Counting absolute numbers of molecules using unique molecular identifiers

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Items 801–900 of 1,001

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2. Use of metagenomics for the detection of pathogens in the environment: A scoping review
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4. SURVEY AND SUMMARY Single-cell RNA-seq: advances and future challenges
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5. Navigating disease phenotypes – A multidimensional single-cell resolution compass leads the way
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6. META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples
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7. „Liquid biopsy“ – Einsatzmöglichkeiten in der molekularen Tumordiagnostik
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8. Modern methods of molecular diagnostics and study the genetic diversity of fruit and small fruit crops viruses based on sequencing
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9. Integrating Metagenomics in the Routine Lab
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10. SASCRiP: A Python workflow for preprocessing UMI count-based scRNA-seq data
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11. Genomic Characterization of a Tomato Yellow Mottle-Associated Virus Collected from a Field Tomato Plant in Chengdu, Southwestern China
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12. Selection Strategies in DNA-Encoded Libraries
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13. Integrated Transcriptome and Small RNA Sequencing Analyses Reveals Insights into the Molecular Mechanism of Seed Germination in Mung Bean
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14. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level
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15. Review of Machine Learning Advancements for Single-Cell Analysis
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16. Gene network inference from single-cell omics data and domain knowledge for constructing COVID-19-specific ICAM1-associated pathways
    Mitsuhiro Odaka, Morgan Magnin, Katsumi Inoue · 2023 · Frontiers in Genetics
17. Micro RNA-175 Targets Claudin-1 to Inhibit Madin–Darby Canine Kidney Cell Adhesion
    Xiaoyun Li, Fangfang Ma, Siya Wang, Tian Tang, Liyuan Ma, Zilin Qiao, Zhongren Ma, Jiamin Wang, Zhenbin Liu · 2024 · Genes
18. How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads
    Pengyao Ping, Tian Lan, Shuquan Su, Wei Liu, Jinyan Li · 2025 · Quantitative Biology
19. Barcodes based on nucleic acid sequences: Applications and challenges (Review)
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20. Characterizing the Role of Sialylated Milk Glycans and the Infant Gut Microbiota in Growth and Metabolism
    Mark R. Charbonneau · 2015 · Open Scholarship Institutional Repository (Washington University in St. Louis)
21. Molecular Methods and Bioinformatic Tools for Adjuvant Characterization by High-Throughput Sequencing
    Steven R. Wiley, Vanitha S. Raman · 2016 · Methods in molecular biology
22. Single-cell technologies in stem cell epigenetics
    Chen Kozulin, Danny Bavli, Oren Ram · 2020 · Elsevier eBooks
23. Single‐Cell Molecular Profiles and Biophysical Assessment of Circulating Tumor Cells
    Devalingam Mahalingam, Paweł A. Osmulski, Chiou‐Miin Wang, Aaron M. Horning, Anna D. Louie, Chun‐Lin Lin, Maria E. Gaczynska, Chun‐Liang Chen · 2016
24. Genome‐Wide Analysis of Single Cells and the Role of Microfluidics
    Sayantan Bose, Peter A. Sims · 2016 · Wiley eBooks
25. Bartender: an ultrafast and accurate clustering algorithm to count barcode and amplicon reads
    Lu Hua Zhao, Zhimin Liu, Sasha F. Levy, Song Wu · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
26. MC4C: Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies
    Amin Allahyar · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
27. Effects of duplicated mapped read PCR artifacts on RNA-seq differential expression analysis based on qRNA-seq
    Anna C. Salzberg, Jiafen Hu, Elizabeth J. Conroy, Nancy M. Cladel, Robert M. Brucklacher, Georgina V. Bixler, Yuka Imamura Kawasawa · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
28. Single-cell ID-seq identifies BMP signaling as a driver of a late stage epidermal differentiation program
    Roderick A. P. M. van Eijl, Jessie A.G.L. van Buggenum, Sabine E.J. Tanis, Joost Hendriks, Klaas W. Mulder · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
29. Development of a CRISPR-based epigenetic screening method
    Anna Köferle · 2017 · UCL Discovery (University College London)
30. Balancing Selection at HLA-G Modulates Fetal Survival, Preeclampsia and Human Birth Sex Ratio
    Satu Wedenoja, Masahito Yoshihara, Hindrek Teder, Hannu V. Sariola, Mika Gissler, Shintaro Katayama, Juho Wedenoja, Inka M K Häkkinen, Sini Ezer, Nina Linder et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
31. Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
    Robert A. Policastro, R. Taylor Raborn, Volker Brendel, Gabriel E. Zentner · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
32. Increased H3K27 trimethylation contributes to cone survival in a mouse model of cone dystrophy
