Counting absolute numbers of molecules using unique molecular identifiers

Cited by (1,001)

Items 901–1,000 of 1,001

1. Use molecular barcodes to study emerging infectious diseases
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7. Reviewer #2 (Public Review): Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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8. eLife Assessment: Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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9. Reviewer #4 (Public Review): Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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10. Reviewer #1 (Public Review): Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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11. Reviewer #3 (Public Review): Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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19. Additional file 2 of Decode-seq: a practical approach to improve differential gene expression analysis
    Yingshu Li, Hang Yang, Hujun Zhang, Yongjie Liu, Hanqiao Shang, Herong Zhao, Ting Zhang, Qiang Tu · 2020 · Figshare
20. Additional file 4 of Decode-seq: a practical approach to improve differential gene expression analysis
    Yingshu Li, Hang Yang, Hujun Zhang, Yongjie Liu, Hanqiao Shang, Herong Zhao, Ting Zhang, Qiang Tu · 2020 · Figshare
21. Additional file 2 of BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
    Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior S. Pachter · 2021 · Figshare
22. Systematic perturbation screens decode regulators of inflammatory macrophage states and identify a role for TNF mRNA m6A modification
    Simone M. Haag, Shiqi Xie, Céline Eidenschenk, Jean‐Philippe Fortin, Marinella G. Callow, Mike Costa, Aaron T. L. Lun, Chris Cox, Sunny Z. Wu, Rachana Pradhan et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
23. Author Response: Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
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24. The Rubicon-WIPI axis regulates exosome biogenesis during aging
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25. How Error Correction Affects PCR Deduplication: A Survey Based on UMI Datasets of Short Reads
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    Yurii Nikolaevich Kuznetsov, I. K. Golubovskaya, Olesya U. Klimova, Мария Викторовна Марченко, N. Yu. Tcvetkov, Кулагин Егор Александрович, А. А. Осипова, Tatiana A Bykova, А. М. Садыков, Ildar Barkhatov et al. · 2024 · Clinical oncohematology
27. An Optimized High-Resolution Mapping Method for Glucocorticoid Receptor-DNA Binding in Mouse Primary Macrophages
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28. Transcriptome and Temporal Transcriptome Analyses in Single Cells
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29. LINNAEUS: Simultaneous Single-Cell Lineage Tracing and Cell Type Identification
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30. Droplet-Based Assays
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31. Advances in single-cell RNA-seq for nascent transcriptome and epitranscriptome
    Minsong Gao, Jianzhao Liu · 2025 · Scientia Sinica Vitae
32. Genome-wide profiling of tRNA modifications reveal the presence of divergent signatures in Plasmodium falciparum
    Qian Li, Ylva Veith, Elena Christ, Johan Ankarklev, Ola Segnestam Larsson, Sherwin Chun-Leung Chan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
33. mclUMI: Markov clustering of unique molecular identifiers enables dynamic removal of PCR duplicates
    Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
34. ABC‐seq Expands Small RNAs Profiling with Successive Nucleic Acid Structure‐Differentiated Enzymatic Recognition
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35. Oxygen levels regulating embryonic genome activation
    Nina Boskovic · 2025
36. MAGNET-seq: A tandem PCR and hybrid capture method for enhanced target enrichment
    Dongin Lee, Tae‐Hoon Kim, Duhee Bang · 2025 · PLoS ONE
37. Evolution of DNA sequencing technologies: An overview of working mechanisms, principles and clinical applications in personalised medicine
    Dharambir Kashyap, Riya Sharma, Harpal Singh Buttar, Vivek Kumar Garg, Douglas W. Wilson, Charles Odilichukwu R. Okpala · 2025 · Elsevier eBooks
38. Heterogeneity in platelet differentiation pathways
    Axel Winroth · 2025
39. An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal
    Sanjana Bhatnagar, Jade Ho, Nour H Sadek, Isha Singh, Michael Zoberman, Bina Koterniak, Yufang Liu, Daniel D. Fusca, Asher D. Cutter, Alan M Moses et al. · 2026 · Nucleic Acids Research
40. Unique Molecular Identifiers Don’t Need to be Unique: A Collision-Aware Estimator for RNA-Seq Quantification
    Dylan Agyemang, Rafael A. Irizarry, Tavor Z. Baharav · 2026 · Journal of Computational Biology
41. Molecule template estimation using Validator Barcodes in multiplex PCR for adaptive immune repertoire profiling
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42. Single cell transcriptomics in prostate cancer research
    Акрамова Элина Ринатовна, Шарифьянова Юлия Вакилевна, D. Kh. Gainullina, Polina Shmelkova, Liliia Kalimullina, В. Н. Павлов, Kadriia Enikeeva · 2025 · Medical Immunology (Russia)
43. Additional file 3 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
44. Additional file 2 of Benefits of applying molecular barcoding systems are not uniform across different genomic applications
    Jonathan Bieler, Slawomir Kubik, Morgane Macheret, Christian Pozzorini, Adrian Willig, Xu, Zhenyu · 2024 · Figshare
45. Additional file 1 of Prediction of P-tau/Aβ42 in the cerebrospinal fluid with blood microRNAs in Alzheimer’s disease
    Longfei Jia, Zhu, Min, Yang, Jianwei, Yana Pang, Wang, Qi, Li, Ying, Li, Tingting, Li, Fangyu, Qigeng Wang, Li, Yan et al. · 2021 · Figshare
46. Additional file 3 of Decode-seq: a practical approach to improve differential gene expression analysis
    Li, Yingshu, Yang, Hang, Hujun Zhang, Liu, Yongjie, Hanqiao Shang, Herong Zhao, Zhang, Ting, Tu, Qiang · 2020 · Figshare
47. Additional file 1 of Benefits of applying molecular barcoding systems are not uniform across different genomic applications
    Jonathan Bieler, Slawomir Kubik, Morgane Macheret, Christian Pozzorini, Adrian Willig, Xu, Zhenyu · 2024 · Figshare
48. Additional file 1 of BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
    Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Pachter, Lior · 2021 · Figshare
49. Additional file 1 of DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate
    Kashima Makoto, Mari Kamitani, Nomura, Yasuyuki, Natsumi Mori-Moriyama, Shigeyuki Betsuyaku, Hirata, Hiromi, Nagano, Atsushi J. · 2022 · Figshare
50. Additional file 2 of Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis
    Oren Ben-Kiki, Akhiad Bercovich, Aviezer Lifshitz, Amos Tanay · 2022 · Figshare
51. Additional file 4 of DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate
    Kashima Makoto, Mari Kamitani, Yasuyuki Nomura, Natsumi Mori-Moriyama, Shigeyuki Betsuyaku, Hirata, Hiromi, Nagano, Atsushi J. · 2022 · Figshare
52. Additional file 1 of Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis
    Oren Ben-Kiki, Akhiad Bercovich, Aviezer Lifshitz, Amos Tanay · 2022 · Figshare
53. Additional file 1 of Decode-seq: a practical approach to improve differential gene expression analysis
    Li, Yingshu, Yang, Hang, Hujun Zhang, Liu, Yongjie, Hanqiao Shang, Herong Zhao, Zhang, Ting, Tu, Qiang · 2020 · Figshare
54. Additional file 2 of DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate
    Kashima Makoto, Mari Kamitani, Yasuyuki Nomura, Natsumi Mori-Moriyama, Shigeyuki Betsuyaku, Hirata, Hiromi, Nagano, Atsushi J. · 2022 · Figshare
55. Additional file 5 of Decode-seq: a practical approach to improve differential gene expression analysis
    Li, Yingshu, Yang, Hang, Hujun Zhang, Liu, Yongjie, Hanqiao Shang, Herong Zhao, Zhang, Ting, Tu, Qiang · 2020 · Figshare
56. Additional file 2 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
57. Additional file 3 of BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
    Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Pachter, Lior · 2021 · Figshare
58. Additional file 1 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
59. Additional file 2 of Prediction of P-tau/Aβ42 in the cerebrospinal fluid with blood microRNAs in Alzheimer’s disease
    Longfei Jia, Zhu, Min, Yang, Jianwei, Yana Pang, Wang, Qi, Li, Ying, Li, Tingting, Li, Fangyu, Qigeng Wang, Li, Yan et al. · 2021 · Figshare
60. Single cell RNA sequencing in autoimmune inflammatory rheumatic diseases
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61. Technical Advancements in Microbial Single-Cell Omics Analysis
    Haruko Takeyama, Masahito Hosokawa, Masahiro Ando, Yohei Nishikawa · 2025 · The microbiomes of humans, animals, plants, and the environment
62. DNA-barcoded microneedle array patch enabling the profiling of in vivo spatiotemporal transcriptomics
    Yuanbin Guo, Yile Zhang, Xinyin Li, Jingwen Kuang, Ke Cao, Feng Chen, Chunhai Fan, Yongxi Zhao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
63. Optimal sequencing depth for single-cell RNA-sequencing in Wasserstein space
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64. CancerSTFormer enables multi-scale analysis of spot-resolution spatial transcriptomes and dissects gene and immune regulatory responses to targeted therapies
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65. Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq
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66. A distributive germline restricts the spread of new mutations
    Justin Scherer, Maa Ahema Gaisie, Sungjin Park, Bradlee D. Nelms · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
67. Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis
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68. RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction
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69. Structure and genomic organization of the human DUX4 homologue bovine DUXC
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70. Single-Molecule Counting for Noninvasive Prenatal Diagnosis of Autosomal Recessive Hearing Loss in at-Risk Families
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71. The antifungal and antimycotoxin efficacy of the tick peptide TickCore3 is associated with a broad and complex transcriptional response in Fusarium graminearum
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72. An innovative approach for magnetic solid supports handling in droplet microfluidics
    Marco Serra · 2018
73. Pre-evolutionary dynamics in autocatalytic RNA networks
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74. Analysis of single cell gene expression reveals cellular heterogeneity and differentiation dynamics of an healthy airway epithelia
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75. Caractérisation transcriptomique des cellules lymphoïdes innées
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77. Développement de nouvelles méthodes algorithmiques pour le traitement des UMI à partir des données de séquençage haut débit.
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78. On the selection of unconventional CD8+ T-cell during human thymopoiesis
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81. The antifungal and antimycotoxin efficacy of the tick peptide TickCore3 is associated with a broad and complex transcriptional response in Fusarium graminearum
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82. CsZAT6/12 response auxin signaling to differentially regulate theanine-dominated nitrogen flow in tea roots (Camellia sinensis)
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85. Single-Cell RNA Sequencing
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86. AviTag-seq unifies nucleotide-resolution maps of CRISPR off-targets and AAV vector integrations
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97. The Phantom of the PCR: detection and consequences of spurious UMIs in mainstream RNA sequencing
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98. Reconstruction of cell diversity and cell lineages from somatic mutations in single-cell transcriptomic data
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99. Pattern-Filter structural validation of single-cell RNA-seq reads reduces artifactual barcodes and improves biological resolution
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100. Fluorescence Event Counting for miRNA Detection Enabled by Surface-Confined Hybridization Chain Reaction with Integrated Optical Gain
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