Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,933 · 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

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015) · Nature Biotechnology · doi:10.1038/nbt.3300 · Cited by 2,873 · see citing works

Transcriptional regulatory code of a eukaryotic genome

Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,116 · see citing works

The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification

Puig, Ó., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado‐Nilsson, E., Wilm, M. S., & Séraphin, B. (2001) · Methods · doi:10.1006/meth.2001.1183 · Cited by 1,784 · see citing works

Effect of benzoic acid on metabolic fluxes in yeasts: A continuous‐culture study on the regulation of respiration and alcoholic fermentation

Verduyn, C., Postma, E., Scheffers, W. A., & van Dijken, J. P. (1992) · Yeast · doi:10.1002/yea.320080703 · Cited by 1,510 · see citing works

Reconstruction of biochemical networks in microorganisms

Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., & Palsson, B. Ø. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1949 · Cited by 859 · see citing works

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 760 · see citing works

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Väremo, L., Nielsen, J., & Nookaew, I. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt111 · Cited by 683 · see citing works

An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains

van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heijnen, J. J., Hoare, M., Lange, H. C., et al. (2000) · Enzyme and Microbial Technology · doi:10.1016/s0141-0229(00)00162-9 · Cited by 598 · cited 1× · see citing works

Metabolism and Regulation of Glycerolipids in the Yeast Saccharomyces cerevisiae

Henry, S. A., Kohlwein, S. D., & Carman, G. M. (2012) · Genetics · doi:10.1534/genetics.111.130286 · Cited by 518 · see citing works

Phospholipid Metabolism Regulated by a Transcription Factor Sensing Phosphatidic Acid

Loewen, C. J. R., Gaspar, M. L., Jesch, S. A., Delon, C., Ktistakis, N. T., Henry, S. A., & Levine, T. P. (2004) · Science · doi:10.1126/science.1096083 · Cited by 492 · see citing works

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

Zhou, Y. J., Buijs, N. A. A., Zhu, Z., Qin, J., Siewers, V., & Nielsen, J. (2016) · Nature Communications · doi:10.1038/ncomms11709 · Cited by 422 · see citing works

The biochemistry of peroxisomal β-oxidation in the yeastSaccharomyces cerevisiae

Hiltunen, J. K., Mursula, A. M., Rottensteiner, H., Wierenga, R. K., Kastaniotis, A. J., & Gurvitz, A. (2003) · FEMS Microbiology Reviews · doi:10.1016/s0168-6445(03)00017-2 · Cited by 349 · see citing works

Microbial acetyl-CoA metabolism and metabolic engineering

Krivoruchko, A., Zhang, Y., Siewers, V., Chen, Y., & Nielsen, J. (2014) · Metabolic Engineering · doi:10.1016/j.ymben.2014.11.009 · Cited by 342 · see citing works

PHOSPHOLIPID BIOSYNTHESIS IN YEAST

Carman, G. M., & Henry, S. A. (1989) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.58.070189.003223 · Cited by 327 · see citing works

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

Seo, S. W., Kim, D., Latif, H., O’Brien, E. J., Szubin, R., & Palsson, B. Ø. (2014) · Nature Communications · doi:10.1038/ncomms5910 · Cited by 318 · see citing works

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

Guo, Y., Mahony, S., & Gifford, D. K. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002638 · Cited by 288 · see citing works

Oxygen Sensing and the Transcriptional Regulation of Oxygen-Responsive Genes in Yeast

Kwast, K. E., Burke, P. V., & Poyton, R. Ο. (1998) · Journal of Experimental Biology · doi:10.1242/jeb.201.8.1177 · Cited by 249 · see citing works

Isolation and Characterization of a Gene Affecting Fatty Acid Elongation in Saccharomyces cerevisiae

Toke, D. A., & Martin, C. E. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.31.18413 · Cited by 214 · see citing works

ChIP‐exo Method for Identifying Genomic Location of DNA‐Binding Proteins with Near‐Single‐Nucleotide Accuracy

Rhee, H. S., & Pugh, B. F. (2012) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2124s100 · Cited by 195 · see citing works