    Annie L. Miller, Paula I. Fuller-Carter, Klaudija Masarini, Marijana Samardzija, Kim W. Carter, Rabab Rashwan, Alicia A. Brunet, Abha Chopra, Ramesh Ram, Christian Grimm et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
33. A hybrid unsupervised approach for accurate short read clustering and barcoded sample demultiplexing in nanopore sequencing
    Renmin Han, Junhai Qi, Yang Xue, Xiujuan Sun, Fa Zhang, Xin Gao, Guojun Li · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
34. WEGS: a cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome
    Claude Bhérer, Robert J. M. Eveleigh, Katerina Trajanoska, Janick St-Cyr, Antoine Paccard, Praveen Nadukkalam Ravindran, Elizabeth A. Caron, Nimara Bader Asbah, Clare Wei, Iris Baumgärtner et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
35. Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
    Alison G. Cole, Tamar Hashimshony, Zhuo Du, Itai Yanai · 2023 · eLife
36. Turn ‘noise’ to signal: accurately rectify millions of erroneous short reads through graph learning on edit distances
    Pengyao Ping, Shuquan Su, Xinhui Cai, Tian Lan, Xuan Zhang, Hui Peng, Yi Pan, Wei Liu, Jinyan Li · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
37. Next Generation Sequencing Data Analysis
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38. Sources of non-uniform coverage in short-read RNA-Seq data
    Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, J. S. Yang, Souparna Purohit, Amruta S. Naik, Emanuela Ricciotti, Shaon Sengupta, Peter S. Choi, Gregory R. Grant · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
39. Transcriptome Analysis
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40. From Noise to Models to Numbers: Evaluating Negative Binomial Models and Parameter Estimations in Single-Cell RNA-seq
    Yiling Wang, Zhanpeng Shu, Zhixing Cao, Ramon Grima · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
41. Identifying pyrogenic contaminants using transcriptomic profiling of monocyte activation test with machine learning
    Tess A. V. Afanasyeva, Bruno F.M. de Albuquerque, Paulien Doodeman, Miranda C. Dieker, Marijke Molenaar‐de Backer, Teunis J. P. van Dam, Anja ten Brinke · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
42. DDX3X-mediated translation of structured cardiac mRNAs is essential for female heart development
    Kayla K. Mason, Seohyun K. Park, James I. Emerson, Yao Wei Lu, Da-Zhi Wang, William F. Marzluff, Frank L. Conlon · 2026 · Genes & Development
43. Proximity Ligation and Barcoding Assays : Tools for analysis of proteins and protein complexes
    Di Wu · 2014 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
44. Genetic studies on primary immunodeficiency diseases
    Emma Maria Haapaniemi · 2015 · Työväentutkimus Vuosikirja
45. Methods to Prepare DNA for Efficient Massive Sequencing
    Sverker Lundin · 2012 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
46. Noninvasive prenatal detection for Pathogenic CNVs
    Xuan Huang, Sheng‐Pei Chen, Jing Juan Zheng, Haojun Jiang, Xiaoyu Pan, Jing Hui Guo, Ning Chen, Hui Jiang, Wei Wang · 2015
47. METHOD Open Access
    Lasse Maretty, Jonas A. Sibbesen, Anders Krogh · 2014
48. Single Cell Transcriptomics for Autoimmune Disorders
    Bhawna Gupta, Sunil K. Raghav · 2015 · Journal of Molecular and Genetic Medicine
49. Technologies for Single Cell Genome Analysis
    Erik Borgström · 2016 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
50. Single-Cell RNA Sequencing of the Bronchial Epithelium in Smokers With Lung Cancer
    Jennifer Beane, Joshua David Campbell, Grant E. Duclos · 2015
51. Analysis and kinase-mediated decay of RNAs with 5´-hydroxyl termini
    Sally E. Peach · 2016
52. Library Preparation for High Throughput DNA Sequencing
    Anders Jemt · 2017 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
53. Normalized Sequence Profiling Diversity Measured with Deep and Age-Related Decrease in TCR Repertoire
    Dmitriy M. Chudakov, Aliona I. Bogdanova, Ilgar Z. Mamedov, Y. B. Lebedev, Dmitriy A. Bolotin, Sergey A. Lukyanov, M. Merzlyak, Maria A. Turchaninova, V. Britanova, Ekaterina V. Putintseva · 2014
54. Directional qRNA-Seq: combining the power of stranded RNA-Seq with the quantitative precision of molecular labels
    Dawn Obermoeller, Radmila Hrdlickov, Jiřı́ Nehyba, Adam R. Morris · 2015
55. Optimizing gene expression by adapting splicing
    Idan Frumkin, Ido Yofe, Raz Bar‐Ziv, Yoav Voichek, Yitzhak Pilpel · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
56. Breathe (in the air) : pulmonary immunology in multiple sclerosis
    Michael Hagemann-Jensen · 2018 · Figshare
57. Genomic normalization for sequencing libraries enrichment for rare somatic retroelement insertions
    Alexander Yu. Komkov, Gaiaz A. Nugmanov, Maria Salutina, Anastasia A. Minervina, Konstantin V. Khodosevich, Yuri B. Lebedev, Ilgar Z. Mamedov · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
58. Single-Cell Dissection of Human Pancreatic Islet Dysfunction in Diabetes
    Michael L. Stitzel · 2017
59. Discovering Rare Hematopoietic Clones Harboring Leukemia-Associated Mutations Using Error-Corrected Sequencing
    Andrew L. Young · 2018 · Open Scholarship Institutional Repository (Washington University in St. Louis)
60. Modelling Crebbp loss in BCL2 driven non-Hodgkin’s lymphoma
    Joanna Dawes · 2015 · Spiral (Imperial College London)
