Stem cell transcriptome profiling via massive-scale mRNA sequencing

Cloonan, Nicole, Forrest, Alistair R R, Kolle, Gabriel, Gardiner, Brooke B A, Faulkner, Geoffrey J, Brown, Mellissa K, Taylor, Darrin F, Steptoe, Anita L +11 more·2008·Nature Methods

Cited by (922)

Items 801–900 of 922

  1. Pathogen-Omics: Challenges and Prospects in Research and Clinical Settings
    Dyuti Purkait, Saif Hameed, Zeeshan Fatima · 2021 · Springer eBooks
  2. Next-generation omics technologies to explore microbial diversity
    Ayushi Sharma, Jitendraa Vashistt, Rahul Shrivastava · 2021 · Elsevier eBooks
  3. Coffee Bean Transcriptome
    Bing Cheng, Robert James Henry · 2019 · Elsevier eBooks
  4. Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences
    P. Bushel, Weida Tong · 2019 · Frontiers Research Topics
  5. Genomics Studies in Hepatocellular Carcinoma via Next-Generation Sequencing
    Xi-Yang Wei, Niya Liu, Xin-Wei Wang, Jun-Fang Ji · 2018 · Molecular pathology library
  6. Transcription Factor Regulatory Networks
    E. Miyamoto-Sato, Hiroyuki Ohashi, H. Sasaki, J. Nishikawa, H. Yanagawa · 2014 · Methods in Molecular Biology
  7. Application of Machine-Learning Methods to Understand Gene Expression Regulation
    Chao Cheng, W. Worzel · 2014 · Genetic Programming Theory and Practice
  8. Detection of Alternatively Spliced or Processed RNAs in Cancer Using Oligonucleotide Microarray.
    M. Gencheva, Lixin Yang, Gong-Biao Lin, Ren-Jang Lin · 2013 · Cancer treatment and research
  9. Novel Next-Generation DNA Sequencing Techniques for Ultra High-Throughput Applications in Bio-Medicine
    W. Ansorge · 2010
  10. Sequence Based Gene Expression Analysis
    Lakshmi K. Matukumalli, Steven Schroeder · 2009 · Springer eBooks
  11. A Novel Approach for Mapping Ambiguous Sequences of Transcriptomes
    Tamer Aldwairi, Bindu Nanduri, Mahalingam Ramkumar, Andy Perkins · 2022 · EPiC series in computing
  12. Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA
    Oswaldo A. Lozoya, Kathryn S. McClelland, Brian N. Papas, Jian‐Liang Li, Humphrey Hung‐Chang Yao · 2020 · Frontiers in Genetics
  13. Angiosperm Sexual Systems: The Role of Transcriptomics in Understanding Sex expression
    Kamana Shandalya, Mukhtar Ahmed, Puranamrita, S. Verma · 2025 · Plant Molecular Biology Reporter
  14. Transcriptomic Insights into the Degradation Mechanisms of Fomitopsis pinicola and Its Host Preference for Coniferous over Broadleaf Deadwood
    Jianbin Xue, Yu-Lian Wei, Li-Ting Chen, Hai-Sheng Yuan · 2025 · Microorganisms
  15. Comprehensive Characterization of tRNA by Ultra High-Performance Liquid Chromatography High-Resolution Accurate Mass Spectrometry
    Robert L. Ross, Ryan E. Cowley, Keeley Murphy, Roberto C. Gamez, Paul Gazis, Jennifer N. Sutton, Min Du · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  16. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.)
