Counting absolute numbers of molecules using unique molecular identifiers

Kivioja, Teemu, Vähärautio, Anna, Karlsson, Kasper, Bonke, Martin, Enge, Martin, Linnarsson, Sten, Taipale, Jussi·2012·Nature Methods
DOI 10.1038/nmeth.1778

Cited by (1,001)

Items 201–300 of 1,001

  1. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells
    Olivier Cuvier, Beat Fierz · 2017 · Nature Reviews Genetics
  2. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model
    Nova Fong, Ryan M. Sheridan, Srinivas Ramachandran, David L. Bentley · 2022 · Molecular Cell
  3. Using Genotype Abundance to Improve Phylogenetic Inference
    William S. DeWitt, Luka Mesin, Gabriel D. Victora, Vladimir N. Minin, Frederick A. Matsen IV · 2018 · Molecular Biology and Evolution
  4. The Mettl3 epitranscriptomic writer amplifies p53 stress responses
    Nitin Raj, Mengxiong Wang, José Antonio Seoane, Richard L. Zhao, Alyssa M. Kaiser, Nancie A. Moonie, János Demeter, Anthony M. Boutelle, Craig H. Kerr, Abigail S. Mulligan et al. · 2022 · Molecular Cell
  5. Application of single-cell genomics in cancer: promise and challenges
    Quin F. Wills, Adam J. Mead · 2015 · Human Molecular Genetics
  6. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins
    Inga Jarmoskaite, Sarah K. Denny, Pavanapuresan P. Vaidyanathan, Winston R. Becker, Johan O. L. Andreasson, Curtis J. Layton, Kalli Kappel, Varun Shivashankar, Raashi Sreenivasan, Rhiju Das et al. · 2019 · Molecular Cell
  7. Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
    Yue You, Luyi Tian, Shian Su, Xueyi Dong, Jafar S. Jabbari, Peter F. Hickey, Matthew E. Ritchie · 2021 · Genome biology
  8. Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns
    Annabel Ebbing, Ábel Vértesy, Marco C. Betist, Bastiaan Spanjaard, Jan Philipp Junker, Eugène Berezikov, Alexander van Oudenaarden, Hendrik C. Korswagen · 2018 · Developmental Cell
  9. Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites
    Sanaz Firouzi, Yosvany López, Yutaka Suzuki, Kenta Nakai, Sumio Sugano, Tadanori Yamochi, Toshiki Watanabe · 2014 · Genome Medicine
  10. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching
    Dave T. P. Tang, Charles Plessy, M. Salimullah, Ana Maria Suzuki, Raffaella Calligaris, Stefano Gustincich, Piero Carninci · 2012 · Nucleic Acids Research
  11. Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy
    Ilenia Aversa, Donatella Malanga, Giuseppe Fiume, Camillo Palmieri · 2020 · International Journal of Molecular Sciences
  12. CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients
    Ekaterina A. Komech, Mikhail V. Pogorelyy, Evgeny S. Egorov, Olga V. Britanova, Denis V. Rebrikov, Anna Georgiyevna Bochkova, Е. Шмидт, Nadejda A. Shostak, Mikhail Shugay, Sergey Lukyanov et al. · 2018 · Lara D. Veeken
  13. Population-scale testing can suppress the spread of COVID-19
    Jussi Taipale, Paul Romer, Sten Linnarsson · 2020 · medRxiv
  14. Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome
    Omer Schwartzman, Angela Maria Savino, Michael Gombert, Chiara Palmi, Gunnar Cario, Martin Schrappe, Cornelia Eckert, Arend von Stackelberg, Jin-Yan Huang, Michal Hameiri-Grossman et al. · 2017 · Proceedings of the National Academy of Sciences
  15. Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
    Florian V. De Rop, Joy N. Ismail, Carmen Bravo González‐Blas, Gert J. Hulselmans, Christopher Flerin, Jasper Janssens, Koen Theunis, Valerie Christiaens, Jasper Wouters, Gabriele Marcassa et al. · 2022 · eLife
