Now showing items 1-20 of 119

    • 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 networks while also accounting for other processes, such as incomplete lineage sorting. However, these methods can only handle a ...
    • A maximum pseudo-likelihood approach for phylogenetic networks 

      Yu, Yun; Nakhleh, Luay (2015)
      Abstract Background Several phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when inferring a species phylogeny. A maximum likelihood approach was introduced recently for inferring species phylogenies in the ...
    • 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 Askey–Wilson blossom can be used to find the Askey–Wilson derivative of a polynomial of any order. We also introduce a corresponding ...
    • A review of parameters and heuristics for guiding metabolic pathfinding 

      Kim, Sarah M; Peña, Matthew I; Moll, Mark; Bennett, George N; Kavraki, Lydia E (2017-09-15)
      Abstract Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells introduces the possibility of ...
    • An Automated System for Interactively Learning Software Testing 

      Smith, Rebecca; Tang, Terry; Warren, Joe; Rixner, Scott (2017)
      Testing is an important, time-consuming, and often difficult part of the software development process. It is therefore critical to introduce testing early in the computer science curriculum, and to provide students with frequent opportunities for practice and feedback. This paper presents an automated system to help introductory students learn how ...
    • An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data 

      (2013)
      Regulatory networks play a central role in cellular behavior and decision making. Learning these regulatory networks is a major task in biology, and devising computational methods and mathematical models for this task is a major endeavor in bioinformatics. Boolean networks have been used extensively for modeling regulatory networks. In this model, ...
    • 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 planner. The key idea is to leverage incremental constraint solving to efficiently incorporate geometric information at the ...
    • 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 peptide-MHC complexes (pMHCs) holds the promise of interpretable and general binding prediction (i.e., testing whether a given ...
    • 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 ...
    • 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 usage. One approach to generate such strategies is called reactive synthesis. Reactive synthesis requires an abstraction, which ...
    • 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 alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified ...
    • Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent 

      Wen, Dingqiao; Yu, Yun; Nakhleh, Luay (2016)
      The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in ...
    • Binding Modes of Peptidomimetics Designed to Inhibit STAT3 

      (2012)
      STAT3 is a transcription factor that has been found to be constitutively activated in a number of human cancers. Dimerization of STAT3 via its SH2 domain and the subsequent translocation of the dimer to the nucleus leads to transcription of anti-apoptotic genes. Prevention of the dimerization is thus an attractive strategy for inhibiting the ...
    • Boosting forward-time population genetic simulators through genotype compression 

      (2013)
      Background: Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various param- eters controlling them. In particular, for certain settings, the data footprint may quickly exceed the memory of a single compute ...
    • 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 ...
    • 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 ...
    • Circular polarization dependent cyclotron resonance in large-area graphene in ultrahigh magnetic fields 

      (2012)
      Using ultrahigh magnetic fields up to 170 T and polarized midinfrared radiation with tunable wavelengths from 9.22 to 10.67 μm, we studied cyclotron resonance in large-area graphene grown by chemical vapor deposition. Circular polarization dependent studies reveal strong p-type doping for as-grown graphene, and the dependence of the cyclotron resonance ...
    • Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data 

      Devaurs, Didier; Antunes, Dinler A.; Papanastasiou, Malvina; Moll, Mark; Ricklin, Daniel; (2017)
      Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between ...
    • 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 ...
    • Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome 

      (2013)
      The protein kinases are a large family of enzymes that play fundamental roles in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug compounds with high specificity among the kinases has proven difficult. However, computational approaches to comparing the 3-dimensional ...