Analysis of human transcriptomes

Direct multiplexed measurement of gene expression with color-coded probe pairs

Geiss, G. K., Bumgarner, R. E., Birditt, B., Dahl, T., Dowidar, N., Dunaway, D. L., Fell, H. P., Ferree, S., George, R. D., Grogan, T., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1385 · Cited by 2,066

A promoter-level mammalian expression atlas

The FANTOM Consortium and the RIKEN PMI and CLST (DGT) (2014) · Nature · doi:10.1038/nature13182 · Cited by 1,982

A draft network of ligand–receptor-mediated multicellular signalling in human

Ramilowski, J. A., Goldberg, T., Harshbarger, J., Kloppmann, E., Lizio, M., Satagopam, V. P., Itoh, M., Kawaji, H., Carninci, P., Rost, B., et al. (2015) · Nature Communications · doi:10.1038/ncomms8866 · Cited by 887

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Ramsköld, D., Wang, E. T., Burge, C. B., & Sandberg, R. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000598 · Cited by 820

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.

't Hoen, P. A. C., Ariyurek, Y., Thygesen, H. H., Vreugdenhil, E., Vossen, R. H. A. M., de Menezes, R. X., Boer, J. M., van Ommen, G.-J. B., & den Dunnen, J. T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn705 · Cited by 742

Single-RNA counting reveals alternative modes of gene expression in yeast

Zenklusen, D., Larson, D. R., & Singer, R. H. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1514 · Cited by 684

Using the transcriptome to annotate the genome

Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E. (2002) · Nature Biotechnology · doi:10.1038/nbt0502-508 · Cited by 630

Profiling the HeLa S3 Transcriptome using Randomly Primed cDNA and Massively Parallel Short-Read Sequencing

Morin, R. D., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T. J., McDonald, H., Varhol, R., Jones, S. J. M., & Marra, M. A. (2008) · BioTechniques · doi:10.2144/000112900 · Cited by 342

The rat blood-brain barrier transcriptome

Enerson, B. E., & Drewes, L. R. (2006) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1038/sj.jcbfm.9600249 · Cited by 205

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

Heimberg, G., Bhatnagar, R., El-Samad, H., & Thomson, M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.001 · Cited by 156

Apolipoprotein E is required for cell proliferation and survival in ovarian cancer

Chen, Y.-C., Pohl, G., Wang, T.-L., Morin, P. J., Risberg, B., Kristensen, G. B., Yu, A., Davidson, B., & Shih, I.-M. (2005) · Cancer Research · doi:10.1158/0008-5472.331.65.1 · Cited by 155

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

Zhao, T., & Schranz, M. E. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801757116 · Cited by 120

Evaluating stably expressed genes in single cells

Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D. M., Speed, T., Yang, J. Y. H., & Yang, P. (2019) · GigaScience · doi:10.1093/gigascience/giz106 · Cited by 84

Differentiation Therapy Targeting the β-Catenin/CBP Interaction in Pancreatic Cancer

Manegold, P., Lai, K., Wu, Y., Teo, J.-L., Lenz, H.-J., Genyk, Y., Pandol, S., Wu, K., Lin, D., Chen, Y., et al. (2018) · Cancers · doi:10.3390/cancers10040095 · Cited by 51

The +4G Site in Kozak Consensus Is Not Related to the Efficiency of Translation Initiation

Xia, X. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000188 · Cited by 45

Digital expression profiles of the prostate androgen-response program

Clegg, N., Eroglu, B., Ferguson, C., Arnold, H., Moorman, A., & Nelson, P. S. (2002) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/s0960-0760(01)00167-4 · Cited by 37

Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability

Pérez-Ortín, J. E., Tordera, V., & Chávez, S. (2019) · RNA Biology · doi:10.1080/15476286.2019.1655352 · Cited by 35

RNA Transfer by Electroporation into Mature Dendritic Cells Leading to Reactivation of Effector-Memory Cytotoxic T Lymphocytes: A Quantitative Analysis

Javorovic, M., Pohla, H., Frankenberger, B., Wölfel, T., & Schendel, D. J. (2005) · Molecular Therapy · doi:10.1016/j.ymthe.2005.03.034 · Cited by 33

Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine

Chu, L.-X., Wang, W.-J., Gu, X.-P., Wu, P., Gao, C., Zhang, Q., Wu, J., Jiang, D.-W., Huang, J.-Q., Ying, X.-W., et al. (2024) · Military Medical Research · doi:10.1186/s40779-024-00537-4 · Cited by 29

Noise robustness and metabolic load determine the principles of central dogma regulation

Lo, T. W., Choi, H. J., Huang, D., & Wiggins, P. A. (2024) · Science Advances · doi:10.1126/sciadv.ado3095 · Cited by 13

RNA Reference Materials for Gene Expression Studies

Gingeras, T. R. (2004) · Clinical Chemistry · doi:10.1373/clinchem.2003.030072 · Cited by 7

Homeostasis in the Central Dogma of Molecular Biology: the importance of mRNA instability

Pérez-Ortín, J. E., Tordera, V., & Chávez, S. (2019) · doi:10.1101/599050 · Cited by 1