  16. Strategies for improving detection of circulating tumor DNA using next generation sequencing
    Roberto Tébar-Martínez, Jorge Martín-Arana, Francisco Gimeno-Valiente, Noelia Tarazona, Pilar Rentero-Garrido, Andrès M.R. Cervantes · 2023 · Cancer Treatment Reviews
  17. Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Paweł Zając, Saiful Islam, Hannah Hochgerner, Peter Lönnerberg, Sten Linnarsson · 2013 · PLoS ONE
  18. Evolution of MHC-based technologies used for detection of antigen-responsive T cells
    Amalie Kai Bentzen, Sine Reker Hadrup · 2017 · Cancer Immunology Immunotherapy
  19. Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology
    Fátima Valdés‐Mora, Kristina Handler, Andrew M. K. Law, Robert Salomon, Samantha Richelle Oakes, Christopher John Ormandy, David Gallego‐Ortega · 2018 · Frontiers in Immunology
  20. HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer
    Manoj M. Pillai, Austin E. Gillen, Tomomi M. Yamamoto, Enos C. Kline, Joseph Brown, Kale Flory, Jay R. Hesselberth, Peter Kabos · 2014 · Breast Cancer Research and Treatment
  21. Deep immunophenotyping at the single-cell level identifies a combination of anti-IL-17 and checkpoint blockade as an effective treatment in a preclinical model of data-guided personalized immunotherapy
    Koji Nagaoka, Masataka Shirai, Kiyomi Taniguchi, Akihiro Hosoi, Changbo Sun, Yukari Kobayashi, Kazuhiro Maejima, Masashi Fujita, Hidewaki Nakagawa, Sachiyo Nomura et al. · 2020 · Journal for ImmunoTherapy of Cancer
  22. An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
    Anders Jemt, Fredrik Salmén, Anna Lundmark, Annelie Mollbrink, José Fernández Navarro, Patrik L. Ståhl, Tülay Yucel‐Lindberg, Joakim Lundeberg · 2016 · Scientific Reports
  23. Single-Cell Genomics: Approaches and Utility in Immunology
    Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly Azeem Khan · 2017 · Trends in Immunology
  24. Chromatin dynamics during DNA replication
    Raz Bar‐Ziv, Yoav Voichek, Naama Barkai · 2016 · Genome Research
  25. T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity
    Minervina, Anastasia, Pogorelyy, Mikhail, Mamedov, Ilgar · 2019 · Transplant International
  26. Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer
    Chiang‐Ching Huang, Meijun Du, Liang Wang · 2019 · Cancers
  27. Specific Induction of Double Negative B Cells During Protective and Pathogenic Immune Responses
    Christoph Ruschil, Gisela Gabernet, Gildas Lepennetier, Simon Heumos, Miriam Kaminski, Zsuzsanna Hracskó, Martin Irmler, Johannes Beckers, Ulf Ziemann, Sven Nahnsen et al. · 2020 · Frontiers in Immunology
  28. RNA 5-Methylcytosine Analysis by Bisulfite Sequencing
    Matthias Schaefer · 2015 · Methods in enzymology on CD-ROM/Methods in enzymology
  29. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data
    Bram Gerritsen, Aridaman Pandit, Arno C. Andeweg, Rob J. de Boer · 2016 · Bioinformatics
  30. Single‐cell RNA‐sequencing of the brain
    Raquel Cuevas‐Díaz Durán, Haichao Wei, Jia Qian Wu · 2017 · Clinical and Translational Medicine
  31. RNase L Targets Distinct Sites in Influenza A Virus RNAs
    Daphne A. Cooper, Shuvojit Banerjee, Arindam Chakrabarti, Adolfo García‐Sastre, Jay R. Hesselberth, Robert H. Silverman, David J. Barton · 2014 · Journal of Virology
  32. A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT
