Biology subjects

Amaral, L. A. N.

Publications and source records attributed to Amaral, L. A. N..

7 recordsLinked to original sources

bioRxiv2025

A principled approach to the identification of biologically relevant transcription factor binding sites

Transcription factors (TF) regulate gene expression in cells by binding to specific DNA sequences. However, previous studies indicate that TF binding is a necessary but not sufficient condition for regulating gene expression.1-3 While recent advances in sequencing technologies such as Chromatin Immunoprecipitation sequencing (ChIP-seq) enable researchers to identify binding sequences at single nucleotide resolution, they often fail to distinguish between biologically relevant and non-relevant - i.e., spurious - binding events. Reliably distinguishing between these two types of binding is essential if one aims for reproducible findings. Here, we report on a systematic study of the sensitivity of "called" TF-target gene interactions to the choice of various data processing parameters. We find that acceptable distance from the transcription start site (TSS) is a critical parameter for reducing subjectivity. We, thus, develop a two-state mechanistic model that captures the positional distribution of both biologically relevant and spurious binding events, allowing us to identify interaction distance thresholds that minimize spurious binding. We validate our model with independent data by showing that biologically relevant binding events identified by our model are capable of recruiting RNA Polymerase II and, subsequently, regulating mRNA expression levels of the target gene. Finally, we investigate the impact of our approach on the detection of genes that are differentially bound and regulated by BCL3, a transcription coactivator, during molecular perturbation experiments. Within the genes expected to show differential expression, our model predicts that over 70% of reported interactions are spurious and we demonstrate the lack of change in mRNA expression in these genes following perturbation. We also identify genes that display a shift from spurious to biologically relevant binding that account for close to 17% of the genes displaying a sharp change in mRNA expression and strong association with known functions of BCL3 such as cell cycle regulation and DNA damage response. By providing a systematic TF-specific method to identify binding events that are directly involved in transcriptional regulation our model will increase reproducibility of analysis.

genomics↗

bioRxiv2025

The evolution of interdisciplinarity and internationalization in scientific journals

There is a widely-held perception that science is becoming increasingly international -- both in terms of collaborations involving authors from multiple countries and in terms of publications from authors from a broader group of countries -- and more interdisciplinary, i.e., drawing on knowledge and methods from multiple scholarship domains. However, these hypothesized trends have not yet been characterized quantitatively at the level of individual discipline. The widespread availability of scholarly metadata on scientific publications makes it possible to examine how science has evolved over time. Here, we use OpenAlex metadata to examine potential trends in two groups of peer-reviewed research journals: disciplinary journals in biology, chemistry, economics, medicine, physics, and political science, and multidisciplinary journals that publish articles from multiple fields. Supporting existing perceptions, we find an almost universal trend towards increasing internationalization of both sets of journals. Nevertheless, we find disparities: journals in medicine are less international than journals in other disciplines and are not increasing their levels of internationalization, whereas journals in physics appear to be segregating between those that are international and those that are not. We also find that multidisciplinary journals have undergone significant shifts in their disciplinary focuses over the past century, whereas disciplinary journals appear to have largely maintained their degree of interdisciplinarity.

scientific communication and education↗

bioRxiv2023

Energy metabolism modulates the regulatory impact of activators on gene expression

Gene expression is a regulated process fueled by ATP consumption. Therefore, regulation must be coupled to constraints imposed by the level of energy metabolism. Here, we explore this relationship both theoretically and experimentally. A stylized mathematical model predicts that activators of gene expression have variable impact depending on metabolic rate. Activators become less essential when metabolic rate is reduced and more essential when metabolic rate is enhanced. We find that in the Drosophila eye, expression dynamics of the yan gene are less affected by loss of EGFR-mediated activation when metabolism is reduced, and the opposite effect is seen when metabolism is enhanced. The effects are also seen at the level of pattern regularity in the adult eye, where loss of EGFR-mediated activation is mitigated by lower metabolism. We propose that gene activation is tuned by energy metabolism to allow for faithful expression dynamics in the face of variable metabolic conditions.

developmental biology↗

bioRxiv2023

Data-driven design of a tool to promote the investigation of understudied genes

Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of - omics studies. To promote the investigation of understudied genes we condense our insights into a tool, find my understudied genes (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.

genomics↗

bioRxiv2020

Information-theory-based benchmarking and feature selection algorithm improve cell type annotation and reproducibility of single cell RNA-seq data analysis pipelines

Single cell RNA sequencing (scRNA-seq) data are now routinely generated in experimental practice because of their promise to enable the quantitative study of biological processes at the single cell level. However, cell type and cell state annotations remain an important computational challenge in analyzing scRNA-seq data. Here, we report on the development of a benchmark dataset where reference annotations are generated independently from transcriptomic measurements. We used this benchmark to systematically investigate the impact on labelling accuracy of different approaches to feature selection, of different clustering algorithms, and of different sets of parameter values. We show that an approach grounded on information theory can provide a general, reliable, and accurate process for discarding uninformative features and to optimize cluster resolution in single cell RNA-seq data analysis.

bioinformatics↗

bioRxiv2018

Ratio-based sensing of two transcription factors regulates the transit to differentiation

Cell state transitions are often triggered by large changes in the absolute concentrations of transcription factors and therefore large differences in the stoichiometric ratios between these factors. Whether cells can elicit state transitions using modest changes in the relative ratios of co-expressed factors is unclear. In this study we investigate how cells in the Drosophila eye resolve cell state transitions by quantifying the expression dynamics of the ETS transcription factors Pnt and Yan. We find that eye progenitor cells maintain a relatively constant ratio of Pnt/Yan protein despite expressing both proteins with pulsatile dynamics. A rapid and sustained two-fold increase in the Pnt/Yan ratio accompanies transitions to photoreceptor fates. Genetic perturbations that modestly disrupt the Pnt/Yan ratio produce fate transition defects consistent with the hypothesis that transitions are normally driven by a two-fold shift in the ratio. A biophysical model based on cooperative Yan-DNA binding coupled with non-cooperative Pnt-DNA binding illustrates how two-fold ratio changes could generate ultrasensitive changes in target gene transcription to drive fate transitions. In this way, coupling cell state transitions to the Pnt/Yan stoichiometric ratio sensitizes the system to modest fold-changes, conferring both robustness and ultrasensitivity to the developmental program.

developmental biology↗

bioRxiv2018

Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.\n\nOne Sentence SummarySingle-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.

systems biology↗