Integrating regulatory motif discovery and genome-wide expression analysis

Cluster analysis and display of genome-wide expression patterns

Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works

Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815 · see citing works

Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

Spellman, P. T., Sherlock, G. J., Zhang, M. Q., Iyer, V. R., Anders, K. R., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.12.3273 · Cited by 4,724 · see citing works

Sequence logos: a new way to display consensus sequences

Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,396 · see citing works

Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i>

Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956 · see citing works

Systematic determination of genetic network architecture

Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., & Church, G. M. (1999) · Nature Genetics · doi:10.1038/10343 · Cited by 2,509 · see citing works

The economics of ribosome biosynthesis in yeast

Warner, J. R. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(99)01460-7 · Cited by 1,933 · see citing works

Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment

Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., & Wootton, J. C. (1993) · Science · doi:10.1126/science.8211139 · Cited by 1,810 · see citing works

Computational identification of Cis -regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae 1 1Edited by F. E. Cohen

Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,008 · see citing works

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

Roth, F. P., Hughes, J. D., Estep, P. W., & Church, G. M. (1998) · Nature Biotechnology · doi:10.1038/nbt1098-939 · Cited by 939 · see citing works

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 1Edited by G. von Heijne

van Helden, J., André, B., & Collado‐Vides, J. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1947 · Cited by 748 · see citing works

Regulatory element detection using correlation with expression

Bussemaker, H. J., Li, H., & Siggia, E. D. (2001) · Nature Genetics · doi:10.1038/84792 · Cited by 721 · see citing works

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

Lieb, J. D., Liu, X., Botstein, D., & Brown, P. O. (2001) · Nature Genetics · doi:10.1038/ng569 · Cited by 707 · see citing works

An algorithm for finding protein–DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments

Liu, X. S., Brutlag, D. L., & Liu, J. S. (2002) · Nature Biotechnology · doi:10.1038/nbt717 · Cited by 670 · see citing works

Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

Simon, I., Barnett, J., Hannett, N. M., Harbison, C. T., Rinaldi, N. J., Volkert, T. L., Wyrick, J. J., Zeitlinger, J., Gifford, D. K., Jaakkola, T., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00494-9 · Cited by 654 · see citing works

Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.10.2987 · Cited by 542 · see citing works

New Components of a System for Phosphate Accumulation and Polyphosphate Metabolism inSaccharomyces cerevisiaeRevealed by Genomic Expression Analysis

Ogawa, N., DeRisi, J. L., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4309 · Cited by 494 · see citing works

Widespread aneuploidy revealed by DNA microarray expression profiling

Hughes, T. R., Roberts, C. J., Dai, H. A., Jones, A. R., Meyer, M. R., Slade, D., Burchard, J., Dow, S., Ward, T. R., Kidd, M. J., et al. (2000) · Nature Genetics · doi:10.1038/77116 · Cited by 482 · see citing works

Identifying protein-binding sites from unaligned DNA fragments.

Stormo, G. D., & Hartzell, G. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.4.1183 · Cited by 481 · see citing works

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

Zhu, J., & Zhang, M. Q. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.7.607 · Cited by 436 · see citing works

Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions

Fernandes, L., Rodrigues-Pousada, C., & Struhl, K. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.12.6982 · Cited by 337 · see citing works

Genome-wide binding map of the histone deacetylase Rpd3 in yeast

Kurdistani, S. K., Robyr, D., Tavazoie, S., & Grunstein, M. (2002) · Nature Genetics · doi:10.1038/ng907 · Cited by 279 · see citing works

Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis

Bussemaker, H. J., Li, H., & Siggia, E. D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.180265397 · Cited by 257 · see citing works

A statistical method for finding transcription factor binding sites.