    Alan Flores-Díaz, Christian Escoto-Sandoval, Felipe Cervantes‐Hernández, José Juan Ordaz-Ortíz, Corina Hayano‐Kanashiro, M. Humberto Reyes‐Valdés, Ana Garcés Claver, Neftalí Ochoa‐Alejo, Octavio Martínez · 2023 · Plants
  17. Characterization of the pars tuberalis and hypothalamus transcriptome in female sheep under different reproductive stages
    K. Lakhssassi, Irene Ureña, Belén Marín, M. P. Sarto, B. Lahoz, J. Alabart, J. Calvo, M. Serrano · 2022 · Animal Biotechnology
  18. PNGSeqR: An R Package for Rapid Candidate Gene Selection through Pooled Next-Generation Sequencing
    Si-Han Zhen, Hong-Wei Zhang, Yuxin Xie, Song Zhang, Yan Chen, Riliang Gu, Sanzhen Liu, Xuemei Du, Jun-Jie Fu · 2022 · Plants
  19. Bioinformatics Study of mtDNA Genes in Two Subspecies of Holstein (Bos taurus) and Cholistani (Bos indicus) Cattle Using RNA-Seq Data
    Ahmad Tamroosi, Gholam Reza Dashab, Mohammad Hossein Banabazi, Ali Maghsoudi · 2021 · Research on Animal Production
  20. Assessing Host-Pathogen Interaction Networks via RNA-Seq Profiling: A Systems Biology Approach
    Sudhesh Dev Sareshma, Subha Bhassu · 2021 · IntechOpen eBooks
  21. Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases
    Haocheng Lu, Jifeng Zhang, Y. Eugene Chen, Minerva T. Garcia-Barrio · 2021 · Cardiovascular Drugs and Therapy
  22. Fundamentos y aplicaciones biomédicas de las principales tecnologías de secuenciación: una revisión de literatura
    Anny Camargo, Karen Nattaly Valero González, Alida Marcela Gómez Rodríguez, Diego Fernando Camargo Mancipe, Carlos Fernando Suárez, Laura Cuy-Chaparro · 2020 · Revista Investigación en Salud Universidad de Boyacá
  23. RNA Sequencing: A Potent Transcription Profiling Tool
    Kaiho Kaisa, Harshit Kumar, Manjit Panigrahi, Triveni Dutt, Bharat Bhushan · 2020 · International Journal of Current Microbiology and Applied Sciences
  24. Targeting endogenous retrovirus gene transcription in human cancers
    Audrey T. Lin, Cindy G. Santander, Emanuele Marchi, Timokratis Karamitros, Aris Katzourakis, Gkikas Magiorkinis · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  25. Impacts of environment on gene expression and epigenetic modification in grazing animals
    Jennifer M. Thomson · 2016 · Journal of Animal Science
  26. Efficient algorithms for de novo assembly of alternative splicing events from RNA-seq data
    Gustavo Sacomoto · 2014 · arXiv.org
  27. Non-Parametric Bayesian Modelling of Digital Gene Expression Data
    Dimitris V. Vavoulis · 2014 · Journal of Computer Science & Systems Biology
  28. SyStem cell biology
    Eran Meshorer · 2013 · Systems Biomedicine
  29. Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices
    Emilie Tisserant · 2011
  30. Generate gene expression profile from high-throughput sequencing data
    Hui Liu, Zhi-Chao Jiang, Xiang-Zhong Fang, Han-Jiang Fu, Xiao-Fei Zheng, L. Cha, Wu-Ju Li · 2011
  31. Values of Single-Cell RNA Sequencing in Development of Cerebral Cortex
    Enqiang Chang, Xiaoguo Ruan, Ruilou Zhu, Yangyang Wang, Jiaqiang Zhang · 2020 · Advances in experimental medicine and biology
  32. Techniques for Genome-Wide Expression Analysis of Noncoding RNA
    Rena Onoguchi‐Mizutani, Toshimichi Yamada, Nobuyoshi Akimitsu · 2017 · Elsevier eBooks
  33. Fluorescence-Activated Cell Sorting and Gene Expression Profiling of GFP-Positive Cells from Transgenic Zebrafish Lines.