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

de Boer, C. G., & Hughes, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr993 · Cited by 193 · see citing works

Identifying transcription factor functions and targets by phenotypic activation

Chua, G., Morris, Q., Sopko, R., Robinson, M. D., Ryan, O. W., Chan, E. T., Frey, B. J., Andrews, B., Boone, C. M., & Hughes, T. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605140103 · Cited by 183 · see citing works

Deep learning for regulatory genomics

Park, Y., & Kellis, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3313 · Cited by 172 · see citing works

Regulatory Elements That Control Transcription Activation and Unsaturated Fatty Acid-mediated Repression of the Saccharomyces cerevisiae OLE1 Gene

Choi, J., Stukey, J., Hwang, S., & Martin, C. E. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.7.3581 · Cited by 155 · see citing works

Global Regulatory Functions of Oaf1p and Pip2p (Oaf2p), Transcription Factors That Regulate Genes Encoding Peroxisomal Proteins in Saccharomyces cerevisiae

Karpichev, I. V., & Small, G. M. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.11.6560 · Cited by 139 · see citing works

Heme Levels Switch the Function of Hap1 of <i>Saccharomyces cerevisiae</i> between Transcriptional Activator and Transcriptional Repressor

Hickman, M. J., & Winston, F. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00887-07 · Cited by 137 · see citing works

Engineering of synthetic, stress-responsive yeast promoters

Rajkumar, A. S., Liu, G., Bergenholm, D., Arsovska, D., Kristensen, M., Nielsen, J., Jensen, M. K., & Keasling, J. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw553 · Cited by 134 · see citing works

Genome-wide Analysis Reveals Inositol, Not Choline, as the Major Effector of Ino2p-Ino4p and Unfolded Protein Response Target Gene Expression in Yeast

Jesch, S. A., Zhao, X., Wells, M. T., & Henry, S. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m411770200 · Cited by 129 · see citing works

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

Gordân, R., Murphy, K. F., McCord, R. P., Zhu, C., Vedenko, A., & Bulyk, M. L. (2011) · Genome biology · doi:10.1186/gb-2011-12-12-r125 · Cited by 119 · see citing works

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

Fang, X. D., Sastry, A. V., Mih, N., Kim, D., Tan, J., Yurkovich, J. T., Lloyd, C. J., Gao, Y., Yang, L., & Palsson, B. Ø. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1702581114 · Cited by 114 · see citing works

Spurious transcription factor binding: Non‐functional or genetically redundant?

Spivakov, M. (2014) · BioEssays · doi:10.1002/bies.201400036 · Cited by 96 · see citing works

Genome Expression Analysis in Yeast Reveals Novel Transcriptional Regulation by Inositol and Choline and New Regulatory Functions for Opi1p, Ino2p, and Ino4p

Santiago, T., & Mamoun, C. B. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303008200 · Cited by 90 · see citing works

Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response

Dang, W., Sutphin, G. L., Dorsey, J. A., Otte, G. L., Cao, K., Perry, R. M., Wanat, J. J., Saviolaki, D., Murakami, C. J., Tsuchiyama, S., et al. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.04.004 · Cited by 83 · see citing works

Backup in gene regulatory networks explains differences between binding and knockout results

Gitter, A., Siegfried, Z., Klutstein, M., Fornés, O., Oliva, B., Simon, I., & Bar‐Joseph, Z. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.33 · Cited by 83 · see citing works

Mapping Yeast Transcriptional Networks

Hughes, T. R., & de Boer, C. G. (2013) · Genetics · doi:10.1534/genetics.113.153262 · Cited by 83 · see citing works

Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae

Khoomrung, S., Chumnanpuen, P., Jansa-Ard, S., Nookaew, I., & Nielsen, J. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4125-x · Cited by 76 · see citing works

Functional Analysis of the Zn2Cys6Transcription Factors Oaf1p and Pip2p

Baumgartner, U., Hamilton, B., Piskáček, M., Ruis, H., & Rottensteiner, H. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.32.22208 · Cited by 68 · see citing works

