Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316

Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., & Hood, L. (2001) · Science · doi:10.1126/science.292.5518.929 · Cited by 2,050

A N EW A PPROACH TO D ECODING L IFE : Systems Biology

Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.343 · Cited by 1,664

Transcriptional enhancers: from properties to genome-wide predictions

Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356

Discovering motifs in ranked lists of DNA sequences

Eden, E., Lipson, D., Yogev, S., & Yakhini, Z. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030039 · Cited by 696

'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns

Hastie, T., Tibshirani, R., Eisen, M. B., Alizadeh, A., Levy, R., Staudt, L., Chan, W. C., Botstein, D., & Brown, P. (2000) · Genome Biology · doi:10.1186/gb-2000-1-2-research0003 · Cited by 547

Absence of a simple code: how transcription factors read the genome

Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537

Molecular taxonomy of major neuronal classes in the adult mouse forebrain

Sugino, K., Hempel, C. M., Miller, M. N., Hattox, A. M., Shapiro, P., Wu, C., Huang, Z. J., & Nelson, S. B. (2006) · Nature Neuroscience · doi:10.1038/nn1618 · Cited by 521

What is Bioinformatics? A Proposed Definition and Overview of the Field

Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001) · Methods of Information in Medicine · doi:10.1055/s-0038-1634431 · Cited by 453

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

Sudarsanam, P., Iyer, V. R., Brown, P. O., & Winston, F. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.7.3364 · Cited by 389

Integrating regulatory motif discovery and genome-wide expression analysis

Conlon, E. M., Liu, X. S., Lieb, J. D., & Liu, J. S. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630591100 · Cited by 343

Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes

Jelinsky, S. A., Estep, P., Church, G. M., & Samson, L. D. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.21.8157-8167.2000 · Cited by 335

Expression-based monitoring of transcription factor activity: the TELiS database

Cole, S. W., Yan, W., Galic, Z., Arevalo, J., & Zack, J. A. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti038 · Cited by 185

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

Csárdi, G., Franks, A., Choi, D. S., Airoldi, E. M., & Drummond, D. A. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005206 · Cited by 181

Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes

Cenik, C., Chua, H. N., Zhang, H., Tarnawsky, S. P., Akef, A., Derti, A., Tasan, M., Moore, M. J., Palazzo, A. F., & Roth, F. P. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001366 · Cited by 87

PARE: a tool for comparing protein abundance and mRNA expression data

Yu, E. Z., Burba, A. E. C., & Gerstein, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-309 · Cited by 20

Translation efficiency covariation identifies conserved coordination patterns across cell types

Liu, Y., Rao, S., Hoskins, I., Geng, M., Zhao, Q., Chacko, J., Ghatpande, V., Qi, K., Persyn, L., Wang, J., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02718-5 · Cited by 15

Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast

Csárdi, G., Franks, A., Choi, D. S., Airoldi, E. M., & Drummond, D. A. (2014) · doi:10.1101/009472 · Cited by 8