RNA-Seq: a revolutionary tool for transcriptomics

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Items 101–200 of 1,061

1. From RNA-seq reads to differential expression results
   Alicia Oshlack, Mark D. Robinson, Matthew D. Young · 2010 · Genome biology
2. An accurate and robust imputation method scImpute for single-cell RNA-seq data
   Wei Vivian Li, Jingyi Jessica Li · 2018 · Nature Communications
3. Classification of low quality cells from single-cell RNA-seq data
   Ilicic, Tomislav, Kim, Jong Kyoung, Kolodziejczyk, Aleksandra A., Bagger, Frederik Otzen, McCarthy, Davis James, Marioni, John C., Teichmann, Sarah A. · 2016 · Genome Biology
4. Adaptation genomics: the next generation
   Jessica Stapley, Julia Reger, Philine G. D. Feulner, Carole M. Smadja, Juan Galindo, Robert Ekblom, Clair Bennison, Alexander D. Ball, Andrew P. Beckerman, Jon Slate · 2010 · Trends in Ecology & Evolution
5. Basal-like and triple-negative breast cancers: a critical review with an emphasis on the implications for pathologists and oncologists
   Sunil Badve, David J. Dabbs, Stuart J. Schnitt, Frederick L. Baehner, Thomas W. Decker, Vincenzo Eusebi, Stephen B. Fox, Shu Ichihara, Jocelyne D. Jacquemier, Sunil R. Lakhani et al. · 2010 · Modern Pathology
6. Corset: enabling differential gene expression analysis for
   N. Davidson, Alicia Oshlack · 2014 · Genome biology
7. Single cell analysis: the new frontier in 'Omics'
   Daojing Wang, Steven Bodovitz · 2010 · Trends in biotechnology
8. Library construction for next-generation sequencing: Overviews and challenges
   Steven Robert Head, H. Kiyomi Komori, Sarah A. LaMere, Thomas C. Whisenant, Filip Van Nieuwerburgh, Daniel R. Salomon, Phillip T. Ordoukhanian · 2014 · BioTechniques
9. Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
   Nicholas T. Ingolia, Gloria Ann Brar, Noam Stern‐Ginossar, Michael S. Harris, Gaëlle J.S. Talross, Sarah Elizabeth Jackson, Mark R. Wills, Jonathan S. Weissman · 2014 · Cell Reports
10. A quantitative atlas of polyadenylation in five mammals
    Adnan Derti, Philip W. Garrett-Engele, Kenzie D. MacIsaac, Richard C. Stevens, Shreedharan Sriram, Ronghua Chen, Carol A. Rohl, Jason Michael Johnson, Tomas Babak · 2012 · Genome Research
11. Applications of next-generation sequencing to phylogeography and phylogenetics
    John E. McCormack, Sarah M. Hird, Amanda J. Zellmer, Bryan C. Carstens, Robb Thomas Brumfield · 2011 · Molecular Phylogenetics and Evolution
12. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
    Zhicheng Ji, Hongkai Ji · 2016 · Nucleic Acids Research
13. Ribosome profiling: new views of translation, from single codons to genome scale
    Nicholas T. Ingolia · 2014 · Nature Reviews Genetics
14. Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals
    Analía Álvarez, Juliana Maria Saez, José Sebastián Dávila Costa, Verónica Leticia Colin, María S. Fuentes, Sergio A. Cuozzo, Claudia S. Benimeli, Marta Alejandra Polti, María Julia Amoroso · 2016 · Chemosphere
15. RNA-Seq differential expression analysis: An extended review and a software tool
    Juliana Costa Silva, Douglas Silva Domingues, Fabrício Martins Lopes · 2017 · PLoS ONE
16. Visualization of omics data for systems biology
    Nils Gehlenborg, Sean I O’Donoghue, Nitin S. Baliga, Alexander Goesmann, Matthew Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum et al. · 2010 · Nature Methods
17. Revisiting Global Gene Expression Analysis
    Lovén, Jakob, Orlando, David A., Sigova, Alla A., Lin, Charles Y., Rahl, Peter B., Burge, Christopher B., Levens, David L., Lee, Tong Ihn, Young, Richard A. · 2012 · Cell
18. Ligand-Targeted Drug Delivery
    Madduri Srinivasarao, Philip Stewart Low · 2017 · Chemical Reviews
19. Genomic views of distant-acting enhancers
    Visel, Axel, Rubin, Edward M., Pennacchio, Len A. · 2009 · Nature
20. Beneficial effects of silicon on salt and drought tolerance in plants
    Yongxing Zhu, Haijun Gong · 2013 · Agronomy for Sustainable Development
21. Increased inflammatory markers identified in the dorsolateral prefrontal cortex of individuals with schizophrenia
    Fillman, S G, Cloonan, N, Catts, V S, Miller, L C, Wong, J, McCrossin, T, Cairns, M, Weickert, C S · 2013 · Molecular Psychiatry