    David Tsao, Sukrit Silas, Brian P. Landry, Nelda P. Itzep, Amy B. Nguyen, Samuel Greenberg, Celeste K. Kanne, Vivien Sheehan, Rani Sharma, Rahul Shukla et al. · 2019 · Scientific Reports
  33. The genotype‐phenotype landscape of an allosteric protein
    Drew S. Tack, Peter D. Tonner, Abe Pressman, Nathan D. Olson, Sasha F. Levy, Eugenia F. Romantseva, Nina Alperovich, Olga B Vasilyeva, David Ross · 2021 · Molecular Systems Biology
  34. Assessing human B cell repertoire diversity and convergence
    Katharina Imkeller, Hedda Wardemann · 2018 · Immunological Reviews
  35. Single-Cell Genomics
    Carmela Paolillo, Eric R. Londin, Paolo M. Fortina · 2019 · Clinical Chemistry
  36. Quantitative single-cell transcriptomics
    Christoph Ziegenhain, Beate Vieth, Swati Parekh, Ines Hellmann, Wolfgang Enard · 2018 · Briefings in Functional Genomics
  37. Single‐Cell Sequencing Methodologies: From Transcriptome to Multi‐Dimensional Measurement
    Yingwen Chen, Jia Tao Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong James Yang · 2021 · Small Methods
  38. Gametophyte genome activation occurs at pollen mitosis I in maize
    Bradlee D. Nelms, Virginia Walbot · 2022 · Science
  39. Coupled catabolism and anabolism in autocatalytic RNA sets
    Arsène, Simon, Ameta, Sandeep, Lehman, Niles, Griffiths, Andrew D, Nghe, Philippe · 2018 · Nucleic Acids Research
  40. TagDust2: a generic method to extract reads from sequencing data
    Timo Lassmann · 2015 · BMC Bioinformatics
  41. Ribonuclease L and metal-ion–independent endoribonuclease cleavage sites in host and viral RNAs
    Daphne A. Cooper, Babal Kant Jha, Robert H. Silverman, Jay R. Hesselberth, David J. Barton · 2014 · Nucleic Acids Research
  42. Modeling genome coverage in single-cell sequencing
    Timothy Daley, Andrew D. Smith · 2014 · Bioinformatics
  43. Comparative analysis of murine T‐cell receptor repertoires
    Mark Izraelson, Tatiana O. Nakonechnaya, Bruno Moltedo, Evgeny S. Egorov, Sofya A. Kasatskaya, Ekaterina V. Putintseva, Ilgar Z. Mamedov, Dmitriy B. Staroverov, Irina I. Shemiakina, Maria Yu. Zakharova et al. · 2017 · Immunology
  44. A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines
    Richa Nayak, Yasha Hasija · 2021 · Genomics
  45. GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution
    Weiguo Shen, Hanxiao Sun, Cong Liu, Yunpeng Yi, Yongkang Hou, Ye Xiao, Yufei Hu, Bo Lu, Jinying Peng, Jing Wang et al. · 2024 · Nature Protocols
  46. Aberrant Methylation of LINE-1 Transposable Elements: A Search for Cancer Biomarkers
    Anastasia A. Ponomaryova, ELENA YU. RYKOVA, Гервас Полина Анатольевна, Н. В. Чердынцева, Ilgar Z. Mamedov, Tatyana L. Azhikina · 2020 · Cells
  47. Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives
    Geyang Luo, Qian Gao, Shuye Zhang, Bo Yan · 2020 · Computational and Structural Biotechnology Journal
  48. Limitations and challenges of genetic barcode quantification
    Lars Thielecke, Tim Aranyossy, Andreas Dahl, Rajiv Lochan Tiwari, Ingo Roeder, Hartmut Geiger, Boris Fehse, Ingmar Glauche, Kerstin Cornils · 2017 · Scientific Reports
  49. Single-Cell RNA Sequencing to Understand Host–Pathogen Interactions
    Cristina Peñaranda, Deborah Tan Hung · 2019 · ACS Infectious Diseases
  50. Single cell transcriptomics: moving towards multi-omics
    Yanling Song, Xing Xu, Wei Wang, Tian Tian, Zhi Zhu, Chaoyong James Yang · 2019 · The Analyst
  51. X-chromosome upregulation is driven by increased burst frequency
