Specific Nucleotide Sequences Research Articles

The Role of FOXA1 in Human Normal Development and Its Functions in Sex Hormone-Related Cancers.

Transcription factors (TFs) are essential proteins regulating gene expression by binding to specific nucleotide sequences upstream of genes. Among TF families, the forkhead box (FOX) proteins, characterized by a conserved DNA-binding domain, play vital roles in various cellular processes, including cancer. The FOXA subfamily, encompassing FOXA1, FOXA2, and FOXA3, stands out for its pivotal role in mammalian development. FOXA1, initially identified in the liver, exhibits diverse expression across multiple organ tissues and plays a critical role in cell proliferation, differentiation, and tumor development. Its structural composition includes transactivation domains and a DNA-binding domain, facilitating its function as a pioneer factor, which is crucial for chromatin interaction and the recruitment of other transcriptional regulators. The involvement of FOXA1 in sex hormone-related tumors underscores its significance in cancer biology. This review provides an overview of multifaceted roles of FOXA1 in normal development and its implications in the pathogenesis of hormone-related cancers, particularly breast cancer and prostate cancer.

Impact of transcription factors KLF1 and GATA1 on red blood cell antigen expression: a review.

KLF transcription factor 1 (KLF1) and GATA binding protein 1 (GATA1) are transcription factors (TFs) that initiate and regulate transcription of the genes involved in erythropoiesis. These TFs possess DNA-binding domains that recognize specific nucleotide sequences in genes, to which they bind and regulate transcription. Variants in the genes that encode either KLF1 or GATA1 can result in a range of hematologic phenotypes-from benign to severe forms of thrombocytopenia and anemia; they can also weaken the expression of blood group antigens. The Lutheran (LU) blood group system is susceptible to TF gene variations, particularly KLF1 variants. Individuals heterozygous for KLF1 gene variants show reduced Lutheran antigens on red blood cells that are not usually detected by routine hemagglutination methods. This reduced antigen expression is referred to as the In(Lu) phenotype. For accurate blood typing, it is important to distinguish between the In(Lu) phenotype, which has very weak antigen expression, and the true Lunull phenotype, which has no antigen expression. The International Society of Blood Transfusion blood group allele database registers KLF1 and GATA1 variants associated with modified Lutheran expression. Here, we review KLF1 and recent novel gene variants defined through investigating blood group phenotype and genotype discrepancies or, for one report, investigating cases with unexplained chronic anemia. In addition, we include a review of the GATA1 TF, including a case report describing the second GATA1 variant associated with a serologic Lu(a-b-) phenotype. Finally, we review both past and recent reports on variations in the DNA sequence motifs on the blood group genes that disrupt the binding of the GATA1 TF and either remove or reduce erythroid antigen expression. This review highlights the diversity and complexity of the transcription process itself and the need to consider these factors as an added component for accurate blood group phenotyping.

Abstract 3492: Comprehensive analysis of hematological malignancies with optical genome mapping and Bionano VIA™Software

Abstract The current standard for analysis of samples with suspected hematological cancer is karyotyping, fluorescence in situ hybridization (FISH), and/or chromosomal microarray (CMA). However, these methods have several limitations for the detection of structural variants (SVs) or copy number variants (CNV) that are smaller than 5 Mbp (karyotyping). Additionally, they are limited in their ability to detect low allele fraction (LAF) events and cannot detect the absence of heterozygosity (AOH) or the loss of heterozygosity (AOH/LOH - FISH and karyotyping). Optical genome mapping (OGM) from Bionano can enable accurate detection of SV and CNV events of sizes down to 5 kbp, with high sensitivity to detect LAF events down to 5% variant allele fraction. Bionano’s VIA™ software provides visualization and analysis support for OGM SV events including an improved Circos plot and ideogram for whole genome review. VIA incorporates CNV calling from OGM data using the SNP-FASST3 algorithm which also allows for accurate copy number calling at allele fractions as low as 10%. CNV detection performance was evaluated using 280 CNV events ranging in size from 175 kbp to 8 Mbp on the 22 autosomal chromosomes. Sensitivity and PPV were calculated for each size range separately. Using SNP-FASST3, VIA also adds the ability to detect AOH/LOH events from OGM data. By analyzing locations where known SNPs disrupt the specific nucleotide sequence motif used by the DLE-1 labeling enzyme, a B-allele frequency can be calculated and enable AOH/LOH detection at low allelic fractions. AOH/LOH performance using SNP-FASST3 was evaluated using a cohort of constitutional and cancer samples analyzed with orthogonal methods as well as with simulated events. Sensitivity for 20-25 Mbp AOH events was 92% with PPV greater than 90% at 25% aberrant cell fraction. The VIA 7.0 release also includes the ability to create a customizable decision tree using supplied reference annotation files for CNV, AOH and SV event pre-classification. VIA resources include a panel of target variants derived from various medical societies for clinical analysis guidelines specific to Acute Myeloid Leukemia (AML), Myelodysplastic Syndrome (MDS) and an aggregation of all hematological malignancy guidelines (pan-heme). These methods, combined with tools for expert review and reclassification of variants, allow users to conduct whole genome interpretation and report results. These new features in VIA provide a streamlined workflow for analyzing heterogeneous hematological cancer samples and demonstrate the analytical performance of updated approaches for detection of CNV and AOH/LOH regions at low allele fractions using optical genome mapping alone. Citation Format: Jacob Wisotsky, Aliz Raski, Westley Sherman, Megan Roytman, Samer Al-Saffar, Jen Hauenstein, Andy Wing Chun Pang, Viren Wasnikar, Neil Miller. Comprehensive analysis of hematological malignancies with optical genome mapping and Bionano VIA™Software [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3492.

Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation.

H-NS is a DNA organizing protein that occurs in Gram-negative bacteria. It can form long filaments between two DNA duplexes by first binding to a high-affinity AT-rich nucleotide sequence and extending from there. Using molecular dynamics simulations and steered molecular dynamics, we are able to determine the free energy of formation and dissociation of a protein-DNA complex comprising an H-NS DNA-binding domain and a specific nucleotide sequence. The molecular dynamics simulations allow detailed characterization of the interactions between the protein and a specific nucleotide sequence. To quantify the strength of the interaction, we employ an additional potential based on protein-DNA contacts to speed up dissociation of the protein-DNA complex. The work required for the dissociation results in an estimate of the free energy of dissociation/complex formation. Our protocol can provide quantitative prediction of protein-DNA complex stability, while also providing high-resolution insights into recognition mechanisms. In this chapter, we have used this approach to quantify the sequence specificity of H-NS DNA-binding domains to various nucleotide sequences, thus elucidating the mechanism with which H-NS can specifically bind to AT-rich DNA.

Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.

XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.

Base-editing mutagenesis maps alleles to tune human T cell functions.

CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with thepotential to accelerate immunotherapy design.

Structural peculiarities of tandem repeats and their clinical significance

While it is well established that a mere 2% of human DNA nucleotides are involved in protein coding, the remainder of the DNA plays a vital role in the preservation of normal cellular genetic function. A significant proportion of tandem repeats (TRs) are present in non-coding DNA. TRs - specific sequences of nucleotides that entail numerous repetitions of a given fragment.In this study, we employed our novel algorithm grounded in finite automata theory, which we refer to as Dafna, to investigate for the first time the likelihood of these nucleotide sequences forming non-canonical DNA structures (NS). Such structures include G-quadruplexes, i-motifs, hairpins, and triplexes. The tandem repeats under consideration in our research encompassed sequences containing 1 to 6 nucleotides per repeated fragment.For comparison, we employed a set of randomly generated sequences of the same length (60 nucleotides) as a benchmark. The outcomes of our research exposed a disparity between the potential for NS formation in random sequences and tandem repeats.Our findings affirm that the propensity of DNA and RNA to form NS is closely tied to various genetic disorders, including Huntington's disease, Fragile X syndrome, and Friedreich's ataxia. In the concluding discussion, we present a proposal for a new therapeutic mechanism to address these diseases. This novel approach revolves around the ability of specific nucleic acid fragments to form multiple types of NS.

Surface adsorption of adenine on pristine and B/N/O/P-doped coronene as a biosensing substrate for DNA detection- DFT study

Nucleobase detection is crucial for the exploration of specific nucleotide sequences. Inspired by the recent realization of two dimensional nanomaterials as DNA detectors as well as sensors, the interactions of pristine and B/N/O/P-doped coronenes with adenine nucleobase have been studied on the basis of Density Functional Theory. Optimal configurations, the corresponding adsorption energies, charge transfer and electrical properties have been calculated for each complex. The adsorption strength and charge transfer in doped coronene have been found larger than that in the pristine coronene. AIM-RDG study suggests that non-covalent interactions existing in the associated interactive region are responsible for the stability of the complexes. The change in electrical conductivity of coronenes after the adsorption indicates its sensitivity towards DNA bases. The predicted energy gap and the prolonged recovery time for adenine-coronene configurations imply that pristine/doped coronene has potential applications in DNA detection.