Sinha, S., & Tompa, M. (2000) · PubMed · Cited by 198 · see citing works

Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA

Blaiseau, P.-L., & Thomas, D. (1998) · The EMBO Journal · doi:10.1093/emboj/17.21.6327 · Cited by 122 · see citing works

Identification of regulatory elements using a feature selection method

Keleş, S., van der Laan, M. J., & Eisen, M. B. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.9.1167 · Cited by 122 · see citing works

Ste12 and Mcm1 Regulate Cell Cycle-Dependent Transcription of FAR1

Oehlen, L. J. W. M., McKinney, J. D., & Cross, F. R. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.6.2830 · Cited by 113 · see citing works

Mining for putative regulatory elements in the yeast genome using gene expression data.

Vilo, J., Brāzma, A., Jonassen, I., Robinson, A. J., & Ukkonen, E. (2000) · PubMed · Cited by 107 · see citing works

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool

Grundy, W. N., Bailey, T. L., & Elkan, C. (1996) · Computer applications in the biosciences · doi:10.1093/bioinformatics/12.4.303 · Cited by 83 · see citing works

Finding regulatory elements using joint likelihoods for sequence and expression profile data.

Holmes, I., & Bruno, W. (2000) · PubMed · Cited by 66 · see citing works

Distribution patterns of over-represented k-mers in non-coding yeast DNA

Hampson, S. E., Kibler, D. F., & Baldi, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.4.513 · Cited by 48 · see citing works

Analysis of a Meiosis-Specific URS1 Site: Sequence Requirements and Involvement of Replication Protein A

Gailus‐Durner, V., Chintamaneni, C. D., Wilson, R., Brill, S. J., & Vershon, A. K. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.7.3536 · Cited by 21 · see citing works

Stability Selection

Meinshausen, N., & Bühlmann, P. (2010) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.1467-9868.2010.00740.x · Cited by 2,314 · see citing works

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050008 · Cited by 1,563 · see citing works

Transposable elements have rewired the core regulatory network of human embryonic stem cells

Kunarso, G., Chia, N., Jeyakani, J., Hwang, C., Lu, X., Chan, Y.-S., Ng, H., & Bourque, G. (2010) · Nature Genetics · doi:10.1038/ng.600 · Cited by 777 · see citing works

ERRα and Gabpa/b specify PGC-1α-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle.

Mootha, V. K., Handschin, C., Arlow, D., Xie, X., St. Pierre, J., Sihag, S., Yang, W., Altshuler, D., Puigserver, P., Patterson, N., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401401101 · Cited by 688 · see citing works

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

Quenneville, S., Verde, G., Corsinotti, A., Kapopoulou, A., Jakobsson, J., Offner, S., Baglivo, I., Pedone, P. V., Grimaldi, G., Riccio, A., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.032 · Cited by 606 · see citing works

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., & Xavier, R. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp425 · Cited by 469 · see citing works

High-dimensional additive modeling

Meier, L., van de Geer, S., & Bühlmann, P. (2009) · The Annals of Statistics · doi:10.1214/09-aos692 · Cited by 464 · see citing works

p -Values for High-Dimensional Regression

Meinshausen, N., Meier, L., & Bühlmann, P. (2009) · Journal of the American Statistical Association · doi:10.1198/jasa.2009.tm08647 · Cited by 447 · see citing works

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Ouyang, Z., Zhou, Q., & Wong, W. H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904863106 · Cited by 329 · see citing works

Variable Selection in Nonparametric Varying-Coefficient Models for Analysis of Repeated Measurements

Wang, L., Li, H., & Huang, J. Z. (2008) · Journal of the American Statistical Association · doi:10.1198/016214508000000788 · Cited by 302 · see citing works

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

de Boer, C. G., Vaishnav, E. D., Sadeh, R., Abeyta, E. L., Friedman, N., & Regev, A. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0315-8 · Cited by 283 · see citing works

Group SCAD regression analysis for microarray time course gene expression data

Wang, L., Chen, G., & Li, H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm125 · Cited by 279 · see citing works