    Anton J. M. Larsson, Christos Coucoravas, Rickard Sandberg, Björn Reinius · 2019 · Nature Structural & Molecular Biology
  52. Inflammatory Bowel Disease Through the Lens of Single-cell RNA-seq Technologies
    Daniele Corridoni, Thomas Chapman, Agne Antanaviciute, Jack J. Satsangi, Alison Simmons · 2020 · Inflammatory Bowel Diseases
  53. Methods, Challenges and Potentials of Single Cell RNA-seq
    Daniel Hebenstreit · 2012 · Biology
  54. Re-Evaluating the Conventional Wisdom about Binding Assays
    Brandon D. Wilson, Hyongsok Tom Soh · 2020 · Trends in Biochemical Sciences
  55. Single-Cell Applications of Next-Generation Sequencing
    Naishitha Anaparthy, Yu-Jui Ho, Luciano Gastón Martelotto, Molly Hammell, James B Hicks · 2019 · Cold Spring Harbor Perspectives in Medicine
  56. Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
    Daniel Liu · 2019 · PeerJ
  57. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
    Mikhail Shugay, Andrew R. Zaretsky, Dmitry A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrey A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov · 2017 · PLoS Computational Biology
  58. A brief review of single-cell transcriptomic technologies
    Tomer Kalisky C, Sarit Oriel, Tali Hana Bar-Lev, Nissim Ben-Haim, Ariel Trink, Yishay Wineberg, Itamar Kanter, Shlomit Gilad, Saumyadipta Pyne · 2017 · Briefings in Functional Genomics
  59. Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients
    E. Christensen, I. Nordentoft, S. Vang, K. Birkenkamp-Demtröder, J. B. Jensen, M. Agerbæk, J. S. Pedersen, L. Dyrskjøt · 2018 · Scientific Reports
  60. Missing Data and Technical Variability in Single-Cell RNA-Sequencing Experiments
    Hicks, Stephanie C., Townes, F. William, Teng, Mingxiang, Irizarry, Rafael A. · 2015
  61. T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis
    José Garrido‐Mesa, Matthew Arthur Brown · 2022 · Current Rheumatology Reports
  62. The Application of Single-Cell RNA Sequencing in Studies of Autoimmune Diseases: a Comprehensive Review
    Mingming Zhao, Jiao Jiang, Ming Zhao, Christopher Chang, Haijing Wu, Qianjin Lu · 2020 · Clinical Reviews in Allergy & Immunology
  63. Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing
    Sally E. Peach, Kerri T. York, Jay R. Hesselberth · 2015 · Nucleic Acids Research
  64. Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics
    Vicent Pelechano, Wei Wu, Lars Michael Steinmetz · 2016 · Nature Protocols
  65. UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution
    Paul Jannis Zurek, Philipp Knyphausen, Katharina Neufeld, Ahir Pushpanath, Florian Hollfelder · 2020 · Nature Communications
  66. Different Modes of Negative Regulation of Plant Immunity by Calmodulin-Related Genes
    You Lu, William Truman, Xiaotong Liu, Gerit Bethke, Man Zhou, Chad L. Myers, Fumiaki Katagiri, Jane Glazebrook · 2018 · PLANT PHYSIOLOGY
  67. Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation
    Juan Mata · 2013 · RNA Biology
  68. Single-cell analysis of glandular T cell receptors in Sjögren’s syndrome
    Michelle L. Joachims, Kerry M. Leehan, Christina Lawrence, Richard C. Pelikan, Jacen S. Moore, Zijian Pan, Astrid Rasmussen, Lida Radfar, David M. Lewis, Kiely M. Grundahl et al. · 2016 · JCI Insight
  69. Novel Approaches to Analyze Immunoglobulin Repertoires
    Hedda Wardemann, Christian E. Busse · 2017 · Trends in Immunology
  70. Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation
    Minoru Kubo, Tomoaki Nishiyama, Yosuke Tamada, Ryosuke Sano, Masaki Ishikawa, Takashi Murata, Akihiro Imai, Daniel Lang, Taku Demura, Ralf Reski et al. · 2019 · Nucleic Acids Research
  71. Beyond protein binding: recent advances in screening DNA-encoded libraries
    Thomas J. Kodadek, Nicholas G. Paciaroni, Madeline Balzarini, Paige Dickson · 2019 · Chemical Communications
  72. Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children
    Ivan V. Zvyagin, Ilgar Z. Mamedov, O V Tatarinova, Ekaterina A. Komech, Elena Kurnikova, Боякова Елена Викторовна, В. В. Бриллиантова, Larisa N. Shelikhova, Dmitry Balashov, Mikhail Shugay et al. · 2016 · Leukemia
  73. Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia
    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. · 2020 · EBioMedicine
  74. Characterizing range-wide divergence in an alpine-endemic bird: a comparison of genetic and genomic approaches
    Kathryn M. Langin, Cameron L. Aldridge, Jennifer A. Fike, Robert S. Cornman, Kathy Martin, Gregory T. Wann, Amy E. Seglund, Michael A. Schroeder, Clait E. Braun, David P. Benson et al. · 2018 · Conservation Genetics
  75. Fibrosis in Pathology of Heart and Kidney: From Deep RNA-Sequencing to Novel Molecular Targets
    Felix Schreibing, Teresa M Anslinger, Rafael Kramann · 2023 · Circulation Research
  76. Opportunities and tradeoffs in single-cell transcriptomic technologies
    Matilde Immacolata Conte, Azahara Fuentes‐Trillo, Cecilia Domínguez Conde · 2023 · Trends in Genetics
  77. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters
    Patricia J. Hare, Travis J. LaGree, Brandon A. Byrd, Angela M. DeMarco, Wendy W. K. Mok · 2021 · Microorganisms
  78. Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq
    Cindo O. Nicholson, Matthew B. Friedersdorf, Jack D. Keene · 2016 · RNA
  79. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes
    Milo S. Johnson, Sandeep Venkataram, Sergey Kryazhimskiy · 2023 · Journal of Molecular Evolution
  80. Heterogeneity of macrophages in atherosclerosis revealed by single‐cell RNA sequencing
    Liwen Yu, Yujie Zhang, Changhao Liu, Xiao Wu, Shasha Wang, Wenhai Sui, Yun Zhang, Cheng Zhang, Meng Zhang · 2023 · The FASEB Journal
  81. Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules
    Jianfeng Sun, Martin Philpott, Danson Shek Chun Loi, Shuang Li, Pablo Monteagudo-Mesas, Gabriela Hoffman, Jonathan Robson, Neelam Mehta, Vicki Gamble, Tom Brown et al. · 2024 · Nature Methods
  82. Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing
    Ulrike Menzel, Victor Greiff, Tarik A. Khan, Ulrike Haessler, Ina Hellmann, Simon Friedensohn, Skylar C. Cook, Mark Pogson, Sai T. Reddy · 2014 · PLoS ONE
  83. Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos
    Ilaria Lavagi, Stefan Krebs, Kilian Simmet, Andrea H. Beck, Valeri Zakhartchenko, Eckhard Wolf, Helmut Blum · 2018 · Scientific Reports
  84. The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis
    Michal Eisenberg‐Bord, Hui Su Tsui, Diana Antunes, Lucía Fernández-del-Río, Michelle C. Bradley, Cory D. Dunn, Theresa P. T. Nguyen, Doron Rapaport, Catherine Freitag Clarke, Maya Schuldiner · 2019 · Contact
  85. Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing
    Toby P. Aicher, Shaina L. Carroll, Gianmarco Raddi, Todd M. Gierahn, Marc H. Wadsworth, Travis K. Hughes, Chris Love, Alex K. Shalek · 2019 · Methods in molecular biology
  86. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics?