Chimeric mouse with humanized liver, an emerging tool for the drug development

Chimeric mouse with humanized liver is an experimental animal which is produced by transplanting normal human hepatocytes into a host mouse having both of immunodeficient and liver-injured characters. PXB-mouse®, which is developed and supplied by PhoenixBio group, is produced by utilizing cDNA-uPA/SCID mouse as a host animal and has a humanized liver containing over 70% of human hepatocytes. It has been utilized in the research fields of drug metabolism such as investigation of human-specific metabolites and pharmacokinetics, prediction of human DILI and development of anti-viral hepatitis drugs. Furthermore, it is expected that PXB-mouse will be valuable for the development of drugs of new modalities as the emerging technologies such as oligonucleotide medicine and gene therapy. Because it has an organ which consists almost entirely of human cells PXB-mouse is expected to be used in validation of efficacy or prediction of off-target effect caused by human specific nucleotide sequence. This paper introduces the character of PXB-mouse focusing on the successful achievements in these research fields.

Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes

ABSTRACT In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive ‘identity code’ that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

Disinfection of SARS-CoV-2 by UV-LED 267 nm: comparing different variants

UV irradiation is an efficient tool for the disinfection of viruses in general and coronavirus specifically. This study explores the disinfection kinetics of SARS-CoV-2 variants wild type (similar to the Wuhan strain) and three variants (Alpha, Delta, and Omicron) by 267 nm UV-LED. All variants showed more than 5 logs average reduction in copy number at 5 mJ/cm2 but inconsistency was evident, especially for the Alpha variant. Increasing the dose to 7 mJ/cm2 did not increase average inactivation but did result in a dramatic decrease in the inactivation inconsistency making this dose the recommended minimum. Sequence analysis suggests that the difference between the variants is likely due to small differences in the frequency of specific UV extra-sensitive nucleotide sequence motifs although this hypothesis requires further experimental testing. In summary, the use of UV-LED with their simple electricity need (can be operated from a battery or photovoltaic panel) and geometrical flexibility could offer many advantages in the prevention of SARS-CoV-2 spread, but minimal UV dose should be carefully considered.

A Qualitative PCR Assay for the Discrimination of Bubaline Herpesvirus 1, Bovine Herpesvirus 1 and Bovine Herpesvirus 5.

Bubaline herpesvirus 1 (BuHV-1), Bovine herpesvirus 1 (BoHV-1) and Bovine herpesvirus 5 (BoHV-5) are classified in the genus Varicellovirus, subfamily Alphaherpesvirinae. BoHV-1 is the causative agent of infectious bovine rhinotracheitis, BoHV-5 induces moderate disease in adult cattle while BuHV-1 has instead been associated with a decline in livestock production of water buffaloes. The aim of this study was to develop a qualitative PCR assay that allows the discrimination of BuHV-1, BoHV-1 and BoHV-5. The alignment of homologous genes identified specific nucleotide sequences of BuHV- 1, BoHV-1 and BoHV-5. The design of the primers and the optimization of the PCR assay were focused on the target sequences located on the portions of gD, gE and gG genes. This assay involved the use of three different PCR end-points: the PCR of a portion of the gD gene identified only the presence of BoHV-1; the PCR of a portion of the gE gene confirmed the presence of both BoHV-5 and BuHV-1; the PCR of a portion of the gG gene discriminated between BoHV-5 and BuHV-1, as the amplification product was observed only for BoHV-5. This qualitative PCR assay allowed the differentiation of BoHV-1 and BoHV-5 infections both in cattle and water buffaloes and heterologous BuHV-1 infections in bovine.

Whole-Mount RNA, Single-Molecule RNA (smRNA), and DNA Fluorescence In Situ Hybridization (FISH) in Mammalian Embryos.

