Kitty Yu-Yeung Lau, Ho Cheung Shum · 2019 · Advanced Biosystems
  49. The Importance of Detailed Epigenomic Profiling of Different Cell Types within Organs
    Theresa Ryan Stueve, Crystal N. Marconett, Beiyun Zhou, Zea Borok, Ite A. Laird‐Offringa · 2016 · Epigenomics
  50. Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism
    Camille Ezran, Shixuan Liu, Stephen Chang, Jingsi Ming, Olga Borisovna Botvinnik, Lolita Penland, Alexander J. Tarashansky, Antoine de Morrée, Kyle J. Travaglini, Jia Zhao et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Single-Cell RNA Sequencing of Human T Cells
    Alexandra–Chloé Villani, Karthik Shekhar · 2016 · Methods in molecular biology
  52. Gene expression effects of lithium and valproic acid in a serotonergic cell line
    Diana Balasubramanian, John F. Pearson, Martin Alexander Kennedy · 2018 · Physiological Genomics
  53. Illuminating Neural Circuits in Alzheimer’s Disease
    Ying Yang, Jian‐Zhi Wang · 2021 · Neuroscience Bulletin
  54. Deep transcriptome analysis of the heat shock response in an Atlantic sturgeon (Acipenser oxyrinchus) cell line
    Elena Santidrián Yebra-Pimentel, Marina Gebert, Hans J. Jansen, Susanne A. Jong-Raadsen, Ron P. Dirks · 2019 · Fish & Shellfish Immunology
  55. Unmasking cellular response of a bloom-forming alga to viral infection by resolving expression profiles at a single-cell level
    Shilo Rosenwasser, Uri Sheyn, Miguel José Frada, David Pilzer, Ron Rotkopf, Assaf Vardi · 2019 · PLoS Pathogens
  56. Precision monitoring of immunotherapies in solid organ and hematopoietic stem cell transplantation
    Rose DiLoreto, Kiran K. Khush, Iwijn De Vlaminck · 2017 · Advanced Drug Delivery Reviews
  57. Current and future perspectives of single-cell multi-omics technologies in cardiovascular research
    Wilson Lek Wen Tan, Wei Qiang Seow, Angela Zhang, Siyeon Rhee, Wing Hung Wong, William James Greenleaf, Joseph C. Wu · 2023 · Nature Cardiovascular Research
  58. CRATER tumor niches facilitate CD8+ T cell engagement and correspond with immunotherapy success
    Aya Ludin, Georgia L. Stirtz, Asaf Tal, Ajit J. Nirmal, Kathleen Lindahl Pfaff, Michael P. Manos, Naomi R. Besson, Nebiyat Eskndir, Billie A. Porter, Stephanie M. Jones et al. · 2025 · Cell
  59. Spatial and single-cell transcriptomics reveal the reorganization of cerebellar microglia with aging
    Andy Po‐Yi Tsai, Douglas E. Henze, Eduardo Ramirez Lopez, James Haberberger, Chuanpeng Dong, Nannan Lu, Micaiah Atkins, Emma K. Costa, Amelia Farinas, Hamilton Se‐Hwee Oh et al. · 2025 · Cell Reports
  60. Cancer systems immunology
    Nathan Edward Reticker-Flynn, Edgar G. Engleman · 2020 · eLife
  61. Revealing the Key MSCs Niches and Pathogenic Genes in Influencing CEP Homeostasis: A Conjoint Analysis of Single-Cell and WGCNA
    Weihang Li, Shilei Zhang, Yingjing Zhao, Dong Wang, Quan Shi, Ziyi Ding, Yongchun Wang, Bo Gao, Ming Yan · 2022 · Frontiers in Immunology
  62. Delineating biological and technical variance in single cell expression data
    Ángeles Arzalluz-Luque, Guillaume Devailly, Anna Mantsoki, Anagha Joshi · 2017 · The International Journal of Biochemistry & Cell Biology
  63. CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq
    Logan A. Walker, Michael G. Sovic, Chi‐Ling Chiang, Eileen Y. Hu, Jiyeon K. Denninger, Xi Chen, Elizabeth D. Kirby, John C. Byrd, Natarajan Muthusamy, Ralf A. Bundschuh et al. · 2020 · Journal of Translational Medicine
  64. Lithium-associated transcriptional regulation of CRMP1 in patient-derived olfactory neurons and symptom changes in bipolar disorder
    Charlee K. McLean, Soumya Narayan, Sandra Y. Lin, Narayan Rai, Youjin Chung, MariaMananita S. Hipolito, Nicola G. Cascella, John I. Nürnberger, Koko Ishizuka, Akira Sawa et al. · 2018 · Translational Psychiatry