61. Faculty of 1000 evaluation for Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.
    Siddharth S. Dey, Alex Chialastri · 2018 · F1000 - Post-publication peer review of the biomedical literature
62. Lineages and molecular heterogeneity in the developing nervous system
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63. Emerging Concepts in Liquid Biopsy
    Siddhartha Sen, Michael Datto, Sarah Rapisardo · 2018 · Advances in Molecular Pathology
64. Single-Cell Transcriptomics
    Marta Prieto‐Vila, Yusuke Yamamoto, Ryou‐u Takahashi, Takahiro Ochiya · 2018 · Springer eBooks
65. Exploring the functional landscape of the fission yeast genome via Hermes transposon mutagenesis
    Leanne Grech · 2018 · UCL Discovery (University College London)
66. Decoding the heterogeneity of skin in homeostasis and regeneration at single-cell resolution
    Simon Joost · 2018 · Figshare
67. Coupling multiplex pre-amplification and droplet digital PCR for longitudinal monitoring of ESR1 and PIK3CA mutations from plasma cell-free DNA
    Huilan Yao, Grant Wu, Subhasree Das, Crystal J. MacKenzie, Hua Gao, Victoria M. Rimkunas, Zhaojie Zhang, Stephanie L Ferro, Amy Roden, Manav Korpal et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
68. Peer Review #2 of "Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language (v0.2)"
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69. Peer Review #2 of "Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language (v0.1)"
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70. Peer Review #1 of "Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language (v0.2)"
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71. Peer Review #1 of "Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language (v0.1)"
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72. Recent Progress in Single-Cell Sequencing
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73. Computational Methods for Inferring Transcriptome Dynamics
    Joshua D. Welch · 2019 · Carolina Digital Repository (University of North Carolina at Chapel Hill)
74. Multi-omics analysis of transcription kinetics in human cells
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75. Genetic and functional analyses of the developing asymmetric zebrafish habenula
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76. Peer Review #2 of "Algorithms for efficiently collapsing reads with Unique Molecular Identifiers (v0.2)"
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77. Peer Review #2 of "Algorithms for efficiently collapsing reads with Unique Molecular Identifiers (v0.1)"
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78. Understanding stem cell heterogeneity – a prerequisite for successful (dental) regeneration
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79. Next Generation Sequencing Methods: Pushing the Boundaries
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80. Parallel genetics of regulatory sequences in vivo
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81. Transcription regulation dynamics
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82. Approaches for Identifying Biases in Single-Cell RNA-Sequencing Data
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83. Pathway-based Lineage Analysis of Time-course Single-cell RNA Sequencing Data
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84. Single cell transcriptomics and epigenomics methods provide high resolution genomics profiling of brain disorders
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85. Single-cell transcriptome analysis reveals thyrocyte diversity in the zebrafish thyroid gland
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86. vehicle / vehicles / new / used
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87. Faculty Opinions recommendation of Detection of ultra-rare mutations by next-generation sequencing.
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88. Peer Review #1 of "DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations (v0.1)"
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89. Peer Review #2 of "Evaluation of ddRADseq for reduced representation metagenome sequencing (v0.1)"
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90. Peer Review #1 of "Effect of method of deduplication on estimation of differential gene expression using RNA-seq (v0.1)"
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91. Peer Review #1 of "DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations (v0.2)"
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94. Peer Review #2 of "DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations (v0.1)"
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95. Peer Review #1 of "Evaluation of ddRADseq for reduced representation metagenome sequencing (v0.1)"
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96. Faculty Opinions recommendation of Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.
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97. Peer Review #1 of "Algorithms for efficiently collapsing reads with Unique Molecular Identifiers (v0.1)"
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98. Peer Review #2 of "Effect of method of deduplication on estimation of differential gene expression using RNA-seq (v0.1)"
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99. Peer Review #2 of "DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations (v0.2)"
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100. Faculty Opinions recommendation of Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.
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