Fluorescence in situ hybridization (FISH) provides a valuable tool for studying the spatial localization of and expression level of genes and cell function in diverse biological contexts. In this chapter, we describe a protocol for the simultaneous detection of RNA (including single-molecule (sm)RNA) and DNA in mammalian embryos using FISH. RNA FISH is a technique that enables the detection and visualization of specific RNA molecules within cells. With advancements in technology, the sensitivity and specificity of RNA FISH has been improved to allow the detection of individual mRNA molecules. Both RNA and smRNA are detected using a set of fluorescent-labeled probes, which are complementary to a specific nucleotide sequence corresponding to the gene of interest. These probes hybridize to the target RNA molecules, enabling the simultaneous detection of multiple RNAs within the same cell or tissue. DNA FISH is performed using probes directed at the DNA sequence to detect the genome region of interest. In this chapter, we provide a protocol to process mammalian embryos for FISH with probe examples specifically for studying X-Chromosome activity. By utilizing other probe designs, this protocol can be adapted for the visualization and quantification of other genes and chromosomal regions of interest.

New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease.

The RNA-guided Cas12a nuclease forms a complex with a CRISPR RNA (crRNA) to cleave the double-stranded DNA target. Among others, Cas12a protein from Lachnospiraceae bacterium (LbCas12a) is widely used for biomedical research. For target recognition, LbCas12a requires a specific nucleotide sequence, named a protospacer adjacent motif (PAM). Besides the canonical TTTV PAM, LbCas12a can recognize other suboptimal PAMs. We examined a novel TTAA PAM for the LbCas12a nuclease and found that the specificity of cleavage was increased. We found that single nucleotide substitutions at all positions of the guide RNA except the 20th position blocked the cleavage of the target DNA. The type of nucleotide substitutions (U-A, U-C or U-G) did not affect the efficiency of cleavage in the 20th position. When we used the canonical PAM under the same conditions, we observed the cleavage of target DNA by LbCas12a in many positions, showing less specificity in given conditions. The efficiency and specificity of the LbCas12a nuclease were evaluated both by gel-electrophoresis and using FAM-labeled single-stranded probes. We were able to assess the change in fluorescence intensity only for several variants of guide RNAs. High specificity allows us to type single nucleotide substitutions and small deletions/insertions (1-2 nucleotides) and look for target mutations when knocking out.

Machine learning techniques for identification of carcinogenic mutations, which cause breast adenocarcinoma

Breast adenocarcinoma is the most common of all cancers that occur in women. According to the United States of America survey, more than 282,000 breast cancer patients are registered each year; most of them are women. Detection of cancer at its early stage saves many lives. Each cell contains the genetic code in the form of gene sequences. Changes in the gene sequences may lead to cancer. Replication and/or recombination in the gene base sometimes lead to a permanent change in the nucleotide sequence of the genome, called a mutation. Cancer driver mutations can lead to cancer. The proposed study develops a framework for the early detection of breast adenocarcinoma using machine learning techniques. Every gene has a specific sequence of nucleotides. A total of 99 genes are identified in various studies whose mutations can lead to breast adenocarcinoma. This study uses the dataset taken from 4127 human samples, including men and women from more than 12 cohorts. A total of 6170 mutations in gene sequences are used in this study. Decision Tree, Random Forest, and Gaussian Naïve Bayes are applied to these gene sequences using three evaluation methods: independent set testing, self-consistency testing, and tenfold cross-validation testing. Evaluation metrics such as accuracy, specificity, sensitivity, and Mathew’s correlation coefficient are calculated. The decision tree algorithm obtains the best accuracy of 99% for each evaluation method.

A unifying network modeling approach for codon optimization.

Synthesizing genes to be expressed in other organisms is an essential tool in biotechnology. While the many-to-one mapping from codons to amino acids makes the genetic code degenerate, codon usage in a particular organism is not random either. This bias in codon use may have a remarkable effect on the level of gene expression. A number of measures have been developed to quantify a given codon sequence's strength to express a gene in a host organism. Codon optimization aims to find a codon sequence that will optimize one or more of these measures. Efficient computational approaches are needed since the possible number of codon sequences grows exponentially as the number of amino acids increases. We develop a unifying modeling approach for codon optimization. With our mathematical formulations based on graph/network representations of amino acid sequences, any combination of measures can be optimized in the same framework by finding a path satisfying additional limitations in an acyclic layered network. We tested our approach on bi-objectives commonly used in the literature, namely, Codon Pair Bias versus Codon Adaptation Index and Relative Codon Pair Bias versus Relative Codon Bias. However, our framework is general enough to handle any number of objectives concurrently with certain restrictions or preferences on the use of specific nucleotide sequences. We implemented our models using Python's Gurobi interface and showed the efficacy of our approach even for the largest proteins available. We also provided experimentation showing that highly expressed genes have objective values close to the optimized values in the bi-objective codon design problem. http://alpersen.bilkent.edu.tr/NetworkCodon.zip. Supplementary data are available at Bioinformatics online.