22. Removing technical variability in RNA-seq data using conditional quantile normalization
    Hansen, K. D., Irizarry, R. A., WU, Z. · 2012 · Biostatistics
23. Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
    Magali Soumillon, Anamaria Necşulea, Manuela Weier, David Brawand, Xiaolan Zhang, Hongcang Gu, Pauline Barthès, Maria Kokkinaki, Serge Nef, Andreas Gnirke et al. · 2013 · Cell Reports
24. From bulk, single-cell to spatial RNA sequencing
    Li, Xinmin, Wang, Cun-Yu · 2021 · International Journal of Oral Science
25. Coordination of microbial metabolism
    Victor Chubukov, Luca Gerosa, Karl Kochanowski, Uwe Sauer · 2014 · Nature Reviews Microbiology
26. Analysis of RNA-Seq Data Using TopHat and Cufflinks
    Sreya Ghosh, Chon‐Kit Kenneth Chan · 2015 · Methods in molecular biology
27. Sequence-specific error profile of Illumina sequencers
    Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Morita Hirai, Hiroki Takahashi et al. · 2011 · Nucleic Acids Research
28. Computational analysis of bacterial RNA-Seq data
    Ryan McClure, Divya Balasubramanian, Yan Sun, Maksym Bobrovskyy, Paul Sumby, Caroline Attardo Genco, Carin K. Vanderpool, Brian C. Tjaden · 2013 · Nucleic Acids Research
29. Next-generation genomics: an integrative approach
    R. David Hawkins, Gary C. Hon, Bing Ren · 2010 · Nature Reviews Genetics
30. Measuring biological age using omics data
    Rutledge, Jarod, Oh, Hamilton, Wyss-Coray, Tony · 2022 · Nature Reviews Genetics
31. Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes
    Jesse W. Rowley, Andrew J. Oler, Neal D. Tolley, Benjamin N. Hunter, Elizabeth N. Low, David Austin Nix, Christian C. Yost, Guy A. Zimmerman, Andrew S. Weyrich · 2011 · Blood
32. Polycomb group proteins: navigators of lineage pathways led astray in cancer
    Bracken, Adrian P., Helin, Kristian · 2009 · Nature Reviews Cancer
33. Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
    Guangming He, Xiaopeng Zhu, Axel A. Elling, Liangbi Chen, Xiangfeng Wang, Lan Ping Guo, Manzhong Liang, Hang He, Huiyong Zhang, Fangfang Chen et al. · 2010 · The Plant Cell
34. Inhibition of microRNA function by antimiR oligonucleotides
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35. Mechanisms regulating zygotic genome activation
    Katharine N. Schulz, Melissa M. Harrison · 2018 · Nature Reviews Genetics
36. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
    Zhi‐Ping Liu, Canglin Wu, Hongyu Miao, Hulin Wu · 2015 · Database
37. Emerging evidence for functional peptides encoded by short open reading frames
    Shea J. Andrews, Joseph A. Rothnagel · 2014 · Nature Reviews Genetics
38. Efficient and quantitative high-throughput tRNA sequencing
    Zheng, Guanqun, Qin, Yidan, Clark, Wesley C, Dai, Qing, Yi, Chengqi, He, Chuan, Lambowitz, Alan M, Pan, Tao · 2015 · Nature Methods
39. Microarrays, deep sequencing and the true measure of the transcriptome
    John H. Malone, Brian Oliver · 2011 · BMC Biology
40. Applications of multi‐omics analysis in human diseases
    Chen, Chongyang, Wang, Jing, Pan, Donghui, Wang, Xinyu, Xu, Yuping, Yan, Junjie, Wang, Lizhen, Yang, Xifei, Yang, Min, Liu, Gong‐Ping · 2023 · MedComm
41. Advances and Trends in Omics Technology Development
    Xiaofeng Dai, Li Shen · 2022 · Frontiers in Medicine
42. Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment–Specific Transcriptomes
    Jae Wook Lee, Chung‐Lin Chou, Mark A. Knepper · 2015 · Journal of the American Society of Nephrology
43. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer
    Zhou Du, Teng Fei, Roel G.W. Verhaak, Zhen Su, Yong Zhang, Myles A Brown, Yiwen Chen, X. Shirley Liu · 2013 · Nature Structural & Molecular Biology
44. New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
    Mohamed Mounir, Marta Lucchetta, Tiago C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo · 2019 · PLoS Computational Biology
45. RNA-seq: from technology to biology
    Samuel Marguerat, Jürg Bähler · 2009 · Cellular and Molecular Life Sciences
46. Piercing the dark matter: bioinformatics of long-range sequencing and mapping
