Now showing items 1-20 of 97

    • 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; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E. (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 ...
    • Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis 

      Roussarie, Jean-Pierre; Yao, Vicky; Rodriguez-Rodriguez, Patricia; Oughtred, Rose; Rust, Jennifer; Plautz, Zakary; Kasturia, Shirin; Albornoz, Christian; Wang, Wei; Schmidt, Eric F.; Dannenfelser, Ruth; Tadych, Alicja; Brichta, Lars; Barnea-Cramer, Alona; Heintz, Nathaniel; Hof, Patrick R.; Heiman, Myriam; Dolinski, Kara; Flajolet, Marc; Troyanskaya, Olga G.; Greengard, Paul (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 ...
    • 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 ...
    • A divide-and-conquer method for scalable phylogenetic network inference from multilocus data 

      Zhu, Jiafan; Liu, Xinhao; Ogilvie, Huw A.; Nakhleh, Luay K. (2019)
      Motivation: Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic ...
    • Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins 

      Devaurs, Didier; Antunes, Dinler A.; Hall-Swan, Sarah; Mitchell, Nicole; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E. (2019)
      Background: Docking large ligands, and especially peptides, to protein receptors is still considered a challenge in computational structural biology. Besides the issue of accurately scoring the binding modes of a protein-ligand ...
    • MetaCarvel: linking assembly graph motifs to biological variants 

      Ghurye, Jay; Treangen, Todd; Fedarko, Marcus; Hervey, W. Judson; Pop, Mihai (2019)
      Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage ...
    • Automated Abstraction of Manipulation Domains for Cost-Based Reactive Synthesis 

      He, Keliang; Lahijanian, Morteza; Kavraki, Lydia E.; Vardi, Moshe Y. (2019)
      When robotic manipulators perform high-level tasks in the presence of another agent, e.g., a human, they must have a strategy that considers possible interferences in order to guarantee task completion and efficient resource ...
    • Rational curves over generalized complex numbers 

      Du, Juan; Goldman, Ron; Wang, Xuhui (2019)
      Complex rational curves have been used to represent circular splines as well as many classical curves including epicycloids, cardioids, Joukowski profiles, and the lemniscate of Bernoulli. Complex rational curves are known ...
    • Point-Based Policy Synthesis for POMDPs With Boolean and Quantitative Objectives 

      Wang, Yue; Chaudhuri, Swarat; Kavraki, Lydia E. (2019)
      Effectively planning robust executions under uncertainty is critical for building autonomous robots. Partially observable Markov decision processes (POMDPs) provide a standard framework for modeling many robot applications ...
    • Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics 

      Bravo, Gustavo A.; Antonelli, Alexandre; Bacon, Christine D.; Bartoszek, Krzysztof; Blom, Mozes P.K.; Huynh, Stella; Jones, Graham; Knowles, L. Lacey; Lamichhaney, Sangeet; Marcussen, Thomas; Morlon, Hélène; Nakhleh, Luay K.; Oxelman, Bengt; Pfeil, Bernard; Schliep, Alexander; Wahlberg, Niklas; Werneck, Fernanda P.; Wiedenhoeft, John; Willows-Munro, Sandi; Edwards, Scott V. (2019)
      Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the ...
    • Macronutrient variability in human milk from donors to a milk bank: Implications for feeding preterm infants 

      John, Ashley; Sun, Ruichen; Maillart, Lisa; Schaefer, Andrew; Spence, Erin Hamilton; Perrin, Maryanne T. (2019)
      Background and objective: The composition of human milk varies widely and impacts the ability to meet nutrient requirements for preterm infants. The purpose of this study is to use a large dataset of milk composition from ...
    • APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations 

      Abella, Jayvee R.; Antunes, Dinler A.; Clementi, Cecilia; Kavraki, Lydia E. (2019)
      The Class I Major Histocompatibility Complex (MHC) is a central protein in immunology as it binds to intracellular peptides and displays them at the cell surface for recognition by T-cells. The structural analysis of bound ...
    • An incremental constraint-based framework for task and motion planning 

      Dantam, Neil T.; Kingston, Zachary K.; Chaudhuri, Swarat; Kavraki, Lydia E. (2018)
      We present a new constraint-based framework for task and motion planning (TMP). Our approach is extensible, probabilistically complete, and offers improved performance and generality compared with a similar, state-of-the-art ...
    • Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods 

      Abella, Jayvee R.; Moll, Mark; Kavraki, Lydia E. (2018)
      The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational ...
    • Quantitative comparison of adaptive sampling methods for protein dynamics 

      Hruska, Eugen; Abella, Jayvee R.; Nüske, Feliks; Kavraki, Lydia E.; Clementi, Cecilia (2018)
      Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. ...
    • Bayesian inference of phylogenetic networks from bi-allelic genetic markers 

      Zhu, Jiafan; Wen, Dingqiao; Yu, Yun; Meudt, Heidi M.; Nakhleh, Luay (2018)
      Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence ...
    • General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept 

      Antunes, Dinler A.; Devaurs, Didier; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E. (2018)
      The class I major histocompatibility complex (MHC) is capable of binding peptides derived from intracellular proteins and displaying them at the cell surface. The recognition of these peptide-MHC (pMHC) complexes by T-cells ...
    • Syzygies for translational surfaces 

      Wang, Haohao; Goldman, Ron (2018)
      A translational surface is a rational tensor product surface generated from two rational space curves by translating one curve along the other curve. Translational surfaces are invariant under rigid motions: translating ...
    • A Polynomial Blossom for the Askey–Wilson Operator 

      Simeonov, Plamen; Goldman, Ron (2018)
      We introduce a blossoming procedure for polynomials related to the Askey–Wilson operator. This new blossom is symmetric, multiaffine, and reduces to the complex representation of the polynomial on a certain diagonal. This ...
    • q-Blossoming for analytic functions 

      Goldman, Ron; Simeonov, Plamen (2018)
      We construct aᅠq-analog of the blossom for analytic functions, the analyticᅠq-blossom. Thisᅠq-analog also extends the notion ofᅠq-blossoming from polynomials to analytic functions. We then apply this analyticᅠq-blossom to ...