Passing Messages between Biological Networks to Refine Predicted Interactions

Glass, K., Huttenhower, C., Quackenbush, J., & Yuan, G.-C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064832 · Cited by 266 · see citing works

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Kazan, H., Ray, D., Chan, E. T., Hughes, T. R., & Morris, Q. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000832 · Cited by 256 · see citing works

Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant

Yildiz, F. H., Liu, X. S., Heydorn, A., & Schoolnik, G. K. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04154.x · Cited by 256 · see citing works

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Gao, F., Foat, B. C., & Bussemaker, H. J. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-31 · Cited by 247 · see citing works

CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling

Zhou, Q., & Wong, W. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402858101 · Cited by 216 · see citing works

Molecular networks in Network Medicine: Development and applications

Silverman, E. K., Schmidt, H. H. H. W., Anastasiadou, E., Altucci, L., Angelini, M., Badimón, L., Balligand, J., Benincasa, G., Capasso, G., Conte, F., et al. (2020) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1489 · Cited by 211 · see citing works

Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica

Zwir, I. J. S., Shin, D., Kato, A., Nishino, K., Latifi, T. N., Solomon, F., Hare, J. M., Huang, H. V., & Groisman, E. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408238102 · Cited by 210 · see citing works

T-profiler: scoring the activity of predefined groups of genes using gene expression data

Boorsma, A., Foat, B. C., Vis, D. J., Klis, F. M., & Bussemaker, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki484 · Cited by 206 · see citing works

Bayesian Variable Selection in Structured High-Dimensional Covariate Spaces With Applications in Genomics

Li, F., & Zhang, N. R. (2010) · Journal of the American Statistical Association · doi:10.1198/jasa.2010.tm08177 · Cited by 198 · see citing works

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion

Yuan, G., & Liu, J. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040013 · Cited by 193 · see citing works

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cellsPreprint

Rowe, H. M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T. S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S. L., & Trono, D. (2012) · Genome Research · doi:10.1101/gr.147678.112 · Cited by 186 · see citing works

Genome-wide gene expression in response to parasitoid attack in Drosophila

Wertheim, B., Kraaijeveld, A. R., Schuster, E. F., Blanc, E., Hopkins, M., Pletcher, S. D., Strand, M. R., Partridge, L., & Godfray, H. C. J. (2005) · Genome biology · doi:10.1186/gb-2005-6-11-r94 · Cited by 181 · see citing works

A survey of motif discovery methods in an integrated framework.

Sandve, G. K., & Drabløs, F. (2006) · Biology Direct · doi:10.1186/1745-6150-1-11 · Cited by 170 · see citing works

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Tunçbağ, N., Gosline, S. J. C., Kedaigle, A. J., Soltis, A. R., Gitter, A., & Fraenkel, E. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004879 · Cited by 173 · see citing works

Identifying combinatorial regulation of transcription factors and binding motifs

Kato, M., Hata, N., Banerjee, N., Futcher, B., & Zhang, M. Q. (2004) · Genome biology · doi:10.1186/gb-2004-5-8-r56 · Cited by 173 · see citing works

Practical Strategies for Discovering Regulatory DNA Sequence Motifs

MacIsaac, K. D., & Fraenkel, E. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020036 · Cited by 167 · see citing works

Understanding transcriptional regulation by integrative analysis of transcription factor binding dataPreprint

Cheng, C., Alexander, R. P., Min, R., Leng, J., Yip, K. Y.-L., Rozowsky, J. S., Yan, K., Dong, X., Djebali, S., Ruan, Y., et al. (2012) · Genome Research · doi:10.1101/gr.136838.111 · Cited by 165 · see citing works

Genomic Analysis of Stationary-Phase and Exit inSaccharomyces cerevisiae: Gene Expression and Identification of Novel Essential Genes

Martinez, M. J., Roy, S., Archuletta, A. B., Wentzell, P. D., Anna-Arriola, S. S., Rodriguez, A. L., Aragon, A. D., Quinones, G. A., Allen, C., & Werner‐Washburne, M. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-11-0856 · Cited by 164 · see citing works

