@misc{noauthor_open_nodate,
	title = {Open {Problems} – {Single}-{Cell} {Perturbations}},
	url = {https://kaggle.com/competitions/open-problems-single-cell-perturbations},
	abstract = {Predict how small molecules change gene expression in different cell types},
	language = {en},
	urldate = {2023-12-08},
}

@misc{noauthor_national_nodate,
	title = {National {Drug} {Codes} {List}},
	url = {https://ndclist.com/},
	journal = {National Drug Codes List},
}

@article{agrawal_predicting_2023,
	title = {Predicting gene expression changes upon epigenomic drug treatment},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10541107/},
	doi = {10.1101/2023.07.20.549955},
	abstract = {Background
Tumors are characterized by global changes in epigenetic changes such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome have been proposed for cancer therapy, notably, histone deacetylase inhibitors (HDACi) such as Vorinostatis and DNA methyltransferase inhibitors (DNMTi) such as Zebularine. However, a fundamental challenge with such approaches is the lack of genomic specificity, i.e., the transcriptional changes at different genomic loci can be highly variable thus making it difficult to predict the consequences on the global transcriptome and drug response. For instance, treatment with DNMTi may upregulate the expression of not only a tumor suppressor but also an oncogene leading to unintended adverse effect.

Methods
Given the pre-treatment transcriptome and epigenomic profile of a sample, we assessed the extent of predictability of locus-specific changes in gene expression upon treatment with HDACi using machine learning.

Results
We found that in two cell lines (HCT116 treated with Largazole at 8 doses and RH4 treated with Entinostat at 1μM) where the appropriate data (pre-treatment transcriptome and epigenome as well as post-treatment transcriptome) is available, our model distinguished the post-treatment up versus downregulated genes with high accuracy (up to ROC of 0.89). Furthermore, a model trained on one cell line is applicable to another cell line suggesting generalizability of the model.

Conclusions
Here we present a first assessment of the predictability of genome-wide transcriptomic changes upon treatment with HDACi. Lack of appropriate omics data from clinical trials of epigenetic drugs currently hampers the assessment of applicability of our approach in clinical setting.},
	urldate = {2023-12-08},
	journal = {bioRxiv},
	author = {Agrawal, Piyush and Gopalan, Vishaka and Hannenhalli, Sridhar},
	month = jul,
	year = {2023},
	pmid = {37781626},
	pmcid = {PMC10541107},
	pages = {2023.07.20.549955},
}

@misc{noauthor_gene_nodate,
	title = {Gene regulation {\textbar} {Biological} {Principles}},
	url = {https://bioprinciples.biosci.gatech.edu/module-4-genes-and-genomes/4-7-gene-regulation/},
	urldate = {2023-12-08},
}

@misc{noauthor_encyclopedia_nodate,
	title = {Encyclopedia of {Bioinformatics} and {Computational} {Biology}},
	url = {http://www.sciencedirect.com:5070/referencework/9780128114322/encyclopedia-of-bioinformatics-and-computational-biology},
	abstract = {Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information t...},
	language = {en},
	urldate = {2023-12-08},
	journal = {ScienceDirect},
}

@article{razin_co-regulated_2021,
	title = {Co-{Regulated} {Genes} and {Gene} {Clusters}},
	volume = {12},
	issn = {2073-4425},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8230824/},
	doi = {10.3390/genes12060907},
	abstract = {There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.},
	number = {6},
	urldate = {2023-12-08},
	journal = {Genes},
	author = {Razin, Sergey V. and Ioudinkova, Elena S. and Kantidze, Omar L. and Iarovaia, Olga V.},
	month = jun,
	year = {2021},
	pmid = {34208174},
	pmcid = {PMC8230824},
	pages = {907},
}

@misc{noauthor_notitle_nodate-1,
	url = {https://open.fda.gov/apis/},
	abstract = {openFDA},
	urldate = {2023-12-08},
}

@misc{pubchem_idelalisib_nodate,
	title = {Idelalisib},
	url = {https://pubchem.ncbi.nlm.nih.gov/compound/11625818},
	abstract = {Idelalisib {\textbar} C22H18FN7O {\textbar} CID 11625818 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more.},
	language = {en},
	urldate = {2023-12-08},
	author = {{PubChem}},
}

@misc{pubchem_vandetanib_nodate,
	title = {Vandetanib},
	url = {https://pubchem.ncbi.nlm.nih.gov/compound/3081361},
	abstract = {Vandetanib {\textbar} C22H24BrFN4O2 {\textbar} CID 3081361 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more.},
	language = {en},
	urldate = {2023-12-08},
	author = {{PubChem}},
}