Transcriptional responses to fatty acid are coordinated by combinatorial control

Smith, J. J., Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., & Aitchison, J. D. (2007) · Molecular Systems Biology · doi:10.1038/msb4100157 · Cited by 59 · see citing works

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

Leyn, S. A., Kazanov, M. D., Sernova, N. V., Ermakova, E. O., Novichkov, P. S., & Rodionov, D. A. (2013) · Journal of Bacteriology · doi:10.1128/jb.00140-13 · Cited by 58 · see citing works

Deep Motif: Visualizing Genomic Sequence ClassificationsPreprint

Lanchantin, J., Singh, R., Lin, Z., & Qi, Y. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1605.01133 · Cited by 54 · see citing works

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

Ozonov, E. A., & van Nimwegen, E. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003181 · Cited by 36 · see citing works

Binding Characteristics and Regulatory Mechanisms of the Transcription Factors Controlling Oleate-responsive Genes in Saccharomyces cerevisiae

Karpichev, I. V., Durand-Heredia, J. M., Luo, Y., & Small, G. M. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m708215200 · Cited by 33 · see citing works

The acetyl‐CoA synthetase gene ACS2 of the yeast Saccharomyces cerevisiae is coregulated with structural genes of fatty acid biosynthesis by the transcriptional activators Ino2p and Ino4p

Hiesinger, M., Wagner, C., & Schüller, H. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)01085-5 · Cited by 32 · see citing works

Mitochondrial transporters involved in oleic acid utilization and glutamate metabolism in yeast

Trotter, P. J., Adamson, A. L., Ghrist, A. C., Rowe, L., Scott, L., Sherman, M. P., Stites, N. C., Sun, Y., Tawiah-Boateng, M. A., Tibbetts, A. S., et al. (2005) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2005.07.016 · Cited by 26 · see citing works

Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

Liu, G., Bergenholm, D., & Nielsen, J. (2016) · mBio · doi:10.1128/mbio.00559-16 · Cited by 26 · see citing works

Integrated analysis, transcriptome-lipidome, reveals the effects of INO- level (INO2 and INO4) on lipid metabolism in yeast

Chumnanpuen, P., Nookaew, I., & Nielsen, J. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-s3-s7 · Cited by 24 · see citing works

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors

Österlund, T., Bordel, S., & Nielsen, J. (2015) · Integrative Biology · doi:10.1039/c4ib00247d · Cited by 22 · see citing works

Multiple Basic Helix-Loop-Helix Proteins Regulate Expression of the ENO1 Gene of Saccharomyces cerevisiae

Chen, M., & Lopes, J. M. (2007) · Eukaryotic Cell · doi:10.1128/ec.00383-06 · Cited by 21 · see citing works

Saccharomyces cerevisiae Pip2p–Oaf1p regulates PEX25 transcription through an adenine‐less ORE

Rottensteiner, H., Hartig, A., Hamilton, B., Ruis, H., Erdmann, R., & Gurvitz, A. (2003) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2003.03575.x · Cited by 21 · see citing works

Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae

Guzmán-Vargas, L., & Santillán, M. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-13 · Cited by 18 · see citing works

Yeast transcription factor Oaf1 forms homodimer and induces some oleate-responsive genes in absence of Pip2

Trzcińska‐Danielewicz, J., Ishikawa, T., Miciałkiewicz, A., & Fronk, J. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.07.105 · Cited by 18 · see citing works

Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol–choline and Snf1 in controlling lipid biosynthesis in yeast

Chumnanpuen, P., Zhang, J., Nookaew, I., & Nielsen, J. (2012) · Molecular Genetics and Genomics · doi:10.1007/s00438-012-0697-5 · Cited by 17 · see citing works

The future of genome‐scale modeling of yeast through integration of a transcriptional regulatory network

Liu, G., Marras, A., & Nielsen, J. (2014) · Quantitative Biology · doi:10.1007/s40484-014-0027-5 · Cited by 9 · see citing works

Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae

Jordá, T., & Puig, S. (2020) · Genes · doi:10.3390/genes11070795 · Cited by 489 · see citing works