Label-free and highly sensitive detection of CRP based on the combination of nicking endonuclease-assisted signal amplification and capillary electrophoresis-UV assay

Elevated C-reactive protein (CRP) levels are linked with bacterial infection, local inflammation in osteoarthritis and the increased risk of developing cardiovascular disease. Here, a sensitive and label-free CRP assay is developed by combining cyclic enzymatic signal amplification and capillary electrophoresis (CE) with UV detection. This assay is constructed of base pairing and target recognition. Thereinto, nicking endonuclease (NEase) can recognize the specific nucleotide sequences in double-stranded DNA (dsDNA), which is formed by a CRP aptamer and its complementary DNA (cDNA). Sequentially, NEase cleaves only cDNA to produce signal DNAs. Therefore, a large number of signal DNAs are generated through continuous enzyme cleavage. In the presence of CRP, the aptamer recognizes and binds to CRP with high affinity and selectivity, which results in a decrease in signal DNAs, and thus the UV absorption value of CE significantly decreases, too. A wide linear range was obtained between 0.0125 and 15 μg mL−1 (0.11–130.5 nM) in 1% human serum with a detection limit of 4 ng mL−1 (35 pM). Additionally, the proposed method is universal and can be applied to analyze other similar substances by altering the matched aptamer.

Efficient Screening of Pesticide Diazinon-Binding Aptamers Using the Sol-Gel-Coated Nanoporous Membrane-Assisted SELEX Process and Next-Generation Sequencing.

Aptamer-based methods for detecting pesticides are more efficient than antibody-based methods by high thermal stability, low molecular weight, easy modification, and low cost. In this study, the systematic evolution of ligands by exponential enrichment (SELEX) process, combined with next-generation sequencing (NGS), was performed to select aptamers specific to the pesticide, diazinon, which was fixed on a sol-gel-coated nanoporous-anodized aluminum oxide membrane to overcome the immobilization effect of general method and simplify the elution step. The frequency of specific nucleotide sequences obtained after SELEX rounds was directly analyzed using NGS to eliminate the time-consuming cloning process used in the general SELEX methods. Nine sequences with the highest frequency after SELEX round 10 followed by NGS were selected and tested to derive their binding affinity with the target, diazinon, through circular dichroism (CD) spectrophotometry. The CD signal difference of the aptamer candidates ranged from 0.13 to 2.242 mdeg between diazinon-only treated and diazinon-aptamer-treated samples at a wavelength near 270nm. Aptamer D-4, which had the highest binding affinity from CD spectrophotometry analysis, showed no cross-reactivity with non-target pesticides, such as baycarb, bifenthrin, and pyridaben, but interacted with the other pesticides, fipronil and 2-phenylphenol. Therefore, an aptamer was effectively screened by selection of high-frequency candidates after SELEX-NGS followed by CD analysis with the highest difference signal. A follow-up study is needed to confirm whether the proposed SELEX process combined with NGS for the discovery of aptamers for new targets can further shorten the SELEX cycle by reducing the number of SELEX rounds to 10 or less.

MonaLisa: an R/Bioconductor package for identifying regulatory motifs.

SummaryProteins binding to specific nucleotide sequences, such as transcription factors, play key roles in the regulation of gene expression. Their binding can be indirectly observed via associated changes in transcription, chromatin accessibility, DNA methylation and histone modifications. Identifying candidate factors that are responsible for these observed experimental changes is critical to understand the underlying biological processes. Here, we present monaLisa, an R/Bioconductor package that implements approaches to identify relevant transcription factors from experimental data. The package can be easily integrated with other Bioconductor packages and enables seamless motif analyses without any software dependencies outside of R. Availability and implementation monaLisa is implemented in R and available on Bioconductor at https://bioconductor.org/packages/monaLisa with the development version hosted on GitHub at https://github.com/fmicompbio/monaLisa.Supplementary information Supplementary data are available at Bioinformatics online.