  65. Prestin and electromotility may serve multiple roles in cochlear outer hair cells
    Jing Zheng, Satoe Takahashi, Yingjie Zhou, Mary Ann Cheatham · 2021 · Hearing Research
  66. Bioinformatics approaches to single-cell analysis in developmental biology
    Dicle Yalcin, Zeynep Hakguder, Hasan H. Otu · 2015 · Molecular Human Reproduction
  67. CRISPR/Cas Genome Editing in Filamentous Fungi
    А. М. Рожкова, Valeriy Yu. Kislitsin · 2021 · Biochemistry (Moscow)
  68. Lamin A/C Is Dispensable to Mechanical Repression of Adipogenesis
    Matthew H. Goelzer, Amel Dudakovic, Melis Olcum, Buer Sen, Engin Özçivici, Janet E. Rubin, André J. van Wijnen, Gunes Uzer · 2021 · International Journal of Molecular Sciences
  69. cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics
    Blasi, Thomas, Buettner, Florian, Strasser, Michael K, Marr, Carsten, Theis, Fabian J · 2017 · Physical Biology
  70. Next-Generation Pathology—Surveillance of Tumor Microecology
    Björn Koos, Masood Kamali‐Moghaddam, Leonor David, Manuel A. Sobrinho-Simões, Anna Dimberg, Mats F. Nilsson, Carolina Wählby, Ola Söderberg · 2015 · Journal of Molecular Biology
  71. Transcriptome analysis of upland cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance
    Qinqin Wang, Xuke Lu, Xiugui Chen, Waqar Afzal Malik, Delong Wang, Lanjie Zhao, Junjuan Wang, Shuai Wang, Lixue Guo, Ruifeng Cui et al. · 2021 · Scientific Reports
  72. Leukemic stem cell signatures in Acute myeloid leukemia- targeting the Guardians with novel approaches
    Deepshi Thakral, Ritu Gupta, Aafreen Khan · 2022 · Stem Cell Reviews and Reports
  73. scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching
    Jonathan Karin, Yonathan Bornfeld, Mor Nitzan · 2023 · Nature Biotechnology
  74. Data Mining of Microarray Datasets in Translational Neuroscience
    Lance M. O’Connor, Blake A. O’Connor, Jialiu Zeng, Chih Hung Lo · 2023 · Brain Sciences
  75. Profiling of Single‐Cell Transcriptomes
    Wanze Chen, Vincent Gardeux, Antonio C.A. Meireles-Filho, Bart Deplancke · 2017 · Current Protocols in Mouse Biology
  76. Opportunities and Challenges in Implementation of Multiparameter Single Cell Analysis Platforms for Clinical Translation
    Susan M. Keating, D. Lansing Taylor, Anne L. Plant, E. David Litwack, Peter Kühn, Emily J. Greenspan, Christopher M. Hartshorn, Caroline C. Sigman, Gary J. Kelloff, David D. Chang et al. · 2018 · Clinical and Translational Science
  77. Technological advances and computational approaches for alternative splicing analysis in single cells
    Wei Xiong Wen, Adam J. Mead, Supat Thongjuea · 2020 · Computational and Structural Biotechnology Journal
  78. Transcriptome Analysis of the Effects of Fasting Caecotrophy on Hepatic Lipid Metabolism in New Zealand Rabbits
    Yadong Wang, Huifen Xu, Guirong Sun, Mingming Xue, Shuaijie Sun, Tao Huang, Jianshe Zhou, Juan J. Loor, Ming Li · 2019 · Animals
  79. Single-Cell Multiomic MALDI-MSI Analysis of Lipids and N-Glycans through Affinity Array Capture
    James W. Dressman, Muhammed Bayram, Peggi M. Angel, Richard R. Drake, Anand S. Mehta · 2025 · Analytical Chemistry
  80. Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body
    Chia, Minghao, Ng, Amanda Hui Qi, Ravikrishnan, Aarthi, Mohamed Naim, Ahmad Nazri, Wearne, Stephen, Common, John, Nagarajan, Niranjan · 2026 · Nature Biotechnology
  81. Single-cell sequencing and organoids: applications in organ development and disease
    Tiantian Li, Jianmei Yin, Yang Hao, Wei Gao, Qirong Li, Qiang Feng, Boqiang Tao, Ming Hao, Yanxin Liu, Chao Lin et al. · 2025 · Molecular Biomedicine
  82. Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution
    Ernesto Marín‐Sedeño, Xabier Martínez de Morentin, José María Pérez-Pomares, David Gómez-Cabrero, Adrián Ruiz‐Villalba · 2021 · Frontiers in Cell and Developmental Biology
  83. Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies
    Xiya Guo, Jin Ning, Yuanze Chen, Guoliang Liu, Liyan Zhao, Yue Fan, Shiquan Sun · 2023 · Briefings in Functional Genomics
  84. Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
    Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masataka Shirai, Koji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama et al. · 2018 · Scientific Reports
  85. Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty
    Ehsan Hajiramezanali, Mahdi Imani, Ulisses Braga-Neto, Xiaoning Qian, Edward R. Dougherty · 2019 · BMC Genomics
  86. Between Fate Choice and Self-Renewal—Heterogeneity of Adult Neural Crest-Derived Stem Cells
    Anna L. Höving, Beatrice Ariane Windmöller, Cornelius Knabbe, Barbara Kaltschmidt, Christian Kaltschmidt, Johannes F. W. Greiner · 2021 · Frontiers in Cell and Developmental Biology
  87. Reconstructing Complex Tissues from Single-Cell Analyses
    Lu Wen, Fuchou Tang · 2014 · Cell
  88. 3D printed microfluidics for cell biological applications
    Liang Zhao, Xiayan Wang · 2022 · TrAC Trends in Analytical Chemistry
  89. Effects of purposeful soccer heading on circulating small extracellular vesicle concentration and cargo
    Eric R. Muñoz, Jaclyn B. Caccese, Brittany E. Wilson, Kyle T. Shuler, Fernando Vanderlinde dos Santos, Carolina T. Cabán, John J. Jeka, Dianne Langford, Matthew B. Hudson · 2020 · Journal of sport and health science/Journal of Sport and Health Science
  90. Are dropout imputation methods for scRNA-seq effective for scHi-C data?
    Chenggong Han, Qing Sheng Xie, Shili Lin · 2020 · Briefings in Bioinformatics
  91. Quantitative single cell gene expression profiling in the avian embryo
    Jason A. Morrison, Andrew Box, Mary Cathleen McKinney, Rebecca McLennan, Paul M. Kulesa · 2015 · Developmental Dynamics
  92. A highly sensitive and accurate gene expression analysis by sequencing (“bead-seq”) for a single cell
    Hiroko Matsunaga, Mari Goto, Koji Arikawa, Masataka Shirai, Hiroyuki Tsunoda, Huan Huang, Hideki Kambara · 2014 · Analytical Biochemistry
  93. zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications
    Koen Van den Berge, Charlotte Soneson, Michael I. Love, Mark D. Robinson, Lieven Clement · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  94. Parallel reverse genetic screening in mutant human cells using transcriptomics
    Gapp, Bianca V, Konopka, Tomasz, Penz, Thomas, Dalal, Vineet, Bürckstümmer, Tilmann, Bock, Christoph, Nijman, Sebastian MB · 2016 · Molecular Systems Biology
  95. Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing
    Peisen Zhao, Sudip Mondal, Chris Martin, Andrew DuPlissis, Shahab Chizari, Ke-Yue Ma, Rajani Maiya, Robert O. Messing, Ning Jenny Jiang, Adela Ben‐Yakar · 2023 · Nature Methods
  96. Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca2+ imaging and electrophysiology
    Joan Camuñas-Soler · 2023 · Biophysical Reviews
  97. Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research
    Jiahuan Chen, Qian Zhou, Yangfan Wang, Kang Ning · 2016 · Scientific Reports
  98. Update on Genomic Databases and Resources at the National Center for Biotechnology Information
    Tatiana A. Tatusova · 2016 · Methods in molecular biology
  99. Highly multiplexed single-cell quantitative PCR
    Michael A. VanInsberghe, Hans Zahn, Adam K. White, Oleh I. Petriv, Carl L. Hansen · 2018 · PLoS ONE
  100. A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
    Shiquan Sun, Yabo Chen, Yang Liu, Xuequn Shang · 2019 · BMC Systems Biology