Yeast Systems Biology: Model Organism and Cell Factory

Nielsen, J. (2019) · Biotechnology Journal · doi:10.1002/biot.201800421 · Cited by 283 · see citing works

Transcription factors and ABC transporters: from pleiotropic drug resistance to cellular signaling in yeast

Buechel, E. R., & Pinkett, H. W. (2020) · FEBS Letters · doi:10.1002/1873-3468.13964 · Cited by 70 · see citing works

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories

Lutz, S., Brion, C., Kliebhan, M., & Albert, F. W. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008375 · Cited by 42 · see citing works

Transcriptional regulation of ergosterol biosynthesis genes in response to iron deficiency

Jordá, T., Barba‐Aliaga, M., Rozés, N., Alepuz, P. M., Martínez‐Pastor, M. T., & Puig, S. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16157 · Cited by 35 · see citing works

Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data

Cynthia, Z., & Brent, M. R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa947 · Cited by 33 · see citing works

Key enzymes involved in the utilization of fatty acids by Saccharomyces cerevisiae: a review

Wang, Z., Su, C., Zhang, Y. F., Shangguan, S., Wang, R., & Su, J. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1294182 · Cited by 35 · see citing works

Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responsesPreprint

Kang, Y., Patel, N., Shively, C. A., Recio, P. S., Chen, X., Wranik, B. J., Kim, G., McIsaac, R. S., Mitra, R. D., & Brent, M. R. (2020) · Genome Research · doi:10.1101/gr.259655.119 · Cited by 29 · see citing works

Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions

Holland, P., Bergenholm, D., Börlin, C. S., Liu, G., & Nielsen, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz253 · Cited by 25 · see citing works

A Thi2p Regulatory Network Controls the Post-glucose Effect of Xylose Utilization in Saccharomyces cerevisiae

Wei, S., Bai, P., Liu, Y., Yang, M., Ma, J., Hou, J., Liu, W., Bao, X., & Shen, Y. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01649 · Cited by 22 · see citing works

New biomarkers underlying acetic acid tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii

Samakkarn, W., Vandecruys, P., Foulquié-Moreno, M. R., Thevelein, J. M., Ratanakhanokchai, K., & Soontorngun, N. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-023-12946-x · Cited by 21 · see citing works

Construction of mini‐chemostats for high‐throughput strain characterization

Bergenholm, D., Liu, G., Hansson, D., & Nielsen, J. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.26931 · Cited by 19 · see citing works

Two Zn 2 Cys 6 -type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta

Wang, C., Zhang, X., Wu, K., Liu, S., Li, X., Zhu, C., Xiao, Y., Fang, Z., & Liu, J. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.00545-24 · Cited by 16 · see citing works

Motifs enable communication efficiency and fault-tolerance in transcriptional networks

Roy, S., Ghosh, P., Barua, D., & Das, S. K. (2020) · Scientific Reports · doi:10.1038/s41598-020-66573-x · Cited by 15 · see citing works

Big data in yeast systems biology

Yu, R., & Nielsen, J. (2019) · FEMS Yeast Research · doi:10.1093/femsyr/foz070 · Cited by 14 · see citing works

Yeast systems biology in understanding principles of physiology underlying complex human diseases

Yu, R., & Nielsen, J. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.11.021 · Cited by 12 · see citing works

Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells

Pascual‐Ahuir, A., González-Cantó, E., Juyoux, P., Pable, J., Poveda-Huertes, D., Saiz-Balbastre, S., Squeo, S., Ureña-Marco, A., Vanacloig-Pedros, E., Zaragoza‐Infante, L., et al. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.02.009 · Cited by 11 · see citing works

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

Nambiar, A., Dubinkina, V. B., Liu, S., & Maslov, S. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011563 · Cited by 10 · see citing works

Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states

Bergen, A. C., Kocik, R. A., Hose, J., McClean, M. N., & Gasch, A. P. (2022) · eLife · doi:10.7554/elife.82017 · Cited by 10 · see citing works

ChEC-seq2: an improved chromatin endogenous cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein–DNA interactions