De novo cis-regulatory module elicitation for eukaryotic genomes

Gupta, M., & Liu, J. S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408743102 · Cited by 138 · see citing works

Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages

Hutchins, A. P., Poulain, S., & Miranda‐Saavedra, D. (2012) · Blood · doi:10.1182/blood-2011-09-381483 · Cited by 134 · see citing works

Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-Reducing Bacterium Shewanella oneidensis

Wan, X., VerBerkmoes, N. C., McCue, L. A., Stanek, D., Connelly, H. M., Hauser, L., Wu, L., Liu, X., Yan, T., Leaphart, A. B., et al. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.24.8385-8400.2004 · Cited by 132 · see citing works

Spatially and genetically distinct control of seed germination by phytochromes A and BPreprint

Lee, K. P., Piskurewicz, U., Turečková, V., Carat, S., Chappuis, R., Strnad, M., Fankhauser, C., & Lopez‐Molina, L. (2012) · Genes & Development · doi:10.1101/gad.194266.112 · Cited by 131 · see citing works

Computational identification of transcriptional regulatory elements in DNA sequence

GuhaThakurta, D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl372 · Cited by 130 · see citing works

DNA motifs in human and mouse proximal promoters predict tissue-specific expression

Smith, A. D., Sumazin, P., Xuan, Z., & Zhang, M. Q. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508169103 · Cited by 120 · see citing works

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

Cheng, C., & Gerstein, M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr752 · Cited by 121 · see citing works

Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells

Topol, A., Zhu, S., Hartley, B. J., English, J., Hauberg, M. E., Tran, N., Rittenhouse, C. A., Simone, A., Ruderfer, D. M., Johnson, J., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.03.090 · Cited by 122 · see citing works

Explicit equilibrium modeling of transcription-factor binding and gene regulation

Granek, J. A., & Clarke, N. D. (2005) · Genome biology · doi:10.1186/gb-2005-6-10-r87 · Cited by 121 · see citing works

Interacting models of cooperative gene regulation

Das, D., Banerjee, N., & Zhang, M. Q. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407365101 · Cited by 120 · see citing works

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences

Li, W., Meyer, C. A., & Liu, X. S. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1046 · Cited by 118 · see citing works

Node harvest

Meinshausen, N. (2010) · The Annals of Applied Statistics · doi:10.1214/10-aoas367 · Cited by 107 · see citing works

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

Hu, M., Yu, J., Taylor, J. M. G., Chinnaiyan, A. M., & Qin, Z. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1180 · Cited by 103 · see citing works

Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation

Wang, W., Cherry, J. M., Nochomovitz, Y. D., Jolly, E. R., Botstein, D., & Li, H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405537102 · Cited by 103 · see citing works

Defining a Centromere-like Element in Bacillus subtilis by Identifying the Binding Sites for the Chromosome-Anchoring Protein RacA

Ben‐Yehuda, S., Fujita, M., Liu, X. S., Gorbatyuk, B., Skoko, D., Yan, J., Marko, J. F., Liu, J. S., Eichenberger, P., Rudner, D. Z., et al. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.023 · Cited by 102 · see citing works

Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in <i>Saccharomyces cerevisiae</i>

Lai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E. (2006) · Eukaryotic Cell · doi:10.1128/ec.00107-06 · Cited by 97 · see citing works

In silico representation and discovery of transcription factor binding sites

Pavesi, G. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.3.217 · Cited by 97 · see citing works

BioOptimizer: a Bayesian scoring function approach to motif discovery

Jensen, S. T., & Liu, J. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth127 · Cited by 94 · see citing works

Bayesian sparse hidden components analysis for transcription regulation networks

Sabatti, C., & James, G. M. (2005) · Bioinformatics · doi:10.1093/bioinformatics/btk017 · Cited by 93 · see citing works

