Abadi, M., Agarwal, A., Barham, P., Brevdo, E., Chen, Z., Citro, C., et al. (2015). TensorFlow: Large-scale machine learning on heterogeneous systems. Software available from: https://www.tensorflow.org

Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166–169.

Article  PubMed  CAS  Google Scholar 

Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Research, 37, W202-208.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bang, I., Khanh Nong, L., Young Park, J., Le Thi, H., Mok Lee, S., & Kim, D. (2023a). ChEAP: ChIP-exo analysis pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions. Computational and Structural Biotechnology Journal, 21, 99–104.

Article  PubMed  CAS  Google Scholar 

Bang, I., Lee, S. M., Park, S., Park, J. Y., Nong, L. K., Gao, Y., Palsson, B. O., & Kim, D. (2023b). Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Briefings in Bioinformatics, 24, bba024.

Article  Google Scholar 

Berger, P., Dumevi, R. M., Berger, M., Hastor, I., Treffon, J., Kouzel, I. U., Kehl, A., Scherff, N., Dobrindt, U., & Mellmann, A. (2024). RpoS acts as a global repressor of virulence gene expression in E. coli O104:H4 and enteroaggregative E. coli. The Journal of Infectious Diseases, 230, 840–851.

PubMed  Google Scholar 

Buck, M. J., & Lieb, J. D. (2004). ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83, 349–360.

Article  PubMed  CAS  Google Scholar 

Cantalapiedra, C. P., Hernandez-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular Biology and Evolution, 38, 5825–5829.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Cho, B. K., Kim, D., Knight, E. M., Zengler, K., & Palsson, B. O. (2014). Genome-scale reconstruction of the sigma factor network in Escherichia coli: Topology and functional states. BMC Biology, 12, 4.

Article  PubMed  PubMed Central  Google Scholar 

Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009). Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422–1423.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Eng, S. K., Pusparajah, P., Mutalib, N. S. A., Ser, H. L., Chan, K. G., & Lee, L. H. (2015). Salmonella: A review on pathogenesis, epidemiology and antibiotic resistance. Frontiers in Life Science, 8, 284–293.

Article  CAS  Google Scholar 

Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2015). Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Research, 43, D261-269.

Article  PubMed  CAS  Google Scholar 

Gao, Y., Bang, I., Seif, Y., Kim, D., & Palsson, B. O. (2023). The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Nucleic Acids Research, 51, 3618–3630.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Haring, M., Offermann, S., Danker, T., Horst, I., Peterhansel, C., & Stam, M. (2007). Chromatin immunoprecipitation: Optimization, quantitative analysis and data normalization. Plant Methods, 3, 11.

Article  PubMed  PubMed Central  Google Scholar 

Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., et al. (2020). Array programming with NumPy. Nature, 585, 357–362.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9, 90–95.

Article  Google Scholar 

Karp, P. D., Billington, R., Caspi, R., Fulcher, C. A., Latendresse, M., Kothari, A., Keseler, I. M., Krummenacker, M., Midford, P. E., Ong, Q., et al. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in Bioinformatics, 20, 1085–1093.

Article  PubMed  CAS  Google Scholar 

Karp, P. D., Paley, S., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., Moore, L. R., Subhraveti, P., Gama-Castro, S., Tierrafria, V. H., et al. (2023). The EcoCyc database (2023). EcoSal plus, 11, eesp00022023.

Article  PubMed  Google Scholar 

Kim, D., Seo, S. W., Gao, Y., Nam, H., Guzman, G. I., Cho, B. K., & Palsson, B. O. (2018). Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Research, 46, 2901–2917.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kim, J. W., Ko, Y. S., Chae, T. U., & Lee, S. Y. (2020). High-level production of 3-hydroxypropionic acid from glycerol as a sole carbon source using metabolically engineered Escherichia coli. Biotechnology and Bioengineering, 117, 2139–2152.

Article  PubMed  CAS  Google Scholar 

Lamichhane, B., Mawad, A. M. M., Saleh, M., Kelley, W. G., Harrington, P. J., 2nd., Lovestad, C. W., Amezcua, J., Sarhan, M. M., El Zowalaty, M. E., Ramadan, H., et al. (2024). Salmonellosis: An overview of epidemiology, pathogenesis, and innovative approaches to mitigate the antimicrobial resistant infections. Antibiotics (Basel), 13, 76.

Article  PubMed  CAS  Google Scholar 

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25. https://doi.org/10.1186/gb-2009-10-3-r25

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lawrence, M., Huber, W., Pages, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M. T., & Carey, V. J. (2013). Software for computing and annotating genomic ranges. PLoS Computational Biology, 9, e1003118.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lee, S. M., Le, H. T., Taizhanova, A., Nong, L. K., Park, J. Y., Lee, E. J., Palsson, B. O., & Kim, D. (2023). Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Frontiers in Microbiology, 14, 1271121.

Article  PubMed  Google Scholar 

Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., & Regev, A. (2010). Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature Methods, 7, 709–715.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078–2079.

Article  PubMed  PubMed Central  Google Scholar 

Li, J., Jaitzig, J., Lu, P., Sussmuth, R. D., & Neubauer, P. (2015). Scale-up bioprocess development for production of the antibiotic valinomycin in Escherichia coli based on consistent fed-batch cultivations. Microbial Cell Factories, 14, 83.

Article  PubMed  PubMed Central  Google Scholar 

Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.

Article  PubMed  PubMed Central  Google Scholar 

Morgan, M., Obenchain, V., Hester, J., & Pagès, H. (2024a). SummarizedExperiment: SummarizedExperiment container. R package version 1.34.0. Available from: https://bioconductor.org/packages/SummarizedExperiment

Morgan, M., Pagès, H., Obenchain, V., & Hayden, N. (2024b). Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 2.20.0. Available from: https://bioconductor.org/packages/Rsamtools

Morgan, M., Wang, J., Obenchain, V., Lang, M., Thompson, R., & Turaga, N. (2024c). BiocParallel: Bioconductor facilities for parallel evaluation. R package version 1.38.0. Available from: https://github.com/Bioconductor/BiocParallel

Pagès, H., Carlson, M., Aboyoun, P., Falcon, S., & Morgan, M. (2024). txdbmaker: Tools for making TxDb objects from genomic annotations. R package version 1.0.1. Available from: https://bioconductor.org/packages/txdbmaker