VanBelzen, J., Duan, C., Brickner, D. G., & Brickner, J. H. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae012 · Cited by 9 · see citing works

Transcriptome analysis reveals the mechanism of tolerance to copper toxicity in the white rot fungus Trametes hirsuta AH28-2

Wang, C., Kun, W., Pang, N., Zhao, H., Liu, S., Zhang, X., Xiao, Y., Fang, Z., & Liu, J. (2025) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2025.118194 · Cited by 7 · see citing works

Trans -acting genetic variation affects the expression of adjacent genes

Dyke, K. V., Lutz, S., Mekonnen, G., Myers, C. L., & Albert, F. W. (2021) · Genetics · doi:10.1093/genetics/iyaa051 · Cited by 6 · see citing works

The importance of regulated resource reallocation during dynamic environmental shifts in yeast

Kocik, R. A., Cytrynbaum, E. G., Ahrens, J. M., McClean, M. N., & Gasch, A. P. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00727-x · Cited by 5 · see citing works

Predicting which genes will respond to transcription factor perturbations

Kang, Y., Jung, W. J., & Brent, M. R. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac144 · Cited by 5 · see citing works

Bioinformatics tools in protein analysis: Structure prediction, interaction modelling, and function relationship

Ogunjobi, T. T., Okorie, I. C., Gigam-Ozuzu, C. D., Olorunleke, J. V., Ogunleye, F. I., Irimoren, E. O., Atanda, D. O., Okafor, A. M.-A., Agbo, E. C., Onasokhare, O. F., et al. (2025) · European Journal of Sustainable Development Research · doi:10.29333/ejosdr/16340 · Cited by 4 · see citing works

A bioinformatic pipeline to analyze ChIP-exo datasets

Börlin, C. S., Bergenholm, D., Holland, P., & Nielsen, J. (2019) · Biology Methods and Protocols · doi:10.1093/biomethods/bpz011 · Cited by 4 · see citing works

Rational gRNA design based on transcription factor binding data

Bergenholm, D., Dabirian, Y., Ferreira, R., Siewers, V., David, F., & Nielsen, J. (2021) · Synthetic Biology · doi:10.1093/synbio/ysab014 · Cited by 3 · see citing works

Gene Regulatory Networks: Dissecting Structure and Dynamics

Hütt, M. ‐., & Lesne, A. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11467-9 · Cited by 3 · see citing works

The leucine zipper domain of the transcriptional repressor Opi1 underlies a signal transduction mechanism regulating lipid synthesis

Fernández-Murray, J. P., Tavasoli, M., Williams, J. G., & McMaster, C. R. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105417 · Cited by 3 · see citing works

Predicting which genes will respond to perturbations of a TF: TF-independent properties of genes are major determinants of their responsivenessPreprint

Kang, Y., & Brent, M. R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.15.422864 · Cited by 1 · see citing works

Trans -acting genetic variation affects the expression of adjacent genesPreprint

Dyke, K. V., Mekonnen, G., Myers, C. L., & Albert, F. W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.05.327130

Design and optimization of sustainable process technologies

Mussatto, S. I., Qin, F., Yamakawa, C. K., Sánchez‐Moguel, I., & Cassano, M. (2017) · Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)

Investigating the Regulatory Relationships Between Transcription Factors and Their Targets in Saccharomyces Cerevisiae Using RNA-seq

Ho, J. (2017) · doi:10.14418/wes01.2.162

Mapping Condition-Dependent Regulation of Lipid Metabolism inSaccharomyces cerevisiae

Jewett, M. C., Workman, C. T., Nookaew, I., Pizarro, F. J., Agosin, E. E., Hellgren, L. I., & Nielsen, J. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.006601 · Cited by 20 · see citing works

Transcriptional networks: reverse-engineering gene regulation on a global scale

Chua, G., Robinson, M. D., Morris, Q., & Hughes, T. R. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.10.009 · Cited by 61 · see citing works

Method for identifying transcription factor binding sites in yeast

Analysis, G., Tsai, H.-K., Huang, G. T.-W., Chou, M.-Y., & Lu, H. H.-S. (2008)