Inferring transcriptional and microRNA‐mediated regulatory programs in glioblastoma

Setty, M. N., Helmy, K. Y., Khan, A. A., Silber, J., Arvey, A. J., Neezen, F., Agius, P., Huse, J. T., Holland, E. C., & Leslie, C. S. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.37 · Cited by 89 · see citing works

A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing

Das, D., Clark, T. A., Schweitzer, A. C., Yamamoto, M. L., Marr, H., Arribere, J., Minovitsky, S., Poliakov, A., Dubchak, I. L., Blume, J. E., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm485 · Cited by 89 · see citing works

Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective

Jensen, S. T., Liu, X. S., Zhou, Q., & Liu, J. S. (2004) · Statistical Science · doi:10.1214/088342304000000107 · Cited by 87 · see citing works

Mining ChIP-chip data for transcription factor and cofactor binding sites

Smith, A. D., Sumazin, P., Das, D., & Zhang, M. Q. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1043 · Cited by 87 · see citing works

A graph-based approach to systematically reconstruct human transcriptional regulatory modules

Yan, X., Mehan, M. R., Huang, Y. S., Waterman, M. S., Yu, P. S., & Zhou, X. J. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm227 · Cited by 86 · see citing works

Inferring activity changes of transcription factors by binding association with sorted expression profiles

Cheng, C., Yan, X., Sun, F., & Li, L. M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-452 · Cited by 86 · see citing works

Genome-wide investigation of light and carbon signaling interactions in Arabidopsis

Thum, K. E., Shin, M. J., Palenchar, P. M., Kouranov, A., & Coruzzi, G. M. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r10 · Cited by 86 · see citing works

Gene Coexpression Networks for the Analysis of DNA Microarray Data

Weirauch, M. T. (2011) · Wiley eBooks · doi:10.1002/9783527638079.ch11 · Cited by 85 · see citing works

Predictive Modeling of Genome-Wide mRNA Expression: From Modules to Molecules

Bussemaker, H. J., Foat, B. C., & Ward, L. D. (2007) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.36.040306.132725 · Cited by 82 · see citing works

RSIR: regularized sliced inverse regression for motif discovery

Zhong, W., Zeng, P., Ma, P., Liu, J. S., & Zhu, Y. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti680 · Cited by 83 · see citing works

Deciphering principles of transcription regulation in eukaryotic genomes

Nguyen, D., & D’haeseleer, P. (2006) · Molecular Systems Biology · doi:10.1038/msb4100054 · Cited by 79 · see citing works

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data

MacIsaac, K. D., Gordon, D. B., Nekludova, L., Odom, D. T., Schreiber, J., Gifford, D. K., Young, R. A., & Fraenkel, E. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti815 · Cited by 74 · see citing works

Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting

Grote, A., Li, Y., Liu, C., Voronin, D., Geber, A. B., Lustigman, S., Unnasch, T. R., Welch, L. R., & Ghedin, E. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0008275 · Cited by 74 · see citing works

Charting gene regulatory networks: strategies, challenges and perspectives

Wei, G., Liu, D., & Liang, C. (2004) · Biochemical Journal · doi:10.1042/bj20040311 · Cited by 72 · see citing works

Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease

Wang, Z., Zhu, S., Jia, Y., Wang, Y., Kubota, N., Fujiwara, N., Gordillo, R., Lewis, C., Zhu, M., Sharma, T., et al. (2023) · Cell · doi:10.1016/j.cell.2023.03.014 · Cited by 72 · see citing works

A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors

Ji, H., Vokes, S. A., & Wong, W. H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl803 · Cited by 69 · see citing works

Predicting Gene Expression from Sequence: A Reexamination

Yuan, Y., Guo, L., Shen, L., & Liu, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030243 · Cited by 69 · see citing works

Inferring yeast cell cycle regulators and interactions using transcription factor activities