    H. Tanabe, M. Seki, M. Itoh, A. Deepak, Pradeep Lal, Terumi Horiuchi, Yutaka Suzuki, K. Kawakami · 2016 · Methods in molecular biology
  34. Characterisation of encapsulated embryonic stem cells using silac-based proteomics
    Sarah F. Alsobaie · 2016
  35. PAR-CLIP: A Genomic Technique to Dissect RNA-Protein Interactions
    Tara Dutka, Aishe A. Sarshad, Markus Hafner · 2016 · Springer eBooks
  36. Advanced Datamining Using RNAseq Data
    Yan Ping Guo, Shilin Zhao, Margot C. Bjoring, Leng Han · 2015 · Advances in bioinformatics and biomedical engineering book series
  37. A next generation of studies: Heterosis and inbreeding depression
    Shreyartha Mukherjee · 2014
  38. Hybrid Plant Systems for Breeding and Gene Confinement in Bioenergy Crops
    Albert Paul Kausch, Adam Deresienski, Joel P. Hague, Michael Tilelli, Stephen L. Dellaporta, Kimberly Nelson, Yi Li · 2013 · Elsevier eBooks
  39. Practical Approaches to Biological Network Discovery
    Brian C. Haynes · 2012 · Open Scholarship Institutional Repository (Washington University in St. Louis)
  40. Gene Expression Profiling Using 3′ Tag Digital Approach
    Y. Asmann, E. Thompson, Jean-Pierre A. Kocher · 2012 · Neuromethods
  41. Sequencing-based Expression Profiling in Zebrafish
    Liang Jin, Gabriel Renaud, Shawn Michael Burgess · 2011 · Methods in cell biology
  42. Investigation and development of statistical method for gene expression data analysis
    Nicholas Bradley Larson · 2011
  43. Signal Sequencing for Gene Expression Profiling
    Biaoyang Lin, Jeremy Wechsler, Leroy Hood · 2010 · Springer eBooks
  44. Genome-based technologies useful for aquaculture research and genetic improvement of aquaculture species.
    Zhan-Jiang Liu · 2009
  45. SpliceCOV: Supervised Filtering of RNA-Seq-Derived Transcript Features Improves Transcriptome Assembly
    Celine Hoh, Ida Shinder, Kuan-Hao Chao, Ales Varabyou, Mihaela Pertea · 2026 · Genes
  46. Exploring Heteroplasmic Variants in mtDNA: Insights from Single-Cell Transcriptomics
    M. Barresi, I. Di Meo, A. Nasca, E. Lamantea, A. Legati, Daniele Ghezzi · 2026 · medRxiv
  47. Comparative transcriptomic profiling of long non-coding RNAs reveals regulatory networks underlying growth divergence in White Leghorn and Black Australorp chickens
