Now showing items 1-20 of 328

• #### Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells ﻿

(2018)
Interrupting the interplay between cancer cells and extracellular matrix (ECM) is a strategy to halt tumor progression and stromal invasion. Perlecan/heparan sulfate proteoglycan 2 (HSPG2) is an extracellular proteoglycan ...
• #### Bayesian inference of phylogenetic networks from bi-allelic genetic markers ﻿

(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 ﻿

(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 ...
• #### An incremental constraint-based framework for task and motion planning ﻿

(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 ﻿

(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 ...
• #### Inference of species phylogenies from bi-allelic markers using pseudo-likelihood ﻿

(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 ...
• #### A Polynomial Blossom for the Askey–Wilson Operator ﻿

(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 ...
• #### Platform-Independent Benchmarks for Task and Motion Planning ﻿

(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 ...
• #### q-Blossoming for analytic functions ﻿

(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 ...
• #### Efficacy of Novel Carbon Nanoparticle Antioxidant Therapy in a Severe Model of Reversible Middle Cerebral Artery Stroke in Acutely Hyperglycemic Rats ﻿

(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 ...
• #### Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data ﻿

(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 ...
• #### Quantitative comparison of adaptive sampling methods for protein dynamics ﻿

(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. ...
• #### Syzygies for translational surfaces ﻿

(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 ...
• #### SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models ﻿

(2017-09-19)
Abstract Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under ...
• #### A review of parameters and heuristics for guiding metabolic pathfinding ﻿

(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, ...
• #### Atlas + X: Sampling-based Planners on Constraint Manifolds ﻿

(2017-06-14)
Sampling-based planners struggle when the valid configurations are constrained to an implicit manifold. Special planners have been proposed for this problem recently. Our new framework is decoupled from any particular ...
• #### Parallel Flow-Sensitive Points-to Analysis ﻿

(2017-02-01)
Points-to analysis is a fundamental requirement for many program analyses, optimizations, and debugging/verification tools. However, finding an effective balance between performance, scalability and precision in points-to ...
• #### Strong $\mu$-Bases for Rational Tensor Product Surfaces and Extraneous Factors Associated to Bad Base Points and Anomalies at Infinity ﻿

(2017)
We investigate conditions under which the resultant of a $\mu$-basis for a rational tensor product surface is the implicit equation of the surface without any extraneous factors. In this case, we also derive a formula for ...
• #### Reasoning about Strategies: on the Satisfiability Problem ﻿

(2017)
Strategy Logic (SL, for short) has been introduced by Mogavero, Murano, and Vardi as a useful formalism for reasoning explicitly about strategies, as first-order objects, in multi-agent concurrent games. This logic turns ...
• #### Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data ﻿

(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 ...