Recent Submissions

  • SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data 

    Zafar, Hamim; Navin, Nicholas; Chen, Ken; Nakhleh, Luay (2019)
    Accumulation and selection of somatic mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity. Recently ...
  • Hepatitis E Virus (HEV)-Specific T Cell Receptor Cross-Recognition: Implications for Immunotherapy 

    Soon, Chai Fen; Zhang, Shihong; Suneetha, Pothakamuri Venkata; Antunes, Dinler Amaral; Manns, Michael Peter; (2019)
    T cell immunotherapy is a concept developed for the treatment of cancer and infectious diseases, based on cytotoxic T lymphocytes to target tumor- or pathogen-specific antigens. Antigen-specificity of the T cell receptors (TCRs) is an important selection criterion in the developmental design of immunotherapy. However, off-target specificity is a ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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.
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Machine Learning-Guided Three-Dimensional Printing of Tissue Engineering Scaffolds 

    Conev, Anja; Litsa, Eleni E.; Perez, Marissa R.; Diba, Mani; Mikos, Antonios G.; (2020)
    Various material compositions have been successfully used in 3D printing with promising applications as scaffolds in tissue engineering. However, identifying suitable printing conditions for new materials requires extensive experimentation in a time and resource-demanding process. This study investigates the use of Machine Learning (ML) for distinguishing ...
  • The Chemical Basis of Intracerebral Hemorrhage and Cell Toxicity With Contributions From Eryptosis and Ferroptosis 

    Derry, Paul J.; Vo, Anh Tran Tram; Gnanansekaran, Aswini; Mitra, Joy; Liopo, Anton V.; (2020)
    Intracerebral hemorrhage (ICH) is a particularly devastating event both because of the direct injury from space-occupying blood to the sequelae of the brain exposed to free blood components from which it is normally protected. Not surprisingly, the usual metabolic and energy pathways are overwhelmed in this situation. In this review article, we detail ...
  • Prediction of drug metabolites using neural machine translation 

    Litsa, Eleni E.; Das, Payel; Kavraki, Lydia E. (2020)
    Metabolic processes in the human body can alter the structure of a drug affecting its efficacy and safety. As a result, the investigation of the metabolic fate of a candidate drug is an essential part of drug design studies. Computational approaches have been developed for the prediction of possible drug metabolites in an effort to assist the traditional ...
  • 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 ...
  • 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, ...
  • 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 ...
  • 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, ...

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