    J. Saalom King, T.X. Seena, Marykutty Thomas, P. M. Rojan, Jinty Sukumaran, K.A. Bindu · 2026 · Gene Reports
  48. Transposase Acting on an RNA/DNA Hybrid in Strand-Specific Sequencing.
    Shihui Zhao, Yan-Yi Huang, Chun-Hong Zheng · 2025 · Analytical Chemistry
  49. Current insight into HIV-1 persistence from single-cell transcriptome profiling in acutely treated cohorts of infection
    Lakshmi S. Iyer, Rasmi Thomas · 2025 · Current Opinion in HIV and AIDS
  50. Density estimation for ordinal biological sequences and its applications
    Wei-Chia Chen, Juan-Nan Zhou, David M. McCandlish · 2024 · Physical Review E
  51. Deciphering Transcriptomic Variations in Hematopoietic Lineages: HSCs, EBs, and MKs
    Swati Dahariya, Anton James Enright, Santosh Kumar, Ravi Kumar Gutti · 2024 · International Journal of Molecular Sciences
  52. Multi-omics Integrative Analysis for Incomplete Data Using Weighted p-Value Adjustment Approaches
    Wenda Zhang, Zichen Ma, Yen‐Yi Ho, Shuyi Yang, Joshua Habiger, Hsin‐Hsiung Huang, Yufei Huang · 2024 · Journal of Agricultural Biological and Environmental Statistics
  53. Techniques of Transcriptomic and Proteomic Data Integration
    Janardan Patil, Li Len, Abhinav Bharat, Xi Li · 2020 · Preprints.org
  54. Tagging Transcription Starting Sites with CAGE
    Piero Carninci · 2009 · Pan Stanford Publishing eBooks
  55. Novel Data Transformations for RNA-seq Data Analysis
    Zeyu Zhang, Danyang Yu, Minseok Seo, C. Hersh, S. Weiss, W. Qiu · 2018 · bioRxiv
  56. Transcriptomics in Cardiovascular Medicine
    Daniela Börnigen, Tanja Zeller · 2017 · Elsevier eBooks
  57. Practical Data Processing Approach for RNA Sequencing of Microorganisms
    Toshitaka Kumagai, Masayuki Machida · 2017 · InTech eBooks
  58. RNA SEQUENCING AND EUKARYOTIC ORGANISMS, WITH SPECIAL REFERENCE TO HAEMONCHUS CONTORTUS: A MINIREVIEW.
    Xun Suo, Saeed A. El-Ashram, IbrahimAl Nasr, Fathi Abouhajer, Rashid Mehmood, Min Hu · 2017 · International Journal of Advanced Research
  59. Exploring the Roles of Genetics and the Epigenetic Mechanism DNA Methylation in Honey Bee ( Apis Mellifera ) Behavior
    Christina M. Burden, Jonathan E. Bobek · 2017
  60. COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY
    Shikha Vashisht · 2017
  61. WITHDRAWN: Identifying differentially expressed genes in the intestine of healthy and diarrheal Rex Rabbits by RNA-Seq
    Jiping Zhao, Bing Song, Shuhui Wang, Zhanjun Ren, Huiling Chen, Ye Xiangyang, Qian Li, Ruiguang Gong, F.X. Meng · 2016 · Gene Reports · Retracted
  62. Etude de la formation du duramen chez le douglas : approches biochimique et transcriptomique
    Idelette Plazanet · 2016
  63. Undiscovered Physiology of Transcript and Protein Networks
    Emma Monte, Manuel Rosa‐Garrido, Thomas M. Vondriska, Jessica Wang · 2016 · Comprehensive physiology
  64. Functional genomics and proteomics in developmental and reproductive toxicology
    Robert M. Cabrera, B. Wlodarczyk, R. Finnell · 2016
  65. Stem cell characterisation: a guide to stem cell types, technologies, and future applications
    Justin Lo Re, Rezma Shrestha, Leonard J. Sciorra · 2015
  66. Gene Regulatory Networks: Real Data Sources and Their Analysis
    Yuji Zhang · 2016
  67. Identifying biological associations from high-throughput datasets
    A. Barghash · 2015
  68. Fatores de transcrição no desenvolvimento inicial do tubo neural posterior.
    Felipe Monteleone Vieceli · 2015
  69. Workflow for Building a Draft Genome Assembly using Public-domain Tools: Toxocara canis as a Case Study
    Jung-Im Won, Jinhwa Kong, S. Huh, Jeehee Yoon · 2014
  70. Statistical and bio-computational applications in animal sciences
    Atmakuri Ramakrishna Rao, Manoswini Dash, Tanmaya Kumar Sahu, Sant Dass Wahi, B K BEHERA, Arti Sharma, V. K. Bhatia · 2014 · The Indian Journal of Animal Sciences
  71. A Powerful Approach for Identification of Differentially Transcribed mRNA Isoforms
    Yuan-De Tan, Joel R. Neilson · 2014 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Modeling and inference of genetic interactions
