Browsing Faculty of Arts and Sciences by Keyword "Bioinformatics"
Now showing items 1-20 of 101
-
A genomics love story: Tying the knot between micro- and macroevolution in the Mycobacterium tuberculosis complex
(2021-08-24)Tuberculosis (TB) is a leading cause of death globally. Understanding the population dynamics and evolution of TB’s causative agent Mycobacterium tuberculosis complex (MTBC) over short time-scales in-host (micro-evolution) ... -
Accelerating the Understanding and Design of Intracellular Biosensors by Massively Multiplexed Experimentation and Machine Learning
(2021-01-06)Recent progress in large-scale DNA synthesis and next-generation DNA sequencing technology have enabled studies of biological processes at a massive scale. These studies can be further coupled to advanced computational ... -
AGE REVERSAL BY TRANSCRIPTOMIC REPROGRAMMING
(2022-11-23)Aging is a progressive multifaceted functional decline of a biological system. Chronic age-related conditions such as cancer, cardiovascular, and neurodegenerative diseases are leading causes of death worldwide. As the ... -
Algorithms and Models for Genome Biology
(2014-02-25)New advances in genomic technology make it possible to address some of the most fundamental questions in biology for the first time. They also highlight a need for new approaches to analyze and model massive amounts of ... -
An Inverse Statistical Physics Method for Biological Sequence Analysis
(2021-05-13)Comparative sequence analysis is a robust tool for determining whether a new biological sequence of unknown function is evolutionarily related, or homologous, to pre-observed sequences or families of sequences. It is common ... -
Analyzing the multidimensionality of aging by using machine learning to predict age from diverse medical datasets
(2021-05-12)The world population is aging, leading to a rise in the prevalence of age-related diseases such as cardiovascular disease and cancer. In parallel to treating the diseases, an attractive idea is to address the problem at ... -
Approaches for understanding relationships between cancer genomes and clinical cancer features
(2021-11-16)Cancer is a disease of the genome. Understanding what somatic alterations drive cancer and how they affect cancer treatment outcomes is a central goal of cancer genomics. Next-generation sequencing of cancer has led to ... -
Bridging single-cell genomics and tissue spatial organization in health and cancer
(2022-06-06)The genomic profile of cells manifests itself in the local and global geometry of tissues. Tissue organization informs both normal physiological function in times of health, such as the rapid deployment of immune cells to ... -
Characterization of the functions and therapeutic potential of deubiquitinating enzymes in oncology
(2021-09-02)DUBs are dysregulated in cancer and other diseases, but there is much that is unknown about the specific substrates and pathways that individual DUBs regulate and their clinical utility remains incompletely explored. In ... -
Characterizing Regulatory Elements and Non-Coding Variants in the Human Genome
(2023-05-02)Regulatory elements and the non-coding variants within them govern the spatiotemporal expression of genes as part of coordinated sets of networks, mediated by the combinatorial binding of transcription factors. The mechanisms ... -
Clinical trial data science to advance precision oncology
(2022-04-04)Clinical trials are the most expensive and highest-stakes experiments in biomedicine, and their results determine which therapies are ultimately used to treat patients. While a typical pivotal trial costs millions of dollars ... -
Combination Antibiotic-Focused Machine Learning Models for Integration into Experimental Workflows
(2022-06-02)Antibiotic resistance is a growing crisis with far-reaching impacts on public and global health [1][2]. With antibiotic resistance impeding the efficacy of antibiotics and the discovery of new antibiotics slowing [2], ... -
Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders
(2013-10-08)Mitochondria are responsible for many fundamental biological pathways and metabolic processes, including aerobic ATP production by the mitochondrial respiratory chain. In humans, mitochondrial dysfunction can lead to severe ... -
Computational Approaches to Developmental Biology
(2021-01-20)The origin and evolution of new genes is an active topic of research, relying on the taxonomical diversity now present in sequence databases. Using those databases, we described how \textit{oskar}, a key determinant of ... -
Computational Prediction of Alternative Translation Events
(2023-12-20)The regulation of gene expression is a fundamental and exquisitely orchestrated molecular process, ensuring the proper synthesis of proteins for cellular function. In the classic canon of molecular biology, mRNA is ... -
Cumulative effect of multi-exposures on complex traits and diseases: derivation and applications of the polyexposure risk score
(2022-05-12)Human diseases and traits are influenced by a combination of genetic and environmental factors. Genetic risk scores, which reflect the aggregate genetic predisposition from many markers across the genome, are being developed ... -
Deciphering the Biological Mechanisms Driving the Phenotype of Interest
(2013-03-15)The two key concepts of Neo-Darwinian evolution theory are genotype and phenotype. Genotype is defined as the genetic constitution of an organism and phenotype refers to the observable characteristics of that organism. ... -
Decoding the function of human variation
(2022-11-23)Gene regulation is fundamental to the identity and survival of every cell. While less than 2% of the human genome is dedicated to protein-coding sequence, at least 19% of the genome is associated with open chromatin or ... -
Deep Learning Models for Variant Pathogenicity Prediction
(2021-06-04)Technological advancements in DNA sequencing have made it a mainstay in the clinic in the form of targeted genetic testing as well as whole exome and whole genome sequencing (WES and WGS, respectively). With increased use ... -
Delineating genome alterations in cancer with long-read and linked-read sequencing
(2023-06-01)Cancer is driven by alterations to the genome. The continued invention and application of new methods has gradually enhanced our ability to characterize of genome alterations in cancer with much greater scale and resolution. ...