    Sedlazeck, Fritz J., Lee, Hayan, Darby, Charlotte A., Schatz, Michael C. · 2018 · Nature Reviews Genetics
47. Sequencing-based methods and resources to study antimicrobial resistance
    Manish Boolchandani, Alaric W. D’Souza, Gautam A. Dantas · 2019 · Nature Reviews Genetics
48. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma
    Leilei Chen, Yan Li, Chi Ho Lin, Tim Hon Man Chan, Raymond Kwok Kei Chow, Yangyang Song, Ming Liu, Yun Fei Yuan, Li Fu, Kar Lok Kong et al. · 2013 · Nature Medicine
49. The BIG Data Center: from deposition to integration to translation
    BIG Data Center Members · 2016 · Nucleic Acids Research
50. Identification of protein coding regions in RNA transcripts
    Shiyuyun Tang, Alexandre Lomsadze, Mark Yu. Borodovsky · 2015 · Nucleic Acids Research
51. High-Throughput Genomic Data in Systematics and Phylogenetics
    Emily Moriarty Lemmon, Alan R. Lemmon · 2013 · Annual Review of Ecology Evolution and Systematics
52. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
    Zhiyu Peng, Yanbing Cheng, Bertrand Chin‐Ming Tan, Lin Kang, Zhijian Tian, Yuankun Zhu, Wenwei Zhang, Yu Liang, Xueda Hu, Xuemei Tan et al. · 2012 · Nature Biotechnology
53. RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Fuchou Tang, Cátálin Bárbácioru, Ellen Nordman, Bin Li, Nanlan Xu, Vladimir I. Bashkirov, Kaiqin Lao, M. Azim Surani · 2010 · Nature Protocols
54. RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg
    Christine I. Wooddell, Man‐Fung Yuen, Henry Lik‐Yuen Chan, Robert Gareth Gish, STEPHEN A LOCARNINI, Deborah Chavez, Carlo I. Ferrari, Bruce D. Given, James Hamilton, Steven Brian Kanner et al. · 2017 · Science Translational Medicine
55. TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
    Yingdong Zhao, Ming‐Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, Paul Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane · 2021 · Journal of Translational Medicine
56. Comparative studies of gene expression and the evolution of gene regulation
    Romero, Irene Gallego, Ruvinsky, Ilya, Gilad, Yoav · 2012 · Nature Reviews Genetics
57. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
    Guojie Zhang, Guangwu Guo, Xueda Hu, Yong Zhang, Qiye Li, Ruiqiang Li, Ruhong Zhuang, Zhike Lu, Zengquan He, Xiaodong Fang et al. · 2010 · Genome Research
58. Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry
    Li Xu, Longfu Zhu, Lili Tu, Linlin Liu, Daojun Yuan, Li Jin, Lu Long, Xianlong Zhang · 2011 · Journal of Experimental Botany
59. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau
    Jun Wen, Jianqiang Zhang, Ze‐Long Nie, Yang Zhong, Hang Sun · 2014 · Frontiers in Genetics
60. An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
    Cristian Del Fabbro, Simone Scalabrin, Michele Morgante, Federico Manuel Giorgi · 2013 · PLoS ONE
61. Saliva diagnostics – Current views and directions
    Karolina Elżbieta Kaczor‐Urbanowicz, Carmen Martín Carreras‐Presas, Katri L. S. Aro, Michael Kai Tu, Franklin Garcı́a-Godoy, David T. Wong · 2016 · Experimental Biology and Medicine
62. High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation
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63. Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases
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64. TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications
    Chang, Hyeshik, Lim, Jaechul, Ha, Minju, Kim, V. Narry · 2014 · Molecular Cell
65. Use of Metatranscriptomics in Microbiome Research
    Stavros Bashiardes, Gili Zilberman-Schapira, Eran Elinav · 2016 · Bioinformatics and Biology Insights
66. Cancer across the tree of life: cooperation and cheating in multicellularity
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67. The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines
    Eizirik, Décio L., Sammeth, Michael, Bouckenooghe, Thomas, Bottu, Guy, Sisino, Giorgia, Igoillo-Esteve, Mariana, Ortis, Fernanda, Santin, Izortze, Colli, Maikel L., Barthson, Jenny et al. · 2012 · PLoS Genetics
68. Annotating non-coding regions of the genome.
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69. Climate refugia: joint inference from fossil records, species distribution models and phylogeography
