76 citations · 351 across the 16 of their papers we have counts for
17 papers
Exact -values for global network alignments via combinatorial analysis of shared GO terms (Subtitle: REFANGO: Rigorous Evaluation of Functional Alignments of Networks using Gene Ontology)
Wayne B. Hayes
Network alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically sim…
An introductory guide to aligning networks using SANA, the Simulated Annealing Network Aligner
Wayne B. Hayes
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological…
No cell left behind: automated physics-based tracking of {\em every} cell in a dense and growing colony
Huy Pham, Emile Ramez Shehada, Shawna Stahlheber +1
A human watching a video of closely-packed cells can generally identify every individual cell, regardless of density and noise, but most currently-available cell-tracking software…
SANA: separating the search algorithm from the objective function in biological network alignment, Part 1: Search
Dillon P. Kanne, Wayne B. Hayes
Biological network alignment is currently in a state of disarray, with more than two dozen network alignment tools having been introduced in the past decade, with no clear winner,…
Galaxy Zoo and SpArcFiRe: Constraints on spiral arm formation mechanisms from spiral arm number and pitch angles
Ross E. Hart, Steven P. Bamford, Wayne B. Hayes +7
In this paper we study the morphological properties of spiral galaxies, including measurements of spiral arm number and pitch angle. Using Galaxy Zoo 2, a stellar mass-complete sam…
Graphettes: Constant-time determination of graphlet and orbit identity including (possibly disconnected) graphlets up to size 8
Adib Hassan, Po-Chien Chung, Wayne B. Hayes
Graphlets are small connected induced subgraphs of a larger graph . Graphlets are now commonly used to quantify local and global topology of networks in the field. Methods exist…
SpArcFiRe: morphological selection effects due to reduced visibility of tightly winding arms in distant spiral galaxies
Tianrui, Peng, John Edward English +3
The Galaxy Zoo has provided morphological data on many galaxies. Several biases have been identified in the Galaxy Zoo data. Here we report on a newly discovered selection effect:…
SANA NetGO: A combinatorial approach to using Gene Ontology (GO) terms to score network alignments
Wayne B. Hayes, Nil Mamano
Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins…
On the nature and correction of the spurious S-wise spiral galaxy winding bias in Galaxy Zoo 1
Wayne Hayes, Darren Davis, Pedro Silva
The Galaxy Zoo 1 catalog displays a bias towards the S-wise winding direction in spiral galaxies which has yet to be explained. The lack of an explanation confounds our attempts to…
SANA: Simulated Annealing Network Alignment Applied to Biological Networks
Nil Mamano, Wayne Hayes
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polyno…
Scalable Automated Detection of Spiral Galaxy Arm Segments
Darren R. Davis, Wayne B. Hayes
Given an approximately centered image of a spiral galaxy, we describe an entirely automated method that finds, centers, and sizes the galaxy and then automatically extracts structu…
Automated Quantitative Description of Spiral Galaxy Arm-Segment Structure
Darren Davis, Wayne Hayes
We describe a system for the automatic quantification of structure in spiral galaxies. This enables translation of sky survey images into data needed to help address fundamental as…
Surfing on the Edge: Chaos vs. Near-Integrability in the System of Jovian Planets
Wayne B. Hayes
We demonstrate that the system of Jovian planets (Sun+Jupiter+Saturn+Uranus+Neptune), integrated for 200 million years as an isolated 5-body system using many sets of initial condi…
Is the outer Solar System chaotic?
Wayne B. Hayes
The existence of chaos in the system of Jovian planets has been in question for the past 15 years. Various investigators have found Lyapunov times ranging from about 5 millions yea…
Shadowing-based reliability decay in softened n-body simulations
Wayne Hayes
A shadow of a numerical solution to a chaotic system is an_exact_ solution to the equations of motion that remains close to the numerical solution for a long time. In a collisionle…
Shadowing high-dimensional Hamiltonian systems: the gravitational n-body problem
Wayne B. Hayes
A {\it shadow} is an exact solution to a chaotic system of equations that remains close to a numerically computed solution for a long time, ending in a {\it glitch}. We study the d…
Fitting random stable solar systems to Titius-Bode laws
Wayne Hayes, Scott Tremaine
Simple ``solar systems'' are generated with planetary orbital radii r distributed uniformly random in log(r) between 0.2 and 50 AU. A conservative stability criterion is imposed by…