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  • Multiple genome alignment in the telomere-to-telomere assembly era 

    Kille, Bryce; Balaji, Advait; Sedlazeck, Fritz J.; Nute, Michael; Treangen, Todd J. (2022)
    With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome alignments commonly serve as the bedrock for comparative ...
  • Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection 

    Adenaiye, Oluwasanmi O; Lai, Jianyu; Bueno de Mesquita, P Jacob; Hong, Filbert; Youssefi, Somayeh; (2022)
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks and variants on aerosol shedding are not well understood.We recruited coronavirus disease 2019 (COVID-19) cases to give blood, saliva, mid-turbinate and fomite (phone) swabs, and 30-minute breath ...
  • Accelerating High-Order Stencils on GPUs 

    Sai, Ryuichi; Mellor-Crummey, John; Meng, Xiaozhu; Araya-Polo, Mauricio; Meng, Jie (2020)
    While implementation strategies for low-order stencils on GPUs have been well-studied in the literature, not all of the techniques work well for high-order stencils, such as those used for seismic imaging. In this paper, we study practical seismic imaging computations on GPUs using high-order stencils on large domains with meaningful boundary conditions. ...
  • A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population 

    Wilder, Aryn P; Dudchenko, Olga; Curry, Caitlin; Korody, Marisa; Turbek, Sheela P; (2022)
    High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model ...
  • MotionBenchMaker: A Tool to Generate and Benchmark Motion Planning Datasets 

    Chamzas, Constantinos; Quintero-Peña, Carlos; Kingston, Zachary; Orthey, Andreas; Rakita, Daniel; (2022)
    Recently, there has been a wealth of development in motion planning for robotic manipulation—new motion planners are continuously proposed, each with their own unique strengths and weaknesses. However, evaluating new planners is challenging and researchers often create their own ad-hoc problems for benchmarking, which is time-consuming, prone to bias, ...
  • SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development 

    Rigo, Mauricio Menegatti; Fasoulis, Romanos; Conev, Anja; Hall-Swan, Sarah; Antunes, Dinler Amaral; (2022)
    The pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope ...
  • Annotation-free delineation of prokaryotic homology groups 

    Yin, Yongze; Ogilvie, Huw A.; Nakhleh, Luay (2022)
    Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate ...
  • Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data 

    Edrisi, Mohammadamin; Valecha, Monica V; Chowdary, Sunkara B V; Robledo, Sergio; Ogilvie, Huw A; (2022)
    Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCIΦ and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these ...
  • Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes 

    Yan, Zhi; Cao, Zhen; Liu, Yushu; Ogilvie, Huw A; Nakhleh, Luay (2022)
    Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been ...
  • Current progress and open challenges for applying deep learning across the biosciences 

    Sapoval, Nicolae; Aghazadeh, Amirali; Nute, Michael G.; Antunes, Dinler A.; Balaji, Advait; (2022)
    Deep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future perspectives of DL on five broad areas: protein structure prediction, protein function prediction, genome ...
  • Fecal Microbiota Transplantation Derived from Alzheimer’s Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls 

    Soriano, Sirena; Curry, Kristen; Wang, Qi; Chow, Elsbeth; Treangen, Todd J.; (2022)
    Traumatic brain injury (TBI) causes neuroinflammation and neurodegeneration, both of which increase the risk and accelerate the progression of Alzheimer’s disease (AD). The gut microbiome is an essential modulator of the immune system, impacting the brain. AD has been related with reduced diversity and alterations in the community composition of the ...
  • Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters 

    Gallego-García, Pilar; Varela, Nair; Estévez-Gómez, Nuria; De Chiara, Loretta; Fernández-Silva, Iria; (2022)
    A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends ...
  • Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data 

    Liu, Yunxi; Kearney, Joshua; Mahmoud, Medhat; Kille, Bryce; Sedlazeck, Fritz J.; (2022)
    Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of ...
  • Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater 

    Robledo-Ruiz, Diana A; Gan, Han Ming; Kaur, Parwinder; Dudchenko, Olga; Weisz, David; (2022)
    The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage ...
  • Chromosome size affects sequence divergence between species through the interplay of recombination and selection 

    Tigano, Anna; Khan, Ruqayya; Omer, Arina D.; Weisz, David; Dudchenko, Olga; (2022)
    The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from ...
  • A CRISPR toolbox for generating intersectional genetic mouse models for functional, molecular, and anatomical circuit mapping 

    Lusk, Savannah J.; McKinney, Andrew; Hunt, Patrick J.; Fahey, Paul G.; Patel, Jay; (2022)
    The functional understanding of genetic interaction networks and cellular mechanisms governing health and disease requires the dissection, and multifaceted study, of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic effector alleles represents a significant and powerful approach to delineate ...
  • Backpropagation-Based Decoding for Multimodal Machine Translation 

    Yang, Ziyan; Pinto-Alva, Leticia; Dernoncourt, Franck; Ordonez, Vicente (2022)
    People are able to describe images using thousands of languages, but languages share only one visual world. The aim of this work is to use the learned intermediate visual representations from a deep convolutional neural network to transfer information across languages for which paired data is not available in any form. Our work proposes using ...
  • Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2 

    Tarabini, Renata Fioravanti; Rigo, Mauricio Menegatti; Faustino Fonseca, André; Rubin, Felipe; Bellé, Rafael; (2022)
    Although not being the first viral pandemic to affect humankind, we are now for the first time faced with a pandemic caused by a coronavirus. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been responsible for the COVID-19 pandemic, which caused more than 4.5 million deaths worldwide. Despite unprecedented efforts, with vaccines ...
  • BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis 

    Bouckaert, Remco; Vaughan, Timothy G.; Barido-Sottani, Joëlle; Duchêne, Sebastián; Fourment, Mathieu; (2019)
    Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including ...
  • 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 ...

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