    Daniel G. Gavin, Matthew C. Fitzpatrick, Paul F. Gugger, Katy D. Heath, Francisco Rodríguez‐Sánchez, Solomon Z. Dobrowski, Arndt Hampe, Feng Sheng Hu, Michael B. Ashcroft, Patrick J. Bartlein et al. · 2014 · New Phytologist
70. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
    Manuel Tardáguila, Lorena de la Fuente, Cristina Martí, Cécile Pereira, Francisco J. Pardo-Palacios, Héctor del Risco, Marc Ferrell, Maravillas Mellado-López, Marissa G. Macchietto, Kenneth Verheggen et al. · 2018 · Genome Research
71. De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification
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72. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity
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73. Noise in biology
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74. MicroRNAs in Cardiovascular Disease
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75. Homoeolog expression bias and expression level dominance in allopolyploid cotton
    M-J Yoo, Emmanuel Szadkowski, Jonathan F. Wendel · 2012 · Heredity
76. Uncovering the Complexity of Transcriptomes with RNA-Seq
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77. A 360° view of circular RNAs: From biogenesis to functions
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78. Principles for the post-GWAS functional characterization of cancer risk loci
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79. Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
    Jun Li, Robert John Tibshirani · 2011 · Statistical Methods in Medical Research
80. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
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81. Cell-cell communication: New insights and clinical implications
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82. Integrated Analysis of Transcriptomic and Proteomic Data
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83. FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
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84. Evolution of multisubunit RNA polymerases in the three domains of life
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85. Most “Dark Matter” Transcripts Are Associated With Known Genes
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86. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs
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87. expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform
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88. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
    Heladia Salgado, Martín Peralta-Gil, Socorro Gama‐Castro, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Verena Weiss, Hilda Solano-Lira, Irma Martínez‐Flores, Alejandra Medina-Rivera et al. · 2012 · Nucleic Acids Research
89. SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
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90. Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions
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91. RNA-sequencing from single nuclei
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92. It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR
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93. Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates
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94. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
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95. Arabidopsis REF6 is a histone H3 lysine 27 demethylase
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96. TubercuList – 10 years after
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97. Long non-coding RNA: Classification, biogenesis and functions in blood cells
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98. Adaptation in the age of ecological genomics: insights from parallelism and convergence
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99. Ribosome Footprint Profiling of Translation throughout the Genome
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100. Multi-Omics Profiling for Health
     Mohan Babu, Michael P. Snyder · 2023 · Molecular & Cellular Proteomics