    Ranadip Pal · 2013 · Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery
  73. Identification of Large Noncoding RNAs that Contribute to Prostate Cancer Progression
    Fang-Ting Wu · 2013
  74. Small RNA studies in Drosophila melanogaster, Stylophora pistillata and Symbiodinium sp.
    Y. Liew · 2013
  75. THE NUANCES OF STATISTICALLY ANALYZING NEXT-GENERATION SEQUENCING DATA
    Sanvesh Srivastava, R. W. Doerge · 2012 · Conference on Applied Statistics in Agriculture
  76. Stranded RNA‐Seq: Strand‐Specific Shotgun Sequencing of RNA
    A. Forrest · 2012
  77. Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data
    J. Bedő, A. Kowalczyk · 2011 · Bioinform.
  78. Advancing transcriptome platforms
    Shuobo Shi · 2011 · Nature Precedings
  79. Next Generation DNA Sequencing Technologies and Applications
    Qingshu Meng, Jun Myoung Yu · 2010 · Wiley eBooks
  80. Proteomic Analysis of Human Pluripotent Cells
    Andy T. Y. Lau, Yan-Ming Xu, J. Chiu · 2010
  81. Genomic Analysis of Pluripotent Stem Cells
    David S. Lapointe · 2010
  82. Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009
    Eric Christian Rouchka, Julia Krushkal · 2009 · BMC Bioinformatics
  83. STATISTICAL ISSUES IN NEXT-GENERATION SEQUENCING
    P. Auer, R. Doerge · 2009
  84. SEQUENCING THE TRANSCRIPTOME IN TOTO
    Sean Michael Grimmond · 2008
  85. A Guide to One of the Genome's Best-Kept Secrets
    Mafalda Martins de Araújo, Juan Valcárcel · 2008 · Molecular Cell
  86. Experimental methods to study protein–nucleic acid interactions
    Roberto Giambruno, Jakob Rupert, Elsa Zacco · 2022 · Elsevier eBooks
  87. Computational intelligence for genomic data
    Parameswar Sahu, Fahmida Khan, Subrat Kumar Pattanayak · 2021 · Elsevier eBooks
  88. Genome and Transcriptome of Amaranth Species
    Sabina Adhikari, Upama Khatri‐Chhetri, Dinesh Adhikary · 2021 · Compendium of plant genomes
  89. Differential Expression Analysis of RNA-Seq Data and Co-expression Networks
    Sana Javed · 2021 · Computational biology
  90. Development of Proximity Ligation Assay variants for single cell proteomics
    Jordi, Christian Alain · 2020 · Repository for Publications and Research Data (ETH Zurich)
  91. Hidden Treasures in Contemporary RNA Sequencing
    S. Mangul, H. Yang, E. Eskin, N. Zaitlen · 2019 · SpringerBriefs in Computer Science
  92. Novel Applications of Machine Learning in Bioinformatics
    Yi Zhang · 2019 · UKnowledge (University of Kentucky)
  93. Omics: Potential Role in Early Phase Drug Development
    Harald Grallert, Carola Marzi, Stefanie M. Hauck, Christian Gieger · 2019 · Springer eBooks
  94. An Integrated Approach to Plant Biology via Multi-Analogous Methods
    Sumira Jan, Parvaiz Ahmad · 2019 · Elsevier eBooks
  95. Differential Expression From Microarray and RNA-seq Experiments
    Marc Delord · 2018 · Elsevier eBooks
  96. OBSOLETE: Transciptomics in Cardiovascular Medicine
    Tanja Zeller · 2017 · Elsevier eBooks
  97. Global Approaches in the Analysis of Cocaine-Induced Gene Expression
    Jodi E. Eipper-Mains, Betty A. Eipper, Richard E. Mains · 2017 · Elsevier eBooks
  98. Gene activity patterns associated with pathological cardiac hypertrophy are mediated by specific chromatin modifying factors
    Chang, Lisa Hsiu Chuan · 2017 · Figshare
  99. Data characterization
    Ranadip Pal · 2016 · Elsevier eBooks
  100. Computational and Statistical Analysis of Sequence and Expression Features of MicroRNA and Long Noncoding RNA in Primate Brains
    Hai-Yang Hu · 2016