Collections in this community

Recent Submissions

  • 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 ...
  • Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes 

    Antunes, Dinler A.; Abella, Jayvee R.; Devaurs, Didier; Rigo, Maurício M.; Kavraki, Lydia E. (2018)
    Understanding the mechanisms involved in the activation of an immune response is essential to many fields in human health, including vaccine development and personalized cancer immunotherapy. A central step in the activation ...
  • 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 ...
  • 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 ...
  • 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 ...
  • How Much Do Unstated Problem Constraints Limit Deep Robotic Reinforcement Learning? 

    Lewis, W. Cannon II; Moll, Mark; Kavraki, Lydia E. (2019)
    Deep Reinforcement Learning is a promising paradigm for robotic control which has been shown to be capable of learning policies for high-dimensional, continuous control of unmodeled systems. However, Robotic Reinforcement ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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. ...
  • Picking up the trash: Exploiting generational GC for memory analysis 

    Pridgen, Adam; Garfinkel, Simson; Wallach, Dan S. (2017)
    Memory analysis is slowly moving up the software stack. Early analysis efforts focused on core OS structures and services. As this field evolves, more information becomes accessible because analysis tools can build on ...
  • Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data 

    Devaurs, Didier; Antunes, Dinler A.; Kavraki, Lydia E. (2018)
    Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein structure. However, experimentally observing and computationally ...
  • Efficacy of Novel Carbon Nanoparticle Antioxidant Therapy in a Severe Model of Reversible Middle Cerebral Artery Stroke in Acutely Hyperglycemic Rats 

    Fabian, Roderic H.; Derry, Paul J.; Rea, Harriett Charmaine; Dalmeida, William V.; Nilewski, Lizanne G.; Sikkema, William K.A.; Mandava, Pitchaiah; Tsai, Ah-Lim; Mendoza, Kimberly; Berka, Vladimir; Tour, James M.; Kent, Thomas A. (2018)
    INTRODUCTION: While oxidative stress can be measured during transient cerebral ischemia, antioxidant therapies for ischemic stroke have been clinically unsuccessful. Many antioxidants are limited in their range and/or ...
  • Inference of species phylogenies from bi-allelic markers using pseudo-likelihood 

    Zhu, Jiafan; Nakhleh, Luay (2018)
    MOTIVATION: Phylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses ...
  • Platform-Independent Benchmarks for Task and Motion Planning 

    Lagriffoul, Fabien; Dantam, Neil T.; Garrett, Caelan; Akbari, Aliakbar; Srivastava, Siddharth; Kavraki, Lydia E. (2018)
    We present the first platform-independent evaluation method for task and motion planning (TAMP). Previously point, various problems have been used to test individual planners for specific aspects of TAMP. However, no common ...
  • 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 ...

View more