Yang, Y.-L., Suen, J. K., Brynildsen, M. P., Galbraith, S. J., & Liao, J. C. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-90 · Cited by 66 · see citing works

Applying whole-genome studies of epigenetic regulation to study human disease

Lieb, J. D., Beck, S., Bulyk, M. L., Farnham, P., Hattori, N., Henikoff, S., Liu, X. S., Okumura, K., Shiota, K., Ushijima, T., et al. (2006) · Cytogenetic and Genome Research · doi:10.1159/000091922 · Cited by 64 · see citing works

Adaptively inferring human transcriptional subnetworks

Das, D., Nahle, Z. A., & Zhang, M. Q. (2006) · Molecular Systems Biology · doi:10.1038/msb4100067 · Cited by 62 · see citing works

Twin Boosting: improved feature selection and prediction

Bühlmann, P., & Hothorn, T. (2009) · Statistics and Computing · doi:10.1007/s11222-009-9148-5 · Cited by 61 · see citing works

A boosting approach for motif modeling using ChIP-chip data

Hong, P., Liu, X. S., Zhou, Q., Lu, X., Liu, J. S., & Wong, W. H. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti402 · Cited by 61 · see citing works

Towards quantitative biology: Integration of biological information to elucidate disease pathways and to guide drug discovery

Fischer, H. (2005) · Biotechnology annual review · doi:10.1016/s1387-2656(05)11001-1 · Cited by 61 · see citing works

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences

Hu, J., Yang, Y. D., & Kihara, D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-342 · Cited by 60 · see citing works

Discussion: One-step sparse estimates in nonconcave penalized likelihood models

Bühlmann, P., & Meier, L. (2008) · The Annals of Statistics · doi:10.1214/07-aos0316a · Cited by 61 · see citing works

Global analysis of gene transcription regulation in prokaryotes

Zhou, D., & Yang, R. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6184-6 · Cited by 58 · see citing works

Regulatory motif finding by logic regression

Keleş, S., van der Laan, M. J., & Vulpe, C. D. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth333 · Cited by 55 · see citing works

Genomic Approaches That Aid in the Identification of Transcription Factor Target Genes

Kirmizis, A., & Farnham, P. (2004) · Experimental Biology and Medicine · doi:10.1177/153537020422900803 · Cited by 54 · see citing works

Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts

Chiang, D. Y., Moses, A. M., Kellis, M., Lander, E. S., & Eisen, M. B. (2003) · Genome biology · doi:10.1186/gb-2003-4-7-r43 · Cited by 53 · see citing works

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

Repunte-Canonigo, V., Shin, W., Vendruscolo, L. F., Lefebvre, C., van der Stap, L., Kawamura, T., Schlosburg, J. E., Alvarez, M., Koob, G. F., Califano, A., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0593-5 · Cited by 52 · see citing works

Extracting Sequence Features to Predict\nProtein–DNA Interactions: A Comparative Study

Zhou, Q., & Liu, J. S. (2008) · Digital Access to Scholarship at Harvard (DASH) (Harvard University) · Cited by 52 · see citing works

CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A., & Vingron, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp682 · Cited by 48 · see citing works

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Wang, J., Xia, S., Arand, B., Zhu, H., Machiraju, R., Huang, K., Ji, H., & Qian, J. X. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004892 · Cited by 50 · see citing works

Genetic dissection of diseases: design and methods

Hoh, J. J., & Ott, J. (2004) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2004.04.006 · Cited by 50 · see citing works

Multi-step adaptive elastic-net: reducing false positives in high-dimensional variable selection

Xiao, N., & Xu, Q. (2015) · Journal of Statistical Computation and Simulation · doi:10.1080/00949655.2015.1016944 · Cited by 49 · see citing works

Variable Selection in Regression Mixture Modeling for the Discovery of Gene Regulatory Networks

