Now showing items 1-20 of 119

    • Domain-driven models yield better predictions at lower cost than reservoir computers in Lorenz systems 

      Pyle, Ryan; Jovanovic, Nikola; Subramanian, Devika; Palem, Krishna V.; Patel, Ankit B. (2021)
      Recent advances in computing algorithms and hardware have rekindled interest in developing high-accuracy, low-cost surrogate models for simulating physical systems. The idea is to replace expensive numerical integration of complex coupled partial differential equations at fine time scales performed on supercomputers, with machine-learned surrogates ...
    • Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome 

      Edwards, Richard J.; Field, Matt A.; Ferguson, James M.; Dudchenko, Olga; Keilwagen, Jens; (2021)
      Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to ...
    • SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission 

      Sapoval, Nicolae; Mahmoud, Medhat; Jochum, Michael D.; Liu, Yunxi; Elworth, R. A. Leo; (2021)
      The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we ...
    • Integrative Generalized Convex Clustering Optimization and Feature Selection for Mixed Multi-View Data 

      Wang, Minjie; Allen, Genevera I. (2021)
      In mixed multi-view data, multiple sets of diverse features are measured on the same set of samples. By integrating all available data sources, we seek to discover common group structure among the samples that may be hidden in individualistic cluster analyses of a single data view. While several techniques for such integrative clustering have been ...
    • Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial 

      Molino, Silvia; Pisarevsky, Andrea; Mingorance, Fabiana Lopez; Vega, Patricia; Stefanolo, Juan Pablo; (2021)
      This research aims to study the efficacy of tannins co-supplementation on disease duration, severity and clinical symptoms, microbiota composition and inflammatory mediators in SARS-CoV2 patients.
    • Downregulation of glial genes involved in synaptic function mitigates Huntington's disease pathogenesis 

      Onur, Tarik Seref; Laitman, Andrew; Zhao, He; Keyho, Ryan; Kim, Hyemin; (2021)
      Most research on neurodegenerative diseases has focused on neurons, yet glia help form and maintain the synapses whose loss is so prominent in these conditions. To investigate the contributions of glia to Huntington's disease (HD), we profiled the gene expression alterations of Drosophila expressing human mutant Huntingtin (mHTT) in either glia or ...
    • Chromatin architecture transitions from zebrafish sperm through early embryogenesis 

      Wike, Candice L.; Guo, Yixuan; Tan, Mengyao; Nakamura, Ryohei; Shaw, Dana Klatt; (2021)
      Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation ...
    • Phylogenomic assessment of the role of hybridization and introgression in trait evolution 

      Wang, Yaxuan; Cao, Zhen; Ogilvie, Huw A.; Nakhleh, Luay (2021)
      Trait evolution among a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding ...
    • Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment 

      Fu, Yilei; Mahmoud, Medhat; Muraliraman, Viginesh Vaibhav; Sedlazeck, Fritz J; Treangen, Todd J (2021)
      Long-read sequencing has enabled unprecedented surveys of structural variation across the entire human genome. To maximize the potential of long-read sequencing in this context, novel mapping methods have emerged that have primarily focused on either speed or accuracy. Various heuristics and scoring schemas have been implemented in widely used read ...
    • DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins 

      Hall-Swan, Sarah; Devaurs, Didier; Rigo, Mauricio M.; Antunes, Dinler A.; Kavraki, Lydia E.; (2021)
      An unprecedented research effort has been undertaken in response to the ongoing COVID-19 pandemic. This has included the determination of hundreds of crystallographic structures of SARS-CoV-2 proteins, and numerous virtual screening projects searching large compound libraries for potential drug inhibitors. Unfortunately, these initiatives have had ...
    • HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy 

      Antunes, Dinler A.; Abella, Jayvee R.; Hall-Swan, Sarah; Devaurs, Didier; Conev, Anja; (2020)
      PURPOSE: HLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because T-cell activation is partially driven by structural features of these peptide-HLA complexes, their structural modeling and analysis are becoming central components of cancer immunotherapy ...
    • Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis 

      Roussarie, Jean-Pierre; Yao, Vicky; Rodriguez-Rodriguez, Patricia; Oughtred, Rose; Rust, Jennifer; (2020)
      A major obstacle to treating Alzheimer's disease (AD) is our lack of understanding of the molecular mechanisms underlying selective neuronal vulnerability, a key characteristic of the disease. Here, we present a framework integrating high-quality neuron-type-specific molecular profiles across the lifetime of the healthy mouse, which we generated using ...
    • Data-driven predictions of a multiscale Lorenz 96 chaotic system using machine-learning methods: reservoir computing, artificial neural network, and long short-term memory network 

      Chattopadhyay, Ashesh; Hassanzadeh, Pedram; Subramanian, Devika (2020)
      In this paper, the performance of three machine-learning methods for predicting short-term evolution and for reproducing the long-term statistics of a multiscale spatiotemporal Lorenz 96 system is examined. The methods are an echo state network (ESN, which is a type of reservoir computing; hereafter RC–ESN), a deep feed-forward artificial neural ...
    • Methods for copy number aberration detection from single-cell DNA-sequencing data 

      Mallory, Xian F.; Edrisi, Mohammadamin; Navin, Nicholas; Nakhleh, Luay (2020)
      Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have been developed for detecting CNAs in scDNAseq data, ...
    • Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data 

      Mallory, Xian F.; Edrisi, Mohammadamin; Navin, Nicholas; Nakhleh, Luay (2020)
      Single-cell DNA sequencing technologies are enabling the study of mutations and their evolutionary trajectories in cancer. Somatic copy number aberrations (CNAs) have been implicated in the development and progression of various types of cancer. A wide array of methods for CNA detection has been either developed specifically for or adapted to single-cell ...
    • Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests 

      Abella, Jayvee R.; Antunes, Dinler A.; Clementi, Cecilia; Kavraki, Lydia E.; Center for Theoretical Biological Physics (2020)
      Prediction of stable peptide binding to Class I HLAs is an important component for designing immunotherapies. While the best performing predictors are based on machine learning algorithms trained on peptide-HLA (pHLA) sequences, the use of structure for training predictors deserves further exploration. Given enough pHLA structures, a predictor based ...
    • Quantifying cognitive resilience in Alzheimer’s Disease: The Alzheimer’s Disease Cognitive Resilience Score 

      Yao, Tianyi; Sweeney, Elizabeth; Nagorski, John; Shulman, Joshua M.; Allen, Genevera I. (2020)
      Even though there is a clear link between Alzheimer’s Disease (AD) related neuropathology and cognitive decline, numerous studies have observed that healthy cognition can exist in the presence of extensive AD pathology, a phenomenon sometimes called Cognitive Resilience (CR). To better understand and study CR, we develop the Alzheimer’s Disease ...
    • Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G 

      Arns, Thais; Antunes, Dinler A.; Abella, Jayvee R.; Rigo, Maurício M.; Kavraki, Lydia E.; (2020)
      HLA-G is considered to be an immune checkpoint molecule, a function that is closely linked to the structure and dynamics of the different HLA-G isoforms. Unfortunately, little is known about the structure and dynamics of these isoforms. For instance, there are only seven crystal structures of HLA-G molecules, being all related to a single isoform, ...
    • Cohesin depleted cells rebuild functional nuclear compartments after endomitosis 

      Cremer, Marion; Brandstetter, Katharina; Maiser, Andreas; Rao, Suhas S.P.; Schmid, Volker J.; (2020)
      Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is less well understood. Using live-cell and super-resolved 3D microscopy, here we find that cohesin depletion in a human colon cancer derived cell line results in endomitosis and a single multilobulated ...