    Matthias Schaefer · 2021 · Genes
  87. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
    Nevena Cvetešić, Harry G. Leitch, Małgorzata Borkowska, Ferenc Müller, Piero Carninci, Petra Hájková, Boris Lenhard · 2018 · Genome Research
  88. LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3’-CCA end for high-throughput sequencing
    Lieselotte Erber, Anne Hoffmann, Jörg Fallmann, Heike Betat, Peter Florian Stadler, Mario Mörl · 2019 · RNA Biology
  89. The hitchhikers’ guide to RNA sequencing and functional analysis
    Jiung-Wen Chen, Lisa Shrestha, George Alexander Green, André Leier, Tatiana T. Marquez‐Lago · 2023 · Briefings in Bioinformatics
  90. Single-Cell Expression Variability Implies Cell Function
    Daniel Osorio, Xue Yu, Yan Zhong, Guanxun Li, Peng Yu, Erchin Serpedin, Jian Huang, James J. Cai · 2019 · Cells
  91. DNA synthesis for true random number generation
    Meiser, Linda C., Koch, Julian, Antkowiak, Philipp L., Stark, Wendelin J., Heckel, Reinhard, Grass, Robert N. · 2020 · Nature Communications
  92. Molecular spikes: a gold standard for single-cell RNA counting
    Christoph Ziegenhain, Gert‐Jan Hendriks, Michael Hagemann-Jensen, Rickard Sandberg · 2022 · Nature Methods
  93. Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing
    Daniel J. O’Connell, Raivo Kolde, Matthew Sooknah, Daniel B. Graham, Thomas B. Sundberg, Isabel J. Latorre, Tarjei Sigurd Mikkelsen, Ramnik J. Xavier · 2016 · Cell Systems
  94. Tracking plasma DNA mutation dynamics in estrogen receptor positive metastatic breast cancer with dPCR-SEQ
    Sunil Kumar, Daniel Lindsay, Q. Brent Chen, Amy Garrett, Xianming M. Tan, Carey K. Anders, LA Carey, Gaorav P. Gupta · 2018 · npj Breast Cancer
  95. Computational methods for ribosome profiling data analysis
    Stephen J. Kiniry, Audrey M. Michel, Pavel V. Baranov · 2019 · Wiley Interdisciplinary Reviews - RNA
  96. Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity
    J. G. Coen van Hasselt, Rayees Rahman, Jens Hansen, Alan D. Stern, Jaehee V. Shim, Yuguang Xiong, Amanda J. Pickard, Gomathi Jayaraman, Bin Hu, Milind C. Mahajan et al. · 2020 · Nature Communications
  97. 24‐nt phasiRNAs move from tapetal to meiotic cells in maize anthers
    Xue Zhou, Kun Huang, Chong Teng, Ahmed Abdelgawad, Mona Batish, Blake C. Meyers, Virginia Walbot · 2022 · New Phytologist
  98. Advances in methods for tRNA sequencing and quantification
    Nigam H. Padhiar, Upendra Katneni, Anton A. Komar, Yuri Motorin, Chava Kimchi‐Sarfaty · 2023 · Trends in Genetics
  99. Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes
    Tatsuhiko Hoshino, Fumio Inagaki · 2017 · PLoS ONE
  100. Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP
    Manakov, Sergei A, Shishkin, Alexander A, Yee, Brian A, Shen, Kylie A, Cox, Diana C, Park, Samuel S, Foster, Heather M, Chapman, Karen B, Yeo, Gene W, Van Nostrand, Eric L · 2022