Gupta, M., & Ibrahim, J. G. (2007) · Journal of the American Statistical Association · doi:10.1198/016214507000000068 · Cited by 48 · see citing works

Repetitive DNA elements, nucleosome binding and human gene expression

Huda, A., Mariño‐Ramírez, L., Landsman, D., & Jordan, I. K. (2009) · Gene · doi:10.1016/j.gene.2009.01.013 · Cited by 46 · see citing works

Sex chromosome evolution in parasitic nematodes of humans

Foster, J. M., Grote, A., Mattick, J., Tracey, A., Tsai, Y., Chung, M. C., Cotton, J. A., Clark, T. A., Geber, A. B., Holroyd, N. E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15654-6 · Cited by 47 · see citing works

Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites

Wang, G., Wang, F., Huang, Q., Li, Y., Liu, Y., & Wang, Y. (2015) · BioMed Research International · doi:10.1155/2015/757530 · Cited by 46 · see citing works

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Tan, K., Tegner, J. N., & Ravasi, T. (2008) · Genomics · doi:10.1016/j.ygeno.2007.11.005 · Cited by 43 · see citing works

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data

Chen, X., Guo, L., Fan, Z., & Jiang, T. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn088 · Cited by 43 · see citing works

Predictive modelling of gene expression from transcriptional regulatory elements

Budden, D., Hurley, D., & Crampin, E. J. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu034 · Cited by 40 · see citing works

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays

Yap, Y. L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki188 · Cited by 41 · see citing works

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., & Akiyama, T. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-404 · Cited by 40 · see citing works

Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation

Zwir, I. J. S., Huang, H. V., & Groisman, E. A. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti672 · Cited by 41 · see citing works

Meta-clustering of gene expression data and literature-based information

Glenisson, P., Mathys, J., & Moor, B. D. (2003) · ACM SIGKDD Explorations Newsletter · doi:10.1145/980972.980985 · Cited by 40 · see citing works

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

Halperin, Y., Linhart, C., Ulitsky, I., & Ron Shamir, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn1064 · Cited by 40 · see citing works

Computational analyses of eukaryotic promoters

Zhang, M. Q. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s6-s3 · Cited by 40 · see citing works

An overview of recent developments in genomics and associated statistical methods

Bickel, P. J., Brown, J. B., Huang, H., & Li, Q. (2009) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2009.0164 · Cited by 38 · see citing works

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

Read, D. F., Cook, K. B., Lu, Y. Y., Roch, K. G. L., & Noble, W. S. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007329 · Cited by 39 · see citing works

High-Throughput Analysis of Promoter Occupancy Reveals New Targets for Arx, a Gene Mutated in Mental Retardation and Interneuronopathies

Quillé, M.-L., Carat, S., Redon, S., Hirchaud, E., Baron, D., Bénech, C., Guihot, J., Placet, M., Mignen, O., Férec, C., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025181 · Cited by 38 · see citing works

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

Caselle, M., Cunto, F. D., & Provero, P. (2002) · BMC Bioinformatics · doi:10.1186/1471-2105-3-7 · Cited by 45 · see citing works

MotifScorer: using a compendium of microarrays to identify regulatory motifs

Brilli, M., Fani, R., & Lió, P. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl607 · Cited by 8 · see citing works

Regulatory element detection using correlation with expression

Bussemaker, H. J., Li, H., & Siggia, E. D. (2001) · Nature Genetics · doi:10.1038/84792 · Cited by 721 · see citing works

Development of Software Facilities to Characterize Regulatory Binding Motifs and Application to Streptococcaceae

Pons, N., Batto, J.-M., Ehrlich, S. D., & Renault, P. (2007) · Microbial Physiology · doi:10.1159/000106084 · Cited by 10 · see citing works

Detecting Transcriptional cis-Regulation from Gene Expression Data

Igarashi, Y., Okuno, Y., Vert, J., & Kanehisa, M. I. (2001) · doi:10.11234/gi1990.12.241